From j.scholtalbers at gmail.com  Mon Feb  1 07:24:29 2010
From: j.scholtalbers at gmail.com (Jelle Scholtalbers)
Date: Mon, 1 Feb 2010 13:24:29 +0100
Subject: [Bioperl-l] Bio::DB::SeqFeature::Store::memory -> filter_by_type
	very slow
Message-ID: <b66932c31002010424l2cccf278uf33ad8774e2f96a6@mail.gmail.com>

Hi,
I used the Bio::DB::SeqFeature::Store::memory module to load in a GFF3 file
which I could then use in my script in a 'queryable' way. To retrieve
features I used for example
        $db->features(-type => 'BAC:FPC', -seq_id=>'chromosome0')
However when doing a profile on my script I found out that 60% of the
running time went into filter_by_type from
Bio::DB::SeqFeature::Store::memory.
Replacing this function with
     my @features = grep{$_->type eq 'BAC:FPC'}
$db->features(-seq_id=>'chromosome0')
which gave me the same results was just a fraction of the earlier run time.
My script went from 60min. to 4min. for the same result and only changing
this function (is called often).
Can/Should this be fixed or is this just the faster way to do it?

Cheers,
Jelle

From cjfields at illinois.edu  Mon Feb  1 08:23:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 1 Feb 2010 07:23:02 -0600
Subject: [Bioperl-l] Bio::DB::SeqFeature::Store::memory ->
	filter_by_type very slow
In-Reply-To: <b66932c31002010424l2cccf278uf33ad8774e2f96a6@mail.gmail.com>
References: <b66932c31002010424l2cccf278uf33ad8774e2f96a6@mail.gmail.com>
Message-ID: <3435CD81-A2B1-4419-995B-751BE3810017@illinois.edu>

Jelle,

Seems reasonable, but Lincoln and Scott know that code better and are better suited to comment on it. Lincoln, Scott?

chris

On Feb 1, 2010, at 6:24 AM, Jelle Scholtalbers wrote:

> Hi,
> I used the Bio::DB::SeqFeature::Store::memory module to load in a GFF3 file
> which I could then use in my script in a 'queryable' way. To retrieve
> features I used for example
>       $db->features(-type => 'BAC:FPC', -seq_id=>'chromosome0')
> However when doing a profile on my script I found out that 60% of the
> running time went into filter_by_type from
> Bio::DB::SeqFeature::Store::memory.
> Replacing this function with
>    my @features = grep{$_->type eq 'BAC:FPC'}
> $db->features(-seq_id=>'chromosome0')
> which gave me the same results was just a fraction of the earlier run time.
> My script went from 60min. to 4min. for the same result and only changing
> this function (is called often).
> Can/Should this be fixed or is this just the faster way to do it?
> 
> Cheers,
> Jelle
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From maj at fortinbras.us  Mon Feb  1 09:39:29 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 1 Feb 2010 09:39:29 -0500
Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlastPlus - Illegal seek
	error running blastn
In-Reply-To: <ECDEAECD-2367-4718-86E4-3AABD8FE203E@bbsrc.ac.uk>
References: <1DB83E7D-DFDE-4BE7-9EC0-F78B8875DF55@bbsrc.ac.uk><56CC8EF7EEAD4E28A3B822ADA8AD74B1@NewLife><05171AE0-71F2-4102-8131-70C6019D0172@bbsrc.ac.uk><FD6E9A89F6034CCB856E22553ED893D7@NewLife>
	<ECDEAECD-2367-4718-86E4-3AABD8FE203E@bbsrc.ac.uk>
Message-ID: <4B93C35AE3564EA1ADFC3F9156517ECC@NewLife>

This issue appears resolved; will close out #3003--
thanks
MAJ
----- Original Message ----- 
From: "mike stubbington (BI)" <mike.stubbington at bbsrc.ac.uk>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <bioperl-l at lists.open-bio.org>; <Brian at portal.open-bio.org>; "Osborne" 
<bosborne11 at verizon.net>
Sent: Friday, January 29, 2010 8:25 AM
Subject: Re: [Bioperl-l] Bio::Tools::Run::StandAloneBlastPlus - Illegal seek 
error running blastn


Hi Mark,

Thanks for your continued help.

It now fails with this:

------------- EXCEPTION -------------
MSG: /usr/local/ncbi/blast/bin/blastn call crashed: There was a problem running 
/usr/local/ncbi/blast/bin/blastn : BLAST Database error: No alias or index file 
found for nucleotide database [MouseGenome] in search path 
[/Volumes/stubbing/PerlScripts/5CTest/trunk::]

STACK Bio::Tools::Run::WrapperBase::_run 
/Library/Perl/5.10.0/Bio/Tools/Run/WrapperBase/CommandExts.pm:1004
STACK Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD 
/Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus.pm:1236
STACK Bio::Tools::Run::StandAloneBlastPlus::run 
/Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm:267
STACK Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD 
/Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus.pm:1233
STACK toplevel ./5CTest.pl:63
-------------------------------------

If I change the factory creation to:
my $blastFactory = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => '/Users/stubbing/localBlast/MouseGenome'
);

it fails with

------------- EXCEPTION -------------
MSG: DB name not valid
STACK Bio::Tools::Run::StandAloneBlastPlus::new 
/Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus.pm:516
STACK toplevel ./5CTest.pl:45
-------------------------------------

However I can run the following successfully from the command line:

blastn -db  /Users/stubbing/localBlast/MouseGenome -query querySequence.fasta

Is there something wrong with how I'm referring to the blast database when I 
construct my factory?

Thanks again,

M



On 28 Jan 2010, at 18:47, Mark A. Jensen wrote:

> Hi Mike,
> Believe I found the real bug causing the problem (was not accounting for
> the db_dir parameter). Crashes should now also throw much more helpful
> errors. Please try the code at r16774, and shout back.
> thanks --
> MAJ
> ----- Original Message ----- 
> From: "mike stubbington (BI)" <mike.stubbington at bbsrc.ac.uk>
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Thursday, January 28, 2010 11:18 AM
> Subject: Re: [Bioperl-l] Bio::Tools::Run::StandAloneBlastPlus - Illegal seek
> error running blastn
>
>
> Hi,
>
> Thanks for the suggestion. Unfortunately it still fails - error as follows:
>
> ------------- EXCEPTION -------------
> MSG: /usr/local/ncbi/blast/bin/blastn call crashed: There was a problem 
> running
> /usr/local/ncbi/blast/bin/blastn : Illegal seek at
> /Library/Perl/5.10.0/Bio/Tools/Run/WrapperBase/CommandExts.pm line 1000, 
> <DATA>
> line 532.
>
> STACK Bio::Tools::Run::WrapperBase::_run
> /Library/Perl/5.10.0/Bio/Tools/Run/WrapperBase/CommandExts.pm:1005
> STACK Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD
> /Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus.pm:1236
> STACK Bio::Tools::Run::StandAloneBlastPlus::run
> /Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm:267
> STACK Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD
> /Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus.pm:1233
> STACK toplevel ./5CTest.pl:63
> -------------------------------------
>
> M
>
> On 28 Jan 2010, at 15:56, Mark A. Jensen wrote:
>
>> Mike - please try updating your bioperl-live (the core) to the latest code
>> (revision 16761 or so).
>> CommandExts is a work in progress; from the stack errors it looks like you've
>> got an older version.
>> Try it then ping us back, if you would--
>> Thanks
>> Mark
>> ----- Original Message ----- 
>> From: "mike stubbington (BI)" <mike.stubbington at bbsrc.ac.uk>
>> To: <bioperl-l at lists.open-bio.org>
>> Sent: Thursday, January 28, 2010 10:41 AM
>> Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlastPlus - Illegal seek 
>> error
>> running blastn
>>
>>
>> Dear all,
>>
>> I am attempting to blast some primers against the mouse genome. I have 
>> created
>> a
>> local mouse genome blast database and I can search against it using 'blastn'
>> at
>> the command line.
>>
>> I have perl code that creates an array of bioperl sequence objects called
>> @primers
>>
>> I then create a StandAloneBlastPlus factory using the following code?
>>
>> my $blastFactory = Bio::Tools::Run::StandAloneBlastPlus->new(
>> -db_dir => '/Users/stubbing/localBlast/',
>> -db_name => 'MouseGenome'
>> );
>>
>> and then attempt to blast my primers using this?
>>
>> my @shortPrimers;
>> my $count=1;
>> foreach (@primers) {
>> my $currentSeq = $_;
>> print "Checking primer $count/$primerNumber ";
>> if ($_->length < 40) {
>> push(@shortPrimers,$_);
>> print "Too short!\n";
>> }
>> else {
>> print "BLASTing...";
>> my $blastResult = $blastFactory->blastn(-query => $currentSeq);
>> }
>> $count++;
>> }
>>
>> This fails with the following error?
>>
>> ------------- EXCEPTION -------------
>> MSG: /usr/local/ncbi/blast/bin/blastn call crashed: There was a problem
>> running
>> /usr/local/ncbi/blast/bin/blastn : Illegal seek at
>> /Library/Perl/5.10.0/Bio/Tools/Run/WrapperBase/CommandExts.pm line 989, 
>> <DATA>
>> line 532.
>>
>> STACK Bio::Tools::Run::WrapperBase::_run
>> /Library/Perl/5.10.0/Bio/Tools/Run/WrapperBase/CommandExts.pm:994
>> STACK Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD
>> /Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus.pm:1236
>> STACK Bio::Tools::Run::StandAloneBlastPlus::run
>> /Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm:267
>> STACK Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD
>> /Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus.pm:1233
>> STACK toplevel ./5CTest.pl:63
>> -------------------------------------
>>
>> Line 63 in my code is (as you might expect) the one that calls blastn on my
>> factory object.
>>
>> I'd appreciate any help you might be able to provide to shed light on this.
>>
>> Thanks in advance,
>>
>> Mike
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason at bioperl.org  Mon Feb  1 14:48:17 2010
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 1 Feb 2010 11:48:17 -0800
Subject: [Bioperl-l] Fwd: megablast using bioperl
References: <624104.84596.qm@web30907.mail.mud.yahoo.com>
Message-ID: <C010E89A-5C94-4773-BF26-DED76D6F13F2@bioperl.org>

Xiujing -
Your message is best asked on the mailing list.

Begin forwarded message:

> From: Xiujing Gu <xiujingg at yahoo.com>
> Date: February 1, 2010 7:58:55 AM PST
> To: jason at bioperl.org
> Subject: megablast using bioperl
>
> Hello Jason:
>
> After numerous googling, I found you might be the only person who  
> knows about this subject. Would you so kindly show me an example of  
> setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
>
> Thanks a lot!
>
> Best regards,
> Xiujing

From Russell.Smithies at agresearch.co.nz  Mon Feb  1 15:12:07 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 2 Feb 2010 09:12:07 +1300
Subject: [Bioperl-l] Fwd: megablast using bioperl
In-Reply-To: <C010E89A-5C94-4773-BF26-DED76D6F13F2@bioperl.org>
References: <624104.84596.qm@web30907.mail.mud.yahoo.com>
	<C010E89A-5C94-4773-BF26-DED76D6F13F2@bioperl.org>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61B820F2@exchsth.agresearch.co.nz>

Have you read the docs? It's very well documented:
http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/StandAloneBlast.pm

Have you searched the BioPerl wiki? Again, well documented with examples:
http://www.bioperl.org/wiki/HOWTO:StandAloneBlast

And if that doesn't help, perhaps you need to improve your Google skills:
http://www.google.com/support/websearch/?ctx=web

--Russell



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Jason Stajich
> Sent: Tuesday, 2 February 2010 8:48 a.m.
> To: BioPerl List
> Cc: xiujingg at yahoo.com
> Subject: [Bioperl-l] Fwd: megablast using bioperl
> 
> Xiujing -
> Your message is best asked on the mailing list.
> 
> Begin forwarded message:
> 
> > From: Xiujing Gu <xiujingg at yahoo.com>
> > Date: February 1, 2010 7:58:55 AM PST
> > To: jason at bioperl.org
> > Subject: megablast using bioperl
> >
> > Hello Jason:
> >
> > After numerous googling, I found you might be the only person who
> > knows about this subject. Would you so kindly show me an example of
> > setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
> >
> > Thanks a lot!
> >
> > Best regards,
> > Xiujing
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
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From maj at fortinbras.us  Mon Feb  1 15:22:40 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 1 Feb 2010 15:22:40 -0500
Subject: [Bioperl-l] Fwd: megablast using bioperl
In-Reply-To: <C010E89A-5C94-4773-BF26-DED76D6F13F2@bioperl.org>
References: <624104.84596.qm@web30907.mail.mud.yahoo.com>
	<C010E89A-5C94-4773-BF26-DED76D6F13F2@bioperl.org>
Message-ID: <68636D1D473B459CAF3DE0FF890F7C40@NewLife>

Xiujing--
If you choose to use blast+, this is pretty easily done with
Bio::Tools::Run::StandAloneBlastPlus :

 use Bio::Tools::Run::StandAloneBlastPlus;
 $ENV{BLASTPLUSDIR} = "/path/to/blast+/bin";
 
 $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
    -db_name => '/path/to/blastdb/mydb'
);
 
 $result = $fac->blastn( -query => 'myqueryseqs.fas' );

 while ($hit = $result->next_hit) {
  # process hits
 }

Here, blastn is used, because in blast+, megablast is the default
algorithm. --to specify others, you set the -task parameter: e.g., 
legacy blastn would be
 
 $result = $fac->blastn( -query =. 'myqueryseqs.fas',
                                     -task => 'blastn' );

For much more information, please look at 
http://bioperl.org/wiki/HOWTO:SearchIO
and
http://bioperl.org/wiki/HOWTO:BlastPlus

Many questions you might have will be answered in those pages.
MAJ




----- Original Message ----- 
From: "Jason Stajich" <jason at bioperl.org>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Cc: <xiujingg at yahoo.com>
Sent: Monday, February 01, 2010 2:48 PM
Subject: [Bioperl-l] Fwd: megablast using bioperl


> Xiujing -
> Your message is best asked on the mailing list.
> 
> Begin forwarded message:
> 
>> From: Xiujing Gu <xiujingg at yahoo.com>
>> Date: February 1, 2010 7:58:55 AM PST
>> To: jason at bioperl.org
>> Subject: megablast using bioperl
>>
>> Hello Jason:
>>
>> After numerous googling, I found you might be the only person who  
>> knows about this subject. Would you so kindly show me an example of  
>> setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
>>
>> Thanks a lot!
>>
>> Best regards,
>> Xiujing
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
>

From abhishek.vit at gmail.com  Mon Feb  1 15:36:18 2010
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Mon, 1 Feb 2010 15:36:18 -0500
Subject: [Bioperl-l] Pulling down data from NCBI
Message-ID: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>

Hi All

I looking to batch download some 34K nucleotide sequences,
corresponding to a NCBI accession number. I tired the following and
getting an error. Has it got anything to do with recent update to code
that Chris was discussing.



my $factory = Bio::DB::EUtilities->new  (
					-eutil	=> 'efecth',
					-db 	=>	'nucleotide',
					-retype	=>	'fasta',
					-id		=> $id
				);


----------- EXCEPTION: Bio::Root::Exception -------------
MSG: efecth not supported
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:357
STACK: Bio::Tools::EUtilities::EUtilParameters::eutil
/usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilParameters.pm:452
STACK: Bio::Root::RootI::_set_from_args
/usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/RootI.pm:546
STACK: Bio::Tools::EUtilities::EUtilParameters::new
/usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilParameters.pm:193
STACK: Bio::DB::EUtilities::new
/usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/EUtilities.pm:74
STACK: ./getDatafromNCBI.pl:9


-Abhi

From cjfields at illinois.edu  Mon Feb  1 15:38:10 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 1 Feb 2010 14:38:10 -0600
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
Message-ID: <7CDCC994-B84A-48B8-8A91-346579A74378@illinois.edu>

that would be 'efetch', not 'efecth'.  

chris

On Feb 1, 2010, at 2:36 PM, Abhishek Pratap wrote:

> Hi All
> 
> I looking to batch download some 34K nucleotide sequences,
> corresponding to a NCBI accession number. I tired the following and
> getting an error. Has it got anything to do with recent update to code
> that Chris was discussing.
> 
> 
> 
> my $factory = Bio::DB::EUtilities->new  (
> 					-eutil	=> 'efecth',
> 					-db 	=>	'nucleotide',
> 					-retype	=>	'fasta',
> 					-id		=> $id
> 				);
> 
> 
> ----------- EXCEPTION: Bio::Root::Exception -------------
> MSG: efecth not supported
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:357
> STACK: Bio::Tools::EUtilities::EUtilParameters::eutil
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilParameters.pm:452
> STACK: Bio::Root::RootI::_set_from_args
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/RootI.pm:546
> STACK: Bio::Tools::EUtilities::EUtilParameters::new
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilParameters.pm:193
> STACK: Bio::DB::EUtilities::new
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/EUtilities.pm:74
> STACK: ./getDatafromNCBI.pl:9
> 
> 
> -Abhi
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From Kevin.M.Brown at asu.edu  Mon Feb  1 15:39:28 2010
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Mon, 1 Feb 2010 13:39:28 -0700
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
Message-ID: <1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>

Looks like you've misspelled one of the parameters. It should be
'efetch' not 'efecth'

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Abhishek Pratap
> Sent: Monday, February 01, 2010 1:36 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Pulling down data from NCBI
> 
> Hi All
> 
> I looking to batch download some 34K nucleotide sequences,
> corresponding to a NCBI accession number. I tired the following and
> getting an error. Has it got anything to do with recent update to code
> that Chris was discussing.
> 
> 
> 
> my $factory = Bio::DB::EUtilities->new  (
> 					-eutil	=> 'efecth',
> 					-db 	=>	'nucleotide',
> 					-retype	=>	'fasta',
> 					-id		=> $id
> 				);
> 
> 
> ----------- EXCEPTION: Bio::Root::Exception -------------
> MSG: efecth not supported
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:357
> STACK: Bio::Tools::EUtilities::EUtilParameters::eutil
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
> ameters.pm:452
> STACK: Bio::Root::RootI::_set_from_args
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/RootI.pm:546
> STACK: Bio::Tools::EUtilities::EUtilParameters::new
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
> ameters.pm:193
> STACK: Bio::DB::EUtilities::new
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/EUtilities.pm:74
> STACK: ./getDatafromNCBI.pl:9
> 
> 
> -Abhi
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From abhishek.vit at gmail.com  Mon Feb  1 15:45:30 2010
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Mon, 1 Feb 2010 15:45:30 -0500
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
Message-ID: <be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>

Thank you guys for very quick responses.  My bad I trusted my fingers.

Now that this is working the output that I am getting is not what I
want. I am sure I am missing the correct way of doing it. So If I
search the Nucleotide db @NCBI for this accession number "
AAPP01000000", I see some 34 k records. What I need to do is pull down
those sequences as fasta files.

I am referring to
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook  but dint quite
find a similar example.

Thanks!
-Abhi

On Mon, Feb 1, 2010 at 3:39 PM, Kevin Brown <Kevin.M.Brown at asu.edu> wrote:
> Looks like you've misspelled one of the parameters. It should be
> 'efetch' not 'efecth'
>
> Kevin Brown
> Center for Innovations in Medicine
> Biodesign Institute
> Arizona State University
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>> Abhishek Pratap
>> Sent: Monday, February 01, 2010 1:36 PM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Pulling down data from NCBI
>>
>> Hi All
>>
>> I looking to batch download some 34K nucleotide sequences,
>> corresponding to a NCBI accession number. I tired the following and
>> getting an error. Has it got anything to do with recent update to code
>> that Chris was discussing.
>>
>>
>>
>> my $factory = Bio::DB::EUtilities->new ?(
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -eutil ?=> 'efecth',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -db ? ? => ? ? ?'nucleotide',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -retype => ? ? ?'fasta',
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -id ? ? ? ? ? ? => $id
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? );
>>
>>
>> ----------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: efecth not supported
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw
>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:357
>> STACK: Bio::Tools::EUtilities::EUtilParameters::eutil
>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
>> ameters.pm:452
>> STACK: Bio::Root::RootI::_set_from_args
>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/RootI.pm:546
>> STACK: Bio::Tools::EUtilities::EUtilParameters::new
>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
>> ameters.pm:193
>> STACK: Bio::DB::EUtilities::new
>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/EUtilities.pm:74
>> STACK: ./getDatafromNCBI.pl:9
>>
>>
>> -Abhi
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>


From senthil.debian at gmail.com  Mon Feb  1 15:45:46 2010
From: senthil.debian at gmail.com (Senthil Kumar M)
Date: Mon, 1 Feb 2010 15:45:46 -0500
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
Message-ID: <56b822011002011245w6f97af9cpfe986daa2e593974@mail.gmail.com>

On Mon, Feb 1, 2010 at 3:36 PM, Abhishek Pratap <abhishek.vit at gmail.com> wrote:
<Snip>
>
> my $factory = Bio::DB::EUtilities->new ?(
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-eutil ?=> 'efecth',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-db ? ? => ? ? ?'nucleotide',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-retype => ? ? ?'fasta',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-id ? ? ? ? ? ? => $id
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?);
>
>
> ----------- EXCEPTION: Bio::Root::Exception -------------
> MSG: efecth not supported
</Snip>

Hi,

Shouldn't that be efetch?

Senthil


From Russell.Smithies at agresearch.co.nz  Mon Feb  1 16:02:12 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 2 Feb 2010 10:02:12 +1300
Subject: [Bioperl-l] Fwd: megablast using bioperl
In-Reply-To: <718515.61675.qm@web30905.mail.mud.yahoo.com>
References: <18DF7D20DFEC044098A1062202F5FFF32C61B820F2@exchsth.agresearch.co.nz>
	<718515.61675.qm@web30905.mail.mud.yahoo.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61B82183@exchsth.agresearch.co.nz>

Sorry, I missed the megablast bit.
There's a Bio::SearchIO module for reading megablast output but I don't think there's any built-in way of executing it.
You may have to use system() to execute the command then read the output back into Bio::SearchIO

Have you had a look at Blastplus?
http://doc.bioperl.org/releases/bioperl-current/bioperl-run/lib/Bio/Tools/Run/BlastPlus.html

--Russell


From: Xiujing Gu [mailto:xiujingg at yahoo.com]
Sent: Tuesday, 2 February 2010 9:39 a.m.
To: 'BioPerl List'; Smithies, Russell
Subject: RE: [Bioperl-l] Fwd: megablast using bioperl

Thanks for the links!
But, they only talk about the regular blastall program, not the megablast.

I am not sure how can I switch from blastall to megablast. I tried to just call megablast, but I got a very differenct report.

$VAR1 = bless( {
                 'primary_seq' => bless( {
                                           'display_id' => 'test',
                                           '_seq_length' => undef,
                                           '_root_verbose' => 0,
                                           'seq' => 'TGAACCTAGAAGTATTTGTTGCTGGGTTTGTCTTCAGGTTCTGTTGCTCGGTTTTCTAGTTCCCCACCTAGTCTGGGTTACTCTGCAGCTACTTTTGCATTACAATGGCCTTGGTGAGACTGGTAGACGGGATTAACTGAGAATTCACAAGGGTGGGTCAGTAGGGGGTGTGCCCGCCAGGAGGGGTGGGTCTAAGGTGATAGAGCCTTCATTATAAATCTAGAGACTCCAGGATTTTAACGTTCTGCTGGACTGAGCTGGTTGCCTCATGTTATTATGCAGGCAACTCACTTTATCCCAATTTCTTGATACTTTTCCTTCTGGAGGTCCTATTTCTCTAACATCTTCCAGAAAAGTCTTAAAGCTGCCTTAACCTTTTTTCCAGTCCACCTCTTAAATTTTTTCCTCCTCTTCCTCTATACTAACATGAGTGTGGATCCAGCTTGTCCCCAAAGCTTGCCTTGCTTTGAAGCATCCGACTGTAAAGAATCTTCACCTATGCCTGTGATTTGTGGGCCTGAAGAAAACTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACGGAGACTGGTAAGAAAGAAATTTATCCTTGAAAGGCCAAGTTCCTTAAGGGAAAAGAGAGAAGGAGAGAGGGTTAAGGGATCATTTCCCTCTTGAGCAATGATGGACCATTACTATAAAGAAGTGTTATTATCAACTAATCCTCTGGAAACCCCTTTTTCCATTATAACTTGGTGGCACCTGCCCTTTGAACTATGTCCCAGGTCTCAGGAGTGTGCATTGAGTTGAAGGACACAGAATTCGGCAGTTGAACAGTGTGCAGTAAGTTTGAGAACCTATGGGCTTAGGCATGGTGGAAACAAAAATGTATCGTTATAGTTAAATGAAGGTGATGTGTACATCTTCACATAGTGCTGGACACATGTGAATAAATAGCAGATTTATTGCTAATTAGCCA GAAGACCTAACGTCATAGCTCAGGGATGAGCATGATTTTGTTTTGCCAAAAATGGCATGGCAAATCACGATGAGATTTCTGTAATACATAATTTGGGTAATTCTTTCTATGTCAGTAACGGCTGTCTCTTCTCCATTCTCTGGGTTTGTGGATGTTACTGGGCAGCTCTGAGTTTGGGAGCACCTCCCATGTCTAATTCTCCTAAGTCCTGGGAAGCGTTGACCCAACTTTATGGTAAAGATAATTCCAGAAAGTTTAATCTACTGACAGTCAAACAGAATGTAGCTAGAAGTCCAGTTTGGCTTCAAAACCTGTGCTAGTACTCATGCTTCTGACTGGTAGCTGCAAGGGGTGGGGGATACTCGGGATACTCATAAAGCCGCTACCACTTTTTTGAAAATCAATTTTTCAGTAGTTTTCAAAAACTTGAGAATGAACCAACTTTACCAAGAATG',
                                           'alphabet' => 'dna'
                                         }, 'Bio::PrimarySeq' ),
                 '_root_verbose' => 0
               }, 'Bio::Seq' );
Can't locate object method "nextSbjct" via package "Bio::Seq"



Thanks,
Xiujing Gu


--- On Mon, 2/1/10, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:

From: Smithies, Russell <Russell.Smithies at agresearch.co.nz>
Subject: RE: [Bioperl-l] Fwd: megablast using bioperl
To: "'BioPerl List'" <bioperl-l at lists.open-bio.org>
Cc: "'xiujingg at yahoo.com'" <xiujingg at yahoo.com>
Date: Monday, February 1, 2010, 3:12 PM
Have you read the docs? It's very well documented:
http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/StandAloneBlast.pm<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/Tools/Run/StandAloneBlast.pm>

Have you searched the BioPerl wiki? Again, well documented with examples:
http://www.bioperl.org/wiki/HOWTO:StandAloneBlast

And if that doesn't help, perhaps you need to improve your Google skills:
http://www.google.com/support/websearch/?ctx=web

--Russell



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org</mc/compose?to=bioperl-l-bounces at lists.open-bio.org> [mailto:bioperl-l-
> bounces at lists.open-bio.org</mc/compose?to=bounces at lists.open-bio.org>] On Behalf Of Jason Stajich
> Sent: Tuesday, 2 February 2010 8:48 a.m.
> To: BioPerl List
> Cc: xiujingg at yahoo.com</mc/compose?to=xiujingg at yahoo.com>
> Subject: [Bioperl-l] Fwd: megablast using bioperl
>
> Xiujing -
> Your message is best asked on the mailing list.
>
> Begin forwarded message:
>
> > From: Xiujing Gu <xiujingg at yahoo.com</mc/compose?to=xiujingg at yahoo.com>>
> > Date: February 1, 2010 7:58:55 AM PST
> > To: jason at bioperl.org</mc/compose?to=jason at bioperl.org>
> > Subject: megablast using bioperl
> >
> > Hello Jason:
> >
> > After numerous googling, I found you might be the only person who
> > knows about this subject. Would you so kindly show me an example of
> > setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
> >
> > Thanks a lot!
> >
> > Best regards,
> > Xiujing
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org</mc/compose?to=Bioperl-l at lists.open-bio.org>
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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From abhishek.vit at gmail.com  Mon Feb  1 16:31:45 2010
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Mon, 1 Feb 2010 16:31:45 -0500
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
Message-ID: <be9b52411002011331u309b1915tbacfadce5092712a@mail.gmail.com>

I was able to work this out. Thanks!

How do I retrieve a long list of sequences using a query? from
Eutilities How To helped.

-Abhi

On Mon, Feb 1, 2010 at 3:45 PM, Abhishek Pratap <abhishek.vit at gmail.com> wrote:
> Thank you guys for very quick responses. ?My bad I trusted my fingers.
>
> Now that this is working the output that I am getting is not what I
> want. I am sure I am missing the correct way of doing it. So If I
> search the Nucleotide db @NCBI for this accession number "
> AAPP01000000", I see some 34 k records. What I need to do is pull down
> those sequences as fasta files.
>
> I am referring to
> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook ?but dint quite
> find a similar example.
>
> Thanks!
> -Abhi
>
> On Mon, Feb 1, 2010 at 3:39 PM, Kevin Brown <Kevin.M.Brown at asu.edu> wrote:
>> Looks like you've misspelled one of the parameters. It should be
>> 'efetch' not 'efecth'
>>
>> Kevin Brown
>> Center for Innovations in Medicine
>> Biodesign Institute
>> Arizona State University
>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>>> Abhishek Pratap
>>> Sent: Monday, February 01, 2010 1:36 PM
>>> To: bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] Pulling down data from NCBI
>>>
>>> Hi All
>>>
>>> I looking to batch download some 34K nucleotide sequences,
>>> corresponding to a NCBI accession number. I tired the following and
>>> getting an error. Has it got anything to do with recent update to code
>>> that Chris was discussing.
>>>
>>>
>>>
>>> my $factory = Bio::DB::EUtilities->new ?(
>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -eutil ?=> 'efecth',
>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -db ? ? => ? ? ?'nucleotide',
>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -retype => ? ? ?'fasta',
>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -id ? ? ? ? ? ? => $id
>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? );
>>>
>>>
>>> ----------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: efecth not supported
>>> STACK: Error::throw
>>> STACK: Bio::Root::Root::throw
>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:357
>>> STACK: Bio::Tools::EUtilities::EUtilParameters::eutil
>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
>>> ameters.pm:452
>>> STACK: Bio::Root::RootI::_set_from_args
>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/RootI.pm:546
>>> STACK: Bio::Tools::EUtilities::EUtilParameters::new
>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
>>> ameters.pm:193
>>> STACK: Bio::DB::EUtilities::new
>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/EUtilities.pm:74
>>> STACK: ./getDatafromNCBI.pl:9
>>>
>>>
>>> -Abhi
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>


From cjfields at illinois.edu  Mon Feb  1 16:31:48 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 1 Feb 2010 15:31:48 -0600
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
Message-ID: <2F1F855C-16BF-42ED-BE91-63CD1B331F90@illinois.edu>

Abhi,

The accession in question is for a record containing a set of sequences, not just one sequence (it's a contig record).  The NCBI web interface is performing an esearch on this to get 34K seqs, the equivalent with EUtilities is:

================================
use Bio::DB::EUtilities;

my $id = 'AAPP01000000[ACCN]';

my $factory = Bio::DB::EUtilities->new  (
       -eutil =>  'esearch',
       -db    =>  'nucleotide',
       -term  =>  $id,
       -usehistory => 'y');

say $factory->get_count;

# do more here...

================================

The 'do more here' part is covered in the cookbook, and will require you retrieving the seqs in chunks. 

chris

On Feb 1, 2010, at 2:45 PM, Abhishek Pratap wrote:

> Thank you guys for very quick responses.  My bad I trusted my fingers.
> 
> Now that this is working the output that I am getting is not what I
> want. I am sure I am missing the correct way of doing it. So If I
> search the Nucleotide db @NCBI for this accession number "
> AAPP01000000", I see some 34 k records. What I need to do is pull down
> those sequences as fasta files.
> 
> I am referring to
> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook  but dint quite
> find a similar example.
> 
> Thanks!
> -Abhi
> 
> On Mon, Feb 1, 2010 at 3:39 PM, Kevin Brown <Kevin.M.Brown at asu.edu> wrote:
>> Looks like you've misspelled one of the parameters. It should be
>> 'efetch' not 'efecth'
>> 
>> Kevin Brown
>> Center for Innovations in Medicine
>> Biodesign Institute
>> Arizona State University
>> 
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>>> Abhishek Pratap
>>> Sent: Monday, February 01, 2010 1:36 PM
>>> To: bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] Pulling down data from NCBI
>>> 
>>> Hi All
>>> 
>>> I looking to batch download some 34K nucleotide sequences,
>>> corresponding to a NCBI accession number. I tired the following and
>>> getting an error. Has it got anything to do with recent update to code
>>> that Chris was discussing.
>>> 
>>> 
>>> 
>>> my $factory = Bio::DB::EUtilities->new  (
>>>                                       -eutil  => 'efecth',
>>>                                       -db     =>      'nucleotide',
>>>                                       -retype =>      'fasta',
>>>                                       -id             => $id
>>>                               );
>>> 
>>> 
>>> ----------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: efecth not supported
>>> STACK: Error::throw
>>> STACK: Bio::Root::Root::throw
>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:357
>>> STACK: Bio::Tools::EUtilities::EUtilParameters::eutil
>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
>>> ameters.pm:452
>>> STACK: Bio::Root::RootI::_set_from_args
>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/RootI.pm:546
>>> STACK: Bio::Tools::EUtilities::EUtilParameters::new
>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
>>> ameters.pm:193
>>> STACK: Bio::DB::EUtilities::new
>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/EUtilities.pm:74
>>> STACK: ./getDatafromNCBI.pl:9
>>> 
>>> 
>>> -Abhi
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From abhishek.vit at gmail.com  Mon Feb  1 16:33:17 2010
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Mon, 1 Feb 2010 16:33:17 -0500
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <2F1F855C-16BF-42ED-BE91-63CD1B331F90@illinois.edu>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
	<2F1F855C-16BF-42ED-BE91-63CD1B331F90@illinois.edu>
Message-ID: <be9b52411002011333h10d27649k46ea581d35be7b8@mail.gmail.com>

Thanks Chris.

I was looking at the same thing in cookbook moments ago. Thanks!
-A

On Mon, Feb 1, 2010 at 4:31 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Abhi,
>
> The accession in question is for a record containing a set of sequences, not just one sequence (it's a contig record). ?The NCBI web interface is performing an esearch on this to get 34K seqs, the equivalent with EUtilities is:
>
> ================================
> use Bio::DB::EUtilities;
>
> my $id = 'AAPP01000000[ACCN]';
>
> my $factory = Bio::DB::EUtilities->new ?(
> ? ? ? -eutil => ?'esearch',
> ? ? ? -db ? ?=> ?'nucleotide',
> ? ? ? -term ?=> ?$id,
> ? ? ? -usehistory => 'y');
>
> say $factory->get_count;
>
> # do more here...
>
> ================================
>
> The 'do more here' part is covered in the cookbook, and will require you retrieving the seqs in chunks.
>
> chris
>
> On Feb 1, 2010, at 2:45 PM, Abhishek Pratap wrote:
>
>> Thank you guys for very quick responses. ?My bad I trusted my fingers.
>>
>> Now that this is working the output that I am getting is not what I
>> want. I am sure I am missing the correct way of doing it. So If I
>> search the Nucleotide db @NCBI for this accession number "
>> AAPP01000000", I see some 34 k records. What I need to do is pull down
>> those sequences as fasta files.
>>
>> I am referring to
>> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook ?but dint quite
>> find a similar example.
>>
>> Thanks!
>> -Abhi
>>
>> On Mon, Feb 1, 2010 at 3:39 PM, Kevin Brown <Kevin.M.Brown at asu.edu> wrote:
>>> Looks like you've misspelled one of the parameters. It should be
>>> 'efetch' not 'efecth'
>>>
>>> Kevin Brown
>>> Center for Innovations in Medicine
>>> Biodesign Institute
>>> Arizona State University
>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>>>> Abhishek Pratap
>>>> Sent: Monday, February 01, 2010 1:36 PM
>>>> To: bioperl-l at lists.open-bio.org
>>>> Subject: [Bioperl-l] Pulling down data from NCBI
>>>>
>>>> Hi All
>>>>
>>>> I looking to batch download some 34K nucleotide sequences,
>>>> corresponding to a NCBI accession number. I tired the following and
>>>> getting an error. Has it got anything to do with recent update to code
>>>> that Chris was discussing.
>>>>
>>>>
>>>>
>>>> my $factory = Bio::DB::EUtilities->new ?(
>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -eutil ?=> 'efecth',
>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -db ? ? => ? ? ?'nucleotide',
>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -retype => ? ? ?'fasta',
>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -id ? ? ? ? ? ? => $id
>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? );
>>>>
>>>>
>>>> ----------- EXCEPTION: Bio::Root::Exception -------------
>>>> MSG: efecth not supported
>>>> STACK: Error::throw
>>>> STACK: Bio::Root::Root::throw
>>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:357
>>>> STACK: Bio::Tools::EUtilities::EUtilParameters::eutil
>>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
>>>> ameters.pm:452
>>>> STACK: Bio::Root::RootI::_set_from_args
>>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/RootI.pm:546
>>>> STACK: Bio::Tools::EUtilities::EUtilParameters::new
>>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
>>>> ameters.pm:193
>>>> STACK: Bio::DB::EUtilities::new
>>>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/EUtilities.pm:74
>>>> STACK: ./getDatafromNCBI.pl:9
>>>>
>>>>
>>>> -Abhi
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From xiujingg at yahoo.com  Mon Feb  1 15:38:39 2010
From: xiujingg at yahoo.com (Xiujing Gu)
Date: Mon, 1 Feb 2010 12:38:39 -0800 (PST)
Subject: [Bioperl-l] Fwd: megablast using bioperl
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32C61B820F2@exchsth.agresearch.co.nz>
Message-ID: <718515.61675.qm@web30905.mail.mud.yahoo.com>

Thanks for the links!
But, they only talk about the regular blastall program, not the megablast.

I am not sure how can I switch from blastall to megablast. I tried to just call megablast, but I got a very differenct report.

$VAR1 = bless( {
???????????????? 'primary_seq' => bless( {
?????????????????????????????????????????? 'display_id' => 'test',
?????????????????????????????????????????? '_seq_length' => undef,
?????????????????????????????????????????? '_root_verbose' => 0,
?????????????????????????????????????????? 'seq' =>
 'TGAACCTAGAAGTATTTGTTGCTGGGTTTGTCTTCAGGTTCTGTTGCTCGGTTTTCTAGTTCCCCACCTAGTCTGGGTTACTCTGCAGCTACTTTTGCATTACAATGGCCTTGGTGAGACTGGTAGACGGGATTAACTGAGAATTCACAAGGGTGGGTCAGTAGGGGGTGTGCCCGCCAGGAGGGGTGGGTCTAAGGTGATAGAGCCTTCATTATAAATCTAGAGACTCCAGGATTTTAACGTTCTGCTGGACTGAGCTGGTTGCCTCATGTTATTATGCAGGCAACTCACTTTATCCCAATTTCTTGATACTTTTCCTTCTGGAGGTCCTATTTCTCTAACATCTTCCAGAAAAGTCTTAAAGCTGCCTTAACCTTTTTTCCAGTCCACCTCTTAAATTTTTTCCTCCTCTTCCTCTATACTAACATGAGTGTGGATCCAGCTTGTCCCCAAAGCTTGCCTTGCTTTGAAGCATCCGACTGTAAAGAATCTTCACCTATGCCTGTGATTTGTGGGCCTGAAGAAAACTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACGGAGACTGGTAAGAAAGAAATTTATCCTTGAAAGGCCAAGTTCCTTAAGGGAAAAGAGAGAAGGAGAGAGGGTTAAGGGATCATTTCCCTCTTGAGCAATGATGGACCATTACTATAAAGAAGTGTTATTATCAACTAATCCTCTGGAAACCCCTTTTTCCATTATAACTTGGTGGCACCTGCCCTTTGAACTATGTCCCAGGTCTCAGGAGTGTGCATTGAGTTGAAGGACACAGAATTCGGCAGTTGAACAGTGTGCAGTAAGTTTGAGAACCTATGGGCTTAGGCATGGTGGAAACAAAAATGTATCGTTATAGTTAAATGAAGGTGATGTGTACATCTTCACATAGTGCTGGACACATGTGAATAAATAGCAGATTTATTGCTAATTAGCCA
GAAGACCTAACGTCATAGCTCAGGGATGAGCATGATTTTGTTTTGCCAAAAATGGCATGGCAAATCACGATGAGATTTCTGTAATACATAATTTGGGTAATTCTTTCTATGTCAGTAACGGCTGTCTCTTCTCCATTCTCTGGGTTTGTGGATGTTACTGGGCAGCTCTGAGTTTGGGAGCACCTCCCATGTCTAATTCTCCTAAGTCCTGGGAAGCGTTGACCCAACTTTATGGTAAAGATAATTCCAGAAAGTTTAATCTACTGACAGTCAAACAGAATGTAGCTAGAAGTCCAGTTTGGCTTCAAAACCTGTGCTAGTACTCATGCTTCTGACTGGTAGCTGCAAGGGGTGGGGGATACTCGGGATACTCATAAAGCCGCTACCACTTTTTTGAAAATCAATTTTTCAGTAGTTTTCAAAAACTTGAGAATGAACCAACTTTACCAAGAATG',
?????????????????????????????????????????? 'alphabet' => 'dna'
???????????????????????????????????????? }, 'Bio::PrimarySeq' ),
???????????????? '_root_verbose' => 0
?????????????? }, 'Bio::Seq' );
Can't locate object method "nextSbjct" via package "Bio::Seq" 



Thanks,
Xiujing Gu


--- On Mon, 2/1/10, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:

From: Smithies, Russell <Russell.Smithies at agresearch.co.nz>
Subject: RE: [Bioperl-l] Fwd: megablast using bioperl
To: "'BioPerl List'" <bioperl-l at lists.open-bio.org>
Cc: "'xiujingg at yahoo.com'" <xiujingg at yahoo.com>
Date: Monday, February 1, 2010, 3:12 PM

Have you read the docs? It's very well documented:
http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/StandAloneBlast.pm

Have you searched the BioPerl wiki? Again, well documented with examples:
http://www.bioperl.org/wiki/HOWTO:StandAloneBlast

And if that doesn't help, perhaps you need to improve your Google skills:
http://www.google.com/support/websearch/?ctx=web

--Russell



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Jason Stajich
> Sent: Tuesday, 2 February 2010 8:48 a.m.
> To: BioPerl List
> Cc: xiujingg at yahoo.com
> Subject: [Bioperl-l] Fwd: megablast using bioperl
> 
> Xiujing -
> Your message is best asked on the mailing list.
> 
> Begin forwarded message:
> 
> > From: Xiujing Gu <xiujingg at yahoo.com>
> > Date: February 1, 2010 7:58:55 AM PST
> > To: jason at bioperl.org
> > Subject: megablast using bioperl
> >
> > Hello Jason:
> >
> > After numerous googling, I found you might be the only person who
> > knows about this subject. Would you so kindly show me an example of
> > setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
> >
> > Thanks a lot!
> >
> > Best regards,
> > Xiujing
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



      

From cjfields at illinois.edu  Mon Feb  1 17:02:43 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 1 Feb 2010 16:02:43 -0600
Subject: [Bioperl-l] Fwd: megablast using bioperl
In-Reply-To: <718515.61675.qm@web30905.mail.mud.yahoo.com>
References: <718515.61675.qm@web30905.mail.mud.yahoo.com>
Message-ID: <786A566A-E72E-441E-A9FE-E4B124332EE8@illinois.edu>

Acc. to the blastall docs MEGABLAST is just setting -n to T for blastall.  Is that what you mean?

pyrimidine1:~ cjfields$ blast-2.2.22/bin/blastall -

blastall 2.2.22   arguments:

  -p  Program Name [String]
  -d  Database [String]
    default = nr
...
  -n  MegaBlast search [T/F]
    default = F

chris

On Feb 1, 2010, at 2:38 PM, Xiujing Gu wrote:

> Thanks for the links!
> But, they only talk about the regular blastall program, not the megablast.
> 
> I am not sure how can I switch from blastall to megablast. I tried to just call megablast, but I got a very differenct report.
> 
> $VAR1 = bless( {
>                  'primary_seq' => bless( {
>                                            'display_id' => 'test',
>                                            '_seq_length' => undef,
>                                            '_root_verbose' => 0,
>                                            'seq' =>
> 'TGAACCTAGAAGTATTTGTTGCTGGGTTTGTCTTCAGGTTCTGTTGCTCGGTTTTCTAGTTCCCCACCTAGTCTGGGTTACTCTGCAGCTACTTTTGCATTACAATGGCCTTGGTGAGACTGGTAGACGGGATTAACTGAGAATTCACAAGGGTGGGTCAGTAGGGGGTGTGCCCGCCAGGAGGGGTGGGTCTAAGGTGATAGAGCCTTCATTATAAATCTAGAGACTCCAGGATTTTAACGTTCTGCTGGACTGAGCTGGTTGCCTCATGTTATTATGCAGGCAACTCACTTTATCCCAATTTCTTGATACTTTTCCTTCTGGAGGTCCTATTTCTCTAACATCTTCCAGAAAAGTCTTAAAGCTGCCTTAACCTTTTTTCCAGTCCACCTCTTAAATTTTTTCCTCCTCTTCCTCTATACTAACATGAGTGTGGATCCAGCTTGTCCCCAAAGCTTGCCTTGCTTTGAAGCATCCGACTGTAAAGAATCTTCACCTATGCCTGTGATTTGTGGGCCTGAAGAAAACTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACGGAGACTGGTAAGAAAGAAATTTATCCTTGAAAGGCCAAGTTCCTTAAGGGAAAAGAGAGAAGGAGAGAGGGTTAAGGGATCATTTCCCTCTTGAGCAATGATGGACCATTACTATAAAGAAGTGTTATTATCAACTAATCCTCTGGAAACCCCTTTTTCCATTATAACTTGGTGGCACCTGCCCTTTGAACTATGTCCCAGGTCTCAGGAGTGTGCATTGAGTTGAAGGACACAGAATTCGGCAGTTGAACAGTGTGCAGTAAGTTTGAGAACCTATGGGCTTAGGCATGGTGGAAACAAAAATGTATCGTTATAGTTAAATGAAGGTGATGTGTACATCTTCACATAGTGCTGGACACATGTGAATAAATAGCAGATTTATTGCTAATTAGCCA
> GAAGACCTAACGTCATAGCTCAGGGATGAGCATGATTTTGTTTTGCCAAAAATGGCATGGCAAATCACGATGAGATTTCTGTAATACATAATTTGGGTAATTCTTTCTATGTCAGTAACGGCTGTCTCTTCTCCATTCTCTGGGTTTGTGGATGTTACTGGGCAGCTCTGAGTTTGGGAGCACCTCCCATGTCTAATTCTCCTAAGTCCTGGGAAGCGTTGACCCAACTTTATGGTAAAGATAATTCCAGAAAGTTTAATCTACTGACAGTCAAACAGAATGTAGCTAGAAGTCCAGTTTGGCTTCAAAACCTGTGCTAGTACTCATGCTTCTGACTGGTAGCTGCAAGGGGTGGGGGATACTCGGGATACTCATAAAGCCGCTACCACTTTTTTGAAAATCAATTTTTCAGTAGTTTTCAAAAACTTGAGAATGAACCAACTTTACCAAGAATG',
>                                            'alphabet' => 'dna'
>                                          }, 'Bio::PrimarySeq' ),
>                  '_root_verbose' => 0
>                }, 'Bio::Seq' );
> Can't locate object method "nextSbjct" via package "Bio::Seq" 
> 
> 
> 
> Thanks,
> Xiujing Gu
> 
> 
> --- On Mon, 2/1/10, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:
> 
> From: Smithies, Russell <Russell.Smithies at agresearch.co.nz>
> Subject: RE: [Bioperl-l] Fwd: megablast using bioperl
> To: "'BioPerl List'" <bioperl-l at lists.open-bio.org>
> Cc: "'xiujingg at yahoo.com'" <xiujingg at yahoo.com>
> Date: Monday, February 1, 2010, 3:12 PM
> 
> Have you read the docs? It's very well documented:
> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/StandAloneBlast.pm
> 
> Have you searched the BioPerl wiki? Again, well documented with examples:
> http://www.bioperl.org/wiki/HOWTO:StandAloneBlast
> 
> And if that doesn't help, perhaps you need to improve your Google skills:
> http://www.google.com/support/websearch/?ctx=web
> 
> --Russell
> 
> 
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Jason Stajich
>> Sent: Tuesday, 2 February 2010 8:48 a.m.
>> To: BioPerl List
>> Cc: xiujingg at yahoo.com
>> Subject: [Bioperl-l] Fwd: megablast using bioperl
>> 
>> Xiujing -
>> Your message is best asked on the mailing list.
>> 
>> Begin forwarded message:
>> 
>>> From: Xiujing Gu <xiujingg at yahoo.com>
>>> Date: February 1, 2010 7:58:55 AM PST
>>> To: jason at bioperl.org
>>> Subject: megablast using bioperl
>>> 
>>> Hello Jason:
>>> 
>>> After numerous googling, I found you might be the only person who
>>> knows about this subject. Would you so kindly show me an example of
>>> setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
>>> 
>>> Thanks a lot!
>>> 
>>> Best regards,
>>> Xiujing
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From Russell.Smithies at agresearch.co.nz  Mon Feb  1 17:42:31 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 2 Feb 2010 11:42:31 +1300
Subject: [Bioperl-l] Fwd: megablast using bioperl
In-Reply-To: <786A566A-E72E-441E-A9FE-E4B124332EE8@illinois.edu>
References: <718515.61675.qm@web30905.mail.mud.yahoo.com>
	<786A566A-E72E-441E-A9FE-E4B124332EE8@illinois.edu>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61B8223C@exchsth.agresearch.co.nz>

I don't think it allows a discontiguous template when run via blastall though.
"blastall -p blastn -n T"  will give you a different result than straight megablast.

--Russell

> -----Original Message-----
> From: Chris Fields [mailto:cjfields at illinois.edu]
> Sent: Tuesday, 2 February 2010 11:03 a.m.
> To: Xiujing Gu
> Cc: 'BioPerl List'; Smithies, Russell
> Subject: Re: [Bioperl-l] Fwd: megablast using bioperl
> 
> Acc. to the blastall docs MEGABLAST is just setting -n to T for blastall.
> Is that what you mean?
> 
> pyrimidine1:~ cjfields$ blast-2.2.22/bin/blastall -
> 
> blastall 2.2.22   arguments:
> 
>   -p  Program Name [String]
>   -d  Database [String]
>     default = nr
> ...
>   -n  MegaBlast search [T/F]
>     default = F
> 
> chris
> 
> On Feb 1, 2010, at 2:38 PM, Xiujing Gu wrote:
> 
> > Thanks for the links!
> > But, they only talk about the regular blastall program, not the
> megablast.
> >
> > I am not sure how can I switch from blastall to megablast. I tried to
> just call megablast, but I got a very differenct report.
> >
> > $VAR1 = bless( {
> >                  'primary_seq' => bless( {
> >                                            'display_id' => 'test',
> >                                            '_seq_length' => undef,
> >                                            '_root_verbose' => 0,
> >                                            'seq' =>
> >
> 'TGAACCTAGAAGTATTTGTTGCTGGGTTTGTCTTCAGGTTCTGTTGCTCGGTTTTCTAGTTCCCCACCTAGTC
> TGGGTTACTCTGCAGCTACTTTTGCATTACAATGGCCTTGGTGAGACTGGTAGACGGGATTAACTGAGAATTCA
> CAAGGGTGGGTCAGTAGGGGGTGTGCCCGCCAGGAGGGGTGGGTCTAAGGTGATAGAGCCTTCATTATAAATCT
> AGAGACTCCAGGATTTTAACGTTCTGCTGGACTGAGCTGGTTGCCTCATGTTATTATGCAGGCAACTCACTTTA
> TCCCAATTTCTTGATACTTTTCCTTCTGGAGGTCCTATTTCTCTAACATCTTCCAGAAAAGTCTTAAAGCTGCC
> TTAACCTTTTTTCCAGTCCACCTCTTAAATTTTTTCCTCCTCTTCCTCTATACTAACATGAGTGTGGATCCAGC
> TTGTCCCCAAAGCTTGCCTTGCTTTGAAGCATCCGACTGTAAAGAATCTTCACCTATGCCTGTGATTTGTGGGC
> CTGAAGAAAACTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACGGAGACTGGTAAGAAAGAAATT
> TATCCTTGAAAGGCCAAGTTCCTTAAGGGAAAAGAGAGAAGGAGAGAGGGTTAAGGGATCATTTCCCTCTTGAG
> CAATGATGGACCATTACTATAAAGAAGTGTTATTATCAACTAATCCTCTGGAAACCCCTTTTTCCATTATAACT
> TGGTGGCACCTGCCCTTTGAACTATGTCCCAGGTCTCAGGAGTGTGCATTGAGTTGAAGGACACAGAATTCGGC
> AGTTGAACAGTGTGCAGTAAGTTTGAGAACCTATGGGCTTAGGCATGGTGGAAACAAAAATGTATCGTTATAGT
> TAAATGAAGGTGATGTGTACATCTTCACATAGTGCTGGACACATGTGAATAAATAGCAGATTTATTGCTAATTA
> GCCA
> >
> GAAGACCTAACGTCATAGCTCAGGGATGAGCATGATTTTGTTTTGCCAAAAATGGCATGGCAAATCACGATGAG
> ATTTCTGTAATACATAATTTGGGTAATTCTTTCTATGTCAGTAACGGCTGTCTCTTCTCCATTCTCTGGGTTTG
> TGGATGTTACTGGGCAGCTCTGAGTTTGGGAGCACCTCCCATGTCTAATTCTCCTAAGTCCTGGGAAGCGTTGA
> CCCAACTTTATGGTAAAGATAATTCCAGAAAGTTTAATCTACTGACAGTCAAACAGAATGTAGCTAGAAGTCCA
> GTTTGGCTTCAAAACCTGTGCTAGTACTCATGCTTCTGACTGGTAGCTGCAAGGGGTGGGGGATACTCGGGATA
> CTCATAAAGCCGCTACCACTTTTTTGAAAATCAATTTTTCAGTAGTTTTCAAAAACTTGAGAATGAACCAACTT
> TACCAAGAATG',
> >                                            'alphabet' => 'dna'
> >                                          }, 'Bio::PrimarySeq' ),
> >                  '_root_verbose' => 0
> >                }, 'Bio::Seq' );
> > Can't locate object method "nextSbjct" via package "Bio::Seq"
> >
> >
> >
> > Thanks,
> > Xiujing Gu
> >
> >
> > --- On Mon, 2/1/10, Smithies, Russell
> <Russell.Smithies at agresearch.co.nz> wrote:
> >
> > From: Smithies, Russell <Russell.Smithies at agresearch.co.nz>
> > Subject: RE: [Bioperl-l] Fwd: megablast using bioperl
> > To: "'BioPerl List'" <bioperl-l at lists.open-bio.org>
> > Cc: "'xiujingg at yahoo.com'" <xiujingg at yahoo.com>
> > Date: Monday, February 1, 2010, 3:12 PM
> >
> > Have you read the docs? It's very well documented:
> > http://search.cpan.org/~cjfields/BioPerl-
> 1.6.1/Bio/Tools/Run/StandAloneBlast.pm
> >
> > Have you searched the BioPerl wiki? Again, well documented with
> examples:
> > http://www.bioperl.org/wiki/HOWTO:StandAloneBlast
> >
> > And if that doesn't help, perhaps you need to improve your Google
> skills:
> > http://www.google.com/support/websearch/?ctx=web
> >
> > --Russell
> >
> >
> >
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >> bounces at lists.open-bio.org] On Behalf Of Jason Stajich
> >> Sent: Tuesday, 2 February 2010 8:48 a.m.
> >> To: BioPerl List
> >> Cc: xiujingg at yahoo.com
> >> Subject: [Bioperl-l] Fwd: megablast using bioperl
> >>
> >> Xiujing -
> >> Your message is best asked on the mailing list.
> >>
> >> Begin forwarded message:
> >>
> >>> From: Xiujing Gu <xiujingg at yahoo.com>
> >>> Date: February 1, 2010 7:58:55 AM PST
> >>> To: jason at bioperl.org
> >>> Subject: megablast using bioperl
> >>>
> >>> Hello Jason:
> >>>
> >>> After numerous googling, I found you might be the only person who
> >>> knows about this subject. Would you so kindly show me an example of
> >>> setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
> >>>
> >>> Thanks a lot!
> >>>
> >>> Best regards,
> >>> Xiujing
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > =======================================================================
> > Attention: The information contained in this message and/or attachments
> > from AgResearch Limited is intended only for the persons or entities
> > to which it is addressed and may contain confidential and/or privileged
> > material. Any review, retransmission, dissemination or other use of, or
> > taking of any action in reliance upon, this information by persons or
> > entities other than the intended recipients is prohibited by AgResearch
> > Limited. If you have received this message in error, please notify the
> > sender immediately.
> > =======================================================================
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l



From Russell.Smithies at agresearch.co.nz  Mon Feb  1 19:27:16 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 2 Feb 2010 13:27:16 +1300
Subject: [Bioperl-l] Fwd: megablast using bioperl
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32C618DD435@exchsth.agresearch.co.nz>
References: <718515.61675.qm@web30905.mail.mud.yahoo.com>
	<786A566A-E72E-441E-A9FE-E4B124332EE8@illinois.edu>
	<18DF7D20DFEC044098A1062202F5FFF32C618DD435@exchsth.agresearch.co.nz>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61B822D1@exchsth.agresearch.co.nz>

As I suspected, default gap penalties are different when running "megablast" and "blastall -p blastn -n T".
Here are hits to the same sequence obtained both ways:

=========================================
Megablast
>gb|FJ882402.1|  Sus scrofa homeodomain transcription factor Nanog-like protein
           mRNA, complete cds
          Length = 925

 Score = 93.7 bits (47), Expect = 2e-15
 Identities = 129/155 (83%), Gaps = 8/155 (5%)
 Strand = Plus / Plus

                                                                       
Query: 427 atgagtgtggatccagcttgtccccaaagcttgccttgctttgaagcatccgactgtaaa 486
           |||||||||||||||||||||||||||||| ||| ||||   ||||||||| | | |  |
Sbjct: 1   atgagtgtggatccagcttgtccccaaagcctgctttgccccgaagcatcc-att-tcca 58

                                                                       
Query: 487 g--aatcttcacctatgcctgtgatttgtgggcctgaagaaaactat-ccatccttgcaa 543
           |  |||||||||| ||||||| | ||| ||||||||||||||| ||| || |||||||| 
Sbjct: 59  gcgaatcttcaccaatgcctgaggtttatgggcctgaagaaaattatgcc-tccttgcag 117

                                              
Query: 544 atgtcttctgctgagatgcctc-acacggagactg 577
           |||||  |||||||||  |||| |||| |||||||
Sbjct: 118 atgtcagctgctgagac-cctcgacaccgagactg 151


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
  GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Jan 26, 2010  5:41 PM
  Number of letters in database: 29,627,559,461
  Number of sequences in database:  10,420,530
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 0, Extension: 0
==========================================================
blastall -p blastn  -n T
>gb|FJ882402.1|  Sus scrofa homeodomain transcription factor Nanog-like protein
           mRNA, complete cds
          Length = 925

 Score = 89.7 bits (45), Expect = 3e-14
 Identities = 111/133 (83%)
 Strand = Plus / Plus

                                                                       
Query: 427 atgagtgtggatccagcttgtccccaaagcttgccttgctttgaagcatccgactgtaaa 486
           |||||||||||||||||||||||||||||| ||| ||||   |||||||||   |  |  
Sbjct: 1   atgagtgtggatccagcttgtccccaaagcctgctttgccccgaagcatccatttccagc 60

                                                                       
Query: 487 gaatcttcacctatgcctgtgatttgtgggcctgaagaaaactatccatccttgcaaatg 546
           ||||||||||| ||||||| | ||| ||||||||||||||| ||| | |||||||| |||
Sbjct: 61  gaatcttcaccaatgcctgaggtttatgggcctgaagaaaattatgcctccttgcagatg 120

                        
Query: 547 tcttctgctgaga 559
           ||  |||||||||
Sbjct: 121 tcagctgctgaga 133


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
  GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Jan 26, 2010  5:41 PM
  Number of letters in database: 29,627,559,461
  Number of sequences in database:  10,420,530
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2







--Russell







> -----Original Message-----
> From: Smithies, Russell
> Sent: Tuesday, 2 February 2010 11:43 a.m.
> To: 'Chris Fields'; 'Xiujing Gu'
> Cc: 'BioPerl List'
> Subject: RE: [Bioperl-l] Fwd: megablast using bioperl
> 
> I don't think it allows a discontiguous template when run via blastall
> though.
> "blastall -p blastn -n T"  will give you a different result than straight
> megablast.
> 
> --Russell
> 
> > -----Original Message-----
> > From: Chris Fields [mailto:cjfields at illinois.edu]
> > Sent: Tuesday, 2 February 2010 11:03 a.m.
> > To: Xiujing Gu
> > Cc: 'BioPerl List'; Smithies, Russell
> > Subject: Re: [Bioperl-l] Fwd: megablast using bioperl
> >
> > Acc. to the blastall docs MEGABLAST is just setting -n to T for
> blastall.
> > Is that what you mean?
> >
> > pyrimidine1:~ cjfields$ blast-2.2.22/bin/blastall -
> >
> > blastall 2.2.22   arguments:
> >
> >   -p  Program Name [String]
> >   -d  Database [String]
> >     default = nr
> > ...
> >   -n  MegaBlast search [T/F]
> >     default = F
> >
> > chris
> >
> > On Feb 1, 2010, at 2:38 PM, Xiujing Gu wrote:
> >
> > > Thanks for the links!
> > > But, they only talk about the regular blastall program, not the
> > megablast.
> > >
> > > I am not sure how can I switch from blastall to megablast. I tried to
> > just call megablast, but I got a very differenct report.
> > >
> > > $VAR1 = bless( {
> > >                  'primary_seq' => bless( {
> > >                                            'display_id' => 'test',
> > >                                            '_seq_length' => undef,
> > >                                            '_root_verbose' => 0,
> > >                                            'seq' =>
> > >
> >
> 'TGAACCTAGAAGTATTTGTTGCTGGGTTTGTCTTCAGGTTCTGTTGCTCGGTTTTCTAGTTCCCCACCTAGTC
> >
> TGGGTTACTCTGCAGCTACTTTTGCATTACAATGGCCTTGGTGAGACTGGTAGACGGGATTAACTGAGAATTCA
> >
> CAAGGGTGGGTCAGTAGGGGGTGTGCCCGCCAGGAGGGGTGGGTCTAAGGTGATAGAGCCTTCATTATAAATCT
> >
> AGAGACTCCAGGATTTTAACGTTCTGCTGGACTGAGCTGGTTGCCTCATGTTATTATGCAGGCAACTCACTTTA
> >
> TCCCAATTTCTTGATACTTTTCCTTCTGGAGGTCCTATTTCTCTAACATCTTCCAGAAAAGTCTTAAAGCTGCC
> >
> TTAACCTTTTTTCCAGTCCACCTCTTAAATTTTTTCCTCCTCTTCCTCTATACTAACATGAGTGTGGATCCAGC
> >
> TTGTCCCCAAAGCTTGCCTTGCTTTGAAGCATCCGACTGTAAAGAATCTTCACCTATGCCTGTGATTTGTGGGC
> >
> CTGAAGAAAACTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACGGAGACTGGTAAGAAAGAAATT
> >
> TATCCTTGAAAGGCCAAGTTCCTTAAGGGAAAAGAGAGAAGGAGAGAGGGTTAAGGGATCATTTCCCTCTTGAG
> >
> CAATGATGGACCATTACTATAAAGAAGTGTTATTATCAACTAATCCTCTGGAAACCCCTTTTTCCATTATAACT
> >
> TGGTGGCACCTGCCCTTTGAACTATGTCCCAGGTCTCAGGAGTGTGCATTGAGTTGAAGGACACAGAATTCGGC
> >
> AGTTGAACAGTGTGCAGTAAGTTTGAGAACCTATGGGCTTAGGCATGGTGGAAACAAAAATGTATCGTTATAGT
> >
> TAAATGAAGGTGATGTGTACATCTTCACATAGTGCTGGACACATGTGAATAAATAGCAGATTTATTGCTAATTA
> > GCCA
> > >
> >
> GAAGACCTAACGTCATAGCTCAGGGATGAGCATGATTTTGTTTTGCCAAAAATGGCATGGCAAATCACGATGAG
> >
> ATTTCTGTAATACATAATTTGGGTAATTCTTTCTATGTCAGTAACGGCTGTCTCTTCTCCATTCTCTGGGTTTG
> >
> TGGATGTTACTGGGCAGCTCTGAGTTTGGGAGCACCTCCCATGTCTAATTCTCCTAAGTCCTGGGAAGCGTTGA
> >
> CCCAACTTTATGGTAAAGATAATTCCAGAAAGTTTAATCTACTGACAGTCAAACAGAATGTAGCTAGAAGTCCA
> >
> GTTTGGCTTCAAAACCTGTGCTAGTACTCATGCTTCTGACTGGTAGCTGCAAGGGGTGGGGGATACTCGGGATA
> >
> CTCATAAAGCCGCTACCACTTTTTTGAAAATCAATTTTTCAGTAGTTTTCAAAAACTTGAGAATGAACCAACTT
> > TACCAAGAATG',
> > >                                            'alphabet' => 'dna'
> > >                                          }, 'Bio::PrimarySeq' ),
> > >                  '_root_verbose' => 0
> > >                }, 'Bio::Seq' );
> > > Can't locate object method "nextSbjct" via package "Bio::Seq"
> > >
> > >
> > >
> > > Thanks,
> > > Xiujing Gu
> > >
> > >
> > > --- On Mon, 2/1/10, Smithies, Russell
> > <Russell.Smithies at agresearch.co.nz> wrote:
> > >
> > > From: Smithies, Russell <Russell.Smithies at agresearch.co.nz>
> > > Subject: RE: [Bioperl-l] Fwd: megablast using bioperl
> > > To: "'BioPerl List'" <bioperl-l at lists.open-bio.org>
> > > Cc: "'xiujingg at yahoo.com'" <xiujingg at yahoo.com>
> > > Date: Monday, February 1, 2010, 3:12 PM
> > >
> > > Have you read the docs? It's very well documented:
> > > http://search.cpan.org/~cjfields/BioPerl-
> > 1.6.1/Bio/Tools/Run/StandAloneBlast.pm
> > >
> > > Have you searched the BioPerl wiki? Again, well documented with
> > examples:
> > > http://www.bioperl.org/wiki/HOWTO:StandAloneBlast
> > >
> > > And if that doesn't help, perhaps you need to improve your Google
> > skills:
> > > http://www.google.com/support/websearch/?ctx=web
> > >
> > > --Russell
> > >
> > >
> > >
> > >> -----Original Message-----
> > >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > >> bounces at lists.open-bio.org] On Behalf Of Jason Stajich
> > >> Sent: Tuesday, 2 February 2010 8:48 a.m.
> > >> To: BioPerl List
> > >> Cc: xiujingg at yahoo.com
> > >> Subject: [Bioperl-l] Fwd: megablast using bioperl
> > >>
> > >> Xiujing -
> > >> Your message is best asked on the mailing list.
> > >>
> > >> Begin forwarded message:
> > >>
> > >>> From: Xiujing Gu <xiujingg at yahoo.com>
> > >>> Date: February 1, 2010 7:58:55 AM PST
> > >>> To: jason at bioperl.org
> > >>> Subject: megablast using bioperl
> > >>>
> > >>> Hello Jason:
> > >>>
> > >>> After numerous googling, I found you might be the only person who
> > >>> knows about this subject. Would you so kindly show me an example of
> > >>> setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
> > >>>
> > >>> Thanks a lot!
> > >>>
> > >>> Best regards,
> > >>> Xiujing
> > >> _______________________________________________
> > >> Bioperl-l mailing list
> > >> Bioperl-l at lists.open-bio.org
> > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >
> =======================================================================
> > > Attention: The information contained in this message and/or
> attachments
> > > from AgResearch Limited is intended only for the persons or entities
> > > to which it is addressed and may contain confidential and/or
> privileged
> > > material. Any review, retransmission, dissemination or other use of,
> or
> > > taking of any action in reliance upon, this information by persons or
> > > entities other than the intended recipients is prohibited by
> AgResearch
> > > Limited. If you have received this message in error, please notify the
> > > sender immediately.
> > >
> =======================================================================
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l



From mmuratet at hudsonalpha.org  Tue Feb  2 07:14:17 2010
From: mmuratet at hudsonalpha.org (Michael Muratet)
Date: Tue, 2 Feb 2010 06:14:17 -0600
Subject: [Bioperl-l] Apparent disagreement between EUtilities and web page
In-Reply-To: <be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
Message-ID: <3D2AF4CC-D10D-479C-868F-E78B9EC3B420@hudsonalpha.org>

Greetings

I am using EUtilities for the first time to retrieve data from NCBI  
and I could use some help trying to isolate a problem I have. I was  
using a script I put together from examples in the How-To and email  
archives

            $factory->set_parameters(-id => \@sub );

            while ( my $docsum =$factory->next_DocSum ) {
               my ($item) = $docsum- 
 >get_Items_by_name('GenomicInfoType');

               my ( $chrloc, $acc, $start, $end) = (
                                       $item- 
 >get_contents_by_name('ChrLoc'),
                                       $item- 
 >get_contents_by_name('ChrAccVer'),
                                       $item- 
 >get_contents_by_name('ChrStart'),
                                       $item- 
 >get_contents_by_name('ChrStop'));

and I found a record that has a suspect ChrStart field and no ChrStop  
field (using another example from the HowTo)

ID: 100039753
Name-Description-Orgname-Status-CurrentID-Chromosome-GeneticSource- 
MapLocation-OtherAliases-OtherDesignations-NomenclatureSymbol- 
NomenclatureName-NomenclatureStatus-TaxID-Mim-GenomicInfo-GeneWeight- 
Summary-ChrSort-ChrStart
Name                :LOC100039753
Description         :similar to putative
Orgname             :Mus musculus
Chromosome          :Y
GeneticSource       :genomic
MapLocation         :Y B
OtherDesignations   :hypothetical protein LOC100039753
TaxID               :10090
GeneWeight          :401
ChrSort             :~~last
ChrStart            :999999999

yet on the NCBI web page it shows a defined start and a stop for the  
locus.

I can fix the perl code so that it won't barf when the field isn't  
defined, but I'd like to get all the data and I can't figure out if  
the problem is on the client side or the server side. All the data  
comes from the same source, doesn't it?

Thanks

Mike


From robert.bradbury at gmail.com  Tue Feb  2 08:57:53 2010
From: robert.bradbury at gmail.com (Robert Bradbury)
Date: Tue, 2 Feb 2010 08:57:53 -0500
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <be9b52411002011333h10d27649k46ea581d35be7b8@mail.gmail.com>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
	<2F1F855C-16BF-42ED-BE91-63CD1B331F90@illinois.edu>
	<be9b52411002011333h10d27649k46ea581d35be7b8@mail.gmail.com>
Message-ID: <deaa866a1002020557v4ed134e4mb783e99e7c33de05@mail.gmail.com>

What species/chromosome is this?

> > my $id = 'AAPP01000000[ACCN]';
>
>
One can usually download the genome sequence files, chromosome files, or
fasta files from the various FTP sites (almost all of the major genomes have
them) or the that would generally be the fastest way to do it.  Or simply
look up the Genome sequence at NCBI and download it using a web browser.
There is standard documentation on how to convert genome sequences into
fasta files.

If you are looking for the "big" genomes which may not be in NCBI yet, go to
the Broad Institute.  Some bacterial sequences may still only be at TIGR or
JGI until they migrate upward.

But using the standard "system" utilities to do this is usually a far better
way to do this then wrestling in BioPerl.  FTP and Web Servers are written
in C or C++ which is compiled and much more efficient than an interpreted
language like Perl or Java.

Robert

From cjfields at illinois.edu  Tue Feb  2 09:04:49 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 2 Feb 2010 08:04:49 -0600
Subject: [Bioperl-l] FeatureIO refactoring
Message-ID: <85A8D301-1E20-4981-9741-C5EC437A639E@illinois.edu>

All,

Based on a few discussions from the BioPerl meeting, I've decided to go ahead, bite the bullet, and (on a branch) pull out the Bio::FeatureIO code from core for refactoring.  FeatureIO-based code now lies in the Bio-FeatureIO repository in bioperl's SVN.  The resulting code (FeatureIO-less) core probably won't be merged back into main trunk until after a 1.6.2 release, at which point we may just proceed towards the long-awaited restructuring scheme for BioPerl.

I'm pretty open for discussion on how to proceed.  My current somewhat loose plans:

1) Rewrite FeatureIO code to remove dependencies specifically on Bio::SeqFeature::Annotated (BSFA).

There have been several arguments on and off list as to BSFA's issues.  I think, due to BSFA's idiosyncracies, it's best to remove use of it from BioPerl and replace it with something more lightweight.

2) Consolidate FeatureIO around Bio::DB::SeqFeature::Store's Loader classes and built-in SeqFeature methods for generating GFF data. 

No need to rehash code if it's already working well (and an opportunity to fix code that needs it).  In particular, the GFF3 loader appears to be working very well.  However, if there are any caveats, this would be the time to air them!  Also, with that mind...

3) Optional type-checking against SO/SOFA using tools already in place (Bio::Ontology::*)

This is a bit trickier, as I don't recall Bio::DB::SeqFeature having any typing mechanism, I'm guessing in keeping with it's lightweight nature.  Should we use the attribute Ontology_term for this?

4) Of course, addressing any FeatureIO-related bugs present in Bugzilla.

 

Feedback and suggestions welcome!

chris

From cjfields at illinois.edu  Tue Feb  2 09:06:09 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 2 Feb 2010 08:06:09 -0600
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <deaa866a1002020557v4ed134e4mb783e99e7c33de05@mail.gmail.com>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
	<2F1F855C-16BF-42ED-BE91-63CD1B331F90@illinois.edu>
	<be9b52411002011333h10d27649k46ea581d35be7b8@mail.gmail.com>
	<deaa866a1002020557v4ed134e4mb783e99e7c33de05@mail.gmail.com>
Message-ID: <8CE3E21B-CBBA-4F43-8D68-0A37030CC5D0@illinois.edu>

On Feb 2, 2010, at 7:57 AM, Robert Bradbury wrote:

> 
> What species/chromosome is this?
> > my $id = 'AAPP01000000[ACCN]';
> 
> 
> One can usually download the genome sequence files, chromosome files, or fasta files from the various FTP sites (almost all of the major genomes have them) or the that would generally be the fastest way to do it.  Or simply look up the Genome sequence at NCBI and download it using a web browser.  There is standard documentation on how to convert genome sequences into fasta files.

Yes, Robert, that is true.  This is just an example sequence file demonstrating the problem; retrieving the sequences via FTP would be more efficient.  However, if one had hundreds of these, and the IDs weren't known ahead of time (they cam from a prior analysis), then this wouldn't be the case.  And this is a common issue.`

> If you are looking for the "big" genomes which may not be in NCBI yet, go to the Broad Institute.  Some bacterial sequences may still only be at TIGR or JGI until they migrate upward.
> 
> But using the standard "system" utilities to do this is usually a far better way to do this then wrestling in BioPerl.  FTP and Web Servers are written in C or C++ which is compiled and much more efficient than an interpreted language like Perl or Java.
> 
> Robert

Actually, most if not all the web services stuff is in Java, and (for many genome sites) they use other languages besides C/C++ (Perl, Python, Ruby, etc).  Ensembl, FlyBase, etc come to mind.

chris

From cjfields at illinois.edu  Tue Feb  2 09:34:46 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 2 Feb 2010 08:34:46 -0600
Subject: [Bioperl-l] Apparent disagreement between EUtilities and web
	page
In-Reply-To: <3D2AF4CC-D10D-479C-868F-E78B9EC3B420@hudsonalpha.org>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
	<3D2AF4CC-D10D-479C-868F-E78B9EC3B420@hudsonalpha.org>
Message-ID: <534C7B91-C42B-4032-A78E-C9202EE44E7B@illinois.edu>

Michael,

This is an unusual one and appears to be server-side.  I've seen this before with older obsoleted gene IDs (see: 435023, which is the older version of 100039753), so I'm wondering if an update going on that hasn't made it's way to the web interface yet.

I'm attempting to contact NCBI about the issue, so hopefully we'll hear back.

chris

On Feb 2, 2010, at 6:14 AM, Michael Muratet wrote:

> Greetings
> 
> I am using EUtilities for the first time to retrieve data from NCBI and I could use some help trying to isolate a problem I have. I was using a script I put together from examples in the How-To and email archives
> 
>           $factory->set_parameters(-id => \@sub );
> 
>           while ( my $docsum =$factory->next_DocSum ) {
>              my ($item) = $docsum->get_Items_by_name('GenomicInfoType');
> 
>              my ( $chrloc, $acc, $start, $end) = (
>                                      $item->get_contents_by_name('ChrLoc'),
>                                      $item->get_contents_by_name('ChrAccVer'),
>                                      $item->get_contents_by_name('ChrStart'),
>                                      $item->get_contents_by_name('ChrStop'));
> 
> and I found a record that has a suspect ChrStart field and no ChrStop field (using another example from the HowTo)
> 
> ID: 100039753
> Name-Description-Orgname-Status-CurrentID-Chromosome-GeneticSource-MapLocation-OtherAliases-OtherDesignations-NomenclatureSymbol-NomenclatureName-NomenclatureStatus-TaxID-Mim-GenomicInfo-GeneWeight-Summary-ChrSort-ChrStart
> Name                :LOC100039753
> Description         :similar to putative
> Orgname             :Mus musculus
> Chromosome          :Y
> GeneticSource       :genomic
> MapLocation         :Y B
> OtherDesignations   :hypothetical protein LOC100039753
> TaxID               :10090
> GeneWeight          :401
> ChrSort             :~~last
> ChrStart            :999999999
> 
> yet on the NCBI web page it shows a defined start and a stop for the locus.
> 
> I can fix the perl code so that it won't barf when the field isn't defined, but I'd like to get all the data and I can't figure out if the problem is on the client side or the server side. All the data comes from the same source, doesn't it?
> 
> Thanks
> 
> Mike
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From shalabh.sharma7 at gmail.com  Tue Feb  2 10:16:26 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 2 Feb 2010 10:16:26 -0500
Subject: [Bioperl-l] Mapping Blast results
Message-ID: <9fcc48c71002020716u2981596ekf3ca36cc693200f0@mail.gmail.com>

Hi,
    I am trying to map blast results on a gene. I am using Bio::Graphics
    http://bioperl.org/wiki/HOWTO:Graphics

This is working fine for small blast files but not for large blast file with
lot of hits. Is there any way i can use this for large blast files?

Thanks
Shalabh

From lsbrath at gmail.com  Tue Feb  2 10:40:45 2010
From: lsbrath at gmail.com (Mgavi Brathwaite)
Date: Tue, 2 Feb 2010 10:40:45 -0500
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <2F1F855C-16BF-42ED-BE91-63CD1B331F90@illinois.edu>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
	<2F1F855C-16BF-42ED-BE91-63CD1B331F90@illinois.edu>
Message-ID: <69367b8f1002020740x23f05aecn633c27b242deb56a@mail.gmail.com>

What "cookbook"?

Mgavi

On Mon, Feb 1, 2010 at 4:31 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Abhi,
>
> The accession in question is for a record containing a set of sequences,
> not just one sequence (it's a contig record).  The NCBI web interface is
> performing an esearch on this to get 34K seqs, the equivalent with
> EUtilities is:
>
> ================================
> use Bio::DB::EUtilities;
>
> my $id = 'AAPP01000000[ACCN]';
>
> my $factory = Bio::DB::EUtilities->new  (
>        -eutil =>  'esearch',
>       -db    =>  'nucleotide',
>       -term  =>  $id,
>       -usehistory => 'y');
>
> say $factory->get_count;
>
> # do more here...
>
> ================================
>
> The 'do more here' part is covered in the cookbook, and will require you
> retrieving the seqs in chunks.
>
> chris
>
> On Feb 1, 2010, at 2:45 PM, Abhishek Pratap wrote:
>
> > Thank you guys for very quick responses.  My bad I trusted my fingers.
> >
> > Now that this is working the output that I am getting is not what I
> > want. I am sure I am missing the correct way of doing it. So If I
> > search the Nucleotide db @NCBI for this accession number "
> > AAPP01000000", I see some 34 k records. What I need to do is pull down
> > those sequences as fasta files.
> >
> > I am referring to
> > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook  but dint quite
> > find a similar example.
> >
> > Thanks!
> > -Abhi
> >
> > On Mon, Feb 1, 2010 at 3:39 PM, Kevin Brown <Kevin.M.Brown at asu.edu>
> wrote:
> >> Looks like you've misspelled one of the parameters. It should be
> >> 'efetch' not 'efecth'
> >>
> >> Kevin Brown
> >> Center for Innovations in Medicine
> >> Biodesign Institute
> >> Arizona State University
> >>
> >>> -----Original Message-----
> >>> From: bioperl-l-bounces at lists.open-bio.org
> >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> >>> Abhishek Pratap
> >>> Sent: Monday, February 01, 2010 1:36 PM
> >>> To: bioperl-l at lists.open-bio.org
> >>> Subject: [Bioperl-l] Pulling down data from NCBI
> >>>
> >>> Hi All
> >>>
> >>> I looking to batch download some 34K nucleotide sequences,
> >>> corresponding to a NCBI accession number. I tired the following and
> >>> getting an error. Has it got anything to do with recent update to code
> >>> that Chris was discussing.
> >>>
> >>>
> >>>
> >>> my $factory = Bio::DB::EUtilities->new  (
> >>>                                       -eutil  => 'efecth',
> >>>                                       -db     =>      'nucleotide',
> >>>                                       -retype =>      'fasta',
> >>>                                       -id             => $id
> >>>                               );
> >>>
> >>>
> >>> ----------- EXCEPTION: Bio::Root::Exception -------------
> >>> MSG: efecth not supported
> >>> STACK: Error::throw
> >>> STACK: Bio::Root::Root::throw
> >>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:357
> >>> STACK: Bio::Tools::EUtilities::EUtilParameters::eutil
> >>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
> >>> ameters.pm:452
> >>> STACK: Bio::Root::RootI::_set_from_args
> >>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/RootI.pm:546
> >>> STACK: Bio::Tools::EUtilities::EUtilParameters::new
> >>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
> >>> ameters.pm:193
> >>> STACK: Bio::DB::EUtilities::new
> >>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/EUtilities.pm:74
> >>> STACK: ./getDatafromNCBI.pl:9
> >>>
> >>>
> >>> -Abhi
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From cjfields at illinois.edu  Tue Feb  2 11:14:01 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 2 Feb 2010 10:14:01 -0600
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <69367b8f1002020740x23f05aecn633c27b242deb56a@mail.gmail.com>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
	<2F1F855C-16BF-42ED-BE91-63CD1B331F90@illinois.edu>
	<69367b8f1002020740x23f05aecn633c27b242deb56a@mail.gmail.com>
Message-ID: <0B50E488-6821-47DF-AD11-C6C297670C40@illinois.edu>

On Feb 2, 2010, at 9:40 AM, Mgavi Brathwaite wrote:

> What "cookbook"?
> 
> Mgavi

http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

chris

From folmerf at gmail.com  Tue Feb  2 11:16:48 2010
From: folmerf at gmail.com (Folmer Fredslund)
Date: Tue, 2 Feb 2010 17:16:48 +0100
Subject: [Bioperl-l] Pulling down data from NCBI
In-Reply-To: <69367b8f1002020740x23f05aecn633c27b242deb56a@mail.gmail.com>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
	<2F1F855C-16BF-42ED-BE91-63CD1B331F90@illinois.edu>
	<69367b8f1002020740x23f05aecn633c27b242deb56a@mail.gmail.com>
Message-ID: <991070401002020816r1fc36982j84a8115efe48600d@mail.gmail.com>

Hi Mgavi,


On 2 February 2010 16:40, Mgavi Brathwaite <lsbrath at gmail.com> wrote:
> What "cookbook"?
>
> Mgavi
>

I don't know much about BioPerl yet, but merely searching for
"ncbi eutilities cookbook"
on google gave me this site
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

I would guess this is the page referred to.

This is just me saying: Please use 2min to get your own answers before
you ask everybody on this list.

Best regards,
Folmer Fredslund



> On Mon, Feb 1, 2010 at 4:31 PM, Chris Fields <cjfields at illinois.edu> wrote:
>
>> Abhi,
>>
>> The accession in question is for a record containing a set of sequences,
>> not just one sequence (it's a contig record). ?The NCBI web interface is
>> performing an esearch on this to get 34K seqs, the equivalent with
>> EUtilities is:
>>
>> ================================
>> use Bio::DB::EUtilities;
>>
>> my $id = 'AAPP01000000[ACCN]';
>>
>> my $factory = Bio::DB::EUtilities->new ?(
>> ? ? ? ?-eutil => ?'esearch',
>> ? ? ? -db ? ?=> ?'nucleotide',
>> ? ? ? -term ?=> ?$id,
>> ? ? ? -usehistory => 'y');
>>
>> say $factory->get_count;
>>
>> # do more here...
>>
>> ================================
>>
>> The 'do more here' part is covered in the cookbook, and will require you
>> retrieving the seqs in chunks.
>>
>> chris
>>
>> On Feb 1, 2010, at 2:45 PM, Abhishek Pratap wrote:
>>
>> > Thank you guys for very quick responses. ?My bad I trusted my fingers.
>> >
>> > Now that this is working the output that I am getting is not what I
>> > want. I am sure I am missing the correct way of doing it. So If I
>> > search the Nucleotide db @NCBI for this accession number "
>> > AAPP01000000", I see some 34 k records. What I need to do is pull down
>> > those sequences as fasta files.
>> >
>> > I am referring to
>> > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook ?but dint quite
>> > find a similar example.
>> >
>> > Thanks!
>> > -Abhi
>> >
>> > On Mon, Feb 1, 2010 at 3:39 PM, Kevin Brown <Kevin.M.Brown at asu.edu>
>> wrote:
>> >> Looks like you've misspelled one of the parameters. It should be
>> >> 'efetch' not 'efecth'
>> >>
>> >> Kevin Brown
>> >> Center for Innovations in Medicine
>> >> Biodesign Institute
>> >> Arizona State University
>> >>
>> >>> -----Original Message-----
>> >>> From: bioperl-l-bounces at lists.open-bio.org
>> >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>> >>> Abhishek Pratap
>> >>> Sent: Monday, February 01, 2010 1:36 PM
>> >>> To: bioperl-l at lists.open-bio.org
>> >>> Subject: [Bioperl-l] Pulling down data from NCBI
>> >>>
>> >>> Hi All
>> >>>
>> >>> I looking to batch download some 34K nucleotide sequences,
>> >>> corresponding to a NCBI accession number. I tired the following and
>> >>> getting an error. Has it got anything to do with recent update to code
>> >>> that Chris was discussing.
>> >>>
>> >>>
>> >>>
>> >>> my $factory = Bio::DB::EUtilities->new ?(
>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -eutil ?=> 'efecth',
>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -db ? ? => ? ? ?'nucleotide',
>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -retype => ? ? ?'fasta',
>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -id ? ? ? ? ? ? => $id
>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? );
>> >>>
>> >>>
>> >>> ----------- EXCEPTION: Bio::Root::Exception -------------
>> >>> MSG: efecth not supported
>> >>> STACK: Error::throw
>> >>> STACK: Bio::Root::Root::throw
>> >>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:357
>> >>> STACK: Bio::Tools::EUtilities::EUtilParameters::eutil
>> >>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
>> >>> ameters.pm:452
>> >>> STACK: Bio::Root::RootI::_set_from_args
>> >>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/RootI.pm:546
>> >>> STACK: Bio::Tools::EUtilities::EUtilParameters::new
>> >>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
>> >>> ameters.pm:193
>> >>> STACK: Bio::DB::EUtilities::new
>> >>> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/EUtilities.pm:74
>> >>> STACK: ./getDatafromNCBI.pl:9
>> >>>
>> >>>
>> >>> -Abhi
>> >>> _______________________________________________
>> >>> Bioperl-l mailing list
>> >>> Bioperl-l at lists.open-bio.org
>> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >>>
>> >>
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From scott at scottcain.net  Tue Feb  2 12:06:07 2010
From: scott at scottcain.net (Scott Cain)
Date: Tue, 2 Feb 2010 12:06:07 -0500
Subject: [Bioperl-l] [Gmod-gbrowse] FeatureIO refactoring
In-Reply-To: <85A8D301-1E20-4981-9741-C5EC437A639E@illinois.edu>
References: <85A8D301-1E20-4981-9741-C5EC437A639E@illinois.edu>
Message-ID: <4536f7701002020906r57979ca4n1833035628fae4b8@mail.gmail.com>

Hi Chris,

This sounds like a really good approach; I particularly like (2) and
tying FeatureIO to SeqFeature::Store.

About ontology checking: I think the only thing that ought to be
(optionally) checked is the type (column 3) against SO (not SOFA).  It
is true that SeqFeature::Store does no type checking, and I don't know
that it needs to, but having the option of doing that through
FeatureIO would be a good thing.

Thanks for getting this started,
Scott


On Tue, Feb 2, 2010 at 9:04 AM, Chris Fields <cjfields at illinois.edu> wrote:
> All,
>
> Based on a few discussions from the BioPerl meeting, I've decided to go ahead, bite the bullet, and (on a branch) pull out the Bio::FeatureIO code from core for refactoring. ?FeatureIO-based code now lies in the Bio-FeatureIO repository in bioperl's SVN. ?The resulting code (FeatureIO-less) core probably won't be merged back into main trunk until after a 1.6.2 release, at which point we may just proceed towards the long-awaited restructuring scheme for BioPerl.
>
> I'm pretty open for discussion on how to proceed. ?My current somewhat loose plans:
>
> 1) Rewrite FeatureIO code to remove dependencies specifically on Bio::SeqFeature::Annotated (BSFA).
>
> There have been several arguments on and off list as to BSFA's issues. ?I think, due to BSFA's idiosyncracies, it's best to remove use of it from BioPerl and replace it with something more lightweight.
>
> 2) Consolidate FeatureIO around Bio::DB::SeqFeature::Store's Loader classes and built-in SeqFeature methods for generating GFF data.
>
> No need to rehash code if it's already working well (and an opportunity to fix code that needs it). ?In particular, the GFF3 loader appears to be working very well. ?However, if there are any caveats, this would be the time to air them! ?Also, with that mind...
>
> 3) Optional type-checking against SO/SOFA using tools already in place (Bio::Ontology::*)
>
> This is a bit trickier, as I don't recall Bio::DB::SeqFeature having any typing mechanism, I'm guessing in keeping with it's lightweight nature. ?Should we use the attribute Ontology_term for this?
>
> 4) Of course, addressing any FeatureIO-related bugs present in Bugzilla.
>
>
>
> Feedback and suggestions welcome!
>
> chris
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From cjfields at illinois.edu  Tue Feb  2 12:54:55 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 2 Feb 2010 11:54:55 -0600
Subject: [Bioperl-l] Apparent disagreement between EUtilities and web
	page
In-Reply-To: <534C7B91-C42B-4032-A78E-C9202EE44E7B@illinois.edu>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
	<3D2AF4CC-D10D-479C-868F-E78B9EC3B420@hudsonalpha.org>
	<534C7B91-C42B-4032-A78E-C9202EE44E7B@illinois.edu>
Message-ID: <600261B2-E43F-465C-B7FA-6033A6795BFB@illinois.edu>

Just to follow up, it appears to be a disparity between the efetch gene data and the summary information (via esummary).  The folks at NCBI are checking up on it.

chris

On Feb 2, 2010, at 8:34 AM, Chris Fields wrote:

> Michael,
> 
> This is an unusual one and appears to be server-side.  I've seen this before with older obsoleted gene IDs (see: 435023, which is the older version of 100039753), so I'm wondering if an update going on that hasn't made it's way to the web interface yet.
> 
> I'm attempting to contact NCBI about the issue, so hopefully we'll hear back.
> 
> chris
> 
> On Feb 2, 2010, at 6:14 AM, Michael Muratet wrote:
> 
>> Greetings
>> 
>> I am using EUtilities for the first time to retrieve data from NCBI and I could use some help trying to isolate a problem I have. I was using a script I put together from examples in the How-To and email archives
>> 
>>          $factory->set_parameters(-id => \@sub );
>> 
>>          while ( my $docsum =$factory->next_DocSum ) {
>>             my ($item) = $docsum->get_Items_by_name('GenomicInfoType');
>> 
>>             my ( $chrloc, $acc, $start, $end) = (
>>                                     $item->get_contents_by_name('ChrLoc'),
>>                                     $item->get_contents_by_name('ChrAccVer'),
>>                                     $item->get_contents_by_name('ChrStart'),
>>                                     $item->get_contents_by_name('ChrStop'));
>> 
>> and I found a record that has a suspect ChrStart field and no ChrStop field (using another example from the HowTo)
>> 
>> ID: 100039753
>> Name-Description-Orgname-Status-CurrentID-Chromosome-GeneticSource-MapLocation-OtherAliases-OtherDesignations-NomenclatureSymbol-NomenclatureName-NomenclatureStatus-TaxID-Mim-GenomicInfo-GeneWeight-Summary-ChrSort-ChrStart
>> Name                :LOC100039753
>> Description         :similar to putative
>> Orgname             :Mus musculus
>> Chromosome          :Y
>> GeneticSource       :genomic
>> MapLocation         :Y B
>> OtherDesignations   :hypothetical protein LOC100039753
>> TaxID               :10090
>> GeneWeight          :401
>> ChrSort             :~~last
>> ChrStart            :999999999
>> 
>> yet on the NCBI web page it shows a defined start and a stop for the locus.
>> 
>> I can fix the perl code so that it won't barf when the field isn't defined, but I'd like to get all the data and I can't figure out if the problem is on the client side or the server side. All the data comes from the same source, doesn't it?
>> 
>> Thanks
>> 
>> Mike
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From mmuratet at hudsonalpha.org  Tue Feb  2 13:22:30 2010
From: mmuratet at hudsonalpha.org (Michael Muratet)
Date: Tue, 2 Feb 2010 12:22:30 -0600
Subject: [Bioperl-l] Apparent disagreement between EUtilities and web
	page
In-Reply-To: <600261B2-E43F-465C-B7FA-6033A6795BFB@illinois.edu>
References: <be9b52411002011236p234865a9wb3b6a0bde14314d7@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B406849E36@EX02.asurite.ad.asu.edu>
	<be9b52411002011245v21e191c8u384f4e0d7baaf76f@mail.gmail.com>
	<3D2AF4CC-D10D-479C-868F-E78B9EC3B420@hudsonalpha.org>
	<534C7B91-C42B-4032-A78E-C9202EE44E7B@illinois.edu>
	<600261B2-E43F-465C-B7FA-6033A6795BFB@illinois.edu>
Message-ID: <746E25CE-BA37-4B06-BB21-ED497127C703@hudsonalpha.org>


On Feb 2, 2010, at 11:54 AM, Chris Fields wrote:

> Just to follow up, it appears to be a disparity between the efetch  
> gene data and the summary information (via esummary).  The folks at  
> NCBI are checking up on it.
>
Chris

Thanks for the help! I put a test for defined into the script and  
managed to pull down the other 9K genes. It was just the one that had  
issues.

Mike
> chris
>
> On Feb 2, 2010, at 8:34 AM, Chris Fields wrote:
>
>> Michael,
>>
>> This is an unusual one and appears to be server-side.  I've seen  
>> this before with older obsoleted gene IDs (see: 435023, which is  
>> the older version of 100039753), so I'm wondering if an update  
>> going on that hasn't made it's way to the web interface yet.
>>
>> I'm attempting to contact NCBI about the issue, so hopefully we'll  
>> hear back.
>>
>> chris
>>
>> On Feb 2, 2010, at 6:14 AM, Michael Muratet wrote:
>>
>>> Greetings
>>>
>>> I am using EUtilities for the first time to retrieve data from  
>>> NCBI and I could use some help trying to isolate a problem I have.  
>>> I was using a script I put together from examples in the How-To  
>>> and email archives
>>>
>>>         $factory->set_parameters(-id => \@sub );
>>>
>>>         while ( my $docsum =$factory->next_DocSum ) {
>>>            my ($item) = $docsum- 
>>> >get_Items_by_name('GenomicInfoType');
>>>
>>>            my ( $chrloc, $acc, $start, $end) = (
>>>                                    $item- 
>>> >get_contents_by_name('ChrLoc'),
>>>                                    $item- 
>>> >get_contents_by_name('ChrAccVer'),
>>>                                    $item- 
>>> >get_contents_by_name('ChrStart'),
>>>                                    $item- 
>>> >get_contents_by_name('ChrStop'));
>>>
>>> and I found a record that has a suspect ChrStart field and no  
>>> ChrStop field (using another example from the HowTo)
>>>
>>> ID: 100039753
>>> Name-Description-Orgname-Status-CurrentID-Chromosome-GeneticSource- 
>>> MapLocation-OtherAliases-OtherDesignations-NomenclatureSymbol- 
>>> NomenclatureName-NomenclatureStatus-TaxID-Mim-GenomicInfo- 
>>> GeneWeight-Summary-ChrSort-ChrStart
>>> Name                :LOC100039753
>>> Description         :similar to putative
>>> Orgname             :Mus musculus
>>> Chromosome          :Y
>>> GeneticSource       :genomic
>>> MapLocation         :Y B
>>> OtherDesignations   :hypothetical protein LOC100039753
>>> TaxID               :10090
>>> GeneWeight          :401
>>> ChrSort             :~~last
>>> ChrStart            :999999999
>>>
>>> yet on the NCBI web page it shows a defined start and a stop for  
>>> the locus.
>>>
>>> I can fix the perl code so that it won't barf when the field isn't  
>>> defined, but I'd like to get all the data and I can't figure out  
>>> if the problem is on the client side or the server side. All the  
>>> data comes from the same source, doesn't it?
>>>
>>> Thanks
>>>
>>> Mike
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806






From scott at scottcain.net  Tue Feb  2 13:34:29 2010
From: scott at scottcain.net (Scott Cain)
Date: Tue, 2 Feb 2010 13:34:29 -0500
Subject: [Bioperl-l] Mapping Blast results
In-Reply-To: <9fcc48c71002020716u2981596ekf3ca36cc693200f0@mail.gmail.com>
References: <9fcc48c71002020716u2981596ekf3ca36cc693200f0@mail.gmail.com>
Message-ID: <4536f7701002021034p253c78e4u5c9b9c71cc0cb62@mail.gmail.com>

Hi Shalabh,

When you say it's not working, what do you mean?  Presumably, you
could write a script that uses Bio::DB::SeqFeature::Store if speed is
the problem, but if you wanted to go that far, your time would
probably be better spent installing GBrowse.

Scott


On Tue, Feb 2, 2010 at 10:16 AM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hi,
> ? ?I am trying to map blast results on a gene. I am using Bio::Graphics
> ? ?http://bioperl.org/wiki/HOWTO:Graphics
>
> This is working fine for small blast files but not for large blast file with
> lot of hits. Is there any way i can use this for large blast files?
>
> Thanks
> Shalabh
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From scott at scottcain.net  Tue Feb  2 13:55:02 2010
From: scott at scottcain.net (Scott Cain)
Date: Tue, 2 Feb 2010 13:55:02 -0500
Subject: [Bioperl-l] Mapping Blast results
In-Reply-To: <9fcc48c71002021047q4058efaes735f9ecbdde8b66a@mail.gmail.com>
References: <9fcc48c71002020716u2981596ekf3ca36cc693200f0@mail.gmail.com>
	<4536f7701002021034p253c78e4u5c9b9c71cc0cb62@mail.gmail.com>
	<9fcc48c71002021047q4058efaes735f9ecbdde8b66a@mail.gmail.com>
Message-ID: <4536f7701002021055l2e6ac98cwa95b5a5d13414f77@mail.gmail.com>

Hi Shalabh,

Please keep your responses on the list.

A few things:

* While it interesting that the resulting png isn't readable (and I
don't know why--perhaps the script is silently crashing?), I have to
wonder if a graphic with 1500 hits for a particular gene will be of
that much use anyway?  Perhaps, but it seems to me that 500 will do
just as well as 1500 :-)

* When you say you don't know how to map hits to a particular gene,
what is the hang up?  Coordinate mapping?  Converting blast results to
GFF?

Scott


On Tue, Feb 2, 2010 at 1:47 PM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hi,
> ?? ? thanks for your quick reply.
> Actually i am getting a png file but its not readable (there are about 1500
> hits).
> I have a working Gbrowse on my system but i don't know how i can map my
> blast reads to a particular gene.
> Thanks
> Shalabh
>
> On Tue, Feb 2, 2010 at 1:34 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Shalabh,
>>
>> When you say it's not working, what do you mean? ?Presumably, you
>> could write a script that uses Bio::DB::SeqFeature::Store if speed is
>> the problem, but if you wanted to go that far, your time would
>> probably be better spent installing GBrowse.
>>
>> Scott
>>
>>
>> On Tue, Feb 2, 2010 at 10:16 AM, shalabh sharma
>> <shalabh.sharma7 at gmail.com> wrote:
>> > Hi,
>> > ? ?I am trying to map blast results on a gene. I am using Bio::Graphics
>> > ? ?http://bioperl.org/wiki/HOWTO:Graphics
>> >
>> > This is working fine for small blast files but not for large blast file
>> > with
>> > lot of hits. Is there any way i can use this for large blast files?
>> >
>> > Thanks
>> > Shalabh
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/) ? ? ? ? ? ? ? ? ? ? 216-392-3087
>> Ontario Institute for Cancer Research
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From shalabh.sharma7 at gmail.com  Tue Feb  2 14:05:17 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Tue, 2 Feb 2010 14:05:17 -0500
Subject: [Bioperl-l] Mapping Blast results
In-Reply-To: <4536f7701002021055l2e6ac98cwa95b5a5d13414f77@mail.gmail.com>
References: <9fcc48c71002020716u2981596ekf3ca36cc693200f0@mail.gmail.com>
	<4536f7701002021034p253c78e4u5c9b9c71cc0cb62@mail.gmail.com>
	<9fcc48c71002021047q4058efaes735f9ecbdde8b66a@mail.gmail.com>
	<4536f7701002021055l2e6ac98cwa95b5a5d13414f77@mail.gmail.com>
Message-ID: <9fcc48c71002021105h60625687q13b013c4fedd0abe@mail.gmail.com>

Hi,
    Its not readable as the reads are so closed that i can just see one
vertical line. Do i need to increase the panel size?
I am not sure that how to convert blast results to gff file.

Thanks
Shalabh

On Tue, Feb 2, 2010 at 1:55 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Shalabh,
>
> Please keep your responses on the list.
>
> A few things:
>
> * While it interesting that the resulting png isn't readable (and I
> don't know why--perhaps the script is silently crashing?), I have to
> wonder if a graphic with 1500 hits for a particular gene will be of
> that much use anyway?  Perhaps, but it seems to me that 500 will do
> just as well as 1500 :-)
>
> * When you say you don't know how to map hits to a particular gene,
> what is the hang up?  Coordinate mapping?  Converting blast results to
> GFF?
>
> Scott
>
>
> On Tue, Feb 2, 2010 at 1:47 PM, shalabh sharma
> <shalabh.sharma7 at gmail.com> wrote:
> > Hi,
> >      thanks for your quick reply.
> > Actually i am getting a png file but its not readable (there are about
> 1500
> > hits).
> > I have a working Gbrowse on my system but i don't know how i can map my
> > blast reads to a particular gene.
> > Thanks
> > Shalabh
> >
> > On Tue, Feb 2, 2010 at 1:34 PM, Scott Cain <scott at scottcain.net> wrote:
> >>
> >> Hi Shalabh,
> >>
> >> When you say it's not working, what do you mean?  Presumably, you
> >> could write a script that uses Bio::DB::SeqFeature::Store if speed is
> >> the problem, but if you wanted to go that far, your time would
> >> probably be better spent installing GBrowse.
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 2, 2010 at 10:16 AM, shalabh sharma
> >> <shalabh.sharma7 at gmail.com> wrote:
> >> > Hi,
> >> >    I am trying to map blast results on a gene. I am using
> Bio::Graphics
> >> >    http://bioperl.org/wiki/HOWTO:Graphics
> >> >
> >> > This is working fine for small blast files but not for large blast
> file
> >> > with
> >> > lot of hits. Is there any way i can use this for large blast files?
> >> >
> >> > Thanks
> >> > Shalabh
> >> > _______________________________________________
> >> > Bioperl-l mailing list
> >> > Bioperl-l at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> >
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> Ontario Institute for Cancer Research
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

From scott at scottcain.net  Tue Feb  2 14:28:08 2010
From: scott at scottcain.net (Scott Cain)
Date: Tue, 2 Feb 2010 14:28:08 -0500
Subject: [Bioperl-l] Mapping Blast results
In-Reply-To: <9fcc48c71002021105h60625687q13b013c4fedd0abe@mail.gmail.com>
References: <9fcc48c71002020716u2981596ekf3ca36cc693200f0@mail.gmail.com>
	<4536f7701002021034p253c78e4u5c9b9c71cc0cb62@mail.gmail.com>
	<9fcc48c71002021047q4058efaes735f9ecbdde8b66a@mail.gmail.com>
	<4536f7701002021055l2e6ac98cwa95b5a5d13414f77@mail.gmail.com>
	<9fcc48c71002021105h60625687q13b013c4fedd0abe@mail.gmail.com>
Message-ID: <4536f7701002021128kcea35cfm50f651b6c9c8ca43@mail.gmail.com>

Ah, not readable as in "my eyes can't make anything out" not as in
"the file is corrupted and my image viewing software won't open it."
That's two different things.  Yes, I imagine making the panel taller
would help, but in Bio::Graphics::Panel you don't have direct control
of the panel height.  Instead, you can try changing the value of the
bump parameter.  Try +1 or +2 to see if that helps.  See the perldoc
for Bio::Graphics::Panel for more info.

For converting blast results to GFF, see the bioperl script bp_search2gff.pl.

Scott


On Tue, Feb 2, 2010 at 2:05 PM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hi,
> ?? ?Its not readable as the reads are so closed that i can just see one
> vertical line. Do i need to increase the panel size?
> I am not sure that how to convert blast results to gff file.
> Thanks
> Shalabh
> On Tue, Feb 2, 2010 at 1:55 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Shalabh,
>>
>> Please keep your responses on the list.
>>
>> A few things:
>>
>> * While it interesting that the resulting png isn't readable (and I
>> don't know why--perhaps the script is silently crashing?), I have to
>> wonder if a graphic with 1500 hits for a particular gene will be of
>> that much use anyway? ?Perhaps, but it seems to me that 500 will do
>> just as well as 1500 :-)
>>
>> * When you say you don't know how to map hits to a particular gene,
>> what is the hang up? ?Coordinate mapping? ?Converting blast results to
>> GFF?
>>
>> Scott
>>
>>
>> On Tue, Feb 2, 2010 at 1:47 PM, shalabh sharma
>> <shalabh.sharma7 at gmail.com> wrote:
>> > Hi,
>> > ?? ? thanks for your quick reply.
>> > Actually i am getting a png file but its not readable (there are about
>> > 1500
>> > hits).
>> > I have a working Gbrowse on my system but i don't know how i can map my
>> > blast reads to a particular gene.
>> > Thanks
>> > Shalabh
>> >
>> > On Tue, Feb 2, 2010 at 1:34 PM, Scott Cain <scott at scottcain.net> wrote:
>> >>
>> >> Hi Shalabh,
>> >>
>> >> When you say it's not working, what do you mean? ?Presumably, you
>> >> could write a script that uses Bio::DB::SeqFeature::Store if speed is
>> >> the problem, but if you wanted to go that far, your time would
>> >> probably be better spent installing GBrowse.
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Tue, Feb 2, 2010 at 10:16 AM, shalabh sharma
>> >> <shalabh.sharma7 at gmail.com> wrote:
>> >> > Hi,
>> >> > ? ?I am trying to map blast results on a gene. I am using
>> >> > Bio::Graphics
>> >> > ? ?http://bioperl.org/wiki/HOWTO:Graphics
>> >> >
>> >> > This is working fine for small blast files but not for large blast
>> >> > file
>> >> > with
>> >> > lot of hits. Is there any way i can use this for large blast files?
>> >> >
>> >> > Thanks
>> >> > Shalabh
>> >> > _______________________________________________
>> >> > Bioperl-l mailing list
>> >> > Bioperl-l at lists.open-bio.org
>> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/) ? ? ? ? ? ? ? ? ? ? 216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/) ? ? ? ? ? ? ? ? ? ? 216-392-3087
>> Ontario Institute for Cancer Research
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From robert.bradbury at gmail.com  Wed Feb  3 04:56:49 2010
From: robert.bradbury at gmail.com (Robert Bradbury)
Date: Wed, 3 Feb 2010 04:56:49 -0500
Subject: [Bioperl-l] Problems at NCBI with Javascript
Message-ID: <deaa866a1002030156q1777dd88i508f9029b3ce6d0e@mail.gmail.com>

Hello, I know there will be people who think that this may be off-topic for
the list, but I don't know of another list that might be better.

The basic problem is the recent trend by NCBI to insist that browsers must
have Javascript turned on to work.

Now I have a real problem with this. All the databases at NCBI have been
writen over the last 15 or so years to produce basic HTML..  Switching this
to a requirement for HTML + Javascript in my mind is simply wrong-headed.  I
will save the list my list of problems I have with Javascrip (it isn't
short)t.   I'll simply provide the first one -- It isn't Green.

So I would like to ask if anyone knows why NCBI is heading in this
direction?  (Tonight they seem to have broken non-Javascript enabled use of
PubMed and that has me a little upset.

Is there a better source to taking with anyone directly at NCBI about this
than the Help Desk (I usually find them unresponsive).  Do they have
something like a Bugzilla bug database or an internal developers mailing
list?

I'm sorry in advance for troubling list members with this but I didn't know
of anwhere else to turn [1].

Thank you,
Robert Bradbury

1. I'll also note that they could at least leave the old interface active
indefinitely.  Google/gmail show that its perfectly possible to write
"enhanced" user interfaces that work with HTML+Javascript and simple HTML.

From rtbio.2009 at gmail.com  Wed Feb  3 08:50:07 2010
From: rtbio.2009 at gmail.com (Roopa Raghuveer)
Date: Wed, 3 Feb 2010 14:50:07 +0100
Subject: [Bioperl-l] string comparision mismatches and matches
Message-ID: <c7cac1601002030550g7b356f47s42d97de2c6168830@mail.gmail.com>

Hello all,

I have a problem. I would like to compare two strings of equal length using
Perl and trying to count the number of matches. I have used an algorithm to
count the matches,but I found them to be time consuming in counting the
mismatches. Could any one suggest a better algorithm for this?

Ex:- Let the two sequences be

input:- ACCTCCTCCTCGAGTATGTG

target:- TATCTTGCGCCGGAGATAAT

The no of matches are 5.

In my program, I have used two indices which run along the string in the
forward direction and reverse direction and extracting two characters at a
time and comparing them with the respective characters in the  output
sequence. i.e.,

i/p:- ACCTCCTCCTCGAGTATGTG

I have extracted 'A' in the forward direction and 'G' in the reverse
direction from the i/p.

target:- TATCTTGCGCCGGAGATAAT

I have extracted 'T' in the forward direction and 'T' in the reverse
direction from the target and compared 'A' with 'T' and 'G' with 'T'. In
this way, I have proceeded along the complete length of the string and
counting the matches . But it seems to be time consuming though its working.
Can anybody suggest a better way?

Regards,
Roopa.

From maj at fortinbras.us  Wed Feb  3 09:50:05 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 3 Feb 2010 09:50:05 -0500
Subject: [Bioperl-l] string comparision mismatches and matches
In-Reply-To: <c7cac1601002030550g7b356f47s42d97de2c6168830@mail.gmail.com>
References: <c7cac1601002030550g7b356f47s42d97de2c6168830@mail.gmail.com>
Message-ID: <DD9E6B53DD0A4B3BBB650B89E73D4DCB@NewLife>

try this:

$in = 'ACCTCCTCCTCGAGTATGTG';
$tgt = 'TATCTTGCGCCGGAGATAAT';
$mask = pack("A*",$in)^pack("A*",$tgt);
$matches = $mask =~ tr/"\x0"/"\x0"/;



----- Original Message ----- 
From: "Roopa Raghuveer" <rtbio.2009 at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Cc: "Chris Fields" <cjfields at illinois.edu>; "Mark A. Jensen" <maj at fortinbras.us>
Sent: Wednesday, February 03, 2010 8:50 AM
Subject: [Bioperl-l] string comparision mismatches and matches


> Hello all,
>
> I have a problem. I would like to compare two strings of equal length using
> Perl and trying to count the number of matches. I have used an algorithm to
> count the matches,but I found them to be time consuming in counting the
> mismatches. Could any one suggest a better algorithm for this?
>
> Ex:- Let the two sequences be
>
> input:- ACCTCCTCCTCGAGTATGTG
>
> target:- TATCTTGCGCCGGAGATAAT
>
> The no of matches are 5.
>
> In my program, I have used two indices which run along the string in the
> forward direction and reverse direction and extracting two characters at a
> time and comparing them with the respective characters in the  output
> sequence. i.e.,
>
> i/p:- ACCTCCTCCTCGAGTATGTG
>
> I have extracted 'A' in the forward direction and 'G' in the reverse
> direction from the i/p.
>
> target:- TATCTTGCGCCGGAGATAAT
>
> I have extracted 'T' in the forward direction and 'T' in the reverse
> direction from the target and compared 'A' with 'T' and 'G' with 'T'. In
> this way, I have proceeded along the complete length of the string and
> counting the matches . But it seems to be time consuming though its working.
> Can anybody suggest a better way?
>
> Regards,
> Roopa.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From laceyanne_sanderson at shaw.ca  Wed Feb  3 10:32:56 2010
From: laceyanne_sanderson at shaw.ca (Lacey Sanderson)
Date: Wed, 03 Feb 2010 09:32:56 -0600
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem to
	change
Message-ID: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>

Hi,

I just checked out bioperl-live from svn as follows
$ sudo svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk  
bioperl-live
$ echo 'export PERL5LIB="/usr/local/share/applications/Bioperl/bioperl- 
live:$PERL5LIB"  #adds path of bioperl-live to PERL5LIB' >> ~/.profile

I then restarted by shell and checked the version using
$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'

Which returned 1.006... I am sure this is the version of bioperl I had  
previously installed and not the new one I just checked out. Is there  
something else I need to do to tell my system to disregard the old  
bioperl and instead use bioperl-live?

I had installed BioPerl earlier using the GMOD GBrowse netinstaller  
although I can't seem to locate where it was installed. Will this  
effect anything? If so, how would I go about uninstalling it (I'm a  
little new to Linux)...

By the way I am running Ubuntu Intrepid

Thanks!
Lacey


From scott at scottcain.net  Wed Feb  3 12:08:26 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Feb 2010 12:08:26 -0500
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
	to change
In-Reply-To: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
Message-ID: <4536f7701002030908p558e697ex79087c2ad0d9970d@mail.gmail.com>

Hi Lacey,

Did it return "1.006" or 1.0069 exactly, which is what it should
return if you are using bioperl-live?  As for older versions of
BioPerl, if you go down the install route (which is what I generally
do), you can do the standard build procedure:

perl Build.PL
./Build
./Build test
sudo ./Build install --uninst 1

and that last part (--uninst 1) will remove older versions of the
modules installed elsewhere.  If you want to hunt down where GBrowse
installed bioperl, first you could look in the typical linuxy places,
like /usr/share/perl or /usr/lib/perl for the Bio directory, but
deleting that directory will also delete Bio::Graphics, which isn't
part of bioperl anymore.

Using PERL5LIB will put your specified bioperl at the front of the
list for when things get used, so even if you have bioperl installed
elsewhere, that one should get used.

Scott


On Wed, Feb 3, 2010 at 10:32 AM, Lacey Sanderson
<laceyanne_sanderson at shaw.ca> wrote:
> Hi,
>
> I just checked out bioperl-live from svn as follows
> $ sudo svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk
> bioperl-live
> $ echo 'export
> PERL5LIB="/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB"
> ?#adds path of bioperl-live to PERL5LIB' >> ~/.profile
>
> I then restarted by shell and checked the version using
> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
>
> Which returned 1.006... I am sure this is the version of bioperl I had
> previously installed and not the new one I just checked out. Is there
> something else I need to do to tell my system to disregard the old bioperl
> and instead use bioperl-live?
>
> I had installed BioPerl earlier using the GMOD GBrowse netinstaller although
> I can't seem to locate where it was installed. Will this effect anything? If
> so, how would I go about uninstalling it (I'm a little new to Linux)...
>
> By the way I am running Ubuntu Intrepid
>
> Thanks!
> Lacey
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From laceyanne_sanderson at shaw.ca  Wed Feb  3 12:32:47 2010
From: laceyanne_sanderson at shaw.ca (Lacey Sanderson)
Date: Wed, 03 Feb 2010 11:32:47 -0600
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't
 seem	to change
In-Reply-To: <4536f7701002030908p558e697ex79087c2ad0d9970d@mail.gmail.com>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
	<4536f7701002030908p558e697ex79087c2ad0d9970d@mail.gmail.com>
Message-ID: <BA76EFBD-C3E0-4B4F-AF62-3D8AF39BC591@shaw.ca>

It returned "1.006"... unfortunately no 9 at the end... Any idea why  
it doesn't seem to be picking up the bioperl-live checkout?

PS. Why do the distributions have version numbers like 1.5.2 and 1.6  
and yet the bioperl-live (which I take to be the most current version  
of bioperl) returns 1.069?

Lacey

On 3-Feb-10, at 11:08 AM, Scott Cain wrote:

> Hi Lacey,
>
> Did it return "1.006" or 1.0069 exactly, which is what it should
> return if you are using bioperl-live?  As for older versions of
> BioPerl, if you go down the install route (which is what I generally
> do), you can do the standard build procedure:
>
> perl Build.PL
> ./Build
> ./Build test
> sudo ./Build install --uninst 1
>
> and that last part (--uninst 1) will remove older versions of the
> modules installed elsewhere.  If you want to hunt down where GBrowse
> installed bioperl, first you could look in the typical linuxy places,
> like /usr/share/perl or /usr/lib/perl for the Bio directory, but
> deleting that directory will also delete Bio::Graphics, which isn't
> part of bioperl anymore.
>
> Using PERL5LIB will put your specified bioperl at the front of the
> list for when things get used, so even if you have bioperl installed
> elsewhere, that one should get used.
>
> Scott
>
>
> On Wed, Feb 3, 2010 at 10:32 AM, Lacey Sanderson
> <laceyanne_sanderson at shaw.ca> wrote:
>> Hi,
>>
>> I just checked out bioperl-live from svn as follows
>> $ sudo svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk
>> bioperl-live
>> $ echo 'export
>> PERL5LIB="/usr/local/share/applications/Bioperl/bioperl-live: 
>> $PERL5LIB"
>>  #adds path of bioperl-live to PERL5LIB' >> ~/.profile
>>
>> I then restarted by shell and checked the version using
>> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
>>
>> Which returned 1.006... I am sure this is the version of bioperl I  
>> had
>> previously installed and not the new one I just checked out. Is there
>> something else I need to do to tell my system to disregard the old  
>> bioperl
>> and instead use bioperl-live?
>>
>> I had installed BioPerl earlier using the GMOD GBrowse netinstaller  
>> although
>> I can't seem to locate where it was installed. Will this effect  
>> anything? If
>> so, how would I go about uninstalling it (I'm a little new to  
>> Linux)...
>>
>> By the way I am running Ubuntu Intrepid
>>
>> Thanks!
>> Lacey
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.


From cjfields at illinois.edu  Wed Feb  3 12:58:26 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Feb 2010 11:58:26 -0600
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't
	seem	to change
In-Reply-To: <BA76EFBD-C3E0-4B4F-AF62-3D8AF39BC591@shaw.ca>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
	<4536f7701002030908p558e697ex79087c2ad0d9970d@mail.gmail.com>
	<BA76EFBD-C3E0-4B4F-AF62-3D8AF39BC591@shaw.ca>
Message-ID: <BDAC8D02-EAD8-4877-B973-2C9CADBBF435@illinois.edu>

If I were to choose a versioning scheme I would probably go with simple bipartite ones, but (by legacy) BioPerl is based on the perl tripartite versioning scheme:

http://www.perl.com/pub/a/2000/04/whatsnew.html#Version_Tuples

For instance, with perl 5.10.1 the vstring v5.10.1 would be 5.010001.  BioPerl 1.6.0 is 1.006000, so you either have an older lingering CPAN installation of 1.6.0 or you are installing that one (I'm guessing the former, as the latest from CPAN is now 1.6.1, or 1.006001).  Effectively, svn trunk is v1.6.900 (roughly the 900th point release).

The reason trunk is set at 1.6.9 is simple, it supercedes any current CPAN release version, and it's very unlikely we'll release another 898 point releases of BioPerl.  It also tags the main trunk as pre-1.7.  I can cherry-pick off trunk into the properly designated 1.6 branch (now at 1.6.1), bump the release there, and push to CPAN.  Once we actively start on 1.7 we'll probably bump trunk up to something higher.  It also enables one to distinguish between a CPAN release of BioPerl vs. the SVN version, as installing from svn has unfortunately become very common practice.  Comes in useful in cases like yours, where we're trying to distinguish what version is being called.  

chris

On Feb 3, 2010, at 11:32 AM, Lacey Sanderson wrote:

> It returned "1.006"... unfortunately no 9 at the end... Any idea why it doesn't seem to be picking up the bioperl-live checkout?
> 
> PS. Why do the distributions have version numbers like 1.5.2 and 1.6 and yet the bioperl-live (which I take to be the most current version of bioperl) returns 1.069?
> 
> Lacey
> 
> On 3-Feb-10, at 11:08 AM, Scott Cain wrote:
> 
>> Hi Lacey,
>> 
>> Did it return "1.006" or 1.0069 exactly, which is what it should
>> return if you are using bioperl-live?  As for older versions of
>> BioPerl, if you go down the install route (which is what I generally
>> do), you can do the standard build procedure:
>> 
>> perl Build.PL
>> ./Build
>> ./Build test
>> sudo ./Build install --uninst 1
>> 
>> and that last part (--uninst 1) will remove older versions of the
>> modules installed elsewhere.  If you want to hunt down where GBrowse
>> installed bioperl, first you could look in the typical linuxy places,
>> like /usr/share/perl or /usr/lib/perl for the Bio directory, but
>> deleting that directory will also delete Bio::Graphics, which isn't
>> part of bioperl anymore.
>> 
>> Using PERL5LIB will put your specified bioperl at the front of the
>> list for when things get used, so even if you have bioperl installed
>> elsewhere, that one should get used.
>> 
>> Scott
>> 
>> 
>> On Wed, Feb 3, 2010 at 10:32 AM, Lacey Sanderson
>> <laceyanne_sanderson at shaw.ca> wrote:
>>> Hi,
>>> 
>>> I just checked out bioperl-live from svn as follows
>>> $ sudo svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk
>>> bioperl-live
>>> $ echo 'export
>>> PERL5LIB="/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB"
>>> #adds path of bioperl-live to PERL5LIB' >> ~/.profile
>>> 
>>> I then restarted by shell and checked the version using
>>> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
>>> 
>>> Which returned 1.006... I am sure this is the version of bioperl I had
>>> previously installed and not the new one I just checked out. Is there
>>> something else I need to do to tell my system to disregard the old bioperl
>>> and instead use bioperl-live?
>>> 
>>> I had installed BioPerl earlier using the GMOD GBrowse netinstaller although
>>> I can't seem to locate where it was installed. Will this effect anything? If
>>> so, how would I go about uninstalling it (I'm a little new to Linux)...
>>> 
>>> By the way I am running Ubuntu Intrepid
>>> 
>>> Thanks!
>>> Lacey
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
>> 
>> 
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
> 
> ---------------------------------
> Lacey Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Department of Plant Sciences
> University of Saskatchewan.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From maj at fortinbras.us  Wed Feb  3 12:50:20 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 3 Feb 2010 12:50:20 -0500
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
	tochange
In-Reply-To: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
Message-ID: <DA946FFE9178432A8E83411DC173C072@NewLife>

Presumably your pwd was
/usr/local/share/applications/Bioperl
when you did the checkout?
----- Original Message ----- 
From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
To: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, February 03, 2010 10:32 AM
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem 
tochange


> Hi,
>
> I just checked out bioperl-live from svn as follows
> $ sudo svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk  bioperl-live
> $ echo 'export PERL5LIB="/usr/local/share/applications/Bioperl/bioperl- 
> live:$PERL5LIB"  #adds path of bioperl-live to PERL5LIB' >> ~/.profile
>
> I then restarted by shell and checked the version using
> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
>
> Which returned 1.006... I am sure this is the version of bioperl I had 
> previously installed and not the new one I just checked out. Is there 
> something else I need to do to tell my system to disregard the old  bioperl 
> and instead use bioperl-live?
>
> I had installed BioPerl earlier using the GMOD GBrowse netinstaller  although 
> I can't seem to locate where it was installed. Will this  effect anything? If 
> so, how would I go about uninstalling it (I'm a  little new to Linux)...
>
> By the way I am running Ubuntu Intrepid
>
> Thanks!
> Lacey
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From laceyanne_sanderson at shaw.ca  Wed Feb  3 12:58:09 2010
From: laceyanne_sanderson at shaw.ca (Lacey Sanderson)
Date: Wed, 03 Feb 2010 11:58:09 -0600
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
 tochange
In-Reply-To: <DA946FFE9178432A8E83411DC173C072@NewLife>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
	<DA946FFE9178432A8E83411DC173C072@NewLife>
Message-ID: <E2830264-A715-480E-B7F7-350D50E0F571@shaw.ca>

Yes, Sorry I forgot to include that. I checked and the bioperl-live  
checkout is where I told export it would be (ie: in /usr/local/share/ 
applications/Bioperl/)

Lacey

On 3-Feb-10, at 11:50 AM, Mark A. Jensen wrote:

> Presumably your pwd was
> /usr/local/share/applications/Bioperl
> when you did the checkout?
> ----- Original Message ----- From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca 
> >
> To: <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, February 03, 2010 10:32 AM
> Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't  
> seem tochange
>
>
>> Hi,
>>
>> I just checked out bioperl-live from svn as follows
>> $ sudo svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk   
>> bioperl-live
>> $ echo 'export PERL5LIB="/usr/local/share/applications/Bioperl/ 
>> bioperl- live:$PERL5LIB"  #adds path of bioperl-live to PERL5LIB'  
>> >> ~/.profile
>>
>> I then restarted by shell and checked the version using
>> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
>>
>> Which returned 1.006... I am sure this is the version of bioperl I  
>> had previously installed and not the new one I just checked out. Is  
>> there something else I need to do to tell my system to disregard  
>> the old  bioperl and instead use bioperl-live?
>>
>> I had installed BioPerl earlier using the GMOD GBrowse  
>> netinstaller  although I can't seem to locate where it was  
>> installed. Will this  effect anything? If so, how would I go about  
>> uninstalling it (I'm a  little new to Linux)...
>>
>> By the way I am running Ubuntu Intrepid
>>
>> Thanks!
>> Lacey
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.


From maj at fortinbras.us  Wed Feb  3 13:10:09 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 3 Feb 2010 13:10:09 -0500
Subject: [Bioperl-l] After Checkout of Bioperl-live version
	doesn'tseem	to change
In-Reply-To: <BDAC8D02-EAD8-4877-B973-2C9CADBBF435@illinois.edu>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca><4536f7701002030908p558e697ex79087c2ad0d9970d@mail.gmail.com><BA76EFBD-C3E0-4B4F-AF62-3D8AF39BC591@shaw.ca>
	<BDAC8D02-EAD8-4877-B973-2C9CADBBF435@illinois.edu>
Message-ID: <D05336F0338549DBB9DA11E39828065D@NewLife>

The practicality of it is that you can do a simple float comparision to check
for prerequisites and such:

if ($Bio::Perl::VERSION < 1.006900) {
    die "You ain't got the freshest."
}

Harder if you're comparing strings "1.6" to "1.6.9".
MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
Cc: <bioperl-l at lists.open-bio.org>; "Scott Cain" <scott at scottcain.net>
Sent: Wednesday, February 03, 2010 12:58 PM
Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn'tseem to 
change


> If I were to choose a versioning scheme I would probably go with simple 
> bipartite ones, but (by legacy) BioPerl is based on the perl tripartite 
> versioning scheme:
>
> http://www.perl.com/pub/a/2000/04/whatsnew.html#Version_Tuples
>
> For instance, with perl 5.10.1 the vstring v5.10.1 would be 5.010001.  BioPerl 
> 1.6.0 is 1.006000, so you either have an older lingering CPAN installation of 
> 1.6.0 or you are installing that one (I'm guessing the former, as the latest 
> from CPAN is now 1.6.1, or 1.006001).  Effectively, svn trunk is v1.6.900 
> (roughly the 900th point release).
>
> The reason trunk is set at 1.6.9 is simple, it supercedes any current CPAN 
> release version, and it's very unlikely we'll release another 898 point 
> releases of BioPerl.  It also tags the main trunk as pre-1.7.  I can 
> cherry-pick off trunk into the properly designated 1.6 branch (now at 1.6.1), 
> bump the release there, and push to CPAN.  Once we actively start on 1.7 we'll 
> probably bump trunk up to something higher.  It also enables one to 
> distinguish between a CPAN release of BioPerl vs. the SVN version, as 
> installing from svn has unfortunately become very common practice.  Comes in 
> useful in cases like yours, where we're trying to distinguish what version is 
> being called.
>
> chris
>
> On Feb 3, 2010, at 11:32 AM, Lacey Sanderson wrote:
>
>> It returned "1.006"... unfortunately no 9 at the end... Any idea why it 
>> doesn't seem to be picking up the bioperl-live checkout?
>>
>> PS. Why do the distributions have version numbers like 1.5.2 and 1.6 and yet 
>> the bioperl-live (which I take to be the most current version of bioperl) 
>> returns 1.069?
>>
>> Lacey
>>
>> On 3-Feb-10, at 11:08 AM, Scott Cain wrote:
>>
>>> Hi Lacey,
>>>
>>> Did it return "1.006" or 1.0069 exactly, which is what it should
>>> return if you are using bioperl-live?  As for older versions of
>>> BioPerl, if you go down the install route (which is what I generally
>>> do), you can do the standard build procedure:
>>>
>>> perl Build.PL
>>> ./Build
>>> ./Build test
>>> sudo ./Build install --uninst 1
>>>
>>> and that last part (--uninst 1) will remove older versions of the
>>> modules installed elsewhere.  If you want to hunt down where GBrowse
>>> installed bioperl, first you could look in the typical linuxy places,
>>> like /usr/share/perl or /usr/lib/perl for the Bio directory, but
>>> deleting that directory will also delete Bio::Graphics, which isn't
>>> part of bioperl anymore.
>>>
>>> Using PERL5LIB will put your specified bioperl at the front of the
>>> list for when things get used, so even if you have bioperl installed
>>> elsewhere, that one should get used.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Feb 3, 2010 at 10:32 AM, Lacey Sanderson
>>> <laceyanne_sanderson at shaw.ca> wrote:
>>>> Hi,
>>>>
>>>> I just checked out bioperl-live from svn as follows
>>>> $ sudo svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk
>>>> bioperl-live
>>>> $ echo 'export
>>>> PERL5LIB="/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB"
>>>> #adds path of bioperl-live to PERL5LIB' >> ~/.profile
>>>>
>>>> I then restarted by shell and checked the version using
>>>> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
>>>>
>>>> Which returned 1.006... I am sure this is the version of bioperl I had
>>>> previously installed and not the new one I just checked out. Is there
>>>> something else I need to do to tell my system to disregard the old bioperl
>>>> and instead use bioperl-live?
>>>>
>>>> I had installed BioPerl earlier using the GMOD GBrowse netinstaller 
>>>> although
>>>> I can't seem to locate where it was installed. Will this effect anything? 
>>>> If
>>>> so, how would I go about uninstalling it (I'm a little new to Linux)...
>>>>
>>>> By the way I am running Ubuntu Intrepid
>>>>
>>>> Thanks!
>>>> Lacey
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>>
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot 
>>> net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>
>> ---------------------------------
>> Lacey Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Department of Plant Sciences
>> University of Saskatchewan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From laceyanne_sanderson at shaw.ca  Wed Feb  3 13:21:03 2010
From: laceyanne_sanderson at shaw.ca (Lacey Sanderson)
Date: Wed, 03 Feb 2010 12:21:03 -0600
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
 tochange
In-Reply-To: <0A23A254827D40A997BF65EE356183E6@NewLife>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
	<DA946FFE9178432A8E83411DC173C072@NewLife>
	<E2830264-A715-480E-B7F7-350D50E0F571@shaw.ca>
	<0A23A254827D40A997BF65EE356183E6@NewLife>
Message-ID: <F0BF6771-7F76-4E7C-8085-3DF5C4C8AF9F@shaw.ca>

That gives me the 1.069 that I was wanting so the problem seems to be  
that perl is finding the wrong installation by default...

Lacey

On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:

> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/bioperl- 
> live -le 'print Bio::Perl->VERSION;'


From Jonathan_Epstein at nih.gov  Wed Feb  3 13:40:56 2010
From: Jonathan_Epstein at nih.gov (Jonathan Epstein)
Date: Wed, 03 Feb 2010 13:40:56 -0500
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't	seem
 to change
In-Reply-To: <BDAC8D02-EAD8-4877-B973-2C9CADBBF435@illinois.edu>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>	<4536f7701002030908p558e697ex79087c2ad0d9970d@mail.gmail.com>	<BA76EFBD-C3E0-4B4F-AF62-3D8AF39BC591@shaw.ca>
	<BDAC8D02-EAD8-4877-B973-2C9CADBBF435@illinois.edu>
Message-ID: <4B69C338.1080501@nih.gov>

Here's a low-tech answer: if I'm having a problem like this with my 
PERL5LIB environment variable [Perl is not doing what I /think/ I've 
told it to do], I try to figure out where Perl is actually looking.

So in this case I'd write a two-line BioPerl program foo.pl like:

    use Bio::Perl;
    $seq_object = get_sequence('swiss',"ROA1_HUMAN");

Start the debugger with "perl -d:ptkdb foo.pl", set a breakpoint before 
line 2, run to that breakpoint, and then step-in with the debugger and 
see in which directory the corresponding source file resides.

My guess is that there are additional subordinates paths within 
/usr/local/share/applications/Bioperl/bioperl-live which must be added 
to your path.

Cheers,

Jonathan








On 2/3/2010 12:58 PM, Chris Fields wrote:
> If I were to choose a versioning scheme I would probably go with simple bipartite ones, but (by legacy) BioPerl is based on the perl tripartite versioning scheme:
>
> http://www.perl.com/pub/a/2000/04/whatsnew.html#Version_Tuples
>
> For instance, with perl 5.10.1 the vstring v5.10.1 would be 5.010001.  BioPerl 1.6.0 is 1.006000, so you either have an older lingering CPAN installation of 1.6.0 or you are installing that one (I'm guessing the former, as the latest from CPAN is now 1.6.1, or 1.006001).  Effectively, svn trunk is v1.6.900 (roughly the 900th point release).
>
> The reason trunk is set at 1.6.9 is simple, it supercedes any current CPAN release version, and it's very unlikely we'll release another 898 point releases of BioPerl.  It also tags the main trunk as pre-1.7.  I can cherry-pick off trunk into the properly designated 1.6 branch (now at 1.6.1), bump the release there, and push to CPAN.  Once we actively start on 1.7 we'll probably bump trunk up to something higher.  It also enables one to distinguish between a CPAN release of BioPerl vs. the SVN version, as installing from svn has unfortunately become very common practice.  Comes in useful in cases like yours, where we're trying to distinguish what version is being called.
>
> chris
>
> On Feb 3, 2010, at 11:32 AM, Lacey Sanderson wrote:
>
>    
>> It returned "1.006"... unfortunately no 9 at the end... Any idea why it doesn't seem to be picking up the bioperl-live checkout?
>>
>> PS. Why do the distributions have version numbers like 1.5.2 and 1.6 and yet the bioperl-live (which I take to be the most current version of bioperl) returns 1.069?
>>
>> Lacey
>>
>> On 3-Feb-10, at 11:08 AM, Scott Cain wrote:
>>
>>      
>>> Hi Lacey,
>>>
>>> Did it return "1.006" or 1.0069 exactly, which is what it should
>>> return if you are using bioperl-live?  As for older versions of
>>> BioPerl, if you go down the install route (which is what I generally
>>> do), you can do the standard build procedure:
>>>
>>> perl Build.PL
>>> ./Build
>>> ./Build test
>>> sudo ./Build install --uninst 1
>>>
>>> and that last part (--uninst 1) will remove older versions of the
>>> modules installed elsewhere.  If you want to hunt down where GBrowse
>>> installed bioperl, first you could look in the typical linuxy places,
>>> like /usr/share/perl or /usr/lib/perl for the Bio directory, but
>>> deleting that directory will also delete Bio::Graphics, which isn't
>>> part of bioperl anymore.
>>>
>>> Using PERL5LIB will put your specified bioperl at the front of the
>>> list for when things get used, so even if you have bioperl installed
>>> elsewhere, that one should get used.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Feb 3, 2010 at 10:32 AM, Lacey Sanderson
>>> <laceyanne_sanderson at shaw.ca>  wrote:
>>>        
>>>> Hi,
>>>>
>>>> I just checked out bioperl-live from svn as follows
>>>> $ sudo svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk
>>>> bioperl-live
>>>> $ echo 'export
>>>> PERL5LIB="/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB"
>>>> #adds path of bioperl-live to PERL5LIB'>>  ~/.profile
>>>>
>>>> I then restarted by shell and checked the version using
>>>> $ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
>>>>
>>>> Which returned 1.006... I am sure this is the version of bioperl I had
>>>> previously installed and not the new one I just checked out. Is there
>>>> something else I need to do to tell my system to disregard the old bioperl
>>>> and instead use bioperl-live?
>>>>
>>>> I had installed BioPerl earlier using the GMOD GBrowse netinstaller although
>>>> I can't seem to locate where it was installed. Will this effect anything? If
>>>> so, how would I go about uninstalling it (I'm a little new to Linux)...
>>>>
>>>> By the way I am running Ubuntu Intrepid
>>>>
>>>> Thanks!
>>>> Lacey
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>          
>>>
>>>
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>        
>> ---------------------------------
>> Lacey Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Department of Plant Sciences
>> University of Saskatchewan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>      
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> .
>
>    

From maj at fortinbras.us  Wed Feb  3 13:56:26 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 3 Feb 2010 13:56:26 -0500
Subject: [Bioperl-l] Fw: After Checkout of Bioperl-live version doesn't seem
	tochange
Message-ID: <9EAAAFBA93614EFCB4BCB7FF5F2FC732@NewLife>

up to list-- MAJ
----- Original Message ----- 
From: "Mark A. Jensen" <maj at fortinbras.us>
To: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
Sent: Wednesday, February 03, 2010 1:34 PM
Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem 
tochange


> Well, that's progress. It hard to debug these things remotely, but now
> you can at least work around the problem by using the -I flag. The next
> weak link I would try to eliminate is the append to the .profile file. Just
> do directly from the command line (don't relogin)
>
> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB
> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>
> If this gives 1.0069, then the problem is in that append (and, you can also do 
> your work!).
> (If you're a sudoer, I'd just edit that file directly.)
>
> cheers MAJ
> ----- Original Message ----- 
> From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, February 03, 2010 1:21 PM
> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem 
> tochange
>
>
>> That gives me the 1.069 that I was wanting so the problem seems to be  that 
>> perl is finding the wrong installation by default...
>>
>> Lacey
>>
>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>
>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/bioperl- live -le 
>>> 'print Bio::Perl->VERSION;'
>>
>>
>>
> 


From zhabizg at yahoo.com  Wed Feb  3 14:05:50 2010
From: zhabizg at yahoo.com (zhabiz golkar)
Date: Wed, 3 Feb 2010 11:05:50 -0800 (PST)
Subject: [Bioperl-l] query
Message-ID: <634371.13033.qm@web34205.mail.mud.yahoo.com>

Dear Sir/Madam
We have done the sequencing of about 50 HIV +ve samples. We have used HIV BLAST database. And identified the subtypes,.. we have used 2 pair primers( reverse and forward) means we have 4 seq. for each sample. NOW
1-????? We are looking for gag, reverse transcriptase and protease(POL) regions of each sample and 
2-????? We want to do comparison of these regions which each other. Please note , when we use database, they do the comparison with the reference genome (HIV-1). But we need to compare theses regions among the isolates. And clustalW and X also is not highlighting the specific region .
I would be great full if you can give suggestion or send the link or software name that we can do application .
?
Looking forward to hear you . and thanking you in anticipation 
Regards
Dr.Zhabiz


      

From cjfields at illinois.edu  Wed Feb  3 14:21:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Feb 2010 13:21:02 -0600
Subject: [Bioperl-l] Fw: After Checkout of Bioperl-live version doesn't
	seem tochange
In-Reply-To: <9EAAAFBA93614EFCB4BCB7FF5F2FC732@NewLife>
References: <9EAAAFBA93614EFCB4BCB7FF5F2FC732@NewLife>
Message-ID: <30452F69-00B3-4E72-9E70-D4B12948E65E@illinois.edu>

Yes, though I'm assuming by .profile you mean the user-specific one ($HOME/.profile) and not the system/global one.  The local one should suffice.

chris

On Feb 3, 2010, at 12:56 PM, Mark A. Jensen wrote:

> up to list-- MAJ
> ----- Original Message ----- From: "Mark A. Jensen" <maj at fortinbras.us>
> To: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
> Sent: Wednesday, February 03, 2010 1:34 PM
> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem tochange
> 
> 
>> Well, that's progress. It hard to debug these things remotely, but now
>> you can at least work around the problem by using the -I flag. The next
>> weak link I would try to eliminate is the append to the .profile file. Just
>> do directly from the command line (don't relogin)
>> 
>> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB
>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>> 
>> If this gives 1.0069, then the problem is in that append (and, you can also do your work!).
>> (If you're a sudoer, I'd just edit that file directly.)
>> 
>> cheers MAJ
>> ----- Original Message ----- From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
>> To: "Mark A. Jensen" <maj at fortinbras.us>
>> Cc: <bioperl-l at lists.open-bio.org>
>> Sent: Wednesday, February 03, 2010 1:21 PM
>> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem tochange
>> 
>> 
>>> That gives me the 1.069 that I was wanting so the problem seems to be  that perl is finding the wrong installation by default...
>>> 
>>> Lacey
>>> 
>>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>> 
>>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/bioperl- live -le 'print Bio::Perl->VERSION;'
>>> 
>>> 
>>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Wed Feb  3 14:22:31 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Feb 2010 13:22:31 -0600
Subject: [Bioperl-l] Fw: After Checkout of Bioperl-live version doesn't
	seem tochange
In-Reply-To: <9EAAAFBA93614EFCB4BCB7FF5F2FC732@NewLife>
References: <9EAAAFBA93614EFCB4BCB7FF5F2FC732@NewLife>
Message-ID: <924CFC00-B1CF-401E-B5A8-815E2E8EB1A1@illinois.edu>

Yes, though I'm assuming by .profile you mean the user-specific one ($HOME/.profile) and not the system/global one.  The local one should suffice.

chris

On Feb 3, 2010, at 12:56 PM, Mark A. Jensen wrote:

> up to list-- MAJ
> ----- Original Message ----- From: "Mark A. Jensen" <maj at fortinbras.us>
> To: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
> Sent: Wednesday, February 03, 2010 1:34 PM
> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem tochange
> 
> 
>> Well, that's progress. It hard to debug these things remotely, but now
>> you can at least work around the problem by using the -I flag. The next
>> weak link I would try to eliminate is the append to the .profile file. Just
>> do directly from the command line (don't relogin)
>> 
>> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB
>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>> 
>> If this gives 1.0069, then the problem is in that append (and, you can also do your work!).
>> (If you're a sudoer, I'd just edit that file directly.)
>> 
>> cheers MAJ
>> ----- Original Message ----- From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
>> To: "Mark A. Jensen" <maj at fortinbras.us>
>> Cc: <bioperl-l at lists.open-bio.org>
>> Sent: Wednesday, February 03, 2010 1:21 PM
>> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem tochange
>> 
>> 
>>> That gives me the 1.069 that I was wanting so the problem seems to be  that perl is finding the wrong installation by default...
>>> 
>>> Lacey
>>> 
>>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>> 
>>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/bioperl- live -le 'print Bio::Perl->VERSION;'
>>> 
>>> 
>>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From laceyanne_sanderson at shaw.ca  Wed Feb  3 14:38:09 2010
From: laceyanne_sanderson at shaw.ca (Lacey Sanderson)
Date: Wed, 03 Feb 2010 13:38:09 -0600
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
 tochange
In-Reply-To: <0A73EA011D85433787444922A42E979C@NewLife>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
	<DA946FFE9178432A8E83411DC173C072@NewLife>
	<E2830264-A715-480E-B7F7-350D50E0F571@shaw.ca>
	<0A23A254827D40A997BF65EE356183E6@NewLife>
	<F0BF6771-7F76-4E7C-8085-3DF5C4C8AF9F@shaw.ca>
	<0A73EA011D85433787444922A42E979C@NewLife>
Message-ID: <2163AB4F-0CD3-44C8-AA04-6DAD0E67F549@shaw.ca>

Okay,
> directly from the command line (don't relogin)
>
> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live: 
> $PERL5LIB
> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
That gives me the correct version... For that user until I log out...

I sudoed in to .profile and added the line directly but that doesn't  
seem to have helped.

How would I tell perl to look in the same place for Bioperl for ALL  
users?

Lacey

On 3-Feb-10, at 12:34 PM, Mark A. Jensen wrote:

> Well, that's progress. It hard to debug these things remotely, but now
> you can at least work around the problem by using the -I flag. The  
> next
> weak link I would try to eliminate is the append to the .profile  
> file. Just
> do directly from the command line (don't relogin)
>
> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live: 
> $PERL5LIB
> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>
> If this gives 1.0069, then the problem is in that append (and, you  
> can also do your work!).
> (If you're a sudoer, I'd just edit that file directly.)
>
> cheers MAJ
> ----- Original Message ----- From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca 
> >
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, February 03, 2010 1:21 PM
> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version  
> doesn't seem tochange
>
>
>> That gives me the 1.069 that I was wanting so the problem seems to  
>> be  that perl is finding the wrong installation by default...
>>
>> Lacey
>>
>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>
>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/bioperl-  
>>> live -le 'print Bio::Perl->VERSION;'
>>
>>
>

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.


From scott at scottcain.net  Wed Feb  3 14:49:21 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Feb 2010 14:49:21 -0500
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
	tochange
In-Reply-To: <2163AB4F-0CD3-44C8-AA04-6DAD0E67F549@shaw.ca>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
	<DA946FFE9178432A8E83411DC173C072@NewLife>
	<E2830264-A715-480E-B7F7-350D50E0F571@shaw.ca>
	<0A23A254827D40A997BF65EE356183E6@NewLife>
	<F0BF6771-7F76-4E7C-8085-3DF5C4C8AF9F@shaw.ca>
	<0A73EA011D85433787444922A42E979C@NewLife>
	<2163AB4F-0CD3-44C8-AA04-6DAD0E67F549@shaw.ca>
Message-ID: <4536f7701002031149j3abd0beavfdd8d67e9219b7e2@mail.gmail.com>

Hi Lacey,

In order for it to be available to all users, I would suggest you go
through the "normal" installation procedure:

perl Build.PL
./Build
./Build test
sudo ./Build install --uninst 1

Scott


On Wed, Feb 3, 2010 at 2:38 PM, Lacey Sanderson
<laceyanne_sanderson at shaw.ca> wrote:
> Okay,
>>
>> directly from the command line (don't relogin)
>>
>> $ export
>> PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB
>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>
> That gives me the correct version... For that user until I log out...
>
> I sudoed in to .profile and added the line directly but that doesn't seem to
> have helped.
>
> How would I tell perl to look in the same place for Bioperl for ALL users?
>
> Lacey
>
> On 3-Feb-10, at 12:34 PM, Mark A. Jensen wrote:
>
>> Well, that's progress. It hard to debug these things remotely, but now
>> you can at least work around the problem by using the -I flag. The next
>> weak link I would try to eliminate is the append to the .profile file.
>> Just
>> do directly from the command line (don't relogin)
>>
>> $ export
>> PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB
>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>>
>> If this gives 1.0069, then the problem is in that append (and, you can
>> also do your work!).
>> (If you're a sudoer, I'd just edit that file directly.)
>>
>> cheers MAJ
>> ----- Original Message ----- From: "Lacey Sanderson"
>> <laceyanne_sanderson at shaw.ca>
>> To: "Mark A. Jensen" <maj at fortinbras.us>
>> Cc: <bioperl-l at lists.open-bio.org>
>> Sent: Wednesday, February 03, 2010 1:21 PM
>> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't
>> seem tochange
>>
>>
>>> That gives me the 1.069 that I was wanting so the problem seems to be
>>> ?that perl is finding the wrong installation by default...
>>>
>>> Lacey
>>>
>>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>>
>>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/bioperl- live
>>>> -le 'print Bio::Perl->VERSION;'
>>>
>>>
>>
>
> ---------------------------------
> Lacey Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Department of Plant Sciences
> University of Saskatchewan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From maj at fortinbras.us  Wed Feb  3 14:55:41 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 3 Feb 2010 14:55:41 -0500
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
	tochange
In-Reply-To: <4536f7701002031149j3abd0beavfdd8d67e9219b7e2@mail.gmail.com>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
	<DA946FFE9178432A8E83411DC173C072@NewLife>
	<E2830264-A715-480E-B7F7-350D50E0F571@shaw.ca>
	<0A23A254827D40A997BF65EE356183E6@NewLife>
	<F0BF6771-7F76-4E7C-8085-3DF5C4C8AF9F@shaw.ca>
	<0A73EA011D85433787444922A42E979C@NewLife>
	<2163AB4F-0CD3-44C8-AA04-6DAD0E67F549@shaw.ca>
	<4536f7701002031149j3abd0beavfdd8d67e9219b7e2@mail.gmail.com>
Message-ID: <5063EF67524746ECA04C060F66E50486@NewLife>

I'll jump in to +1 on this; the Build will make sure you have all the necessary 
prequisites, and install those automatically (I *think* it still does this....). 
It will also do comprehensive tests. These will save MANY headaches down the 
road.

[I speak as someone who didn't build in the beginning, until one day Dave 
Messina
blithely said to me "why don't you just run ./Build test ?". Three days later, I 
was back up...]

----- Original Message ----- 
From: "Scott Cain" <scott at scottcain.net>
To: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
Cc: "Mark A. Jensen" <maj at fortinbras.us>; <bioperl-l at lists.open-bio.org>
Sent: Wednesday, February 03, 2010 2:49 PM
Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem 
tochange


Hi Lacey,

In order for it to be available to all users, I would suggest you go
through the "normal" installation procedure:

perl Build.PL
./Build
./Build test
sudo ./Build install --uninst 1

Scott


On Wed, Feb 3, 2010 at 2:38 PM, Lacey Sanderson
<laceyanne_sanderson at shaw.ca> wrote:
> Okay,
>>
>> directly from the command line (don't relogin)
>>
>> $ export
>> PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB
>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>
> That gives me the correct version... For that user until I log out...
>
> I sudoed in to .profile and added the line directly but that doesn't seem to
> have helped.
>
> How would I tell perl to look in the same place for Bioperl for ALL users?
>
> Lacey
>
> On 3-Feb-10, at 12:34 PM, Mark A. Jensen wrote:
>
>> Well, that's progress. It hard to debug these things remotely, but now
>> you can at least work around the problem by using the -I flag. The next
>> weak link I would try to eliminate is the append to the .profile file.
>> Just
>> do directly from the command line (don't relogin)
>>
>> $ export
>> PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB
>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>>
>> If this gives 1.0069, then the problem is in that append (and, you can
>> also do your work!).
>> (If you're a sudoer, I'd just edit that file directly.)
>>
>> cheers MAJ
>> ----- Original Message ----- From: "Lacey Sanderson"
>> <laceyanne_sanderson at shaw.ca>
>> To: "Mark A. Jensen" <maj at fortinbras.us>
>> Cc: <bioperl-l at lists.open-bio.org>
>> Sent: Wednesday, February 03, 2010 1:21 PM
>> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't
>> seem tochange
>>
>>
>>> That gives me the 1.069 that I was wanting so the problem seems to be
>>> that perl is finding the wrong installation by default...
>>>
>>> Lacey
>>>
>>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>>
>>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/bioperl- live
>>>> -le 'print Bio::Perl->VERSION;'
>>>
>>>
>>
>
> ---------------------------------
> Lacey Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Department of Plant Sciences
> University of Saskatchewan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



From cjfields at illinois.edu  Wed Feb  3 15:05:16 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Feb 2010 14:05:16 -0600
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
	tochange
In-Reply-To: <5063EF67524746ECA04C060F66E50486@NewLife>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
	<DA946FFE9178432A8E83411DC173C072@NewLife>
	<E2830264-A715-480E-B7F7-350D50E0F571@shaw.ca>
	<0A23A254827D40A997BF65EE356183E6@NewLife>
	<F0BF6771-7F76-4E7C-8085-3DF5C4C8AF9F@shaw.ca>
	<0A73EA011D85433787444922A42E979C@NewLife>
	<2163AB4F-0CD3-44C8-AA04-6DAD0E67F549@shaw.ca>
	<4536f7701002031149j3abd0beavfdd8d67e9219b7e2@mail.gmail.com>
	<5063EF67524746ECA04C060F66E50486@NewLife>
Message-ID: <85545C48-7DEB-4D92-B5F8-3781BEE5D8AA@illinois.edu>

Also, remember if you are installing from svn you are installing from the bleeding edge code.  IIRC the last svn co I made had several tests failing for various reasons; nothing that should affect your installation, but something to be aware of.

chris

On Feb 3, 2010, at 1:55 PM, Mark A. Jensen wrote:

> I'll jump in to +1 on this; the Build will make sure you have all the necessary prequisites, and install those automatically (I *think* it still does this....). It will also do comprehensive tests. These will save MANY headaches down the road.
> 
> [I speak as someone who didn't build in the beginning, until one day Dave Messina
> blithely said to me "why don't you just run ./Build test ?". Three days later, I was back up...]
> 
> ----- Original Message ----- From: "Scott Cain" <scott at scottcain.net>
> To: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
> Cc: "Mark A. Jensen" <maj at fortinbras.us>; <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, February 03, 2010 2:49 PM
> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem tochange
> 
> 
> Hi Lacey,
> 
> In order for it to be available to all users, I would suggest you go
> through the "normal" installation procedure:
> 
> perl Build.PL
> ./Build
> ./Build test
> sudo ./Build install --uninst 1
> 
> Scott
> 
> 
> On Wed, Feb 3, 2010 at 2:38 PM, Lacey Sanderson
> <laceyanne_sanderson at shaw.ca> wrote:
>> Okay,
>>> 
>>> directly from the command line (don't relogin)
>>> 
>>> $ export
>>> PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB
>>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>> 
>> That gives me the correct version... For that user until I log out...
>> 
>> I sudoed in to .profile and added the line directly but that doesn't seem to
>> have helped.
>> 
>> How would I tell perl to look in the same place for Bioperl for ALL users?
>> 
>> Lacey
>> 
>> On 3-Feb-10, at 12:34 PM, Mark A. Jensen wrote:
>> 
>>> Well, that's progress. It hard to debug these things remotely, but now
>>> you can at least work around the problem by using the -I flag. The next
>>> weak link I would try to eliminate is the append to the .profile file.
>>> Just
>>> do directly from the command line (don't relogin)
>>> 
>>> $ export
>>> PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live:$PERL5LIB
>>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>>> 
>>> If this gives 1.0069, then the problem is in that append (and, you can
>>> also do your work!).
>>> (If you're a sudoer, I'd just edit that file directly.)
>>> 
>>> cheers MAJ
>>> ----- Original Message ----- From: "Lacey Sanderson"
>>> <laceyanne_sanderson at shaw.ca>
>>> To: "Mark A. Jensen" <maj at fortinbras.us>
>>> Cc: <bioperl-l at lists.open-bio.org>
>>> Sent: Wednesday, February 03, 2010 1:21 PM
>>> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't
>>> seem tochange
>>> 
>>> 
>>>> That gives me the 1.069 that I was wanting so the problem seems to be
>>>> that perl is finding the wrong installation by default...
>>>> 
>>>> Lacey
>>>> 
>>>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>>> 
>>>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/bioperl- live
>>>>> -le 'print Bio::Perl->VERSION;'
>>>> 
>>>> 
>>> 
>> 
>> ---------------------------------
>> Lacey Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Department of Plant Sciences
>> University of Saskatchewan.
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From maj at fortinbras.us  Wed Feb  3 14:47:24 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 3 Feb 2010 14:47:24 -0500
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
	tochange
In-Reply-To: <2163AB4F-0CD3-44C8-AA04-6DAD0E67F549@shaw.ca>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca><DA946FFE9178432A8E83411DC173C072@NewLife><E2830264-A715-480E-B7F7-350D50E0F571@shaw.ca><0A23A254827D40A997BF65EE356183E6@NewLife><F0BF6771-7F76-4E7C-8085-3DF5C4C8AF9F@shaw.ca><0A73EA011D85433787444922A42E979C@NewLife>
	<2163AB4F-0CD3-44C8-AA04-6DAD0E67F549@shaw.ca>
Message-ID: <3934A7E8419D47178E80C9844EDC4B7E@NewLife>

You probably want to change the file
/etc/profile
(no .) --MAJ
----- Original Message ----- 
From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, February 03, 2010 2:38 PM
Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem 
tochange


> Okay,
>> directly from the command line (don't relogin)
>>
>> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live: 
>> $PERL5LIB
>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
> That gives me the correct version... For that user until I log out...
>
> I sudoed in to .profile and added the line directly but that doesn't  seem to 
> have helped.
>
> How would I tell perl to look in the same place for Bioperl for ALL  users?
>
> Lacey
>
> On 3-Feb-10, at 12:34 PM, Mark A. Jensen wrote:
>
>> Well, that's progress. It hard to debug these things remotely, but now
>> you can at least work around the problem by using the -I flag. The  next
>> weak link I would try to eliminate is the append to the .profile  file. Just
>> do directly from the command line (don't relogin)
>>
>> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live: 
>> $PERL5LIB
>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>>
>> If this gives 1.0069, then the problem is in that append (and, you  can also 
>> do your work!).
>> (If you're a sudoer, I'd just edit that file directly.)
>>
>> cheers MAJ
>> ----- Original Message ----- From: "Lacey Sanderson" 
>> <laceyanne_sanderson at shaw.ca
>> >
>> To: "Mark A. Jensen" <maj at fortinbras.us>
>> Cc: <bioperl-l at lists.open-bio.org>
>> Sent: Wednesday, February 03, 2010 1:21 PM
>> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version  doesn't seem 
>> tochange
>>
>>
>>> That gives me the 1.069 that I was wanting so the problem seems to  be  that 
>>> perl is finding the wrong installation by default...
>>>
>>> Lacey
>>>
>>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>>
>>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/bioperl-  live -le 
>>>> 'print Bio::Perl->VERSION;'
>>>
>>>
>>
>
> ---------------------------------
> Lacey Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Department of Plant Sciences
> University of Saskatchewan.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From laceyanne_sanderson at shaw.ca  Wed Feb  3 15:49:22 2010
From: laceyanne_sanderson at shaw.ca (Lacey Sanderson)
Date: Wed, 03 Feb 2010 14:49:22 -0600
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
 tochange
In-Reply-To: <4536f7701002031149j3abd0beavfdd8d67e9219b7e2@mail.gmail.com>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca>
	<DA946FFE9178432A8E83411DC173C072@NewLife>
	<E2830264-A715-480E-B7F7-350D50E0F571@shaw.ca>
	<0A23A254827D40A997BF65EE356183E6@NewLife>
	<F0BF6771-7F76-4E7C-8085-3DF5C4C8AF9F@shaw.ca>
	<0A73EA011D85433787444922A42E979C@NewLife>
	<2163AB4F-0CD3-44C8-AA04-6DAD0E67F549@shaw.ca>
	<4536f7701002031149j3abd0beavfdd8d67e9219b7e2@mail.gmail.com>
Message-ID: <6278A3EC-95AC-4CE2-AE77-593D97BEA871@shaw.ca>

Okay, running Build from the base of the bioperl-live directory Worked.

Version is now 1.0069 !!

For all users, even after re-logging in...

Thanks!
Lacey

On 3-Feb-10, at 1:49 PM, Scott Cain wrote:

> Hi Lacey,
>
> In order for it to be available to all users, I would suggest you go
> through the "normal" installation procedure:
>
> perl Build.PL
> ./Build
> ./Build test
> sudo ./Build install --uninst 1
>
> Scott
>
>
> On Wed, Feb 3, 2010 at 2:38 PM, Lacey Sanderson
> <laceyanne_sanderson at shaw.ca> wrote:
>> Okay,
>>>
>>> directly from the command line (don't relogin)
>>>
>>> $ export
>>> PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live: 
>>> $PERL5LIB
>>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>>
>> That gives me the correct version... For that user until I log out...
>>
>> I sudoed in to .profile and added the line directly but that  
>> doesn't seem to
>> have helped.
>>
>> How would I tell perl to look in the same place for Bioperl for ALL  
>> users?
>>
>> Lacey
>>
>> On 3-Feb-10, at 12:34 PM, Mark A. Jensen wrote:
>>
>>> Well, that's progress. It hard to debug these things remotely, but  
>>> now
>>> you can at least work around the problem by using the -I flag. The  
>>> next
>>> weak link I would try to eliminate is the append to the .profile  
>>> file.
>>> Just
>>> do directly from the command line (don't relogin)
>>>
>>> $ export
>>> PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live: 
>>> $PERL5LIB
>>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>>>
>>> If this gives 1.0069, then the problem is in that append (and, you  
>>> can
>>> also do your work!).
>>> (If you're a sudoer, I'd just edit that file directly.)
>>>
>>> cheers MAJ
>>> ----- Original Message ----- From: "Lacey Sanderson"
>>> <laceyanne_sanderson at shaw.ca>
>>> To: "Mark A. Jensen" <maj at fortinbras.us>
>>> Cc: <bioperl-l at lists.open-bio.org>
>>> Sent: Wednesday, February 03, 2010 1:21 PM
>>> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version  
>>> doesn't
>>> seem tochange
>>>
>>>
>>>> That gives me the 1.069 that I was wanting so the problem seems  
>>>> to be
>>>>  that perl is finding the wrong installation by default...
>>>>
>>>> Lacey
>>>>
>>>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>>>
>>>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/ 
>>>>> bioperl- live
>>>>> -le 'print Bio::Perl->VERSION;'
>>>>
>>>>
>>>
>>
>> ---------------------------------
>> Lacey Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Department of Plant Sciences
>> University of Saskatchewan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.


From jason at bioperl.org  Wed Feb  3 15:52:04 2010
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 3 Feb 2010 12:52:04 -0800
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
	tochange
In-Reply-To: <3934A7E8419D47178E80C9844EDC4B7E@NewLife>
References: <FCF02388-37A6-4F7E-8808-58DAEB7549D2@shaw.ca><DA946FFE9178432A8E83411DC173C072@NewLife><E2830264-A715-480E-B7F7-350D50E0F571@shaw.ca><0A23A254827D40A997BF65EE356183E6@NewLife><F0BF6771-7F76-4E7C-8085-3DF5C4C8AF9F@shaw.ca><0A73EA011D85433787444922A42E979C@NewLife>
	<2163AB4F-0CD3-44C8-AA04-6DAD0E67F549@shaw.ca>
	<3934A7E8419D47178E80C9844EDC4B7E@NewLife>
Message-ID: <34A48A92-6ECF-4401-8D92-F15EC91FA040@bioperl.org>

Or add a file on centos/rh to set global variables in the more modular  
way than editing /etc/profile

$ cat /etc/profile.d/perl.sh
LIBS=/usr/local/pkg/bioperl/core
if [ -z "${PERL5LIB}" ]
then
     PERL5LIB=$LIBS; export PERL5LIB
else
     PERL5LIB=$LIBS:$PERL5LIB; export PERL5LIB
fi

-jason
On Feb 3, 2010, at 11:47 AM, Mark A. Jensen wrote:

> You probably want to change the file
> /etc/profile
> (no .) --MAJ
> ----- Original Message ----- From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca 
> >
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, February 03, 2010 2:38 PM
> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version  
> doesn't seem tochange
>
>
>> Okay,
>>> directly from the command line (don't relogin)
>>>
>>> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl- 
>>> live: $PERL5LIB
>>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>> That gives me the correct version... For that user until I log out...
>>
>> I sudoed in to .profile and added the line directly but that  
>> doesn't  seem to have helped.
>>
>> How would I tell perl to look in the same place for Bioperl for  
>> ALL  users?
>>
>> Lacey
>>
>> On 3-Feb-10, at 12:34 PM, Mark A. Jensen wrote:
>>
>>> Well, that's progress. It hard to debug these things remotely, but  
>>> now
>>> you can at least work around the problem by using the -I flag.  
>>> The  next
>>> weak link I would try to eliminate is the append to the .profile   
>>> file. Just
>>> do directly from the command line (don't relogin)
>>>
>>> $ export PERL5LIB=/usr/local/share/applications/Bioperl/bioperl- 
>>> live: $PERL5LIB
>>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>>>
>>> If this gives 1.0069, then the problem is in that append (and,  
>>> you  can also do your work!).
>>> (If you're a sudoer, I'd just edit that file directly.)
>>>
>>> cheers MAJ
>>> ----- Original Message ----- From: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca
>>> >
>>> To: "Mark A. Jensen" <maj at fortinbras.us>
>>> Cc: <bioperl-l at lists.open-bio.org>
>>> Sent: Wednesday, February 03, 2010 1:21 PM
>>> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version   
>>> doesn't seem tochange
>>>
>>>
>>>> That gives me the 1.069 that I was wanting so the problem seems  
>>>> to  be  that perl is finding the wrong installation by default...
>>>>
>>>> Lacey
>>>>
>>>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>>>
>>>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/ 
>>>>> bioperl-  live -le 'print Bio::Perl->VERSION;'
>>>>
>>>>
>>>
>>
>> ---------------------------------
>> Lacey Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Department of Plant Sciences
>> University of Saskatchewan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/
http://twitter.com/hyphaltip


From dan.kortschak at adelaide.edu.au  Wed Feb  3 17:30:50 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Thu, 04 Feb 2010 09:00:50 +1030
Subject: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem
 to change
In-Reply-To: <mailman.34143.1265225894.2696.bioperl-l@lists.open-bio.org>
References: <mailman.34143.1265225894.2696.bioperl-l@lists.open-bio.org>
Message-ID: <1265236250.5663.30.camel@zoidberg.mbs.adelaide.edu.au>

Hi Chris,

I too have had strangeness with version reporting - not with the svn
checkouts, but with the CPAN package which I use on my production
machine (v 1.6.1 installed).

cpanp 'o' reports the version of bioperl (actually 'Bio::Root::RootI')
installed as 'Unparsable', with the available upgrade as 1.006001 as you
would expect, 'l' gives the following:

CPAN Terminal> l Bio::Root::RootI

Details for 'Bio::Root::RootI'
Author                   Christopher Fields (cjfields at bioperl.org)    
Description              None given
Development Stage        Unknown
Installed File           /usr/local/share/perl/5.10.0/Bio/Root/RootI.pm
Interface Style          Unknown
Language Used            Unknown
Package                  BioPerl-1.6.1.tar.gz
Public License           Unknown
Support Level            Unknown
Version Installed        0.0
Version on CPAN          1.006001

etc

The head line of B:R:RI:

# $Id: RootI.pm 16090 2009-09-15 21:57:56Z cjfields $

and the cpanp install logs show 1.6.1 is actually installed.


This has never really worried me, but since version reporting was raised
I thought I'd bring it up. Also curious about why BioPerl.pm isn't
installed/manified on bioperl install as I wonder around the distro.

cheers
Dan


From irisbuiton at gmail.com  Thu Feb  4 11:06:25 2010
From: irisbuiton at gmail.com (Iris Buiton)
Date: Thu, 4 Feb 2010 08:06:25 -0800 (PST)
Subject: [Bioperl-l] clone ID to Accession ID genbank
Message-ID: <62377232-beb8-4aa3-aa4a-10f6d926a8ee@m35g2000prh.googlegroups.com>

Hi members of Bioperl,

I am trying to run some code that given a clone ID (for instance,
CH255-149A8) get the accesion ID (AC238489.2).

The problem is that using this ID, it works perfectly, but using this
other ID (CH251-558O8) I do not get anything (not $seq object is
obtained). Checking to Genbank, this clone exist, there is seqeunce,
and the accession ID should be AC147515.1

This is the code:

 my $name_file="CH251-558O8";

  my $query = Bio::DB::Query::GenBank->new
        (-query   => $name_file,
         -reldate => '30',
     -db      => 'nucleotide');
    #eval 'my $seqio = $gb->get_Stream_by_query($query)';
    print $query->count,"\n";


    my $gb = Bio::DB::GenBank->new();

    my $seqio = $gb->get_Stream_by_query($query);

    print "Running $name_file.....\n";


    while( my $seq =  $seqio->next_seq ) {
      if ($seq->accession_number)
      {
      print "$name_file = ", $seq->accession_number," = ", $seq-
>length,"\n" ;
      }else
      {
      print "$name_file = #N/A \n" ;
      }
    }

Any ideas what am I doing wrong?

Thanks!

Iris

From MEC at stowers.org  Thu Feb  4 12:15:12 2010
From: MEC at stowers.org (Cook, Malcolm)
Date: Thu, 4 Feb 2010 11:15:12 -0600
Subject: [Bioperl-l] clone ID to Accession ID genbank
In-Reply-To: <62377232-beb8-4aa3-aa4a-10f6d926a8ee@m35g2000prh.googlegroups.com>
References: <62377232-beb8-4aa3-aa4a-10f6d926a8ee@m35g2000prh.googlegroups.com>
Message-ID: <BD62CBAC4395B94096109020651BE2EC12E0CA06A1@EXCHMB-02.stowers-institute.org>

remove the -reldate

Malcolm Cook
Stowers Institute for Medical Research -  Bioinformatics
Kansas City, Missouri  USA
 
 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Iris Buiton
> Sent: Thursday, February 04, 2010 10:06 AM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] clone ID to Accession ID genbank
> 
> Hi members of Bioperl,
> 
> I am trying to run some code that given a clone ID (for instance,
> CH255-149A8) get the accesion ID (AC238489.2).
> 
> The problem is that using this ID, it works perfectly, but 
> using this other ID (CH251-558O8) I do not get anything (not 
> $seq object is obtained). Checking to Genbank, this clone 
> exist, there is seqeunce, and the accession ID should be AC147515.1
> 
> This is the code:
> 
>  my $name_file="CH251-558O8";
> 
>   my $query = Bio::DB::Query::GenBank->new
>         (-query   => $name_file,
>          -reldate => '30',
>      -db      => 'nucleotide');
>     #eval 'my $seqio = $gb->get_Stream_by_query($query)';
>     print $query->count,"\n";
> 
> 
>     my $gb = Bio::DB::GenBank->new();
> 
>     my $seqio = $gb->get_Stream_by_query($query);
> 
>     print "Running $name_file.....\n";
> 
> 
>     while( my $seq =  $seqio->next_seq ) {
>       if ($seq->accession_number)
>       {
>       print "$name_file = ", $seq->accession_number," = ", $seq-
> >length,"\n" ;
>       }else
>       {
>       print "$name_file = #N/A \n" ;
>       }
>     }
> 
> Any ideas what am I doing wrong?
> 
> Thanks!
> 
> Iris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

From Irisbuiton at gmail.com  Thu Feb  4 12:26:57 2010
From: Irisbuiton at gmail.com (Irisbuiton at gmail.com)
Date: Thu, 04 Feb 2010 17:26:57 +0000
Subject: [Bioperl-l] clone ID to Accession ID genbank
In-Reply-To: <BD62CBAC4395B94096109020651BE2EC12E0CA06A1@EXCHMB-02.stowers-institute.org>
Message-ID: <00504502e11453f33b047ec9a4b5@google.com>

Many thanks!

Such a stupid mistake...

IRis.

On Feb 4, 2010 9:15am, "Cook, Malcolm" <MEC at stowers.org> wrote:
> remove the -reldate



> Malcolm Cook

> Stowers Institute for Medical Research - Bioinformatics

> Kansas City, Missouri USA







> > -----Original Message-----

> > From: bioperl-l-bounces at lists.open-bio.org

> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Iris Buiton

> > Sent: Thursday, February 04, 2010 10:06 AM

> > To: bioperl-l at bioperl.org

> > Subject: [Bioperl-l] clone ID to Accession ID genbank

> >

> > Hi members of Bioperl,

> >

> > I am trying to run some code that given a clone ID (for instance,

> > CH255-149A8) get the accesion ID (AC238489.2).

> >

> > The problem is that using this ID, it works perfectly, but

> > using this other ID (CH251-558O8) I do not get anything (not

> > $seq object is obtained). Checking to Genbank, this clone

> > exist, there is seqeunce, and the accession ID should be AC147515.1

> >

> > This is the code:

> >

> > my $name_file="CH251-558O8";

> >

> > my $query = Bio::DB::Query::GenBank->new

> > (-query => $name_file,

> > -reldate => '30',

> > -db => 'nucleotide');

> > #eval 'my $seqio = $gb->get_Stream_by_query($query)';

> > print $query->count,"\n";

> >

> >

> > my $gb = Bio::DB::GenBank->new();

> >

> > my $seqio = $gb->get_Stream_by_query($query);

> >

> > print "Running $name_file.....\n";

> >

> >

> > while( my $seq = $seqio->next_seq ) {

> > if ($seq->accession_number)

> > {

> > print "$name_file = ", $seq->accession_number," = ", $seq-

> > >length,"\n" ;

> > }else

> > {

> > print "$name_file = #N/A \n" ;

> > }

> > }

> >

> > Any ideas what am I doing wrong?

> >

> > Thanks!

> >

> > Iris

> > _______________________________________________

> > Bioperl-l mailing list

> > Bioperl-l at lists.open-bio.org

> > http://lists.open-bio.org/mailman/listinfo/bioperl-l

> >

From sharmashalu.bio at gmail.com  Thu Feb  4 17:01:35 2010
From: sharmashalu.bio at gmail.com (shalu sharma)
Date: Thu, 4 Feb 2010 17:01:35 -0500
Subject: [Bioperl-l] Refseq Version
Message-ID: <465b5a661002041401u3b8ac5fdp483f7032ce35139b@mail.gmail.com>

Hi All,
      This is not a bioperl query.
Is there any way to check refseq version (release). Actually i am using some
server to blast my sequences (blastall) against refseq. Is there any way i
can get the version information on the refseq database (from the blast file
or directly from the database)?

Thanks
Shalu

From Russell.Smithies at agresearch.co.nz  Thu Feb  4 18:39:55 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Fri, 5 Feb 2010 12:39:55 +1300
Subject: [Bioperl-l] Refseq Version
In-Reply-To: <465b5a661002041401u3b8ac5fdp483f7032ce35139b@mail.gmail.com>
References: <465b5a661002041401u3b8ac5fdp483f7032ce35139b@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61BED520@exchsth.agresearch.co.nz>

If you have access to the blast database, use fastacmd -I -d databasename
Otherwise, it's usually at the bottom of your blast result.

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of shalu sharma
> Sent: Friday, 5 February 2010 11:02 a.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Refseq Version
> 
> Hi All,
>       This is not a bioperl query.
> Is there any way to check refseq version (release). Actually i am using
> some
> server to blast my sequences (blastall) against refseq. Is there any way i
> can get the version information on the refseq database (from the blast
> file
> or directly from the database)?
> 
> Thanks
> Shalu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From pisceanpranav at gmail.com  Thu Feb  4 21:17:05 2010
From: pisceanpranav at gmail.com (pranav karkhanis)
Date: Fri, 5 Feb 2010 07:47:05 +0530
Subject: [Bioperl-l] (no subject)
Message-ID: <3122b9be1002041817v5f8704afwca44f282d35f4140@mail.gmail.com>

Where can I find the examples or source code for running BLAST with a
input SEQUENCE
using RemoteBlast.pm?

From maj at fortinbras.us  Thu Feb  4 21:20:10 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 4 Feb 2010 21:20:10 -0500
Subject: [Bioperl-l] (no subject)
In-Reply-To: <3122b9be1002041817v5f8704afwca44f282d35f4140@mail.gmail.com>
References: <3122b9be1002041817v5f8704afwca44f282d35f4140@mail.gmail.com>
Message-ID: <911C931932FA4836936C2E0AD23CE284@NewLife>

http://bioperl.org/wiki/HOWTOs
----- Original Message ----- 
From: "pranav karkhanis" <pisceanpranav at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Cc: "Rahul parakkat" <rahulparakkat at gmail.com>
Sent: Thursday, February 04, 2010 9:17 PM
Subject: [Bioperl-l] (no subject)


> Where can I find the examples or source code for running BLAST with a
> input SEQUENCE
> using RemoteBlast.pm?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
>

From fungazid at yahoo.com  Thu Feb  4 21:52:53 2010
From: fungazid at yahoo.com (Fungazid)
Date: Thu, 4 Feb 2010 18:52:53 -0800 (PST)
Subject: [Bioperl-l] Too many links at LoadHelper.pm
Message-ID: <34328.58710.qm@web65506.mail.ac4.yahoo.com>

Bioperl hi,

I have multiple gff3 files that look like:

--------------------------------------------------------
##gff-version 3
# file: temp1.gff3
contig453278    hs    contig    1    699    .    +    .    Name=contig453278
contig453278    hs    alignment    1    194    .    +    .    Name=hs.ENST00000258455
contig453278    hs    alignment    252    699    .    +    .    Name=hs.ENST00000258455
contig453278    hs    mi2    194    252    .    +    .    Name=mi2
contig453278    hs    transcript    104    183    .    +    .    Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
contig453278    hs    transcript    1    9    .    +    .    Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
contig453278    hs    transcript    73    103    .    +    .    Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
contig453278    hs    transcript    10    72    .    +    .    Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
---------------------------------------------------------



I uploaded gff3 files to mysql and view the tracks in gBrowse like this:

--------------------------------------------
Bio::DB::SeqFeature::Store->new(...)
$loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
for($i=0; $i<$#files+1; $i++){
$loader->load($file[$i]);
}
--------------------------------------------

Eventually after uploading ~15000 small gff3 files I got the error:

Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory /tmp/9bbpdE5ibf: Too many links at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49



I am trying to see what went wrong, maybe you can rescue me,
Avi


      


From jason at bioperl.org  Thu Feb  4 22:31:06 2010
From: jason at bioperl.org (Jason Stajich)
Date: Thu, 4 Feb 2010 19:31:06 -0800
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
Message-ID: <FAA3D0CE-0723-400D-9485-840A79377B18@bioperl.org>

why are you not using the bp_seqfeature_load script?

On Feb 4, 2010, at 6:52 PM, Fungazid wrote:

> Bioperl hi,
>
> I have multiple gff3 files that look like:
>
> --------------------------------------------------------
> ##gff-version 3
> # file: temp1.gff3
> contig453278    hs    contig    1    699    .    +    .     
> Name=contig453278
> contig453278    hs    alignment    1    194    .    +    .     
> Name=hs.ENST00000258455
> contig453278    hs    alignment    252    699    .    +    .     
> Name=hs.ENST00000258455
> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
> contig453278    hs    transcript    104    183    .    +    .     
> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
> contig453278    hs    transcript    1    9    .    +    .     
> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
> contig453278    hs    transcript    73    103    .    +    .     
> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
> contig453278    hs    transcript    10    72    .    +    .     
> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
> ---------------------------------------------------------
>
>
>
> I uploaded gff3 files to mysql and view the tracks in gBrowse like  
> this:
>
> --------------------------------------------
> Bio::DB::SeqFeature::Store->new(...)
> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
> for($i=0; $i<$#files+1; $i++){
> $loader->load($file[$i]);
> }
> --------------------------------------------
>
> Eventually after uploading ~15000 small gff3 files I got the error:
>
> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create  
> directory /tmp/9bbpdE5ibf: Too many links at /usr/local/share/perl/ 
> 5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
>
>
>
> I am trying to see what went wrong, maybe you can rescue me,
> Avi
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/
http://twitter.com/hyphaltip


From scott at scottcain.net  Thu Feb  4 22:38:52 2010
From: scott at scottcain.net (Scott Cain)
Date: Thu, 4 Feb 2010 22:38:52 -0500
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
Message-ID: <4536f7701002041938m3ad2d6ddgf8fa56312d62c28a@mail.gmail.com>

Hi Avi,

Off hand, I have no idea what is happening.  Is there a reason you
aren't using bp_seqfeature_load.pl?

Scott


On Thu, Feb 4, 2010 at 9:52 PM, Fungazid <fungazid at yahoo.com> wrote:
> Bioperl hi,
>
> I have multiple gff3 files that look like:
>
> --------------------------------------------------------
> ##gff-version 3
> # file: temp1.gff3
> contig453278 ? ?hs ? ?contig ? ?1 ? ?699 ? ?. ? ?+ ? ?. ? ?Name=contig453278
> contig453278 ? ?hs ? ?alignment ? ?1 ? ?194 ? ?. ? ?+ ? ?. ? ?Name=hs.ENST00000258455
> contig453278 ? ?hs ? ?alignment ? ?252 ? ?699 ? ?. ? ?+ ? ?. ? ?Name=hs.ENST00000258455
> contig453278 ? ?hs ? ?mi2 ? ?194 ? ?252 ? ?. ? ?+ ? ?. ? ?Name=mi2
> contig453278 ? ?hs ? ?transcript ? ?104 ? ?183 ? ?. ? ?+ ? ?. ? ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
> contig453278 ? ?hs ? ?transcript ? ?1 ? ?9 ? ?. ? ?+ ? ?. ? ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
> contig453278 ? ?hs ? ?transcript ? ?73 ? ?103 ? ?. ? ?+ ? ?. ? ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
> contig453278 ? ?hs ? ?transcript ? ?10 ? ?72 ? ?. ? ?+ ? ?. ? ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
> ---------------------------------------------------------
>
>
>
> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>
> --------------------------------------------
> Bio::DB::SeqFeature::Store->new(...)
> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
> for($i=0; $i<$#files+1; $i++){
> $loader->load($file[$i]);
> }
> --------------------------------------------
>
> Eventually after uploading ~15000 small gff3 files I got the error:
>
> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory /tmp/9bbpdE5ibf: Too many links at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
>
>
>
> I am trying to see what went wrong, maybe you can rescue me,
> Avi
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From maj at fortinbras.us  Fri Feb  5 07:27:46 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 5 Feb 2010 07:27:46 -0500
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
Message-ID: <BD5DAE3180434255A2E6ADD94595AC94@NewLife>

The tempfiles are not being unlinked before there are too many for the OS to 
handle.
Sounds like this may be your job, fungazid, if you're not employing the script 
(but
not sure about that)
----- Original Message ----- 
From: "Fungazid" <fungazid at yahoo.com>
To: <Bioperl-l at lists.open-bio.org>
Sent: Thursday, February 04, 2010 9:52 PM
Subject: [Bioperl-l] Too many links at LoadHelper.pm


> Bioperl hi,
>
> I have multiple gff3 files that look like:
>
> --------------------------------------------------------
> ##gff-version 3
> # file: temp1.gff3
> contig453278    hs    contig    1    699    .    +    .    Name=contig453278
> contig453278    hs    alignment    1    194    .    +    . 
> Name=hs.ENST00000258455
> contig453278    hs    alignment    252    699    .    +    . 
> Name=hs.ENST00000258455
> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
> contig453278    hs    transcript    104    183    .    +    . 
> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
> contig453278    hs    transcript    1    9    .    +    . 
> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
> contig453278    hs    transcript    73    103    .    +    . 
> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
> contig453278    hs    transcript    10    72    .    +    . 
> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
> ---------------------------------------------------------
>
>
>
> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>
> --------------------------------------------
> Bio::DB::SeqFeature::Store->new(...)
> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
> for($i=0; $i<$#files+1; $i++){
> $loader->load($file[$i]);
> }
> --------------------------------------------
>
> Eventually after uploading ~15000 small gff3 files I got the error:
>
> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory 
> /tmp/9bbpdE5ibf: Too many links at 
> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
>
>
>
> I am trying to see what went wrong, maybe you can rescue me,
> Avi
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From sharmashalu.bio at gmail.com  Fri Feb  5 09:55:55 2010
From: sharmashalu.bio at gmail.com (shalu sharma)
Date: Fri, 5 Feb 2010 09:55:55 -0500
Subject: [Bioperl-l] Refseq Version
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32C61BED520@exchsth.agresearch.co.nz>
References: <465b5a661002041401u3b8ac5fdp483f7032ce35139b@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED520@exchsth.agresearch.co.nz>
Message-ID: <465b5a661002050655u34ff94acwdf8fe72512dec4b3@mail.gmail.com>

Hi Russell,
               Thanks for your response.
I am getting the number of sequence in the database but not the release
number (like 38, 39).
This is what i did:

$ fastacmd -I -d /db/ncbiblast/refseq/refseq_protein
Database: NCBI Protein Reference Sequences
           7,585,993 sequences; 2,644,770,521 total letters

File names:
/db/ncbiblast/refseq/refseq_protein.00
   Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 36,805 res
/db/ncbiblast/refseq/refseq_protein.01
   Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 33,403 res
/db/ncbiblast/refseq/refseq_protein.02
   Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 15,830 res

I am still confuse that how i can get the release number. I know refseq 39
was released on Jan 30, 2010 but i don't know how to confirm this. I also
tried look refseq release file but was not able to get any thing.

I would really appreciate if anyone can help me out with this.

Thanks
Shalu


On Thu, Feb 4, 2010 at 6:39 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:

> If you have access to the blast database, use fastacmd -I -d databasename
> Otherwise, it's usually at the bottom of your blast result.
>
> --Russell
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of shalu sharma
> > Sent: Friday, 5 February 2010 11:02 a.m.
> > To: bioperl-l at lists.open-bio.org
> > Subject: [Bioperl-l] Refseq Version
> >
> > Hi All,
> >       This is not a bioperl query.
> > Is there any way to check refseq version (release). Actually i am using
> > some
> > server to blast my sequences (blastall) against refseq. Is there any way
> i
> > can get the version information on the refseq database (from the blast
> > file
> > or directly from the database)?
> >
> > Thanks
> > Shalu
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
>

From maj at fortinbras.us  Fri Feb  5 10:03:49 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 5 Feb 2010 10:03:49 -0500
Subject: [Bioperl-l] Refseq Version
In-Reply-To: <465b5a661002050655u34ff94acwdf8fe72512dec4b3@mail.gmail.com>
References: <465b5a661002041401u3b8ac5fdp483f7032ce35139b@mail.gmail.com><18DF7D20DFEC044098A1062202F5FFF32C61BED520@exchsth.agresearch.co.nz>
	<465b5a661002050655u34ff94acwdf8fe72512dec4b3@mail.gmail.com>
Message-ID: <296EA2B4017347E9B8700FBC37836445@NewLife>

Hey guys-- thanks for this conversation, pls resist the temptation to go offlist 
with this.
When Russell provides the info, we can possibly add a new accesor for the
version info.
thanks MAJ
----- Original Message ----- 
From: "shalu sharma" <sharmashalu.bio at gmail.com>
To: "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 9:55 AM
Subject: Re: [Bioperl-l] Refseq Version


> Hi Russell,
>               Thanks for your response.
> I am getting the number of sequence in the database but not the release
> number (like 38, 39).
> This is what i did:
>
> $ fastacmd -I -d /db/ncbiblast/refseq/refseq_protein
> Database: NCBI Protein Reference Sequences
>           7,585,993 sequences; 2,644,770,521 total letters
>
> File names:
> /db/ncbiblast/refseq/refseq_protein.00
>   Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 36,805 res
> /db/ncbiblast/refseq/refseq_protein.01
>   Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 33,403 res
> /db/ncbiblast/refseq/refseq_protein.02
>   Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 15,830 res
>
> I am still confuse that how i can get the release number. I know refseq 39
> was released on Jan 30, 2010 but i don't know how to confirm this. I also
> tried look refseq release file but was not able to get any thing.
>
> I would really appreciate if anyone can help me out with this.
>
> Thanks
> Shalu
>
>
> On Thu, Feb 4, 2010 at 6:39 PM, Smithies, Russell <
> Russell.Smithies at agresearch.co.nz> wrote:
>
>> If you have access to the blast database, use fastacmd -I -d databasename
>> Otherwise, it's usually at the bottom of your blast result.
>>
>> --Russell
>>
>> > -----Original Message-----
>> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> > bounces at lists.open-bio.org] On Behalf Of shalu sharma
>> > Sent: Friday, 5 February 2010 11:02 a.m.
>> > To: bioperl-l at lists.open-bio.org
>> > Subject: [Bioperl-l] Refseq Version
>> >
>> > Hi All,
>> >       This is not a bioperl query.
>> > Is there any way to check refseq version (release). Actually i am using
>> > some
>> > server to blast my sequences (blastall) against refseq. Is there any way
>> i
>> > can get the version information on the refseq database (from the blast
>> > file
>> > or directly from the database)?
>> >
>> > Thanks
>> > Shalu
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> =======================================================================
>> Attention: The information contained in this message and/or attachments
>> from AgResearch Limited is intended only for the persons or entities
>> to which it is addressed and may contain confidential and/or privileged
>> material. Any review, retransmission, dissemination or other use of, or
>> taking of any action in reliance upon, this information by persons or
>> entities other than the intended recipients is prohibited by AgResearch
>> Limited. If you have received this message in error, please notify the
>> sender immediately.
>> =======================================================================
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From j.scholtalbers at gmail.com  Fri Feb  5 10:36:50 2010
From: j.scholtalbers at gmail.com (Jelle Scholtalbers)
Date: Fri, 5 Feb 2010 16:36:50 +0100
Subject: [Bioperl-l] Bio::DB::SeqFeature::Store::memory ->
	filter_by_type very slow
In-Reply-To: <3435CD81-A2B1-4419-995B-751BE3810017@illinois.edu>
References: <b66932c31002010424l2cccf278uf33ad8774e2f96a6@mail.gmail.com>
	<3435CD81-A2B1-4419-995B-751BE3810017@illinois.edu>
Message-ID: <b66932c31002050736gf922661r107034a05316c5c7@mail.gmail.com>

Hi,
a different issue I encountered today with the
Bio::DB::SeqFeature::Store::memory  is with the BINSIZE that this module
sets:

use constant BINSIZE => 10_000;

It would be nice to be able to set this dynamically since different GFF
files ask for different indexing rules. I ran into this as a problem when I
used a file that had its position multiplied by 1000 and at that point the
program ran fairly quick, 3-4min. After dividing the positions by 1000
(which is desired) the program took ~30min. to finish. The slowdown was
traceable to Bio::DB::SeqFeature::Store::memory::filter_by_location. By
setting the BINSIZE to 1 the issue was solved. However for another GFF file
this size is way too low.
Is this already possible and did I not see it or would this be an option to
add?

Cheers,
Jelle


2010/2/1 Chris Fields <cjfields at illinois.edu>

> Jelle,
>
> Seems reasonable, but Lincoln and Scott know that code better and are
> better suited to comment on it. Lincoln, Scott?
>
> chris
>
> On Feb 1, 2010, at 6:24 AM, Jelle Scholtalbers wrote:
>
> > Hi,
> > I used the Bio::DB::SeqFeature::Store::memory module to load in a GFF3
> file
> > which I could then use in my script in a 'queryable' way. To retrieve
> > features I used for example
> >       $db->features(-type => 'BAC:FPC', -seq_id=>'chromosome0')
> > However when doing a profile on my script I found out that 60% of the
> > running time went into filter_by_type from
> > Bio::DB::SeqFeature::Store::memory.
> > Replacing this function with
> >    my @features = grep{$_->type eq 'BAC:FPC'}
> > $db->features(-seq_id=>'chromosome0')
> > which gave me the same results was just a fraction of the earlier run
> time.
> > My script went from 60min. to 4min. for the same result and only changing
> > this function (is called often).
> > Can/Should this be fixed or is this just the faster way to do it?
> >
> > Cheers,
> > Jelle
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

From lincoln.stein at gmail.com  Fri Feb  5 10:46:02 2010
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Fri, 5 Feb 2010 10:46:02 -0500
Subject: [Bioperl-l] Bio::DB::SeqFeature::Store::memory ->
	filter_by_type very slow
In-Reply-To: <b66932c31002010424l2cccf278uf33ad8774e2f96a6@mail.gmail.com>
References: <b66932c31002010424l2cccf278uf33ad8774e2f96a6@mail.gmail.com>
Message-ID: <6dce9a0b1002050746o1271259dxf52972ef41d591f0@mail.gmail.com>

I think the problem with the filter function is that the type you request
may be "BAC" but the feature's type is "BAC:FPC", and you want to be able to
filter by the more generic type terms. Nevertheless I'm sure we can do
better than 60 min running time and so I'll have to look at how this
function works more carefully. I can't do this right now, unfortunately, so
perhaps someone on the mailing list would be willing to take a look?

Lincoln

On Mon, Feb 1, 2010 at 7:24 AM, Jelle Scholtalbers <j.scholtalbers at gmail.com
> wrote:

> Hi,
> I used the Bio::DB::SeqFeature::Store::memory module to load in a GFF3 file
> which I could then use in my script in a 'queryable' way. To retrieve
> features I used for example
>        $db->features(-type => 'BAC:FPC', -seq_id=>'chromosome0')
> However when doing a profile on my script I found out that 60% of the
> running time went into filter_by_type from
> Bio::DB::SeqFeature::Store::memory.
> Replacing this function with
>     my @features = grep{$_->type eq 'BAC:FPC'}
> $db->features(-seq_id=>'chromosome0')
> which gave me the same results was just a fraction of the earlier run time.
> My script went from 60min. to 4min. for the same result and only changing
> this function (is called often).
> Can/Should this be fixed or is this just the faster way to do it?
>
> Cheers,
> Jelle
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>

From mauricio at open-bio.org  Fri Feb  5 10:48:30 2010
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Fri, 05 Feb 2010 09:48:30 -0600
Subject: [Bioperl-l] Fwd: Changes to NCBI BLAST and E-utilities.
Message-ID: <4B6C3DCE.2070808@open-bio.org>

Forwarding to the proper lists...

-------- Original Message --------
Subject: [O|B|F Helpdesk #889] Changes to NCBI BLAST and E-utilities.
Date: Fri, 5 Feb 2010 10:08:51 -0500
From: mcginnis via RT <support at helpdesk.open-bio.org>
Reply-To: support at helpdesk.open-bio.org
To: chris at bioteam.net, heikki at sanbi.ac.za, hlapp at gmx.net, 
jason at bioperl.org,        mauricio at open-bio.org


Fri Feb 05 10:08:51 2010: Request 889 was acted upon.
Transaction: Ticket created by mcginnis at ncbi.nlm.nih.gov
        Queue: support at open-bio.org
      Subject: Changes to NCBI BLAST and E-utilities.
        Owner: Nobody
   Requestors: mcginnis at ncbi.nlm.nih.gov
       Status: new
  Ticket <URL: https://helpdesk.open-bio.org/rt/Ticket/Display.html?id=889 >


Dear Colleague:

There are two changes I'd like to make you aware of.

As you may or may not have noticed, we have been working on a new C++ 
version of the BLAST binaries. In the coming months we will be moving 
the C++ binaries into prominence and (slowly) phasing out the C toolkit 
binaries.

There are many changes not least of which is a move to individual 
binaries for each program (blastn, blastp, etc).  We are not sure how 
many of your users use BioPerl with the BLAST binaries, my understanding 
is that many use BioPerl to to remote BLAST. However, there isa change 
to the BLAST results in Text and presumably HTML. This could have an 
effect on any parsers which scrape these formats and do not use XML. For 
obvious reason, we want to support only the XML format for parsing, but 
we thought we should give you heads up on this.
blast 2.2.22

Query: 3307 ------------------------------------------------------------ 
3307

Sbjct: 390  GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP 449

blast 2.2.22+

Query        ------------------------------------------------------------

Sbjct  390 
GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP  449

A single line of gaps lacks the Query numbering in the blast+ output. 
The C version of blast has numbering in this case. Sample alignment 
shown below. According to users the blast+ output without the numbering 
breaks bioperl parsers. Wehave heard forma few but I think they may be 
older parsers?
The second issue is a policy concerning E-utilities. This was announced 
on the utilities-announce at ncbi.nlm.nih.gov mail-list but you may not 
have seen it.

As part of an ongoing effort to ensure efficient access to the Entrez 
Utilities (E-utilities) by all users, NCBI has decided to change the 
usage policy for the E-utilities effective June 1, 2010. Effective on 
June 1, 2010, all E-utility requests, either using standard URLs or 
SOAP, must contain non-null values for both the &tool and &email 
parameters. Any E-utility request made after June 1, 2010 that does not 
contain values for both parameters will return an error explaining that 
these parameters must be included in E-utility requests.

The value of the &tool parameter should be a URI-safe string that is the 
name of the software package, script or web page producing the E-utility 
request.

The value of the &email parameter should be a valid e-mail address for 
the appropriate contact person or group responsible for maintaining the 
tool producing the E-utility request.

NCBI uses these parameters to contact users whose use of the E-utilities 
violates the standard usage policies described 
athttp://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements. 
These usage policies are designed to prevent excessive requests from a 
small group of users from reducing or eliminating the wider community's 
access to the E-utilities. NCBI will attempt to contact a user at the 
e-mail address provided in the &email parameter prior to blocking access 
to the E-utilities.

NCBI realizes that this policy change will require many of our users to 
change their code. Based on past experience, we anticipate that most of 
our users should be able to make the necessary changes before the June 
1, 2010 deadline. If you have any concerns about making these changes by 
that date, or if you have any questions about these policies, please 
contact eutilities at ncbi.nlm.nih.gov.

Thank you for your understanding and cooperation in helping us continue 
to deliver a reliable and efficient web service.

I think you already adhere to this policy but should a user's script not 
meet these requirements, than the script will fail and requests will be 
turned away with an error message.

Scott D. McGinnis M.A.
NCBI/NLM/NIH
45 Center Drive, MSC 6511
Bldg 45, Room 4AN.44C
Bethesda, MD 20892
mcginnis at ncbi.nlm.nih.gov














From maj at fortinbras.us  Fri Feb  5 10:57:29 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 5 Feb 2010 10:57:29 -0500
Subject: [Bioperl-l] Bio::DB::SeqFeature::Store::memory ->filter_by_type
	very slow
In-Reply-To: <6dce9a0b1002050746o1271259dxf52972ef41d591f0@mail.gmail.com>
References: <b66932c31002010424l2cccf278uf33ad8774e2f96a6@mail.gmail.com>
	<6dce9a0b1002050746o1271259dxf52972ef41d591f0@mail.gmail.com>
Message-ID: <F946652818FB474FB642E6BA4942CFAF@NewLife>

my guess is ..memory::find_types is costly, as it descends into
Bio::DB::GFF::Typename objects...could implement a cache
or memo?
----- Original Message ----- 
From: "Lincoln Stein" <lincoln.stein at gmail.com>
To: "Jelle Scholtalbers" <j.scholtalbers at gmail.com>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 10:46 AM
Subject: Re: [Bioperl-l] Bio::DB::SeqFeature::Store::memory ->filter_by_type 
very slow


>I think the problem with the filter function is that the type you request
> may be "BAC" but the feature's type is "BAC:FPC", and you want to be able to
> filter by the more generic type terms. Nevertheless I'm sure we can do
> better than 60 min running time and so I'll have to look at how this
> function works more carefully. I can't do this right now, unfortunately, so
> perhaps someone on the mailing list would be willing to take a look?
>
> Lincoln
>
> On Mon, Feb 1, 2010 at 7:24 AM, Jelle Scholtalbers <j.scholtalbers at gmail.com
>> wrote:
>
>> Hi,
>> I used the Bio::DB::SeqFeature::Store::memory module to load in a GFF3 file
>> which I could then use in my script in a 'queryable' way. To retrieve
>> features I used for example
>>        $db->features(-type => 'BAC:FPC', -seq_id=>'chromosome0')
>> However when doing a profile on my script I found out that 60% of the
>> running time went into filter_by_type from
>> Bio::DB::SeqFeature::Store::memory.
>> Replacing this function with
>>     my @features = grep{$_->type eq 'BAC:FPC'}
>> $db->features(-seq_id=>'chromosome0')
>> which gave me the same results was just a fraction of the earlier run time.
>> My script went from 60min. to 4min. for the same result and only changing
>> this function (is called often).
>> Can/Should this be fixed or is this just the faster way to do it?
>>
>> Cheers,
>> Jelle
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> -- 
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From cjfields at illinois.edu  Fri Feb  5 11:16:29 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Feb 2010 10:16:29 -0600
Subject: [Bioperl-l] Fwd: Changes to NCBI BLAST and E-utilities.
In-Reply-To: <4B6C3DCE.2070808@open-bio.org>
References: <4B6C3DCE.2070808@open-bio.org>
Message-ID: <B69B91B7-8F18-4C52-95E7-C54342D19C73@illinois.edu>

Thanks Mauricio.  I think the only thing of impact will be the BLAST+ stuff (and Mark has developed a wrapper for it).  We'll need to update the SearchIO parser, so any BLAST+ output examples would be tremendously helpful.

chris

On Feb 5, 2010, at 9:48 AM, Mauricio Herrera Cuadra wrote:

> Forwarding to the proper lists...
> 
> -------- Original Message --------
> Subject: [O|B|F Helpdesk #889] Changes to NCBI BLAST and E-utilities.
> Date: Fri, 5 Feb 2010 10:08:51 -0500
> From: mcginnis via RT <support at helpdesk.open-bio.org>
> Reply-To: support at helpdesk.open-bio.org
> To: chris at bioteam.net, heikki at sanbi.ac.za, hlapp at gmx.net, jason at bioperl.org,        mauricio at open-bio.org
> 
> 
> Fri Feb 05 10:08:51 2010: Request 889 was acted upon.
> Transaction: Ticket created by mcginnis at ncbi.nlm.nih.gov
>       Queue: support at open-bio.org
>     Subject: Changes to NCBI BLAST and E-utilities.
>       Owner: Nobody
>  Requestors: mcginnis at ncbi.nlm.nih.gov
>      Status: new
> Ticket <URL: https://helpdesk.open-bio.org/rt/Ticket/Display.html?id=889 >
> 
> 
> Dear Colleague:
> 
> There are two changes I'd like to make you aware of.
> 
> As you may or may not have noticed, we have been working on a new C++ version of the BLAST binaries. In the coming months we will be moving the C++ binaries into prominence and (slowly) phasing out the C toolkit binaries.
> 
> There are many changes not least of which is a move to individual binaries for each program (blastn, blastp, etc).  We are not sure how many of your users use BioPerl with the BLAST binaries, my understanding is that many use BioPerl to to remote BLAST. However, there isa change to the BLAST results in Text and presumably HTML. This could have an effect on any parsers which scrape these formats and do not use XML. For obvious reason, we want to support only the XML format for parsing, but we thought we should give you heads up on this.
> blast 2.2.22
> 
> Query: 3307 ------------------------------------------------------------ 3307
> 
> Sbjct: 390  GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP 449
> 
> blast 2.2.22+
> 
> Query        ------------------------------------------------------------
> 
> Sbjct  390 GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP  449
> 
> A single line of gaps lacks the Query numbering in the blast+ output. The C version of blast has numbering in this case. Sample alignment shown below. According to users the blast+ output without the numbering breaks bioperl parsers. Wehave heard forma few but I think they may be older parsers?
> The second issue is a policy concerning E-utilities. This was announced on the utilities-announce at ncbi.nlm.nih.gov mail-list but you may not have seen it.
> 
> As part of an ongoing effort to ensure efficient access to the Entrez Utilities (E-utilities) by all users, NCBI has decided to change the usage policy for the E-utilities effective June 1, 2010. Effective on June 1, 2010, all E-utility requests, either using standard URLs or SOAP, must contain non-null values for both the &tool and &email parameters. Any E-utility request made after June 1, 2010 that does not contain values for both parameters will return an error explaining that these parameters must be included in E-utility requests.
> 
> The value of the &tool parameter should be a URI-safe string that is the name of the software package, script or web page producing the E-utility request.
> 
> The value of the &email parameter should be a valid e-mail address for the appropriate contact person or group responsible for maintaining the tool producing the E-utility request.
> 
> NCBI uses these parameters to contact users whose use of the E-utilities violates the standard usage policies described athttp://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements. These usage policies are designed to prevent excessive requests from a small group of users from reducing or eliminating the wider community's access to the E-utilities. NCBI will attempt to contact a user at the e-mail address provided in the &email parameter prior to blocking access to the E-utilities.
> 
> NCBI realizes that this policy change will require many of our users to change their code. Based on past experience, we anticipate that most of our users should be able to make the necessary changes before the June 1, 2010 deadline. If you have any concerns about making these changes by that date, or if you have any questions about these policies, please contact eutilities at ncbi.nlm.nih.gov.
> 
> Thank you for your understanding and cooperation in helping us continue to deliver a reliable and efficient web service.
> 
> I think you already adhere to this policy but should a user's script not meet these requirements, than the script will fail and requests will be turned away with an error message.
> 
> Scott D. McGinnis M.A.
> NCBI/NLM/NIH
> 45 Center Drive, MSC 6511
> Bldg 45, Room 4AN.44C
> Bethesda, MD 20892
> mcginnis at ncbi.nlm.nih.gov
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From fungazid at yahoo.com  Fri Feb  5 11:25:00 2010
From: fungazid at yahoo.com (Fungazid)
Date: Fri, 5 Feb 2010 08:25:00 -0800 (PST)
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <4536f7701002041938m3ad2d6ddgf8fa56312d62c28a@mail.gmail.com>
Message-ID: <654818.36134.qm@web65508.mail.ac4.yahoo.com>

Scott, Jason, hi,

I replaced my code with:

for(...) {system("bp_seqfeature_load.pl -d contigs -u root -p xxxx ./$file[$i]")==0 or die;}

run it, and it went smoothly (or seem to be like that ).

The reason I used an alternative script is that it is almost identical to bp_seqfeature_load.pl but it calls the following functions only once:

Bio::DB::SeqFeature::Store->new(..)
Bio::DB::SeqFeature::Store::GFF3Loader->new(...)


Thanks,
Avi


--- On Fri, 2/5/10, Scott Cain <scott at scottcain.net> wrote:

> From: Scott Cain <scott at scottcain.net>
> Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm
> To: "Fungazid" <fungazid at yahoo.com>
> Cc: Bioperl-l at lists.open-bio.org
> Date: Friday, February 5, 2010, 5:38 AM
> Hi Avi,
> 
> Off hand, I have no idea what is happening.? Is there
> a reason you
> aren't using bp_seqfeature_load.pl?
> 
> Scott
> 
> 
> On Thu, Feb 4, 2010 at 9:52 PM, Fungazid <fungazid at yahoo.com>
> wrote:
> > Bioperl hi,
> >
> > I have multiple gff3 files that look like:
> >
> >
> --------------------------------------------------------
> > ##gff-version 3
> > # file: temp1.gff3
> > contig453278 ? ?hs ? ?contig ? ?1 ? ?699 ?
> ?. ? ?+ ? ?. ? ?Name=contig453278
> > contig453278 ? ?hs ? ?alignment ? ?1 ? ?194 ?
> ?. ? ?+ ? ?. ? ?Name=hs.ENST00000258455
> > contig453278 ? ?hs ? ?alignment ? ?252 ? ?699
> ? ?. ? ?+ ? ?. ? ?Name=hs.ENST00000258455
> > contig453278 ? ?hs ? ?mi2 ? ?194 ? ?252 ? ?.
> ? ?+ ? ?. ? ?Name=mi2
> > contig453278 ? ?hs ? ?transcript ? ?104 ? ?183
> ? ?. ? ?+ ? ?. ?
> ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
> > contig453278 ? ?hs ? ?transcript ? ?1 ? ?9 ?
> ?. ? ?+ ? ?. ?
> ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
> > contig453278 ? ?hs ? ?transcript ? ?73 ? ?103
> ? ?. ? ?+ ? ?. ?
> ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
> > contig453278 ? ?hs ? ?transcript ? ?10 ? ?72
> ? ?. ? ?+ ? ?. ?
> ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
> >
> ---------------------------------------------------------
> >
> >
> >
> > I uploaded gff3 files to mysql and view the tracks in
> gBrowse like this:
> >
> > --------------------------------------------
> > Bio::DB::SeqFeature::Store->new(...)
> >
> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
> > for($i=0; $i<$#files+1; $i++){
> > $loader->load($file[$i]);
> > }
> > --------------------------------------------
> >
> > Eventually after uploading ~15000 small gff3 files I
> got the error:
> >
> > Error in tempdir() using /tmp/XXXXXXXXXX: Could not
> create directory /tmp/9bbpdE5ibf: Too many links at
> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm
> line 49
> >
> >
> >
> > I am trying to see what went wrong, maybe you can
> rescue me,
> > Avi
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.? ? ? ? ? ?
> ? ? ? ? ? ? ? ?
> ? ? ???scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)? ? ? ? ?
> ? ? ? ? ???216-392-3087
> Ontario Institute for Cancer Research
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


      



From scott at scottcain.net  Fri Feb  5 11:50:59 2010
From: scott at scottcain.net (Scott Cain)
Date: Fri, 5 Feb 2010 11:50:59 -0500
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <654818.36134.qm@web65508.mail.ac4.yahoo.com>
References: <4536f7701002041938m3ad2d6ddgf8fa56312d62c28a@mail.gmail.com>
	<654818.36134.qm@web65508.mail.ac4.yahoo.com>
Message-ID: <4536f7701002050850h65a242f7o84b5df6cec0a51f2@mail.gmail.com>

I believe you can call the loading script with more than one GFF file
as the argument, eliminating the need for the for loop.



On Fri, Feb 5, 2010 at 11:25 AM, Fungazid <fungazid at yahoo.com> wrote:
> Scott, Jason, hi,
>
> I replaced my code with:
>
> for(...) {system("bp_seqfeature_load.pl -d contigs -u root -p xxxx ./$file[$i]")==0 or die;}
>
> run it, and it went smoothly (or seem to be like that ).
>
> The reason I used an alternative script is that it is almost identical to bp_seqfeature_load.pl but it calls the following functions only once:
>
> Bio::DB::SeqFeature::Store->new(..)
> Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>
>
> Thanks,
> Avi
>
>
> --- On Fri, 2/5/10, Scott Cain <scott at scottcain.net> wrote:
>
>> From: Scott Cain <scott at scottcain.net>
>> Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm
>> To: "Fungazid" <fungazid at yahoo.com>
>> Cc: Bioperl-l at lists.open-bio.org
>> Date: Friday, February 5, 2010, 5:38 AM
>> Hi Avi,
>>
>> Off hand, I have no idea what is happening.? Is there
>> a reason you
>> aren't using bp_seqfeature_load.pl?
>>
>> Scott
>>
>>
>> On Thu, Feb 4, 2010 at 9:52 PM, Fungazid <fungazid at yahoo.com>
>> wrote:
>> > Bioperl hi,
>> >
>> > I have multiple gff3 files that look like:
>> >
>> >
>> --------------------------------------------------------
>> > ##gff-version 3
>> > # file: temp1.gff3
>> > contig453278 ? ?hs ? ?contig ? ?1 ? ?699
>> ?. ? ?+ ? ?. ? ?Name=contig453278
>> > contig453278 ? ?hs ? ?alignment ? ?1 ? ?194
>> ?. ? ?+ ? ?. ? ?Name=hs.ENST00000258455
>> > contig453278 ? ?hs ? ?alignment ? ?252 ? ?699
>> ? ?. ? ?+ ? ?. ? ?Name=hs.ENST00000258455
>> > contig453278 ? ?hs ? ?mi2 ? ?194 ? ?252 ? ?.
>> ? ?+ ? ?. ? ?Name=mi2
>> > contig453278 ? ?hs ? ?transcript ? ?104 ? ?183
>> ? ?. ? ?+ ? ?.
>> ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
>> > contig453278 ? ?hs ? ?transcript ? ?1 ? ?9
>> ?. ? ?+ ? ?.
>> ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
>> > contig453278 ? ?hs ? ?transcript ? ?73 ? ?103
>> ? ?. ? ?+ ? ?.
>> ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
>> > contig453278 ? ?hs ? ?transcript ? ?10 ? ?72
>> ? ?. ? ?+ ? ?.
>> ?Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
>> >
>> ---------------------------------------------------------
>> >
>> >
>> >
>> > I uploaded gff3 files to mysql and view the tracks in
>> gBrowse like this:
>> >
>> > --------------------------------------------
>> > Bio::DB::SeqFeature::Store->new(...)
>> >
>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>> > for($i=0; $i<$#files+1; $i++){
>> > $loader->load($file[$i]);
>> > }
>> > --------------------------------------------
>> >
>> > Eventually after uploading ~15000 small gff3 files I
>> got the error:
>> >
>> > Error in tempdir() using /tmp/XXXXXXXXXX: Could not
>> create directory /tmp/9bbpdE5ibf: Too many links at
>> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm
>> line 49
>> >
>> >
>> >
>> > I am trying to see what went wrong, maybe you can
>> rescue me,
>> > Avi
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.
>>
>> ? ? ???scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)
>> ? ? ? ? ???216-392-3087
>> Ontario Institute for Cancer Research
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From maj at fortinbras.us  Fri Feb  5 11:32:12 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 5 Feb 2010 11:32:12 -0500
Subject: [Bioperl-l] Fwd: Changes to NCBI BLAST and E-utilities.
In-Reply-To: <B69B91B7-8F18-4C52-95E7-C54342D19C73@illinois.edu>
References: <4B6C3DCE.2070808@open-bio.org>
	<B69B91B7-8F18-4C52-95E7-C54342D19C73@illinois.edu>
Message-ID: <8DEC18FA40C04635B6E7598DF27C3906@NewLife>

all -- note too that blast+ has remote searches built in, and you can
access this functionality in StandAloneBlastPlus by specifying
-remote => 1 to the factory-- cheers MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mauricio Herrera Cuadra" <mauricio at open-bio.org>
Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 11:16 AM
Subject: Re: [Bioperl-l] Fwd: Changes to NCBI BLAST and E-utilities.


> Thanks Mauricio.  I think the only thing of impact will be the BLAST+ stuff 
> (and Mark has developed a wrapper for it).  We'll need to update the SearchIO 
> parser, so any BLAST+ output examples would be tremendously helpful.
>
> chris
>
> On Feb 5, 2010, at 9:48 AM, Mauricio Herrera Cuadra wrote:
>
>> Forwarding to the proper lists...
>>
>> -------- Original Message --------
>> Subject: [O|B|F Helpdesk #889] Changes to NCBI BLAST and E-utilities.
>> Date: Fri, 5 Feb 2010 10:08:51 -0500
>> From: mcginnis via RT <support at helpdesk.open-bio.org>
>> Reply-To: support at helpdesk.open-bio.org
>> To: chris at bioteam.net, heikki at sanbi.ac.za, hlapp at gmx.net, jason at bioperl.org, 
>> mauricio at open-bio.org
>>
>>
>> Fri Feb 05 10:08:51 2010: Request 889 was acted upon.
>> Transaction: Ticket created by mcginnis at ncbi.nlm.nih.gov
>>       Queue: support at open-bio.org
>>     Subject: Changes to NCBI BLAST and E-utilities.
>>       Owner: Nobody
>>  Requestors: mcginnis at ncbi.nlm.nih.gov
>>      Status: new
>> Ticket <URL: https://helpdesk.open-bio.org/rt/Ticket/Display.html?id=889 >
>>
>>
>> Dear Colleague:
>>
>> There are two changes I'd like to make you aware of.
>>
>> As you may or may not have noticed, we have been working on a new C++ version 
>> of the BLAST binaries. In the coming months we will be moving the C++ 
>> binaries into prominence and (slowly) phasing out the C toolkit binaries.
>>
>> There are many changes not least of which is a move to individual binaries 
>> for each program (blastn, blastp, etc).  We are not sure how many of your 
>> users use BioPerl with the BLAST binaries, my understanding is that many use 
>> BioPerl to to remote BLAST. However, there isa change to the BLAST results in 
>> Text and presumably HTML. This could have an effect on any parsers which 
>> scrape these formats and do not use XML. For obvious reason, we want to 
>> support only the XML format for parsing, but we thought we should give you 
>> heads up on this.
>> blast 2.2.22
>>
>> Query: 3307 ------------------------------------------------------------ 3307
>>
>> Sbjct: 390  GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP 449
>>
>> blast 2.2.22+
>>
>> Query        ------------------------------------------------------------
>>
>> Sbjct  390 GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP  449
>>
>> A single line of gaps lacks the Query numbering in the blast+ output. The C 
>> version of blast has numbering in this case. Sample alignment shown below. 
>> According to users the blast+ output without the numbering breaks bioperl 
>> parsers. Wehave heard forma few but I think they may be older parsers?
>> The second issue is a policy concerning E-utilities. This was announced on 
>> the utilities-announce at ncbi.nlm.nih.gov mail-list but you may not have seen 
>> it.
>>
>> As part of an ongoing effort to ensure efficient access to the Entrez 
>> Utilities (E-utilities) by all users, NCBI has decided to change the usage 
>> policy for the E-utilities effective June 1, 2010. Effective on June 1, 2010, 
>> all E-utility requests, either using standard URLs or SOAP, must contain 
>> non-null values for both the &tool and &email parameters. Any E-utility 
>> request made after June 1, 2010 that does not contain values for both 
>> parameters will return an error explaining that these parameters must be 
>> included in E-utility requests.
>>
>> The value of the &tool parameter should be a URI-safe string that is the name 
>> of the software package, script or web page producing the E-utility request.
>>
>> The value of the &email parameter should be a valid e-mail address for the 
>> appropriate contact person or group responsible for maintaining the tool 
>> producing the E-utility request.
>>
>> NCBI uses these parameters to contact users whose use of the E-utilities 
>> violates the standard usage policies described 
>> athttp://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements. 
>> These usage policies are designed to prevent excessive requests from a small 
>> group of users from reducing or eliminating the wider community's access to 
>> the E-utilities. NCBI will attempt to contact a user at the e-mail address 
>> provided in the &email parameter prior to blocking access to the E-utilities.
>>
>> NCBI realizes that this policy change will require many of our users to 
>> change their code. Based on past experience, we anticipate that most of our 
>> users should be able to make the necessary changes before the June 1, 2010 
>> deadline. If you have any concerns about making these changes by that date, 
>> or if you have any questions about these policies, please contact 
>> eutilities at ncbi.nlm.nih.gov.
>>
>> Thank you for your understanding and cooperation in helping us continue to 
>> deliver a reliable and efficient web service.
>>
>> I think you already adhere to this policy but should a user's script not meet 
>> these requirements, than the script will fail and requests will be turned 
>> away with an error message.
>>
>> Scott D. McGinnis M.A.
>> NCBI/NLM/NIH
>> 45 Center Drive, MSC 6511
>> Bldg 45, Room 4AN.44C
>> Bethesda, MD 20892
>> mcginnis at ncbi.nlm.nih.gov
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From miquel.ramia at uab.cat  Fri Feb  5 12:43:17 2010
From: miquel.ramia at uab.cat (Miquel Ramia)
Date: Fri, 05 Feb 2010 18:43:17 +0100
Subject: [Bioperl-l] Bio::Graphics inside PHP
Message-ID: <4B6C58B5.3080304@uab.cat>

Hi,

I'm working in a database with a web interface developed in php. I'm 
displaying Bio::Graphic images inside an IFrame, but doesn't look very well.

Anybody knows if it's possible to include a Bio::Graphics image directly 
in a php page?

Thank you

Miquel R?mia

From sharmashalu.bio at gmail.com  Fri Feb  5 14:21:36 2010
From: sharmashalu.bio at gmail.com (shalu sharma)
Date: Fri, 5 Feb 2010 14:21:36 -0500
Subject: [Bioperl-l] Aligning Reads
Message-ID: <465b5a661002051121l50402168s7a715e62da6812ee@mail.gmail.com>

Hi All,
            Is there any program available which can align reads (200-400bp
in fasta format) against a reference sequence and the whole alignment can be
viewed graphically.
I tried bowtie but i think it only takes fastaq format.

Thanks
shalu

From j.scholtalbers at gmail.com  Fri Feb  5 14:22:43 2010
From: j.scholtalbers at gmail.com (Jelle Scholtalbers)
Date: Fri, 5 Feb 2010 20:22:43 +0100
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <4536f7701002050850h65a242f7o84b5df6cec0a51f2@mail.gmail.com>
References: <4536f7701002041938m3ad2d6ddgf8fa56312d62c28a@mail.gmail.com>
	<654818.36134.qm@web65508.mail.ac4.yahoo.com>
	<4536f7701002050850h65a242f7o84b5df6cec0a51f2@mail.gmail.com>
Message-ID: <b66932c31002051122j68783a24s94eda175e41d37b9@mail.gmail.com>

Also specifying the -f(ast) option could be beneficial for you. Probably you
have a limit in how many files you can specify on the commandline, so could
it also be an idea for you to concatenate the files before loading them? Or
take a look at xargs when on linux: "find -maxdepth 1 -name '*.gff'  | xargs
bp_seqfeature_load.pl -d contigs -u root -p xxxx -f"

2010/2/5 Scott Cain <scott at scottcain.net>

> I believe you can call the loading script with more than one GFF file
> as the argument, eliminating the need for the for loop.
>
>
>
> On Fri, Feb 5, 2010 at 11:25 AM, Fungazid <fungazid at yahoo.com> wrote:
> > Scott, Jason, hi,
> >
> > I replaced my code with:
> >
> > for(...) {system("bp_seqfeature_load.pl -d contigs -u root -p xxxx
> ./$file[$i]")==0 or die;}
> >
> > run it, and it went smoothly (or seem to be like that ).
> >
> > The reason I used an alternative script is that it is almost identical to
> bp_seqfeature_load.pl but it calls the following functions only once:
> >
> > Bio::DB::SeqFeature::Store->new(..)
> > Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
> >
> >
> > Thanks,
> > Avi
> >
> >
> > --- On Fri, 2/5/10, Scott Cain <scott at scottcain.net> wrote:
> >
> >> From: Scott Cain <scott at scottcain.net>
> >> Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm
> >> To: "Fungazid" <fungazid at yahoo.com>
> >> Cc: Bioperl-l at lists.open-bio.org
> >> Date: Friday, February 5, 2010, 5:38 AM
> >> Hi Avi,
> >>
> >> Off hand, I have no idea what is happening.  Is there
> >> a reason you
> >> aren't using bp_seqfeature_load.pl?
> >>
> >> Scott
> >>
> >>
> >> On Thu, Feb 4, 2010 at 9:52 PM, Fungazid <fungazid at yahoo.com>
> >> wrote:
> >> > Bioperl hi,
> >> >
> >> > I have multiple gff3 files that look like:
> >> >
> >> >
> >> --------------------------------------------------------
> >> > ##gff-version 3
> >> > # file: temp1.gff3
> >> > contig453278    hs    contig    1    699
> >>  .    +    .    Name=contig453278
> >> > contig453278    hs    alignment    1    194
> >>  .    +    .    Name=hs.ENST00000258455
> >> > contig453278    hs    alignment    252    699
> >>    .    +    .    Name=hs.ENST00000258455
> >> > contig453278    hs    mi2    194    252    .
> >>    +    .    Name=mi2
> >> > contig453278    hs    transcript    104    183
> >>    .    +    .
> >>  Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
> >> > contig453278    hs    transcript    1    9
> >>  .    +    .
> >>  Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
> >> > contig453278    hs    transcript    73    103
> >>    .    +    .
> >>  Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
> >> > contig453278    hs    transcript    10    72
> >>    .    +    .
> >>  Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
> >> >
> >> ---------------------------------------------------------
> >> >
> >> >
> >> >
> >> > I uploaded gff3 files to mysql and view the tracks in
> >> gBrowse like this:
> >> >
> >> > --------------------------------------------
> >> > Bio::DB::SeqFeature::Store->new(...)
> >> >
> >> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
> >> > for($i=0; $i<$#files+1; $i++){
> >> > $loader->load($file[$i]);
> >> > }
> >> > --------------------------------------------
> >> >
> >> > Eventually after uploading ~15000 small gff3 files I
> >> got the error:
> >> >
> >> > Error in tempdir() using /tmp/XXXXXXXXXX: Could not
> >> create directory /tmp/9bbpdE5ibf: Too many links at
> >> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm
> >> line 49
> >> >
> >> >
> >> >
> >> > I am trying to see what went wrong, maybe you can
> >> rescue me,
> >> > Avi
> >> >
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > Bioperl-l mailing list
> >> > Bioperl-l at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> >
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.
> >>
> >>        scott at scottcain dot net
> >> GMOD Coordinator (http://gmod.org/)
> >>            216-392-3087
> >> Ontario Institute for Cancer Research
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From awitney at sgul.ac.uk  Fri Feb  5 14:14:30 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Fri, 5 Feb 2010 19:14:30 +0000
Subject: [Bioperl-l] Bio::Graphics inside PHP
In-Reply-To: <4B6C58B5.3080304@uab.cat>
References: <4B6C58B5.3080304@uab.cat>
Message-ID: <7E0F3ED7-682E-492B-99D7-45C77041F6F5@sgul.ac.uk>


you could output an <img ..> tag where the source is a perl script that generates the image. eg

<img src="cgi-bin/biographics_script.cgi" />

that perl script would then use Bio::Graphics to generate the image

HTH

adam


On 5 Feb 2010, at 17:43, Miquel Ramia wrote:

> Hi,
> 
> I'm working in a database with a web interface developed in php. I'm displaying Bio::Graphic images inside an IFrame, but doesn't look very well.
> 
> Anybody knows if it's possible to include a Bio::Graphics image directly in a php page?
> 
> Thank you
> 
> Miquel R?mia
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From sdavis2 at mail.nih.gov  Fri Feb  5 14:40:05 2010
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Fri, 5 Feb 2010 14:40:05 -0500
Subject: [Bioperl-l] Aligning Reads
In-Reply-To: <465b5a661002051121l50402168s7a715e62da6812ee@mail.gmail.com>
References: <465b5a661002051121l50402168s7a715e62da6812ee@mail.gmail.com>
Message-ID: <264855a01002051140sa9d309cw302c3266f628e9a3@mail.gmail.com>

On Fri, Feb 5, 2010 at 2:21 PM, shalu sharma <sharmashalu.bio at gmail.com> wrote:
> Hi All,
> ? ? ? ? ? ?Is there any program available which can align reads (200-400bp
> in fasta format) against a reference sequence and the whole alignment can be
> viewed graphically.
> I tried bowtie but i think it only takes fastaq format.

Take a look at the -f option for bowtie.

Sean


From abhishek.vit at gmail.com  Fri Feb  5 15:23:26 2010
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Fri, 5 Feb 2010 15:23:26 -0500
Subject: [Bioperl-l] Aligning Reads
In-Reply-To: <264855a01002051140sa9d309cw302c3266f628e9a3@mail.gmail.com>
References: <465b5a661002051121l50402168s7a715e62da6812ee@mail.gmail.com>
	<264855a01002051140sa9d309cw302c3266f628e9a3@mail.gmail.com>
Message-ID: <be9b52411002051223k6d284f60u67358dd55835e8fb@mail.gmail.com>

I would also try Mosaik. It can take fasta as input and align both
short and long reads.

-Abhi

On Fri, Feb 5, 2010 at 2:40 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Fri, Feb 5, 2010 at 2:21 PM, shalu sharma <sharmashalu.bio at gmail.com> wrote:
>> Hi All,
>> ? ? ? ? ? ?Is there any program available which can align reads (200-400bp
>> in fasta format) against a reference sequence and the whole alignment can be
>> viewed graphically.
>> I tried bowtie but i think it only takes fastaq format.
>
> Take a look at the -f option for bowtie.
>
> Sean
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From thomas.kallman at ebc.uu.se  Fri Feb  5 16:23:50 2010
From: thomas.kallman at ebc.uu.se (=?ISO-8859-1?Q?Thomas_K=E4llman?=)
Date: Fri, 5 Feb 2010 22:23:50 +0100
Subject: [Bioperl-l] Aligning Reads
In-Reply-To: <465b5a661002051121l50402168s7a715e62da6812ee@mail.gmail.com>
References: <465b5a661002051121l50402168s7a715e62da6812ee@mail.gmail.com>
Message-ID: <FCA10D57-027C-4F2F-B6A3-EB3FE05BC2FB@ebc.uu.se>

Hi Shalu,

Not really related to bioperl, but you can find a nice list of  
software aligning short read data at http://seqanswers.com/forums/showthread.php?t=43

/thomas
On Feb 5, 2010, at 8:21 PM, shalu sharma wrote:

> Hi All,
>            Is there any program available which can align reads  
> (200-400bp
> in fasta format) against a reference sequence and the whole  
> alignment can be
> viewed graphically.
> I tried bowtie but i think it only takes fastaq format.
>
> Thanks
> shalu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From sharmashalu.bio at gmail.com  Fri Feb  5 16:43:26 2010
From: sharmashalu.bio at gmail.com (shalu sharma)
Date: Fri, 5 Feb 2010 16:43:26 -0500
Subject: [Bioperl-l] Aligning Reads
In-Reply-To: <FCA10D57-027C-4F2F-B6A3-EB3FE05BC2FB@ebc.uu.se>
References: <465b5a661002051121l50402168s7a715e62da6812ee@mail.gmail.com>
	<FCA10D57-027C-4F2F-B6A3-EB3FE05BC2FB@ebc.uu.se>
Message-ID: <465b5a661002051343o5791a021yf10972239a389718@mail.gmail.com>

Thanks a lot for your valuable suggestions.

Thanks
Shalu


2010/2/5 Thomas K?llman <thomas.kallman at ebc.uu.se>

> Hi Shalu,
>
> Not really related to bioperl, but you can find a nice list of software
> aligning short read data at
> http://seqanswers.com/forums/showthread.php?t=43
>
> /thomas
>
> On Feb 5, 2010, at 8:21 PM, shalu sharma wrote:
>
>  Hi All,
>>           Is there any program available which can align reads (200-400bp
>> in fasta format) against a reference sequence and the whole alignment can
>> be
>> viewed graphically.
>> I tried bowtie but i think it only takes fastaq format.
>>
>> Thanks
>> shalu
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>


From florent.angly at gmail.com  Fri Feb  5 21:56:56 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Sat, 06 Feb 2010 12:56:56 +1000
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <F9A7B451-C47F-40B9-AB19-4391BD373A94@bioperl.org>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>	<1191261780.47013654cb81b@webmail.sas.upenn.edu>	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>	<58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>	<1191264531.47014113f2b54@webmail.sas.upenn.edu>
	<F9A7B451-C47F-40B9-AB19-4391BD373A94@bioperl.org>
Message-ID: <4B6CDA78.9060906@gmail.com>

Hi,
I've used Bio::Phylo for drawing SVG trees non-interactively. It's not 
part of Bioperl but draws nice trees:
http://search.cpan.org/~rvosa/Bio-Phylo/ 
<http://search.cpan.org/%7Ervosa/Bio-Phylo/>
Florent

On 02/10/07 05:32, Jason Stajich wrote:
> I'd definitely recommend  Bio::Tree::Draw::Cladogram over svggraph
> for prettier trees - you get postscript out but you can render this
> to png or jpg with unix tools.  If there is a better stand alone tree
> drawing engine we're happy to try and integrate it into bioperl - the
> modules here are native Perl only and you can use the bioperl-run
> modules that wrap DrawTree and DrawGram from EMBOSS to get other PS
> rendering output.
>
> Mesquite, TreeView or other tools are usually much better but not
> always an option if you want to auto-render these images for a
> website, etc.
>
> -jason
>
>
> On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:
>
>    
>> Yes,
>> that's the issue about those commands, trees are not pretty at all
>> that's why for a one tree only kind of thing I rather use ITOL
>> other thing to try is the tree drawer of the Mesquite package
>> glad I could help
>>
>> Lucia
>>
>> Quoting Shameer Khadar<shameer at ncbs.res.in>:
>>
>>      
>>> Dear Lucia,
>>>
>>> Thanks for the mail. Now I got it. I didnt used this TreeIO /
>>> Tree::Draw
>>> methods. Some how missed this excellent HOWTO :
>>> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as
>>> well. I
>>> tried that and it worked very nicely. I have to work around to
>>> beautify
>>> the tree and I am just going to do that.
>>>
>>> Thanks&  Cheers,
>>> Shameer
>>>
>>>        
>>>> OK
>>>>
>>>> you can use the implementations in Bio::TreeIO
>>>>
>>>> you can basically read the tree in newick format and out as an
>>>> svg graph
>>>> something like this:
>>>>
>>>> my $in = new Bio::TreeIO(-file =>  'input',
>>>>                           -format =>  'newick');
>>>> my $out = new Bio::TreeIO(-file =>  '>mytree.svg',
>>>>                            -format =>  'svggraph');
>>>> while( my $tree = $in->next_tree ) {
>>>>      $out->write_tree($tree);
>>>> }
>>>>
>>>> you can also use Bio::Tree::Draw
>>>>
>>>> hope that helps
>>>>
>>>> Lucia
>>>>
>>>>
>>>> Quoting Shameer Khadar<shameer at ncbs.res.in>:
>>>>
>>>>          
>>>>> Hi,
>>>>>
>>>>> Thanks for your mail. I have to create these trees as a part of a
>>>>> webserver. i need to generate them dynamically using users input
>>>>> sequence.
>>>>> I think ITOL is not the stuff best suited for my purpose.
>>>>>
>>>>>            
>>>>>> I think you'll have better luck using some of already available
>>>>>>              
>>>>> programs
>>>>>            
>>>>>> to do
>>>>>> that, you'll get better looking trees. If you just have one
>>>>>> tree to
>>>>>>              
>>>>> draw I
>>>>>            
>>>>>> recommend you use:
>>>>>> http://itol.embl.de/
>>>>>>
>>>>>> Lucia
>>>>>>
>>>>>>
>>>>>> Quoting Shameer Khadar<shameer at ncbs.res.in>:
>>>>>>
>>>>>>              
>>>>>>> Dear All,
>>>>>>>
>>>>>>> Is it possible to draw a phylogeny tree file in PNG format using
>>>>>>>                
>>>>> Bioperl
>>>>>            
>>>>>>> ?
>>>>>>>   My input file are in phylip  treefile format. Any Modules /
>>>>>>> codes in
>>>>>>> Bio::Graphics / Phylogeny sections ?
>>>>>>>
>>>>>>> Input file :
>>>>>>>
>>>>>>>                
>>>>>>              
>>>>>            
>>>>          
>>>        
>> ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,
>> (((((((_E_499_500:2.75000,_E_250_251:2.75000):
>> 0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):
>> 1.51514,_H_255_263:6.20895):0.83877,
>> (_L_246_249:4.30000,_H_244_245:4.30000):2.74772):
>> 0.92645,_H_520_534:7.97418):0.15279,
>> (_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):
>> 1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,
>> ((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):
>> 0.50000,_L_445_447:7.75000):0.50300):1.08808,
>> (((((_E_381_382:2.65000,_E_377_378:2.65000):
>> 0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):
>> 1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):
>> 0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):
>> 1.52226,_H_463_464:5.42226):0.94093,
>> (_E_427_435:5.15000,_E_369_372:5.15000):1.21319):
>> 1.64489,_L_336_343:8.00808):0.88402,
>> (((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,
>> (_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,
>> (((((_E_470_474:3.85000,_E_344_348:
>>      
>>>>>   3.
>>>>>            
>>>>>>>                
>>>>>>              
>>>>>            
>>>>          
>>>        
>> 85000):0.89054,_L_475_478:4.74054):1.20107,
>> (_E_329_335:3.85000,_E_315_317:3.85000):2.09161):
>> 0.71112,_L_513_519:6.65273):0.67204,
>> ((_L_296_304:5.00000,_H_292_295:5.00000):
>> 0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):
>> 0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):
>> 1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,
>> (_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):
>> 4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):
>> 1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):
>> 1.08193,_H_229_243:7.93459):0.18730,
>> (_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,
>> ((((_H_159_171:7.00000,_L_156_158:7.00000):
>> 0.07448,_L_120_122:7.07448):1.59389,
>> ((((_L__90__91:2.65000,_E__88__89:2.65000):
>> 0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):
>> 1.74719,_L_147_155:6.52780):2.14057):2.44189,
>> ((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,
>> (_L_172_178:3.95000,_L__77__79:3.95000):1.70544):
>> 0.42200,_E_138_146:6.07744):0.46209,_E__51__
>>      
>>>>>   5
>>>>>            
>>>>>>>                
>>>>>>              
>>>>>            
>>>>          
>>>        
>> 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,
>> (_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,
>> ((((_L_108_109:4.30000,_E_104_107:4.30000):
>> 1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,
>> (_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,
>> ((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,
>> (((((_H___3___6:3.30000,_L___1___2:3.30000):
>> 0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):
>> 0.88488,_E__40__48:5.79344):0.60814,
>> (_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):
>> 1.25080):0.17461):6.94325);
>>      
>>>>>>>                
>>>>> --
>>>>> Shameer Khadar
>>>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>>>>> National Centre for Biological Sciences (TIFR)
>>>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>>>>> T - 91-080-23666001 EXT - 6251
>>>>> W - http://www.ncbs.res.in
>>>>>
>>>>>            
>>>>
>>>> Lucia Peixoto
>>>> Department of Biology,SAS
>>>> University of Pennsylvania
>>>>
>>>>          
>>>
>>> --
>>> Shameer Khadar
>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>>> National Centre for Biological Sciences (TIFR)
>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>>> T - 91-080-23666001 EXT - 6251
>>> W - http://www.ncbs.res.in
>>>
>>>        
>>
>> Lucia Peixoto
>> Department of Biology,SAS
>> University of Pennsylvania
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>      
> --
> Jason Stajich
> jason at bioperl.org
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>    


From florent.angly at gmail.com  Fri Feb  5 22:06:08 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Sat, 06 Feb 2010 13:06:08 +1000
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <BD5DAE3180434255A2E6ADD94595AC94@NewLife>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
	<BD5DAE3180434255A2E6ADD94595AC94@NewLife>
Message-ID: <4B6CDCA0.6060700@gmail.com>

I've run into this issue very recently, albeit working on something 
unrelated to loading GFF files: generating many small independent 
assemblies. Maybe there's a bug in the tempdir() code, or its 
documentation is not clear. I will take a look at it when I have some time.
Florent


On 05/02/10 22:27, Mark A. Jensen wrote:
> The tempfiles are not being unlinked before there are too many for the 
> OS to handle.
> Sounds like this may be your job, fungazid, if you're not employing 
> the script (but
> not sure about that)
> ----- Original Message ----- From: "Fungazid" <fungazid at yahoo.com>
> To: <Bioperl-l at lists.open-bio.org>
> Sent: Thursday, February 04, 2010 9:52 PM
> Subject: [Bioperl-l] Too many links at LoadHelper.pm
>
>
>> Bioperl hi,
>>
>> I have multiple gff3 files that look like:
>>
>> --------------------------------------------------------
>> ##gff-version 3
>> # file: temp1.gff3
>> contig453278    hs    contig    1    699    .    +    .    
>> Name=contig453278
>> contig453278    hs    alignment    1    194    .    +    . 
>> Name=hs.ENST00000258455
>> contig453278    hs    alignment    252    699    .    +    . 
>> Name=hs.ENST00000258455
>> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
>> contig453278    hs    transcript    104    183    .    +    . 
>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
>> contig453278    hs    transcript    1    9    .    +    . 
>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
>> contig453278    hs    transcript    73    103    .    +    . 
>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
>> contig453278    hs    transcript    10    72    .    +    . 
>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
>> ---------------------------------------------------------
>>
>>
>>
>> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>>
>> --------------------------------------------
>> Bio::DB::SeqFeature::Store->new(...)
>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>> for($i=0; $i<$#files+1; $i++){
>> $loader->load($file[$i]);
>> }
>> --------------------------------------------
>>
>> Eventually after uploading ~15000 small gff3 files I got the error:
>>
>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory 
>> /tmp/9bbpdE5ibf: Too many links at 
>> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm 
>> line 49
>>
>>
>>
>> I am trying to see what went wrong, maybe you can rescue me,
>> Avi
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From cjfields at illinois.edu  Fri Feb  5 22:13:48 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Feb 2010 21:13:48 -0600
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <4B6CDCA0.6060700@gmail.com>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
	<BD5DAE3180434255A2E6ADD94595AC94@NewLife>
	<4B6CDCA0.6060700@gmail.com>
Message-ID: <E3E8F68F-21F5-4FF9-8557-91D6E0755FB9@illinois.edu>

Florent,

The Bio::Assembly error is documented in Bugzilla:

http://bugzilla.open-bio.org/show_bug.cgi?id=2577

Switching to a Bio::SeqFeature::CollectionI capable of distinguishing features by seq_id (such as Bio::DB::SeqFeature::Store) may be the best way to go.

chris

On Feb 5, 2010, at 9:06 PM, Florent Angly wrote:

> I've run into this issue very recently, albeit working on something unrelated to loading GFF files: generating many small independent assemblies. Maybe there's a bug in the tempdir() code, or its documentation is not clear. I will take a look at it when I have some time.
> Florent
> 
> 
> On 05/02/10 22:27, Mark A. Jensen wrote:
>> The tempfiles are not being unlinked before there are too many for the OS to handle.
>> Sounds like this may be your job, fungazid, if you're not employing the script (but
>> not sure about that)
>> ----- Original Message ----- From: "Fungazid" <fungazid at yahoo.com>
>> To: <Bioperl-l at lists.open-bio.org>
>> Sent: Thursday, February 04, 2010 9:52 PM
>> Subject: [Bioperl-l] Too many links at LoadHelper.pm
>> 
>> 
>>> Bioperl hi,
>>> 
>>> I have multiple gff3 files that look like:
>>> 
>>> --------------------------------------------------------
>>> ##gff-version 3
>>> # file: temp1.gff3
>>> contig453278    hs    contig    1    699    .    +    .    Name=contig453278
>>> contig453278    hs    alignment    1    194    .    +    . Name=hs.ENST00000258455
>>> contig453278    hs    alignment    252    699    .    +    . Name=hs.ENST00000258455
>>> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
>>> contig453278    hs    transcript    104    183    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
>>> contig453278    hs    transcript    1    9    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
>>> contig453278    hs    transcript    73    103    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
>>> contig453278    hs    transcript    10    72    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
>>> ---------------------------------------------------------
>>> 
>>> 
>>> 
>>> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>>> 
>>> --------------------------------------------
>>> Bio::DB::SeqFeature::Store->new(...)
>>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>>> for($i=0; $i<$#files+1; $i++){
>>> $loader->load($file[$i]);
>>> }
>>> --------------------------------------------
>>> 
>>> Eventually after uploading ~15000 small gff3 files I got the error:
>>> 
>>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory /tmp/9bbpdE5ibf: Too many links at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
>>> 
>>> 
>>> 
>>> I am trying to see what went wrong, maybe you can rescue me,
>>> Avi
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From maj at fortinbras.us  Fri Feb  5 22:16:54 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 5 Feb 2010 22:16:54 -0500
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <4B6CDCA0.6060700@gmail.com>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com><BD5DAE3180434255A2E6ADD94595AC94@NewLife>
	<4B6CDCA0.6060700@gmail.com>
Message-ID: <E7C9280EE44D4F16A981FF838871CB5D@NewLife>

I do tend to use File::Temp directly, rather than rely on Bio::Root::IO, 
because I more sure of what will happen. Would be excellent if you would
review the code! MAJ
----- Original Message ----- 
From: "Florent Angly" <florent.angly at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 10:06 PM
Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm


> I've run into this issue very recently, albeit working on something 
> unrelated to loading GFF files: generating many small independent 
> assemblies. Maybe there's a bug in the tempdir() code, or its 
> documentation is not clear. I will take a look at it when I have some time.
> Florent
> 
> 
> On 05/02/10 22:27, Mark A. Jensen wrote:
>> The tempfiles are not being unlinked before there are too many for the 
>> OS to handle.
>> Sounds like this may be your job, fungazid, if you're not employing 
>> the script (but
>> not sure about that)
>> ----- Original Message ----- From: "Fungazid" <fungazid at yahoo.com>
>> To: <Bioperl-l at lists.open-bio.org>
>> Sent: Thursday, February 04, 2010 9:52 PM
>> Subject: [Bioperl-l] Too many links at LoadHelper.pm
>>
>>
>>> Bioperl hi,
>>>
>>> I have multiple gff3 files that look like:
>>>
>>> --------------------------------------------------------
>>> ##gff-version 3
>>> # file: temp1.gff3
>>> contig453278    hs    contig    1    699    .    +    .    
>>> Name=contig453278
>>> contig453278    hs    alignment    1    194    .    +    . 
>>> Name=hs.ENST00000258455
>>> contig453278    hs    alignment    252    699    .    +    . 
>>> Name=hs.ENST00000258455
>>> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
>>> contig453278    hs    transcript    104    183    .    +    . 
>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
>>> contig453278    hs    transcript    1    9    .    +    . 
>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
>>> contig453278    hs    transcript    73    103    .    +    . 
>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
>>> contig453278    hs    transcript    10    72    .    +    . 
>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
>>> ---------------------------------------------------------
>>>
>>>
>>>
>>> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>>>
>>> --------------------------------------------
>>> Bio::DB::SeqFeature::Store->new(...)
>>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>>> for($i=0; $i<$#files+1; $i++){
>>> $loader->load($file[$i]);
>>> }
>>> --------------------------------------------
>>>
>>> Eventually after uploading ~15000 small gff3 files I got the error:
>>>
>>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory 
>>> /tmp/9bbpdE5ibf: Too many links at 
>>> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm 
>>> line 49
>>>
>>>
>>>
>>> I am trying to see what went wrong, maybe you can rescue me,
>>> Avi
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
>

From florent.angly at gmail.com  Fri Feb  5 22:24:40 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Sat, 06 Feb 2010 13:24:40 +1000
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <E3E8F68F-21F5-4FF9-8557-91D6E0755FB9@illinois.edu>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
	<BD5DAE3180434255A2E6ADD94595AC94@NewLife>
	<4B6CDCA0.6060700@gmail.com>
	<E3E8F68F-21F5-4FF9-8557-91D6E0755FB9@illinois.edu>
Message-ID: <4B6CE0F8.2090707@gmail.com>

It can't be, Chris, because I use the workaround mentioned here: 
http://bugzilla.open-bio.org/show_bug.cgi?id=2577#c5

It seems like temporary files keep accumulating assembly after assembly. 
Looking at the lsof command, I get a lot of files described as 
"(deleted)". I am thinking that maybe some filehandle is not closed or 
something.

I'll investigate...

Florent

On 06/02/10 13:13, Chris Fields wrote:
> Florent,
>
> The Bio::Assembly error is documented in Bugzilla:
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2577
>
> Switching to a Bio::SeqFeature::CollectionI capable of distinguishing features by seq_id (such as Bio::DB::SeqFeature::Store) may be the best way to go.
>
> chris
>
> On Feb 5, 2010, at 9:06 PM, Florent Angly wrote:
>
>    
>> I've run into this issue very recently, albeit working on something unrelated to loading GFF files: generating many small independent assemblies. Maybe there's a bug in the tempdir() code, or its documentation is not clear. I will take a look at it when I have some time.
>> Florent
>>
>>
>> On 05/02/10 22:27, Mark A. Jensen wrote:
>>      
>>> The tempfiles are not being unlinked before there are too many for the OS to handle.
>>> Sounds like this may be your job, fungazid, if you're not employing the script (but
>>> not sure about that)
>>> ----- Original Message ----- From: "Fungazid"<fungazid at yahoo.com>
>>> To:<Bioperl-l at lists.open-bio.org>
>>> Sent: Thursday, February 04, 2010 9:52 PM
>>> Subject: [Bioperl-l] Too many links at LoadHelper.pm
>>>
>>>
>>>        
>>>> Bioperl hi,
>>>>
>>>> I have multiple gff3 files that look like:
>>>>
>>>> --------------------------------------------------------
>>>> ##gff-version 3
>>>> # file: temp1.gff3
>>>> contig453278    hs    contig    1    699    .    +    .    Name=contig453278
>>>> contig453278    hs    alignment    1    194    .    +    . Name=hs.ENST00000258455
>>>> contig453278    hs    alignment    252    699    .    +    . Name=hs.ENST00000258455
>>>> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
>>>> contig453278    hs    transcript    104    183    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
>>>> contig453278    hs    transcript    1    9    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
>>>> contig453278    hs    transcript    73    103    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
>>>> contig453278    hs    transcript    10    72    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
>>>> ---------------------------------------------------------
>>>>
>>>>
>>>>
>>>> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>>>>
>>>> --------------------------------------------
>>>> Bio::DB::SeqFeature::Store->new(...)
>>>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>>>> for($i=0; $i<$#files+1; $i++){
>>>> $loader->load($file[$i]);
>>>> }
>>>> --------------------------------------------
>>>>
>>>> Eventually after uploading ~15000 small gff3 files I got the error:
>>>>
>>>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory /tmp/9bbpdE5ibf: Too many links at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
>>>>
>>>>
>>>>
>>>> I am trying to see what went wrong, maybe you can rescue me,
>>>> Avi
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>          
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>        
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>      
>    


From maj at fortinbras.us  Fri Feb  5 23:06:16 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 5 Feb 2010 23:06:16 -0500
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <4B6CE0F8.2090707@gmail.com>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com><BD5DAE3180434255A2E6ADD94595AC94@NewLife><4B6CDCA0.6060700@gmail.com><E3E8F68F-21F5-4FF9-8557-91D6E0755FB9@illinois.edu>
	<4B6CE0F8.2090707@gmail.com>
Message-ID: <B1C64CD0FF0244E2A001DA264ED6F109@NewLife>

That's a good thought; when writing a Bioperl
tempfile, I find I must

($fh, $fn) = tempfile();
$fh->close;
$seqio = Bio::SeqIO( -file => ">$fn", -format=>'fasta');

since the better way (always using the filehandle)

($fh, $fn) = tempfile;
$seqio = Bio::SeqIO( -fh => $fh, -format=>'fasta');

doesn't seem to work, though $fh should be open
for both writing and reading. If people do the former
kludge without closing the handle, File::Temp can't
auto-unlink, but it won't cluck about it either.

If I missing something about writing to temp filehandles
here, please set me straight-
cheers MAJ
----- Original Message ----- 
From: "Florent Angly" <florent.angly at gmail.com>
To: "Chris Fields" <cjfields at illinois.edu>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 10:24 PM
Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm


> It can't be, Chris, because I use the workaround mentioned here: 
> http://bugzilla.open-bio.org/show_bug.cgi?id=2577#c5
>
> It seems like temporary files keep accumulating assembly after assembly. 
> Looking at the lsof command, I get a lot of files described as "(deleted)". I 
> am thinking that maybe some filehandle is not closed or something.
>
> I'll investigate...
>
> Florent
>
> On 06/02/10 13:13, Chris Fields wrote:
>> Florent,
>>
>> The Bio::Assembly error is documented in Bugzilla:
>>
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2577
>>
>> Switching to a Bio::SeqFeature::CollectionI capable of distinguishing 
>> features by seq_id (such as Bio::DB::SeqFeature::Store) may be the best way 
>> to go.
>>
>> chris
>>
>> On Feb 5, 2010, at 9:06 PM, Florent Angly wrote:
>>
>>
>>> I've run into this issue very recently, albeit working on something 
>>> unrelated to loading GFF files: generating many small independent 
>>> assemblies. Maybe there's a bug in the tempdir() code, or its documentation 
>>> is not clear. I will take a look at it when I have some time.
>>> Florent
>>>
>>>
>>> On 05/02/10 22:27, Mark A. Jensen wrote:
>>>
>>>> The tempfiles are not being unlinked before there are too many for the OS 
>>>> to handle.
>>>> Sounds like this may be your job, fungazid, if you're not employing the 
>>>> script (but
>>>> not sure about that)
>>>> ----- Original Message ----- From: "Fungazid"<fungazid at yahoo.com>
>>>> To:<Bioperl-l at lists.open-bio.org>
>>>> Sent: Thursday, February 04, 2010 9:52 PM
>>>> Subject: [Bioperl-l] Too many links at LoadHelper.pm
>>>>
>>>>
>>>>
>>>>> Bioperl hi,
>>>>>
>>>>> I have multiple gff3 files that look like:
>>>>>
>>>>> --------------------------------------------------------
>>>>> ##gff-version 3
>>>>> # file: temp1.gff3
>>>>> contig453278    hs    contig    1    699    .    +    . 
>>>>> Name=contig453278
>>>>> contig453278    hs    alignment    1    194    .    +    . 
>>>>> Name=hs.ENST00000258455
>>>>> contig453278    hs    alignment    252    699    .    +    . 
>>>>> Name=hs.ENST00000258455
>>>>> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
>>>>> contig453278    hs    transcript    104    183    .    +    . 
>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
>>>>> contig453278    hs    transcript    1    9    .    +    . 
>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
>>>>> contig453278    hs    transcript    73    103    .    +    . 
>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
>>>>> contig453278    hs    transcript    10    72    .    +    . 
>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
>>>>> ---------------------------------------------------------
>>>>>
>>>>>
>>>>>
>>>>> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>>>>>
>>>>> --------------------------------------------
>>>>> Bio::DB::SeqFeature::Store->new(...)
>>>>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>>>>> for($i=0; $i<$#files+1; $i++){
>>>>> $loader->load($file[$i]);
>>>>> }
>>>>> --------------------------------------------
>>>>>
>>>>> Eventually after uploading ~15000 small gff3 files I got the error:
>>>>>
>>>>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory 
>>>>> /tmp/9bbpdE5ibf: Too many links at 
>>>>> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
>>>>>
>>>>>
>>>>>
>>>>> I am trying to see what went wrong, maybe you can rescue me,
>>>>> Avi
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From cjfields at illinois.edu  Fri Feb  5 23:33:20 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Feb 2010 22:33:20 -0600
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <B1C64CD0FF0244E2A001DA264ED6F109@NewLife>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com><BD5DAE3180434255A2E6ADD94595AC94@NewLife><4B6CDCA0.6060700@gmail.com><E3E8F68F-21F5-4FF9-8557-91D6E0755FB9@illinois.edu>
	<4B6CE0F8.2090707@gmail.com>
	<B1C64CD0FF0244E2A001DA264ED6F109@NewLife>
Message-ID: <6A63C057-9319-47AA-A972-0720AED70270@illinois.edu>

On Feb 5, 2010, at 10:06 PM, Mark A. Jensen wrote:

> That's a good thought; when writing a Bioperl
> tempfile, I find I must
> 
> ($fh, $fn) = tempfile();
> $fh->close;
> $seqio = Bio::SeqIO( -file => ">$fn", -format=>'fasta');
> 
> since the better way (always using the filehandle)
> 
> ($fh, $fn) = tempfile;
> $seqio = Bio::SeqIO( -fh => $fh, -format=>'fasta');
> 
> doesn't seem to work, though $fh should be open
> for both writing and reading. If people do the former
> kludge without closing the handle, File::Temp can't
> auto-unlink, but it won't cluck about it either.
> 
> If I missing something about writing to temp filehandles
> here, please set me straight-
> cheers MAJ

No, I think you're on the right track.  There isn't any reason why using a temp filehandle shouldn't work with the various *IO that I can think of, so I would consider that a bug.  Does the same thing occur when using Bio::Root::IO::tempfile() (which just wraps File::Temp)?

chris

From maj at fortinbras.us  Fri Feb  5 23:40:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 5 Feb 2010 23:40:25 -0500
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <6A63C057-9319-47AA-A972-0720AED70270@illinois.edu>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com><BD5DAE3180434255A2E6ADD94595AC94@NewLife><4B6CDCA0.6060700@gmail.com><E3E8F68F-21F5-4FF9-8557-91D6E0755FB9@illinois.edu>
	<4B6CE0F8.2090707@gmail.com>
	<B1C64CD0FF0244E2A001DA264ED6F109@NewLife>
	<6A63C057-9319-47AA-A972-0720AED70270@illinois.edu>
Message-ID: <22F7FF69165C4175AAB639DE9331B668@NewLife>

sth to check--
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Florent Angly" <florent.angly at gmail.com>; <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 11:33 PM
Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm


On Feb 5, 2010, at 10:06 PM, Mark A. Jensen wrote:

> That's a good thought; when writing a Bioperl
...
Does the same thing occur when using Bio::Root::IO::tempfile() (which just wraps 
File::Temp)?

chris


From cjfields at illinois.edu  Fri Feb  5 23:41:57 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Feb 2010 22:41:57 -0600
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <4B6CE0F8.2090707@gmail.com>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
	<BD5DAE3180434255A2E6ADD94595AC94@NewLife>
	<4B6CDCA0.6060700@gmail.com>
	<E3E8F68F-21F5-4FF9-8557-91D6E0755FB9@illinois.edu>
	<4B6CE0F8.2090707@gmail.com>
Message-ID: <8D50C6AA-2BD5-43AD-8798-929A0B656CC9@illinois.edu>

The only place I can think of tempfiles being generated offhand are Bio::SeqFeature::Collection (actually, tied handles), but as you mention this may not be related.  There are calls to tempfile from Bio::Assembly::IO::sam/bowtie (one using Root::IO, one using File::Temp directly).

chris

On Feb 5, 2010, at 9:24 PM, Florent Angly wrote:

> It can't be, Chris, because I use the workaround mentioned here: http://bugzilla.open-bio.org/show_bug.cgi?id=2577#c5
> 
> It seems like temporary files keep accumulating assembly after assembly. Looking at the lsof command, I get a lot of files described as "(deleted)". I am thinking that maybe some filehandle is not closed or something.
> 
> I'll investigate...
> 
> Florent
> 
> On 06/02/10 13:13, Chris Fields wrote:
>> Florent,
>> 
>> The Bio::Assembly error is documented in Bugzilla:
>> 
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2577
>> 
>> Switching to a Bio::SeqFeature::CollectionI capable of distinguishing features by seq_id (such as Bio::DB::SeqFeature::Store) may be the best way to go.
>> 
>> chris
>> 
>> On Feb 5, 2010, at 9:06 PM, Florent Angly wrote:
>> 
>>   
>>> I've run into this issue very recently, albeit working on something unrelated to loading GFF files: generating many small independent assemblies. Maybe there's a bug in the tempdir() code, or its documentation is not clear. I will take a look at it when I have some time.
>>> Florent
>>> 
>>> 
>>> On 05/02/10 22:27, Mark A. Jensen wrote:
>>>     
>>>> The tempfiles are not being unlinked before there are too many for the OS to handle.
>>>> Sounds like this may be your job, fungazid, if you're not employing the script (but
>>>> not sure about that)
>>>> ----- Original Message ----- From: "Fungazid"<fungazid at yahoo.com>
>>>> To:<Bioperl-l at lists.open-bio.org>
>>>> Sent: Thursday, February 04, 2010 9:52 PM
>>>> Subject: [Bioperl-l] Too many links at LoadHelper.pm
>>>> 
>>>> 
>>>>       
>>>>> Bioperl hi,
>>>>> 
>>>>> I have multiple gff3 files that look like:
>>>>> 
>>>>> --------------------------------------------------------
>>>>> ##gff-version 3
>>>>> # file: temp1.gff3
>>>>> contig453278    hs    contig    1    699    .    +    .    Name=contig453278
>>>>> contig453278    hs    alignment    1    194    .    +    . Name=hs.ENST00000258455
>>>>> contig453278    hs    alignment    252    699    .    +    . Name=hs.ENST00000258455
>>>>> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
>>>>> contig453278    hs    transcript    104    183    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
>>>>> contig453278    hs    transcript    1    9    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
>>>>> contig453278    hs    transcript    73    103    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
>>>>> contig453278    hs    transcript    10    72    .    +    . Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
>>>>> ---------------------------------------------------------
>>>>> 
>>>>> 
>>>>> 
>>>>> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>>>>> 
>>>>> --------------------------------------------
>>>>> Bio::DB::SeqFeature::Store->new(...)
>>>>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>>>>> for($i=0; $i<$#files+1; $i++){
>>>>> $loader->load($file[$i]);
>>>>> }
>>>>> --------------------------------------------
>>>>> 
>>>>> Eventually after uploading ~15000 small gff3 files I got the error:
>>>>> 
>>>>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory /tmp/9bbpdE5ibf: Too many links at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
>>>>> 
>>>>> 
>>>>> 
>>>>> I am trying to see what went wrong, maybe you can rescue me,
>>>>> Avi
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>>> 
>>>>>         
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>       
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>     
>>   
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From maj at fortinbras.us  Fri Feb  5 23:49:34 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 5 Feb 2010 23:49:34 -0500
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <8D50C6AA-2BD5-43AD-8798-929A0B656CC9@illinois.edu>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com><BD5DAE3180434255A2E6ADD94595AC94@NewLife><4B6CDCA0.6060700@gmail.com><E3E8F68F-21F5-4FF9-8557-91D6E0755FB9@illinois.edu><4B6CE0F8.2090707@gmail.com>
	<8D50C6AA-2BD5-43AD-8798-929A0B656CC9@illinois.edu>
Message-ID: <68FE1652EDB34C3097DDAB00C2F6D6CA@NewLife>

Dan has been partial to temp in Root::IO (bowtie); I scurried off to File::Temp 
(sam)--
any issues with tempfile handles, Dan?
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Florent Angly" <florent.angly at gmail.com>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 11:41 PM
Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm


> The only place I can think of tempfiles being generated offhand are 
> Bio::SeqFeature::Collection (actually, tied handles), but as you mention this 
> may not be related.  There are calls to tempfile from 
> Bio::Assembly::IO::sam/bowtie (one using Root::IO, one using File::Temp 
> directly).
>
> chris
>
> On Feb 5, 2010, at 9:24 PM, Florent Angly wrote:
>
>> It can't be, Chris, because I use the workaround mentioned here: 
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2577#c5
>>
>> It seems like temporary files keep accumulating assembly after assembly. 
>> Looking at the lsof command, I get a lot of files described as "(deleted)". I 
>> am thinking that maybe some filehandle is not closed or something.
>>
>> I'll investigate...
>>
>> Florent
>>
>> On 06/02/10 13:13, Chris Fields wrote:
>>> Florent,
>>>
>>> The Bio::Assembly error is documented in Bugzilla:
>>>
>>> http://bugzilla.open-bio.org/show_bug.cgi?id=2577
>>>
>>> Switching to a Bio::SeqFeature::CollectionI capable of distinguishing 
>>> features by seq_id (such as Bio::DB::SeqFeature::Store) may be the best way 
>>> to go.
>>>
>>> chris
>>>
>>> On Feb 5, 2010, at 9:06 PM, Florent Angly wrote:
>>>
>>>
>>>> I've run into this issue very recently, albeit working on something 
>>>> unrelated to loading GFF files: generating many small independent 
>>>> assemblies. Maybe there's a bug in the tempdir() code, or its documentation 
>>>> is not clear. I will take a look at it when I have some time.
>>>> Florent
>>>>
>>>>
>>>> On 05/02/10 22:27, Mark A. Jensen wrote:
>>>>
>>>>> The tempfiles are not being unlinked before there are too many for the OS 
>>>>> to handle.
>>>>> Sounds like this may be your job, fungazid, if you're not employing the 
>>>>> script (but
>>>>> not sure about that)
>>>>> ----- Original Message ----- From: "Fungazid"<fungazid at yahoo.com>
>>>>> To:<Bioperl-l at lists.open-bio.org>
>>>>> Sent: Thursday, February 04, 2010 9:52 PM
>>>>> Subject: [Bioperl-l] Too many links at LoadHelper.pm
>>>>>
>>>>>
>>>>>
>>>>>> Bioperl hi,
>>>>>>
>>>>>> I have multiple gff3 files that look like:
>>>>>>
>>>>>> --------------------------------------------------------
>>>>>> ##gff-version 3
>>>>>> # file: temp1.gff3
>>>>>> contig453278    hs    contig    1    699    .    +    . 
>>>>>> Name=contig453278
>>>>>> contig453278    hs    alignment    1    194    .    +    . 
>>>>>> Name=hs.ENST00000258455
>>>>>> contig453278    hs    alignment    252    699    .    +    . 
>>>>>> Name=hs.ENST00000258455
>>>>>> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
>>>>>> contig453278    hs    transcript    104    183    .    +    . 
>>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
>>>>>> contig453278    hs    transcript    1    9    .    +    . 
>>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
>>>>>> contig453278    hs    transcript    73    103    .    +    . 
>>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
>>>>>> contig453278    hs    transcript    10    72    .    +    . 
>>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
>>>>>> ---------------------------------------------------------
>>>>>>
>>>>>>
>>>>>>
>>>>>> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>>>>>>
>>>>>> --------------------------------------------
>>>>>> Bio::DB::SeqFeature::Store->new(...)
>>>>>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>>>>>> for($i=0; $i<$#files+1; $i++){
>>>>>> $loader->load($file[$i]);
>>>>>> }
>>>>>> --------------------------------------------
>>>>>>
>>>>>> Eventually after uploading ~15000 small gff3 files I got the error:
>>>>>>
>>>>>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory 
>>>>>> /tmp/9bbpdE5ibf: Too many links at 
>>>>>> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
>>>>>>
>>>>>>
>>>>>>
>>>>>> I am trying to see what went wrong, maybe you can rescue me,
>>>>>> Avi
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From dan.kortschak at adelaide.edu.au  Sat Feb  6 00:11:23 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Sat, 06 Feb 2010 15:41:23 +1030
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <68FE1652EDB34C3097DDAB00C2F6D6CA@NewLife>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com>
	<BD5DAE3180434255A2E6ADD94595AC94@NewLife> <4B6CDCA0.6060700@gmail.com>
	<E3E8F68F-21F5-4FF9-8557-91D6E0755FB9@illinois.edu>
	<4B6CE0F8.2090707@gmail.com>
	<8D50C6AA-2BD5-43AD-8798-929A0B656CC9@illinois.edu>
	<68FE1652EDB34C3097DDAB00C2F6D6CA@NewLife>
Message-ID: <1265433083.4676.7.camel@epistle>

When I was working through those issues (I was having problems with
Bio::DB::Sam causing tempfiles to be released before they were finished
with) I paid quite close attention to having a clean /tmp after running
tests, so I pretty confident that my modules are working with
Bio::Root::IO properly and that Bio::Root::IO is working properly with
them.

Sorry I can't be more helpful.
Dan

On Fri, 2010-02-05 at 23:49 -0500, Mark A. Jensen wrote:
> Dan has been partial to temp in Root::IO (bowtie); I scurried off to File::Temp 
> (sam)--
> any issues with tempfile handles, Dan?
> ----- Original Message ----- 
> From: "Chris Fields" <cjfields at illinois.edu>
> To: "Florent Angly" <florent.angly at gmail.com>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Friday, February 05, 2010 11:41 PM
> Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm
> 
> 
> > The only place I can think of tempfiles being generated offhand are 
> > Bio::SeqFeature::Collection (actually, tied handles), but as you mention this 
> > may not be related.  There are calls to tempfile from 
> > Bio::Assembly::IO::sam/bowtie (one using Root::IO, one using File::Temp 
> > directly).
> >
> > chris
> >
> > On Feb 5, 2010, at 9:24 PM, Florent Angly wrote:
> >
> >> It can't be, Chris, because I use the workaround mentioned here: 
> >> http://bugzilla.open-bio.org/show_bug.cgi?id=2577#c5
> >>
> >> It seems like temporary files keep accumulating assembly after assembly. 
> >> Looking at the lsof command, I get a lot of files described as "(deleted)". I 
> >> am thinking that maybe some filehandle is not closed or something.
> >>
> >> I'll investigate...
> >>
> >> Florent
> >>
> >> On 06/02/10 13:13, Chris Fields wrote:
> >>> Florent,
> >>>
> >>> The Bio::Assembly error is documented in Bugzilla:
> >>>
> >>> http://bugzilla.open-bio.org/show_bug.cgi?id=2577
> >>>
> >>> Switching to a Bio::SeqFeature::CollectionI capable of distinguishing 
> >>> features by seq_id (such as Bio::DB::SeqFeature::Store) may be the best way 
> >>> to go.
> >>>
> >>> chris
> >>>
> >>> On Feb 5, 2010, at 9:06 PM, Florent Angly wrote:
> >>>
> >>>
> >>>> I've run into this issue very recently, albeit working on something 
> >>>> unrelated to loading GFF files: generating many small independent 
> >>>> assemblies. Maybe there's a bug in the tempdir() code, or its documentation 
> >>>> is not clear. I will take a look at it when I have some time.
> >>>> Florent
> >>>>
> >>>>
> >>>> On 05/02/10 22:27, Mark A. Jensen wrote:
> >>>>
> >>>>> The tempfiles are not being unlinked before there are too many for the OS 
> >>>>> to handle.
> >>>>> Sounds like this may be your job, fungazid, if you're not employing the 
> >>>>> script (but
> >>>>> not sure about that)
> >>>>> ----- Original Message ----- From: "Fungazid"<fungazid at yahoo.com>
> >>>>> To:<Bioperl-l at lists.open-bio.org>
> >>>>> Sent: Thursday, February 04, 2010 9:52 PM
> >>>>> Subject: [Bioperl-l] Too many links at LoadHelper.pm
> >>>>>
> >>>>>
> >>>>>
> >>>>>> Bioperl hi,
> >>>>>>
> >>>>>> I have multiple gff3 files that look like:
> >>>>>>
> >>>>>> --------------------------------------------------------
> >>>>>> ##gff-version 3
> >>>>>> # file: temp1.gff3
> >>>>>> contig453278    hs    contig    1    699    .    +    . 
> >>>>>> Name=contig453278
> >>>>>> contig453278    hs    alignment    1    194    .    +    . 
> >>>>>> Name=hs.ENST00000258455
> >>>>>> contig453278    hs    alignment    252    699    .    +    . 
> >>>>>> Name=hs.ENST00000258455
> >>>>>> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
> >>>>>> contig453278    hs    transcript    104    183    .    +    . 
> >>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
> >>>>>> contig453278    hs    transcript    1    9    .    +    . 
> >>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
> >>>>>> contig453278    hs    transcript    73    103    .    +    . 
> >>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
> >>>>>> contig453278    hs    transcript    10    72    .    +    . 
> >>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
> >>>>>> ---------------------------------------------------------
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
> >>>>>>
> >>>>>> --------------------------------------------
> >>>>>> Bio::DB::SeqFeature::Store->new(...)
> >>>>>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
> >>>>>> for($i=0; $i<$#files+1; $i++){
> >>>>>> $loader->load($file[$i]);
> >>>>>> }
> >>>>>> --------------------------------------------
> >>>>>>
> >>>>>> Eventually after uploading ~15000 small gff3 files I got the error:
> >>>>>>
> >>>>>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory 
> >>>>>> /tmp/9bbpdE5ibf: Too many links at 
> >>>>>> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> I am trying to see what went wrong, maybe you can rescue me,
> >>>>>> Avi
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Bioperl-l mailing list
> >>>>>> Bioperl-l at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>> _______________________________________________
> >>>>> Bioperl-l mailing list
> >>>>> Bioperl-l at lists.open-bio.org
> >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > 



From pisceanpranav at gmail.com  Sat Feb  6 01:17:49 2010
From: pisceanpranav at gmail.com (pranav karkhanis)
Date: Sat, 6 Feb 2010 11:47:49 +0530
Subject: [Bioperl-l] Remote Blast
Message-ID: <3122b9be1002052217t6749866cw42cb22935be08a44@mail.gmail.com>

Where can I find the examples or source code for running BLAST with a
input SEQUENCE using RemoteBlast.pm?

From ross at cuhk.edu.hk  Sat Feb  6 06:09:27 2010
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sat, 6 Feb 2010 19:09:27 +0800
Subject: [Bioperl-l] get a full taxonomy path from  Bio::Taxon
Message-ID: <000001caa71c$d9308900$8b919b00$@edu.hk>

In 2003, there's an old post asking about a way to get a full taxonomy.

 

http://osdir.com/ml/lang.perl.bio.general/2003-08/msg00206.html

 

Then Bio::Taxonomy is deprecated and now combination with Bio::Tree has to
use in order to work out the story. 

 

In 

 

http://search.cpan.org/dist/bioperl/Bio/Taxon.pm

 

it also gives an example by explicitly stating what to retrieve. However,
what I need is to just provide a GI or accession number and to get a full
taxonomy and I find there is no simple way (at least I don't know .) to do
so. Would anybody advise?

 

Thanks a lot,

Ross

 


From maj at fortinbras.us  Sat Feb  6 08:52:31 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Sat, 6 Feb 2010 08:52:31 -0500
Subject: [Bioperl-l] get a full taxonomy path from  Bio::Taxon
In-Reply-To: <000001caa71c$d9308900$8b919b00$@edu.hk>
References: <000001caa71c$d9308900$8b919b00$@edu.hk>
Message-ID: <C1301F86CBC544FCAB44038B52CE30F8@NewLife>

Try this, Ross:

use Bio::DB::SoapEUtilities;
my $fac = Bio::DB::SoapEUtilities->new();
my $links = $fac->elink( -db => 'taxonomy', -db_from => protein, -id => $accn )
                         ->run( -auto_adapt => 1 );

my $spcio = $fac->efetch( -db => 'taxonomy', -id => [ $links->id_map( $accn ) ])
                             ->run( -auto_adapt => 1);

my $species = $spcio->next_species;
my @fullpath = $species->classification;

Bio::DB::SoapEUtilities is in the bioperl-run trunk.

MAJ


----- Original Message ----- 
From: "Ross KK Leung" <ross at cuhk.edu.hk>
To: <bioperl-l at bioperl.org>
Sent: Saturday, February 06, 2010 6:09 AM
Subject: [Bioperl-l] get a full taxonomy path from Bio::Taxon


> In 2003, there's an old post asking about a way to get a full taxonomy.
>
>
>
> http://osdir.com/ml/lang.perl.bio.general/2003-08/msg00206.html
>
>
>
> Then Bio::Taxonomy is deprecated and now combination with Bio::Tree has to
> use in order to work out the story.
>
>
>
> In
>
>
>
> http://search.cpan.org/dist/bioperl/Bio/Taxon.pm
>
>
>
> it also gives an example by explicitly stating what to retrieve. However,
> what I need is to just provide a GI or accession number and to get a full
> taxonomy and I find there is no simple way (at least I don't know .) to do
> so. Would anybody advise?
>
>
>
> Thanks a lot,
>
> Ross
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From florent.angly at gmail.com  Sat Feb  6 09:27:53 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Sun, 07 Feb 2010 00:27:53 +1000
Subject: [Bioperl-l] Too many links at LoadHelper.pm
In-Reply-To: <1265433083.4676.7.camel@epistle>
References: <34328.58710.qm@web65506.mail.ac4.yahoo.com>	
	<BD5DAE3180434255A2E6ADD94595AC94@NewLife>
	<4B6CDCA0.6060700@gmail.com>	
	<E3E8F68F-21F5-4FF9-8557-91D6E0755FB9@illinois.edu>	
	<4B6CE0F8.2090707@gmail.com>	
	<8D50C6AA-2BD5-43AD-8798-929A0B656CC9@illinois.edu>	
	<68FE1652EDB34C3097DDAB00C2F6D6CA@NewLife>
	<1265433083.4676.7.camel@epistle>
Message-ID: <4B6D7C69.2050704@gmail.com>

Ok, so I looked at my code, and it's a totally unrelated issue that 
caused files/filehandles to not be removed/closed properly.
The BioPerl tempdir() system seems to be doing fine :)
Florent

On 06/02/10 15:11, Dan Kortschak wrote:
> When I was working through those issues (I was having problems with
> Bio::DB::Sam causing tempfiles to be released before they were finished
> with) I paid quite close attention to having a clean /tmp after running
> tests, so I pretty confident that my modules are working with
> Bio::Root::IO properly and that Bio::Root::IO is working properly with
> them.
>
> Sorry I can't be more helpful.
> Dan
>
> On Fri, 2010-02-05 at 23:49 -0500, Mark A. Jensen wrote:
>    
>> Dan has been partial to temp in Root::IO (bowtie); I scurried off to File::Temp
>> (sam)--
>> any issues with tempfile handles, Dan?
>> ----- Original Message -----
>> From: "Chris Fields"<cjfields at illinois.edu>
>> To: "Florent Angly"<florent.angly at gmail.com>
>> Cc:<bioperl-l at lists.open-bio.org>
>> Sent: Friday, February 05, 2010 11:41 PM
>> Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm
>>
>>
>>      
>>> The only place I can think of tempfiles being generated offhand are
>>> Bio::SeqFeature::Collection (actually, tied handles), but as you mention this
>>> may not be related.  There are calls to tempfile from
>>> Bio::Assembly::IO::sam/bowtie (one using Root::IO, one using File::Temp
>>> directly).
>>>
>>> chris
>>>
>>> On Feb 5, 2010, at 9:24 PM, Florent Angly wrote:
>>>
>>>        
>>>> It can't be, Chris, because I use the workaround mentioned here:
>>>> http://bugzilla.open-bio.org/show_bug.cgi?id=2577#c5
>>>>
>>>> It seems like temporary files keep accumulating assembly after assembly.
>>>> Looking at the lsof command, I get a lot of files described as "(deleted)". I
>>>> am thinking that maybe some filehandle is not closed or something.
>>>>
>>>> I'll investigate...
>>>>
>>>> Florent
>>>>
>>>> On 06/02/10 13:13, Chris Fields wrote:
>>>>          
>>>>> Florent,
>>>>>
>>>>> The Bio::Assembly error is documented in Bugzilla:
>>>>>
>>>>> http://bugzilla.open-bio.org/show_bug.cgi?id=2577
>>>>>
>>>>> Switching to a Bio::SeqFeature::CollectionI capable of distinguishing
>>>>> features by seq_id (such as Bio::DB::SeqFeature::Store) may be the best way
>>>>> to go.
>>>>>
>>>>> chris
>>>>>
>>>>> On Feb 5, 2010, at 9:06 PM, Florent Angly wrote:
>>>>>
>>>>>
>>>>>            
>>>>>> I've run into this issue very recently, albeit working on something
>>>>>> unrelated to loading GFF files: generating many small independent
>>>>>> assemblies. Maybe there's a bug in the tempdir() code, or its documentation
>>>>>> is not clear. I will take a look at it when I have some time.
>>>>>> Florent
>>>>>>
>>>>>>
>>>>>> On 05/02/10 22:27, Mark A. Jensen wrote:
>>>>>>
>>>>>>              
>>>>>>> The tempfiles are not being unlinked before there are too many for the OS
>>>>>>> to handle.
>>>>>>> Sounds like this may be your job, fungazid, if you're not employing the
>>>>>>> script (but
>>>>>>> not sure about that)
>>>>>>> ----- Original Message ----- From: "Fungazid"<fungazid at yahoo.com>
>>>>>>> To:<Bioperl-l at lists.open-bio.org>
>>>>>>> Sent: Thursday, February 04, 2010 9:52 PM
>>>>>>> Subject: [Bioperl-l] Too many links at LoadHelper.pm
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>                
>>>>>>>> Bioperl hi,
>>>>>>>>
>>>>>>>> I have multiple gff3 files that look like:
>>>>>>>>
>>>>>>>> --------------------------------------------------------
>>>>>>>> ##gff-version 3
>>>>>>>> # file: temp1.gff3
>>>>>>>> contig453278    hs    contig    1    699    .    +    .
>>>>>>>> Name=contig453278
>>>>>>>> contig453278    hs    alignment    1    194    .    +    .
>>>>>>>> Name=hs.ENST00000258455
>>>>>>>> contig453278    hs    alignment    252    699    .    +    .
>>>>>>>> Name=hs.ENST00000258455
>>>>>>>> contig453278    hs    mi2    194    252    .    +    .    Name=mi2
>>>>>>>> contig453278    hs    transcript    104    183    .    +    .
>>>>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
>>>>>>>> contig453278    hs    transcript    1    9    .    +    .
>>>>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
>>>>>>>> contig453278    hs    transcript    73    103    .    +    .
>>>>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
>>>>>>>> contig453278    hs    transcript    10    72    .    +    .
>>>>>>>> Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
>>>>>>>> ---------------------------------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I uploaded gff3 files to mysql and view the tracks in gBrowse like this:
>>>>>>>>
>>>>>>>> --------------------------------------------
>>>>>>>> Bio::DB::SeqFeature::Store->new(...)
>>>>>>>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>>>>>>>> for($i=0; $i<$#files+1; $i++){
>>>>>>>> $loader->load($file[$i]);
>>>>>>>> }
>>>>>>>> --------------------------------------------
>>>>>>>>
>>>>>>>> Eventually after uploading ~15000 small gff3 files I got the error:
>>>>>>>>
>>>>>>>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory
>>>>>>>> /tmp/9bbpdE5ibf: Too many links at
>>>>>>>> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm line 49
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I am trying to see what went wrong, maybe you can rescue me,
>>>>>>>> Avi
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>                  
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>                
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>              
>>>>>            
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>          
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>        
>
>    


From fungazid at yahoo.com  Sat Feb  6 18:36:57 2010
From: fungazid at yahoo.com (Fungazid)
Date: Sat, 6 Feb 2010 15:36:57 -0800 (PST)
Subject: [Bioperl-l] Bio::seqFeature functions coresponding to specific
	gBrowse variables
Message-ID: <963778.13913.qm@web65505.mail.ac4.yahoo.com>

Hello everybody,

thanks for you help, here is another small question, and I would be grateful for your help: 

In the gBrowse .conf file of gBrowse I have the following lines

-------------------------------------------------------------------
balloon hover = =<h2>Gene</h2>
balloon click = 
<a href='http://localhost/cgi-bin/gbrowse_details/gBrowseTest4?name=$name;class=Sequence;ref=$ref;start=$start;end=$end;feature_id=$id'>gene regions</a><br>
---------------------------------------------------------------------

As you can see above, gBrowse recognizes the properties $name,$ref, $start, $end, $id


Now, lets say I wrote this:
---------------------------
balloon click = sub {											my $feature = shift;
$name = $feature->?????();
$ref = $feature->?????();
...
}
---------------------------

what are the seqFeature parallel functions/variables ?

Avi


      


From Russell.Smithies at agresearch.co.nz  Sun Feb  7 15:47:00 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 8 Feb 2010 09:47:00 +1300
Subject: [Bioperl-l] Refseq Version
In-Reply-To: <465b5a661002050655u34ff94acwdf8fe72512dec4b3@mail.gmail.com>
References: <465b5a661002041401u3b8ac5fdp483f7032ce35139b@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED520@exchsth.agresearch.co.nz>
	<465b5a661002050655u34ff94acwdf8fe72512dec4b3@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61BED76C@exchsth.agresearch.co.nz>

Release 39 was Jan 30 and according to the README releases only come out in odd months (January, March, May, July, September, November)
The stats file is here: ftp://ftp.ncbi.nih.gov/refseq/release/release-statistics/RefSeq-release39.01232010.stats.txt

The numbers of sequences between the fasta release and the pre-build blast databases seem to differ but I guess only NCBI can explain that.
I can't see any way of extracting the release number from the pre-build blast databases (apart from the build date) but it might be worth asking NCBI if they'd include the information in future releases.


FYI, here's the old release stats.
(I wget'ed and grep'ed all the stats files)

Release

Date

Year

Organisms

Nucleotide Bases

Amino Acids

Records

1

Jun-30

2003

            4,672,871,949

            263,588,685

          1,061,675

2

Oct-21

2003

        2,124

            7,745,398,573

            286,957,682

          1,097,404

3

Jan-13

2004

        2,218

            7,992,741,222

            294,647,847

          1,101,244

4

Mar-24

2004

        2,358

            8,175,128,887

            318,253,841

          1,193,457

5

May-02

2004

        2,395

            8,325,515,623

            337,229,387

          1,255,613

6

Jul-05

2004

        2,467

            8,696,371,716

            365,446,682

          1,367,206

7

Sep-12

2004

        2,558

          21,072,808,460

            405,233,619

          1,579,579

8

Oct-31

2004

        2,645

          26,814,386,658

            430,300,369

          1,709,723

9

Jan-09

2005

        2,780

          36,786,975,473

            470,534,907

          1,843,944

10

Mar-06

2005

        2,827

          36,893,741,150

            482,862,858

          1,893,478

11

May-08

2005

        2,928

          39,731,702,362

            507,980,644

          2,477,893

12

Jul-10

2005

        2,969

          43,043,256,058

            608,493,108

          2,869,675

13

Sep-11

2005

        3,060

          44,727,484,853

            686,768,902

          3,400,773

14

Nov-20

2005

        3,198

          47,364,955,367

            763,761,075

          3,272,776

15

Jan-01

2006

        3,244

          52,645,441,913

            810,009,733

          3,436,263

16

Mar-11

2006

        3,397

          56,175,443,059

            887,509,001

          3,715,260

17

May-01

2006

        3,497

          62,130,037,371

            927,587,669

          3,999,859

18

Jul-11

2006

        3,695

          70,474,041,999

            974,374,765

          4,186,692

19

Sep-10

2006

        3,774

          70,694,879,544

         1,012,985,077

          4,311,543

20

Nov-05

2006

        3,919

          72,679,681,505

         1,061,797,276

          4,567,569

21

Jan-06

2007

        4,079

          73,864,990,566

         1,144,795,927

          4,742,335

22

Mar-05

2007

        4,187

          82,441,128,546

         1,215,085,694

          5,207,865

23

May-08

2007

        4,300

          83,148,327,110

         1,291,050,995

          5,503,385

24

Jul-10

2007

        4,511

          89,856,995,521

         1,365,916,222

          6,073,814

25

Sep-11

2007

        4,646

          91,265,840,843

         1,470,475,398

          6,515,132

26

Nov-04

2007

        4,737

          99,105,705,485

         1,495,032,507

          6,698,250

27

Jan-06

2008

        4,926

         101,059,552,113

         1,556,356,987

          7,025,715

28

Mar-09

2008

        5,059

         102,051,350,525

         1,770,627,427

          7,914,560

29

May-04

2008

        5,168

         104,671,101,150

         1,870,214,220

          8,376,141

30

Jul-07

2008

        5,395

         105,074,486,709

         1,913,447,691

          8,572,852

31

Aug-30

2008

        5,513

         109,214,348,591

         2,026,768,719

          9,145,702

32

Nov-10

2008

        5,726

         111,122,203,221

         2,089,596,746

          9,501,764

33

Jan-16

2009

        7,773

         116,001,583,818

         2,204,073,443

        10,325,282

34

Mar-06

2009

        8,054

         111,792,574,830

         2,299,682,138

        10,021,870

35

May-04

2009

        8,393

         113,210,655,336

         2,565,199,170

        10,993,891

36

Jul-02

2009

        8,665

         117,013,741,530

         2,756,884,219

        12,141,825

37

Sep-03

2009

        9,005

         119,151,229,820

         2,965,450,333

        12,941,750

38

Nov-07

2009

        9,166

         119,196,622,435

         3,115,246,540

        13,436,447



--Russell


From: shalu sharma [mailto:sharmashalu.bio at gmail.com]
Sent: Saturday, 6 February 2010 3:56 a.m.
To: Smithies, Russell
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Refseq Version

Hi Russell,
               Thanks for your response.
I am getting the number of sequence in the database but not the release number (like 38, 39).
This is what i did:

$ fastacmd -I -d /db/ncbiblast/refseq/refseq_protein
Database: NCBI Protein Reference Sequences
           7,585,993 sequences; 2,644,770,521 total letters

File names:
/db/ncbiblast/refseq/refseq_protein.00
   Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 36,805 res
/db/ncbiblast/refseq/refseq_protein.01
   Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 33,403 res
/db/ncbiblast/refseq/refseq_protein.02
   Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 15,830 res

I am still confuse that how i can get the release number. I know refseq 39 was released on Jan 30, 2010 but i don't know how to confirm this. I also tried look refseq release file but was not able to get any thing.

I would really appreciate if anyone can help me out with this.

Thanks
Shalu

On Thu, Feb 4, 2010 at 6:39 PM, Smithies, Russell <Russell.Smithies at agresearch.co.nz<mailto:Russell.Smithies at agresearch.co.nz>> wrote:
If you have access to the blast database, use fastacmd -I -d databasename
Otherwise, it's usually at the bottom of your blast result.

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-bounces at lists.open-bio.org> [mailto:bioperl-l-<mailto:bioperl-l->
> bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>] On Behalf Of shalu sharma
> Sent: Friday, 5 February 2010 11:02 a.m.
> To: bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>
> Subject: [Bioperl-l] Refseq Version
>
> Hi All,
>       This is not a bioperl query.
> Is there any way to check refseq version (release). Actually i am using
> some
> server to blast my sequences (blastall) against refseq. Is there any way i
> can get the version information on the refseq database (from the blast
> file
> or directly from the database)?
>
> Thanks
> Shalu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org<mailto:Bioperl-l at lists.open-bio.org>
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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From Russell.Smithies at agresearch.co.nz  Sun Feb  7 15:59:28 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 8 Feb 2010 09:59:28 +1300
Subject: [Bioperl-l] Refseq Version
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32C61BED76C@exchsth.agresearch.co.nz>
References: <465b5a661002041401u3b8ac5fdp483f7032ce35139b@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED520@exchsth.agresearch.co.nz>
	<465b5a661002050655u34ff94acwdf8fe72512dec4b3@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED76C@exchsth.agresearch.co.nz>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61BED78C@exchsth.agresearch.co.nz>

I should have known it would break the formatting :-(

Try this:

Release 1:June 30, 2003;Release Size: 4672871949 bases, 263588685 amino acids, 1061675 records
Release 2:October 21, 2003;Release Size: 2124 organisms, 7745398573 nucleotide bases, 286957682 amino acids, 1097404 records
Release 3:January 13, 2004;Release Size: 2218 organisms, 7992741222 nucleotide bases, 294647847 amino acids, 1101244 records
Release 4:March 24, 2004;Release Size: 2358 organisms, 8175128887 nucleotide bases, 318253841 amino acids, 1193457 records
Release 5:May 2 , 2004;Release Size: 2395 organisms, 8325515623 nucleotide bases, 337229387 amino acids, 1255613 records
Release 6:July 5, 2004;Release Size: 2467 organisms, 8696371716 nucleotide bases, 365446682 amino acids, 1367206 records
Release 7:September 12, 2004;Release Size: 2558 organisms, 21072808460 nucleotide bases, 405233619 amino acids, 1579579 records
Release 8:October 31, 2004;Release Size: 2645 organisms, 26814386658 nucleotide bases, 430300369 amino acids, 1709723 records
Release 9:January 9, 2005;Release Size:  2780 organisms, 36786975473 nucleotide bases, 470534907 amino acids, 1843944 records
Release 10:March 6, 2005;Release Size:2827 organisms, 36893741150 nucleotide bases, 482862858 amino acids, 1893478 records
Release 11:May 8, 2005;Release Size:2928 organisms, 39731702362 nucleotide bases, 507980644 amino acids, 2477893 records
Release 12:July 10, 2005;Release Size:2969 organisms, 43043256058 nucleotide bases, 608493108 amino acids, 2869675 records
Release 13:September 11, 2005;Release Size:3060 organisms, 44727484853 nucleotide bases, 686768902 amino acids, 3400773 records
Release 14:November 20, 2005;Release Size:3198 organisms, 47364955367 nucleotide bases, 763761075 amino acids, 3272776 records
Release 15:January 1, 2006;Release Size:3244 organisms, 52645441913 nucleotide bases, 810009733 amino acids, 3436263 records
Release 16:March 11, 2006;Release Size:3397 organisms, 56175443059 nucleotide bases, 887509001 amino acids, 3715260 records
Release 17:May 1, 2006;Release Size:3497 organisms, 62130037371 nucleotide bases, 927587669 amino acids, 3999859 records
Release 18:July 11, 2006;Release Size:3695 organisms, 70474041999 nucleotide bases, 974374765 amino acids, 4186692 records
Release 19:September 10, 2006;Release Size: 3774 organisms, 70694879544 nucleotide bases, 1012985077 amino acids, 4311543 records
Release 20:November 5, 2006;Release Size:3919 organisms, 72679681505 nucleotide bases, 1061797276 amino acids, 4567569 records
Release 21:January 6, 2007;Release Size:4079 organisms, 73864990566 nucleotide bases, 1144795927 amino acids, 4742335 records
Release 22:March 5, 2007;Release Size:4187 organisms, 82441128546 nucleotide bases, 1215085694 amino acids, 5207865 records
Release 23:May 8, 2007;Release Size:4300 organisms, 83148327110 nucleotide bases, 1291050995 amino acids, 5503385 records
Release 24:July 10, 2007;Release Size:4511 organisms, 89856995521 nucleotide bases, 1365916222 amino acids, 6073814 records
Release 25:September 11, 2007;Release Size:4646 organisms, 91265840843 nucleotide bases, 1470475398 amino acids, 6515132 records
Release 26:November 4, 2007;Release Size:4737 organisms, 99105705485 nucleotide bases, 1495032507 amino acids, 6698250 records
Release 27:January 6, 2008;Release Size:4926 organisms, 101059552113 nucleotide bases, 1556356987 amino acids, 7025715 records
Release 28:March 9, 2008;Release Size: 5059 organisms, 102051350525 nucleotide bases, 1770627427 amino acids, 7914560 records
Release 29:May 4, 2008;Release Size:5168 organisms, 104671101150 nucleotide bases, 1870214220 amino acids, 8376141 records
Release 30:July 7, 2008;Release Size:5395 organisms, 105074486709 nucleotide bases, 1913447691 amino acids, 8572852 records
Release 31:August 30, 2008;Release Size: 5513 organisms, 109214348591 nucleotide bases, 2026768719 amino acids, 9145702 records
Release 32:November 10, 2008;Release Size: 5726 organisms, 111122203221 nucleotide bases, 2089596746 amino acids, 9501764 records
Release 33:January 16, 2009;Release Size:7773 organisms, 116001583818 nucleotide bases, 2204073443 amino acids, 10325282 records
Release 34:March 6, 2009;Release Size: 8054 organisms, 111792574830 nucleotide bases, 2299682138 amino acids, 10021870 records
Release 35:May 4, 2009;Release Size: 8393 organisms, 113210655336 nucleotide bases, 2565199170 amino acids, 10993891 records
Release 36:July 2, 2009;Release Size: 8665 organisms, 117013741530 nucleotide bases, 2756884219 amino acids, 12141825 records
Release 37:September 3, 2009;Release Size: 9005 organisms, 119151229820 nucleotide bases, 2965450333 amino acids, 12941750 records
Release 38:November 7, 2009;Release Size: 9166 organisms, 119196622435 nucleotide bases, 3115246540 amino acids, 13436447 records



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Smithies, Russell
> Sent: Monday, 8 February 2010 9:47 a.m.
> To: 'shalu sharma'
> Cc: 'bioperl-l at lists.open-bio.org'
> Subject: Re: [Bioperl-l] Refseq Version
>
> Release 39 was Jan 30 and according to the README releases only come out
> in odd months (January, March, May, July, September, November)
> The stats file is here: ftp://ftp.ncbi.nih.gov/refseq/release/release-
> statistics/RefSeq-release39.01232010.stats.txt
>
> The numbers of sequences between the fasta release and the pre-build blast
> databases seem to differ but I guess only NCBI can explain that.
> I can't see any way of extracting the release number from the pre-build
> blast databases (apart from the build date) but it might be worth asking
> NCBI if they'd include the information in future releases.
>
>
> FYI, here's the old release stats.
> (I wget'ed and grep'ed all the stats files)
>
> Release
>
> Date
>
> Year
>
> Organisms
>
> Nucleotide Bases
>
> Amino Acids
>
> Records
>
> 1
>
> Jun-30
>
> 2003
>
>             4,672,871,949
>
>             263,588,685
>
>           1,061,675
>
> 2
>
> Oct-21
>
> 2003
>
>         2,124
>
>             7,745,398,573
>
>             286,957,682
>
>           1,097,404
>
> 3
>
> Jan-13
>
> 2004
>
>         2,218
>
>             7,992,741,222
>
>             294,647,847
>
>           1,101,244
>
> 4
>
> Mar-24
>
> 2004
>
>         2,358
>
>             8,175,128,887
>
>             318,253,841
>
>           1,193,457
>
> 5
>
> May-02
>
> 2004
>
>         2,395
>
>             8,325,515,623
>
>             337,229,387
>
>           1,255,613
>
> 6
>
> Jul-05
>
> 2004
>
>         2,467
>
>             8,696,371,716
>
>             365,446,682
>
>           1,367,206
>
> 7
>
> Sep-12
>
> 2004
>
>         2,558
>
>           21,072,808,460
>
>             405,233,619
>
>           1,579,579
>
> 8
>
> Oct-31
>
> 2004
>
>         2,645
>
>           26,814,386,658
>
>             430,300,369
>
>           1,709,723
>
> 9
>
> Jan-09
>
> 2005
>
>         2,780
>
>           36,786,975,473
>
>             470,534,907
>
>           1,843,944
>
> 10
>
> Mar-06
>
> 2005
>
>         2,827
>
>           36,893,741,150
>
>             482,862,858
>
>           1,893,478
>
> 11
>
> May-08
>
> 2005
>
>         2,928
>
>           39,731,702,362
>
>             507,980,644
>
>           2,477,893
>
> 12
>
> Jul-10
>
> 2005
>
>         2,969
>
>           43,043,256,058
>
>             608,493,108
>
>           2,869,675
>
> 13
>
> Sep-11
>
> 2005
>
>         3,060
>
>           44,727,484,853
>
>             686,768,902
>
>           3,400,773
>
> 14
>
> Nov-20
>
> 2005
>
>         3,198
>
>           47,364,955,367
>
>             763,761,075
>
>           3,272,776
>
> 15
>
> Jan-01
>
> 2006
>
>         3,244
>
>           52,645,441,913
>
>             810,009,733
>
>           3,436,263
>
> 16
>
> Mar-11
>
> 2006
>
>         3,397
>
>           56,175,443,059
>
>             887,509,001
>
>           3,715,260
>
> 17
>
> May-01
>
> 2006
>
>         3,497
>
>           62,130,037,371
>
>             927,587,669
>
>           3,999,859
>
> 18
>
> Jul-11
>
> 2006
>
>         3,695
>
>           70,474,041,999
>
>             974,374,765
>
>           4,186,692
>
> 19
>
> Sep-10
>
> 2006
>
>         3,774
>
>           70,694,879,544
>
>          1,012,985,077
>
>           4,311,543
>
> 20
>
> Nov-05
>
> 2006
>
>         3,919
>
>           72,679,681,505
>
>          1,061,797,276
>
>           4,567,569
>
> 21
>
> Jan-06
>
> 2007
>
>         4,079
>
>           73,864,990,566
>
>          1,144,795,927
>
>           4,742,335
>
> 22
>
> Mar-05
>
> 2007
>
>         4,187
>
>           82,441,128,546
>
>          1,215,085,694
>
>           5,207,865
>
> 23
>
> May-08
>
> 2007
>
>         4,300
>
>           83,148,327,110
>
>          1,291,050,995
>
>           5,503,385
>
> 24
>
> Jul-10
>
> 2007
>
>         4,511
>
>           89,856,995,521
>
>          1,365,916,222
>
>           6,073,814
>
> 25
>
> Sep-11
>
> 2007
>
>         4,646
>
>           91,265,840,843
>
>          1,470,475,398
>
>           6,515,132
>
> 26
>
> Nov-04
>
> 2007
>
>         4,737
>
>           99,105,705,485
>
>          1,495,032,507
>
>           6,698,250
>
> 27
>
> Jan-06
>
> 2008
>
>         4,926
>
>          101,059,552,113
>
>          1,556,356,987
>
>           7,025,715
>
> 28
>
> Mar-09
>
> 2008
>
>         5,059
>
>          102,051,350,525
>
>          1,770,627,427
>
>           7,914,560
>
> 29
>
> May-04
>
> 2008
>
>         5,168
>
>          104,671,101,150
>
>          1,870,214,220
>
>           8,376,141
>
> 30
>
> Jul-07
>
> 2008
>
>         5,395
>
>          105,074,486,709
>
>          1,913,447,691
>
>           8,572,852
>
> 31
>
> Aug-30
>
> 2008
>
>         5,513
>
>          109,214,348,591
>
>          2,026,768,719
>
>           9,145,702
>
> 32
>
> Nov-10
>
> 2008
>
>         5,726
>
>          111,122,203,221
>
>          2,089,596,746
>
>           9,501,764
>
> 33
>
> Jan-16
>
> 2009
>
>         7,773
>
>          116,001,583,818
>
>          2,204,073,443
>
>         10,325,282
>
> 34
>
> Mar-06
>
> 2009
>
>         8,054
>
>          111,792,574,830
>
>          2,299,682,138
>
>         10,021,870
>
> 35
>
> May-04
>
> 2009
>
>         8,393
>
>          113,210,655,336
>
>          2,565,199,170
>
>         10,993,891
>
> 36
>
> Jul-02
>
> 2009
>
>         8,665
>
>          117,013,741,530
>
>          2,756,884,219
>
>         12,141,825
>
> 37
>
> Sep-03
>
> 2009
>
>         9,005
>
>          119,151,229,820
>
>          2,965,450,333
>
>         12,941,750
>
> 38
>
> Nov-07
>
> 2009
>
>         9,166
>
>          119,196,622,435
>
>          3,115,246,540
>
>         13,436,447
>
>
>
> --Russell
>
>
> From: shalu sharma [mailto:sharmashalu.bio at gmail.com]
> Sent: Saturday, 6 February 2010 3:56 a.m.
> To: Smithies, Russell
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Refseq Version
>
> Hi Russell,
>                Thanks for your response.
> I am getting the number of sequence in the database but not the release
> number (like 38, 39).
> This is what i did:
>
> $ fastacmd -I -d /db/ncbiblast/refseq/refseq_protein
> Database: NCBI Protein Reference Sequences
>            7,585,993 sequences; 2,644,770,521 total letters
>
> File names:
> /db/ncbiblast/refseq/refseq_protein.00
>    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 36,805
> res
> /db/ncbiblast/refseq/refseq_protein.01
>    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 33,403
> res
> /db/ncbiblast/refseq/refseq_protein.02
>    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 15,830
> res
>
> I am still confuse that how i can get the release number. I know refseq 39
> was released on Jan 30, 2010 but i don't know how to confirm this. I also
> tried look refseq release file but was not able to get any thing.
>
> I would really appreciate if anyone can help me out with this.
>
> Thanks
> Shalu
>
> On Thu, Feb 4, 2010 at 6:39 PM, Smithies, Russell
> <Russell.Smithies at agresearch.co.nz<mailto:Russell.Smithies at agresearch.co.n
> z>> wrote:
> If you have access to the blast database, use fastacmd -I -d databasename
> Otherwise, it's usually at the bottom of your blast result.
>
> --Russell
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-
> bounces at lists.open-bio.org> [mailto:bioperl-l-<mailto:bioperl-l->
> > bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>] On Behalf
> Of shalu sharma
> > Sent: Friday, 5 February 2010 11:02 a.m.
> > To: bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>
> > Subject: [Bioperl-l] Refseq Version
> >
> > Hi All,
> >       This is not a bioperl query.
> > Is there any way to check refseq version (release). Actually i am using
> > some
> > server to blast my sequences (blastall) against refseq. Is there any way
> i
> > can get the version information on the refseq database (from the blast
> > file
> > or directly from the database)?
> >
> > Thanks
> > Shalu
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org<mailto:Bioperl-l at lists.open-bio.org>
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> =======================================================================
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> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
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> =======================================================================
>
>
> _______________________________________________
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> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From Russell.Smithies at agresearch.co.nz  Sun Feb  7 16:05:17 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 8 Feb 2010 10:05:17 +1300
Subject: [Bioperl-l] Refseq Version
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32C61BED78C@exchsth.agresearch.co.nz>
References: <465b5a661002041401u3b8ac5fdp483f7032ce35139b@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED520@exchsth.agresearch.co.nz>
	<465b5a661002050655u34ff94acwdf8fe72512dec4b3@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED76C@exchsth.agresearch.co.nz>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED78C@exchsth.agresearch.co.nz>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61BED795@exchsth.agresearch.co.nz>

AAArrrgg, what is it with Outlook this morning!!!
Formatting kaput again but I'm sure you can work it out from there!

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Smithies, Russell
> Sent: Monday, 8 February 2010 9:59 a.m.
> To: 'shalu sharma'
> Cc: 'bioperl-l at lists.open-bio.org'
> Subject: Re: [Bioperl-l] Refseq Version
>
> I should have known it would break the formatting :-(
>
> Try this:
>
> Release 1:June 30, 2003;Release Size: 4672871949 bases, 263588685 amino
> acids, 1061675 records
> Release 2:October 21, 2003;Release Size: 2124 organisms, 7745398573
> nucleotide bases, 286957682 amino acids, 1097404 records
> Release 3:January 13, 2004;Release Size: 2218 organisms, 7992741222
> nucleotide bases, 294647847 amino acids, 1101244 records
> Release 4:March 24, 2004;Release Size: 2358 organisms, 8175128887
> nucleotide bases, 318253841 amino acids, 1193457 records
> Release 5:May 2 , 2004;Release Size: 2395 organisms, 8325515623 nucleotide
> bases, 337229387 amino acids, 1255613 records
> Release 6:July 5, 2004;Release Size: 2467 organisms, 8696371716 nucleotide
> bases, 365446682 amino acids, 1367206 records
> Release 7:September 12, 2004;Release Size: 2558 organisms, 21072808460
> nucleotide bases, 405233619 amino acids, 1579579 records
> Release 8:October 31, 2004;Release Size: 2645 organisms, 26814386658
> nucleotide bases, 430300369 amino acids, 1709723 records
> Release 9:January 9, 2005;Release Size:  2780 organisms, 36786975473
> nucleotide bases, 470534907 amino acids, 1843944 records
> Release 10:March 6, 2005;Release Size:2827 organisms, 36893741150
> nucleotide bases, 482862858 amino acids, 1893478 records
> Release 11:May 8, 2005;Release Size:2928 organisms, 39731702362 nucleotide
> bases, 507980644 amino acids, 2477893 records
> Release 12:July 10, 2005;Release Size:2969 organisms, 43043256058
> nucleotide bases, 608493108 amino acids, 2869675 records
> Release 13:September 11, 2005;Release Size:3060 organisms, 44727484853
> nucleotide bases, 686768902 amino acids, 3400773 records
> Release 14:November 20, 2005;Release Size:3198 organisms, 47364955367
> nucleotide bases, 763761075 amino acids, 3272776 records
> Release 15:January 1, 2006;Release Size:3244 organisms, 52645441913
> nucleotide bases, 810009733 amino acids, 3436263 records
> Release 16:March 11, 2006;Release Size:3397 organisms, 56175443059
> nucleotide bases, 887509001 amino acids, 3715260 records
> Release 17:May 1, 2006;Release Size:3497 organisms, 62130037371 nucleotide
> bases, 927587669 amino acids, 3999859 records
> Release 18:July 11, 2006;Release Size:3695 organisms, 70474041999
> nucleotide bases, 974374765 amino acids, 4186692 records
> Release 19:September 10, 2006;Release Size: 3774 organisms, 70694879544
> nucleotide bases, 1012985077 amino acids, 4311543 records
> Release 20:November 5, 2006;Release Size:3919 organisms, 72679681505
> nucleotide bases, 1061797276 amino acids, 4567569 records
> Release 21:January 6, 2007;Release Size:4079 organisms, 73864990566
> nucleotide bases, 1144795927 amino acids, 4742335 records
> Release 22:March 5, 2007;Release Size:4187 organisms, 82441128546
> nucleotide bases, 1215085694 amino acids, 5207865 records
> Release 23:May 8, 2007;Release Size:4300 organisms, 83148327110 nucleotide
> bases, 1291050995 amino acids, 5503385 records
> Release 24:July 10, 2007;Release Size:4511 organisms, 89856995521
> nucleotide bases, 1365916222 amino acids, 6073814 records
> Release 25:September 11, 2007;Release Size:4646 organisms, 91265840843
> nucleotide bases, 1470475398 amino acids, 6515132 records
> Release 26:November 4, 2007;Release Size:4737 organisms, 99105705485
> nucleotide bases, 1495032507 amino acids, 6698250 records
> Release 27:January 6, 2008;Release Size:4926 organisms, 101059552113
> nucleotide bases, 1556356987 amino acids, 7025715 records
> Release 28:March 9, 2008;Release Size: 5059 organisms, 102051350525
> nucleotide bases, 1770627427 amino acids, 7914560 records
> Release 29:May 4, 2008;Release Size:5168 organisms, 104671101150
> nucleotide bases, 1870214220 amino acids, 8376141 records
> Release 30:July 7, 2008;Release Size:5395 organisms, 105074486709
> nucleotide bases, 1913447691 amino acids, 8572852 records
> Release 31:August 30, 2008;Release Size: 5513 organisms, 109214348591
> nucleotide bases, 2026768719 amino acids, 9145702 records
> Release 32:November 10, 2008;Release Size: 5726 organisms, 111122203221
> nucleotide bases, 2089596746 amino acids, 9501764 records
> Release 33:January 16, 2009;Release Size:7773 organisms, 116001583818
> nucleotide bases, 2204073443 amino acids, 10325282 records
> Release 34:March 6, 2009;Release Size: 8054 organisms, 111792574830
> nucleotide bases, 2299682138 amino acids, 10021870 records
> Release 35:May 4, 2009;Release Size: 8393 organisms, 113210655336
> nucleotide bases, 2565199170 amino acids, 10993891 records
> Release 36:July 2, 2009;Release Size: 8665 organisms, 117013741530
> nucleotide bases, 2756884219 amino acids, 12141825 records
> Release 37:September 3, 2009;Release Size: 9005 organisms, 119151229820
> nucleotide bases, 2965450333 amino acids, 12941750 records
> Release 38:November 7, 2009;Release Size: 9166 organisms, 119196622435
> nucleotide bases, 3115246540 amino acids, 13436447 records
>
>
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Smithies, Russell
> > Sent: Monday, 8 February 2010 9:47 a.m.
> > To: 'shalu sharma'
> > Cc: 'bioperl-l at lists.open-bio.org'
> > Subject: Re: [Bioperl-l] Refseq Version
> >
> > Release 39 was Jan 30 and according to the README releases only come out
> > in odd months (January, March, May, July, September, November)
> > The stats file is here: ftp://ftp.ncbi.nih.gov/refseq/release/release-
> > statistics/RefSeq-release39.01232010.stats.txt
> >
> > The numbers of sequences between the fasta release and the pre-build
> blast
> > databases seem to differ but I guess only NCBI can explain that.
> > I can't see any way of extracting the release number from the pre-build
> > blast databases (apart from the build date) but it might be worth asking
> > NCBI if they'd include the information in future releases.
> >
> >
> > FYI, here's the old release stats.
> > (I wget'ed and grep'ed all the stats files)
> >
> > Release
> >
> > Date
> >
> > Year
> >
> > Organisms
> >
> > Nucleotide Bases
> >
> > Amino Acids
> >
> > Records
> >
> > 1
> >
> > Jun-30
> >
> > 2003
> >
> >             4,672,871,949
> >
> >             263,588,685
> >
> >           1,061,675
> >
> > 2
> >
> > Oct-21
> >
> > 2003
> >
> >         2,124
> >
> >             7,745,398,573
> >
> >             286,957,682
> >
> >           1,097,404
> >
> > 3
> >
> > Jan-13
> >
> > 2004
> >
> >         2,218
> >
> >             7,992,741,222
> >
> >             294,647,847
> >
> >           1,101,244
> >
> > 4
> >
> > Mar-24
> >
> > 2004
> >
> >         2,358
> >
> >             8,175,128,887
> >
> >             318,253,841
> >
> >           1,193,457
> >
> > 5
> >
> > May-02
> >
> > 2004
> >
> >         2,395
> >
> >             8,325,515,623
> >
> >             337,229,387
> >
> >           1,255,613
> >
> > 6
> >
> > Jul-05
> >
> > 2004
> >
> >         2,467
> >
> >             8,696,371,716
> >
> >             365,446,682
> >
> >           1,367,206
> >
> > 7
> >
> > Sep-12
> >
> > 2004
> >
> >         2,558
> >
> >           21,072,808,460
> >
> >             405,233,619
> >
> >           1,579,579
> >
> > 8
> >
> > Oct-31
> >
> > 2004
> >
> >         2,645
> >
> >           26,814,386,658
> >
> >             430,300,369
> >
> >           1,709,723
> >
> > 9
> >
> > Jan-09
> >
> > 2005
> >
> >         2,780
> >
> >           36,786,975,473
> >
> >             470,534,907
> >
> >           1,843,944
> >
> > 10
> >
> > Mar-06
> >
> > 2005
> >
> >         2,827
> >
> >           36,893,741,150
> >
> >             482,862,858
> >
> >           1,893,478
> >
> > 11
> >
> > May-08
> >
> > 2005
> >
> >         2,928
> >
> >           39,731,702,362
> >
> >             507,980,644
> >
> >           2,477,893
> >
> > 12
> >
> > Jul-10
> >
> > 2005
> >
> >         2,969
> >
> >           43,043,256,058
> >
> >             608,493,108
> >
> >           2,869,675
> >
> > 13
> >
> > Sep-11
> >
> > 2005
> >
> >         3,060
> >
> >           44,727,484,853
> >
> >             686,768,902
> >
> >           3,400,773
> >
> > 14
> >
> > Nov-20
> >
> > 2005
> >
> >         3,198
> >
> >           47,364,955,367
> >
> >             763,761,075
> >
> >           3,272,776
> >
> > 15
> >
> > Jan-01
> >
> > 2006
> >
> >         3,244
> >
> >           52,645,441,913
> >
> >             810,009,733
> >
> >           3,436,263
> >
> > 16
> >
> > Mar-11
> >
> > 2006
> >
> >         3,397
> >
> >           56,175,443,059
> >
> >             887,509,001
> >
> >           3,715,260
> >
> > 17
> >
> > May-01
> >
> > 2006
> >
> >         3,497
> >
> >           62,130,037,371
> >
> >             927,587,669
> >
> >           3,999,859
> >
> > 18
> >
> > Jul-11
> >
> > 2006
> >
> >         3,695
> >
> >           70,474,041,999
> >
> >             974,374,765
> >
> >           4,186,692
> >
> > 19
> >
> > Sep-10
> >
> > 2006
> >
> >         3,774
> >
> >           70,694,879,544
> >
> >          1,012,985,077
> >
> >           4,311,543
> >
> > 20
> >
> > Nov-05
> >
> > 2006
> >
> >         3,919
> >
> >           72,679,681,505
> >
> >          1,061,797,276
> >
> >           4,567,569
> >
> > 21
> >
> > Jan-06
> >
> > 2007
> >
> >         4,079
> >
> >           73,864,990,566
> >
> >          1,144,795,927
> >
> >           4,742,335
> >
> > 22
> >
> > Mar-05
> >
> > 2007
> >
> >         4,187
> >
> >           82,441,128,546
> >
> >          1,215,085,694
> >
> >           5,207,865
> >
> > 23
> >
> > May-08
> >
> > 2007
> >
> >         4,300
> >
> >           83,148,327,110
> >
> >          1,291,050,995
> >
> >           5,503,385
> >
> > 24
> >
> > Jul-10
> >
> > 2007
> >
> >         4,511
> >
> >           89,856,995,521
> >
> >          1,365,916,222
> >
> >           6,073,814
> >
> > 25
> >
> > Sep-11
> >
> > 2007
> >
> >         4,646
> >
> >           91,265,840,843
> >
> >          1,470,475,398
> >
> >           6,515,132
> >
> > 26
> >
> > Nov-04
> >
> > 2007
> >
> >         4,737
> >
> >           99,105,705,485
> >
> >          1,495,032,507
> >
> >           6,698,250
> >
> > 27
> >
> > Jan-06
> >
> > 2008
> >
> >         4,926
> >
> >          101,059,552,113
> >
> >          1,556,356,987
> >
> >           7,025,715
> >
> > 28
> >
> > Mar-09
> >
> > 2008
> >
> >         5,059
> >
> >          102,051,350,525
> >
> >          1,770,627,427
> >
> >           7,914,560
> >
> > 29
> >
> > May-04
> >
> > 2008
> >
> >         5,168
> >
> >          104,671,101,150
> >
> >          1,870,214,220
> >
> >           8,376,141
> >
> > 30
> >
> > Jul-07
> >
> > 2008
> >
> >         5,395
> >
> >          105,074,486,709
> >
> >          1,913,447,691
> >
> >           8,572,852
> >
> > 31
> >
> > Aug-30
> >
> > 2008
> >
> >         5,513
> >
> >          109,214,348,591
> >
> >          2,026,768,719
> >
> >           9,145,702
> >
> > 32
> >
> > Nov-10
> >
> > 2008
> >
> >         5,726
> >
> >          111,122,203,221
> >
> >          2,089,596,746
> >
> >           9,501,764
> >
> > 33
> >
> > Jan-16
> >
> > 2009
> >
> >         7,773
> >
> >          116,001,583,818
> >
> >          2,204,073,443
> >
> >         10,325,282
> >
> > 34
> >
> > Mar-06
> >
> > 2009
> >
> >         8,054
> >
> >          111,792,574,830
> >
> >          2,299,682,138
> >
> >         10,021,870
> >
> > 35
> >
> > May-04
> >
> > 2009
> >
> >         8,393
> >
> >          113,210,655,336
> >
> >          2,565,199,170
> >
> >         10,993,891
> >
> > 36
> >
> > Jul-02
> >
> > 2009
> >
> >         8,665
> >
> >          117,013,741,530
> >
> >          2,756,884,219
> >
> >         12,141,825
> >
> > 37
> >
> > Sep-03
> >
> > 2009
> >
> >         9,005
> >
> >          119,151,229,820
> >
> >          2,965,450,333
> >
> >         12,941,750
> >
> > 38
> >
> > Nov-07
> >
> > 2009
> >
> >         9,166
> >
> >          119,196,622,435
> >
> >          3,115,246,540
> >
> >         13,436,447
> >
> >
> >
> > --Russell
> >
> >
> > From: shalu sharma [mailto:sharmashalu.bio at gmail.com]
> > Sent: Saturday, 6 February 2010 3:56 a.m.
> > To: Smithies, Russell
> > Cc: bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] Refseq Version
> >
> > Hi Russell,
> >                Thanks for your response.
> > I am getting the number of sequence in the database but not the release
> > number (like 38, 39).
> > This is what i did:
> >
> > $ fastacmd -I -d /db/ncbiblast/refseq/refseq_protein
> > Database: NCBI Protein Reference Sequences
> >            7,585,993 sequences; 2,644,770,521 total letters
> >
> > File names:
> > /db/ncbiblast/refseq/refseq_protein.00
> >    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 36,805
> > res
> > /db/ncbiblast/refseq/refseq_protein.01
> >    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 33,403
> > res
> > /db/ncbiblast/refseq/refseq_protein.02
> >    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 15,830
> > res
> >
> > I am still confuse that how i can get the release number. I know refseq
> 39
> > was released on Jan 30, 2010 but i don't know how to confirm this. I
> also
> > tried look refseq release file but was not able to get any thing.
> >
> > I would really appreciate if anyone can help me out with this.
> >
> > Thanks
> > Shalu
> >
> > On Thu, Feb 4, 2010 at 6:39 PM, Smithies, Russell
> >
> <Russell.Smithies at agresearch.co.nz<mailto:Russell.Smithies at agresearch.co.n
> > z>> wrote:
> > If you have access to the blast database, use fastacmd -I -d
> databasename
> > Otherwise, it's usually at the bottom of your blast result.
> >
> > --Russell
> >
> > > -----Original Message-----
> > > From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-
> > bounces at lists.open-bio.org> [mailto:bioperl-l-<mailto:bioperl-l->
> > > bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>] On
> Behalf
> > Of shalu sharma
> > > Sent: Friday, 5 February 2010 11:02 a.m.
> > > To: bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>
> > > Subject: [Bioperl-l] Refseq Version
> > >
> > > Hi All,
> > >       This is not a bioperl query.
> > > Is there any way to check refseq version (release). Actually i am
> using
> > > some
> > > server to blast my sequences (blastall) against refseq. Is there any
> way
> > i
> > > can get the version information on the refseq database (from the blast
> > > file
> > > or directly from the database)?
> > >
> > > Thanks
> > > Shalu
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org<mailto:Bioperl-l at lists.open-bio.org>
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > =======================================================================
> > Attention: The information contained in this message and/or attachments
> > from AgResearch Limited is intended only for the persons or entities
> > to which it is addressed and may contain confidential and/or privileged
> > material. Any review, retransmission, dissemination or other use of, or
> > taking of any action in reliance upon, this information by persons or
> > entities other than the intended recipients is prohibited by AgResearch
> > Limited. If you have received this message in error, please notify the
> > sender immediately.
> > =======================================================================
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From Russell.Smithies at agresearch.co.nz  Sun Feb  7 16:09:59 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 8 Feb 2010 10:09:59 +1300
Subject: [Bioperl-l] Bio::Graphics inside PHP
In-Reply-To: <4B6C58B5.3080304@uab.cat>
References: <4B6C58B5.3080304@uab.cat>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61BED7A0@exchsth.agresearch.co.nz>

We looked at this a year or so, you can base64 encode an image and use that in the img src tag but only a few browsers support it. Easiest way is write the image as a png (with a unique name) to a temp dir.

--Russell 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Miquel Ramia
> Sent: Saturday, 6 February 2010 6:43 a.m.
> To: BioPerl List
> Subject: [Bioperl-l] Bio::Graphics inside PHP
> 
> Hi,
> 
> I'm working in a database with a web interface developed in php. I'm
> displaying Bio::Graphic images inside an IFrame, but doesn't look very
> well.
> 
> Anybody knows if it's possible to include a Bio::Graphics image directly
> in a php page?
> 
> Thank you
> 
> Miquel R?mia
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From sdavis2 at mail.nih.gov  Sun Feb  7 18:00:34 2010
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Sun, 7 Feb 2010 18:00:34 -0500
Subject: [Bioperl-l] Bio::Graphics inside PHP
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32C61BED7A0@exchsth.agresearch.co.nz>
References: <4B6C58B5.3080304@uab.cat>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED7A0@exchsth.agresearch.co.nz>
Message-ID: <264855a01002071500r6c4662cbq7814a78b22b416b2@mail.gmail.com>

On Sun, Feb 7, 2010 at 4:09 PM, Smithies, Russell
<Russell.Smithies at agresearch.co.nz> wrote:
> We looked at this a year or so, you can base64 encode an image and use that in the img src tag but only a few browsers support it. Easiest way is write the image as a png (with a unique name) to a temp dir.
>

You could also have a separate URL that returns the image and then
embed that URL in the generated page, thus avoiding the temp file.

Sean

>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Miquel Ramia
>> Sent: Saturday, 6 February 2010 6:43 a.m.
>> To: BioPerl List
>> Subject: [Bioperl-l] Bio::Graphics inside PHP
>>
>> Hi,
>>
>> I'm working in a database with a web interface developed in php. I'm
>> displaying Bio::Graphic images inside an IFrame, but doesn't look very
>> well.
>>
>> Anybody knows if it's possible to include a Bio::Graphics image directly
>> in a php page?
>>
>> Thank you
>>
>> Miquel R?mia
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From jessica.sun at gmail.com  Sun Feb  7 21:53:56 2010
From: jessica.sun at gmail.com (Jessica Sun)
Date: Sun, 7 Feb 2010 21:53:56 -0500
Subject: [Bioperl-l] questions
Message-ID: <9adc0e9b1002071853v2fd4bbe8gb34a6228d346a948@mail.gmail.com>

Does any one knows how to add locations(CDS, Joins(600,140;...) to the new
sequence object as feature,'
or if anyone knows how to keep the feature of truncated sequences object.

thx

-- 
Jessica Jingping Sun

From roy.chaudhuri at gmail.com  Mon Feb  8 06:09:29 2010
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Mon, 08 Feb 2010 11:09:29 +0000
Subject: [Bioperl-l] questions
In-Reply-To: <9adc0e9b1002071853v2fd4bbe8gb34a6228d346a948@mail.gmail.com>
References: <9adc0e9b1002071853v2fd4bbe8gb34a6228d346a948@mail.gmail.com>
Message-ID: <4B6FF0E9.3040704@gmail.com>

Hi Jessica,

> Does any one knows how to add locations(CDS, Joins(600,140;...) to the new
> sequence object as feature,'

use Bio::SeqIO;
use Bio::Seq;
use Bio::Location::Split;
use Bio::Location::Simple;
use Bio::SeqFeature::Generic;
my $seq=Bio::Seq->new(-seq=>'ACTGATCGATGCATGATGTAGATCGATAGCTGCTA');
my $loc=Bio::Location::Split->new;
$loc->add_sub_Location(Bio::Location::Simple->new(-start=>4, -end=>6, 
-strand=>1);
$loc->add_sub_Location(Bio::Location::Simple->new(-start=>10, -end=>12, 
-strand=>1);
my $feat=Bio::SeqFeature::Generic->new(-primary_tag=>'misc_feat', 
-location=>$loc);
$seq->add_SeqFeature($feat);
my $out=Bio::SeqIO->new(-format=>'genbank';
$out->write_seq($seq);

> or if anyone knows how to keep the feature of truncated sequences object.

Look at the trunc_with_features method in Bio::SeqUtils:

use Bio::SeqUtils;
my $trunc=Bio::SeqUtils->trunc_with_features($seq, 2, 12);
$out->write_seq($trunc);


Hope this helps.
Roy.

From maj at fortinbras.us  Mon Feb  8 09:38:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 8 Feb 2010 09:38:25 -0500
Subject: [Bioperl-l] server maintenace occurring
Message-ID: <8F69A20965E64983887DE6028356911A@NewLife>

Hi All, 
Chris Dag informs us that necessary server changes are taking place 
over the next couple of days. There could be temporary outages
at the wiki and codebase. Thanks for your patience.
MAJ

From bluecurio at gmail.com  Mon Feb  8 11:20:43 2010
From: bluecurio at gmail.com (Daniel Renfro)
Date: Mon, 8 Feb 2010 10:20:43 -0600
Subject: [Bioperl-l] Bio::Graphics inside PHP
Message-ID: <25c0f63d1002080820l60e9f9d2p837b9afd8bb1f90d@mail.gmail.com>

I've been trying different ways to do this same thing. At EcoliWiki.net we
use GBrowse to show all the strains of Ecoli and assoc phage, plasmids, etc.
so this is definitely something I think many other model-organism databases
could use.

The final solution was to construct a link to gbrowse_img with all the
necessary variables coming in from $_REQUEST and throw it in the src=""
attribute of the <img> tag. This works pretty good for what we're doing.
Good luck.

-Daniel Renfro

Hu Lab Research Associate
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4055

From lincoln.stein at gmail.com  Mon Feb  8 11:33:18 2010
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Mon, 8 Feb 2010 11:33:18 -0500
Subject: [Bioperl-l] Bio::Graphics inside PHP
In-Reply-To: <25c0f63d1002080820l60e9f9d2p837b9afd8bb1f90d@mail.gmail.com>
References: <25c0f63d1002080820l60e9f9d2p837b9afd8bb1f90d@mail.gmail.com>
Message-ID: <6dce9a0b1002080833o3ad29300kfcee727ed499e74e@mail.gmail.com>

There's an embeddable version of gbrowse_img that generates the imagemap so
it is clickable. If you use an <iframe> the formatting usually works out
pretty well.

Lincoln

On Mon, Feb 8, 2010 at 11:20 AM, Daniel Renfro <bluecurio at gmail.com> wrote:

> I've been trying different ways to do this same thing. At EcoliWiki.net we
> use GBrowse to show all the strains of Ecoli and assoc phage, plasmids,
> etc.
> so this is definitely something I think many other model-organism databases
> could use.
>
> The final solution was to construct a link to gbrowse_img with all the
> necessary variables coming in from $_REQUEST and throw it in the src=""
> attribute of the <img> tag. This works pretty good for what we're doing.
> Good luck.
>
> -Daniel Renfro
>
> Hu Lab Research Associate
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4055
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>

From sharmashalu.bio at gmail.com  Mon Feb  8 11:37:54 2010
From: sharmashalu.bio at gmail.com (shalu sharma)
Date: Mon, 8 Feb 2010 11:37:54 -0500
Subject: [Bioperl-l] Refseq Version
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32C61BED795@exchsth.agresearch.co.nz>
References: <465b5a661002041401u3b8ac5fdp483f7032ce35139b@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED520@exchsth.agresearch.co.nz>
	<465b5a661002050655u34ff94acwdf8fe72512dec4b3@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED76C@exchsth.agresearch.co.nz>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED78C@exchsth.agresearch.co.nz>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED795@exchsth.agresearch.co.nz>
Message-ID: <465b5a661002080837v76b0215ctc7039c516bb0c82d@mail.gmail.com>

Thanks a lot Russell.
But i am still confused. Actually i asked the server admin and he said that
this is Refseq's latest vesrion (the one i am using).
But the number of sequences which i am getting from blast report are not
matching with the refseq 38 release ( or i don't know which numbers to
match).

Like from blast report i am getting :
$ fastacmd -I -d /db/ncbiblast/refseq/refseq_
protein
Database: NCBI Protein Reference Sequences
           7,585,993 sequences; 2,644,770,521 total letters

And when i am looking at refseq release notes , i don't understand that
which numbers to match with because i don't see these numbers in release
notes.

Thanks a lot, I really appreciate your help.

Thanks
Shalu




On Sun, Feb 7, 2010 at 4:05 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:

> AAArrrgg, what is it with Outlook this morning!!!
> Formatting kaput again but I'm sure you can work it out from there!
>
> --Russell
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Smithies, Russell
> > Sent: Monday, 8 February 2010 9:59 a.m.
> > To: 'shalu sharma'
> > Cc: 'bioperl-l at lists.open-bio.org'
> > Subject: Re: [Bioperl-l] Refseq Version
> >
> > I should have known it would break the formatting :-(
> >
> > Try this:
> >
> > Release 1:June 30, 2003;Release Size: 4672871949 bases, 263588685 amino
> > acids, 1061675 records
> > Release 2:October 21, 2003;Release Size: 2124 organisms, 7745398573
> > nucleotide bases, 286957682 amino acids, 1097404 records
> > Release 3:January 13, 2004;Release Size: 2218 organisms, 7992741222
> > nucleotide bases, 294647847 amino acids, 1101244 records
> > Release 4:March 24, 2004;Release Size: 2358 organisms, 8175128887
> > nucleotide bases, 318253841 amino acids, 1193457 records
> > Release 5:May 2 , 2004;Release Size: 2395 organisms, 8325515623
> nucleotide
> > bases, 337229387 amino acids, 1255613 records
> > Release 6:July 5, 2004;Release Size: 2467 organisms, 8696371716
> nucleotide
> > bases, 365446682 amino acids, 1367206 records
> > Release 7:September 12, 2004;Release Size: 2558 organisms, 21072808460
> > nucleotide bases, 405233619 amino acids, 1579579 records
> > Release 8:October 31, 2004;Release Size: 2645 organisms, 26814386658
> > nucleotide bases, 430300369 amino acids, 1709723 records
> > Release 9:January 9, 2005;Release Size:  2780 organisms, 36786975473
> > nucleotide bases, 470534907 amino acids, 1843944 records
> > Release 10:March 6, 2005;Release Size:2827 organisms, 36893741150
> > nucleotide bases, 482862858 amino acids, 1893478 records
> > Release 11:May 8, 2005;Release Size:2928 organisms, 39731702362
> nucleotide
> > bases, 507980644 amino acids, 2477893 records
> > Release 12:July 10, 2005;Release Size:2969 organisms, 43043256058
> > nucleotide bases, 608493108 amino acids, 2869675 records
> > Release 13:September 11, 2005;Release Size:3060 organisms, 44727484853
> > nucleotide bases, 686768902 amino acids, 3400773 records
> > Release 14:November 20, 2005;Release Size:3198 organisms, 47364955367
> > nucleotide bases, 763761075 amino acids, 3272776 records
> > Release 15:January 1, 2006;Release Size:3244 organisms, 52645441913
> > nucleotide bases, 810009733 amino acids, 3436263 records
> > Release 16:March 11, 2006;Release Size:3397 organisms, 56175443059
> > nucleotide bases, 887509001 amino acids, 3715260 records
> > Release 17:May 1, 2006;Release Size:3497 organisms, 62130037371
> nucleotide
> > bases, 927587669 amino acids, 3999859 records
> > Release 18:July 11, 2006;Release Size:3695 organisms, 70474041999
> > nucleotide bases, 974374765 amino acids, 4186692 records
> > Release 19:September 10, 2006;Release Size: 3774 organisms, 70694879544
> > nucleotide bases, 1012985077 amino acids, 4311543 records
> > Release 20:November 5, 2006;Release Size:3919 organisms, 72679681505
> > nucleotide bases, 1061797276 amino acids, 4567569 records
> > Release 21:January 6, 2007;Release Size:4079 organisms, 73864990566
> > nucleotide bases, 1144795927 amino acids, 4742335 records
> > Release 22:March 5, 2007;Release Size:4187 organisms, 82441128546
> > nucleotide bases, 1215085694 amino acids, 5207865 records
> > Release 23:May 8, 2007;Release Size:4300 organisms, 83148327110
> nucleotide
> > bases, 1291050995 amino acids, 5503385 records
> > Release 24:July 10, 2007;Release Size:4511 organisms, 89856995521
> > nucleotide bases, 1365916222 amino acids, 6073814 records
> > Release 25:September 11, 2007;Release Size:4646 organisms, 91265840843
> > nucleotide bases, 1470475398 amino acids, 6515132 records
> > Release 26:November 4, 2007;Release Size:4737 organisms, 99105705485
> > nucleotide bases, 1495032507 amino acids, 6698250 records
> > Release 27:January 6, 2008;Release Size:4926 organisms, 101059552113
> > nucleotide bases, 1556356987 amino acids, 7025715 records
> > Release 28:March 9, 2008;Release Size: 5059 organisms, 102051350525
> > nucleotide bases, 1770627427 amino acids, 7914560 records
> > Release 29:May 4, 2008;Release Size:5168 organisms, 104671101150
> > nucleotide bases, 1870214220 amino acids, 8376141 records
> > Release 30:July 7, 2008;Release Size:5395 organisms, 105074486709
> > nucleotide bases, 1913447691 amino acids, 8572852 records
> > Release 31:August 30, 2008;Release Size: 5513 organisms, 109214348591
> > nucleotide bases, 2026768719 amino acids, 9145702 records
> > Release 32:November 10, 2008;Release Size: 5726 organisms, 111122203221
> > nucleotide bases, 2089596746 amino acids, 9501764 records
> > Release 33:January 16, 2009;Release Size:7773 organisms, 116001583818
> > nucleotide bases, 2204073443 amino acids, 10325282 records
> > Release 34:March 6, 2009;Release Size: 8054 organisms, 111792574830
> > nucleotide bases, 2299682138 amino acids, 10021870 records
> > Release 35:May 4, 2009;Release Size: 8393 organisms, 113210655336
> > nucleotide bases, 2565199170 amino acids, 10993891 records
> > Release 36:July 2, 2009;Release Size: 8665 organisms, 117013741530
> > nucleotide bases, 2756884219 amino acids, 12141825 records
> > Release 37:September 3, 2009;Release Size: 9005 organisms, 119151229820
> > nucleotide bases, 2965450333 amino acids, 12941750 records
> > Release 38:November 7, 2009;Release Size: 9166 organisms, 119196622435
> > nucleotide bases, 3115246540 amino acids, 13436447 records
> >
> >
> >
> > > -----Original Message-----
> > > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > > bounces at lists.open-bio.org] On Behalf Of Smithies, Russell
> > > Sent: Monday, 8 February 2010 9:47 a.m.
> > > To: 'shalu sharma'
> > > Cc: 'bioperl-l at lists.open-bio.org'
> > > Subject: Re: [Bioperl-l] Refseq Version
> > >
> > > Release 39 was Jan 30 and according to the README releases only come
> out
> > > in odd months (January, March, May, July, September, November)
> > > The stats file is here: ftp://ftp.ncbi.nih.gov/refseq/release/release-
> > > statistics/RefSeq-release39.01232010.stats.txt
> > >
> > > The numbers of sequences between the fasta release and the pre-build
> > blast
> > > databases seem to differ but I guess only NCBI can explain that.
> > > I can't see any way of extracting the release number from the pre-build
> > > blast databases (apart from the build date) but it might be worth
> asking
> > > NCBI if they'd include the information in future releases.
> > >
> > >
> > > FYI, here's the old release stats.
> > > (I wget'ed and grep'ed all the stats files)
> > >
> > > Release
> > >
> > > Date
> > >
> > > Year
> > >
> > > Organisms
> > >
> > > Nucleotide Bases
> > >
> > > Amino Acids
> > >
> > > Records
> > >
> > > 1
> > >
> > > Jun-30
> > >
> > > 2003
> > >
> > >             4,672,871,949
> > >
> > >             263,588,685
> > >
> > >           1,061,675
> > >
> > > 2
> > >
> > > Oct-21
> > >
> > > 2003
> > >
> > >         2,124
> > >
> > >             7,745,398,573
> > >
> > >             286,957,682
> > >
> > >           1,097,404
> > >
> > > 3
> > >
> > > Jan-13
> > >
> > > 2004
> > >
> > >         2,218
> > >
> > >             7,992,741,222
> > >
> > >             294,647,847
> > >
> > >           1,101,244
> > >
> > > 4
> > >
> > > Mar-24
> > >
> > > 2004
> > >
> > >         2,358
> > >
> > >             8,175,128,887
> > >
> > >             318,253,841
> > >
> > >           1,193,457
> > >
> > > 5
> > >
> > > May-02
> > >
> > > 2004
> > >
> > >         2,395
> > >
> > >             8,325,515,623
> > >
> > >             337,229,387
> > >
> > >           1,255,613
> > >
> > > 6
> > >
> > > Jul-05
> > >
> > > 2004
> > >
> > >         2,467
> > >
> > >             8,696,371,716
> > >
> > >             365,446,682
> > >
> > >           1,367,206
> > >
> > > 7
> > >
> > > Sep-12
> > >
> > > 2004
> > >
> > >         2,558
> > >
> > >           21,072,808,460
> > >
> > >             405,233,619
> > >
> > >           1,579,579
> > >
> > > 8
> > >
> > > Oct-31
> > >
> > > 2004
> > >
> > >         2,645
> > >
> > >           26,814,386,658
> > >
> > >             430,300,369
> > >
> > >           1,709,723
> > >
> > > 9
> > >
> > > Jan-09
> > >
> > > 2005
> > >
> > >         2,780
> > >
> > >           36,786,975,473
> > >
> > >             470,534,907
> > >
> > >           1,843,944
> > >
> > > 10
> > >
> > > Mar-06
> > >
> > > 2005
> > >
> > >         2,827
> > >
> > >           36,893,741,150
> > >
> > >             482,862,858
> > >
> > >           1,893,478
> > >
> > > 11
> > >
> > > May-08
> > >
> > > 2005
> > >
> > >         2,928
> > >
> > >           39,731,702,362
> > >
> > >             507,980,644
> > >
> > >           2,477,893
> > >
> > > 12
> > >
> > > Jul-10
> > >
> > > 2005
> > >
> > >         2,969
> > >
> > >           43,043,256,058
> > >
> > >             608,493,108
> > >
> > >           2,869,675
> > >
> > > 13
> > >
> > > Sep-11
> > >
> > > 2005
> > >
> > >         3,060
> > >
> > >           44,727,484,853
> > >
> > >             686,768,902
> > >
> > >           3,400,773
> > >
> > > 14
> > >
> > > Nov-20
> > >
> > > 2005
> > >
> > >         3,198
> > >
> > >           47,364,955,367
> > >
> > >             763,761,075
> > >
> > >           3,272,776
> > >
> > > 15
> > >
> > > Jan-01
> > >
> > > 2006
> > >
> > >         3,244
> > >
> > >           52,645,441,913
> > >
> > >             810,009,733
> > >
> > >           3,436,263
> > >
> > > 16
> > >
> > > Mar-11
> > >
> > > 2006
> > >
> > >         3,397
> > >
> > >           56,175,443,059
> > >
> > >             887,509,001
> > >
> > >           3,715,260
> > >
> > > 17
> > >
> > > May-01
> > >
> > > 2006
> > >
> > >         3,497
> > >
> > >           62,130,037,371
> > >
> > >             927,587,669
> > >
> > >           3,999,859
> > >
> > > 18
> > >
> > > Jul-11
> > >
> > > 2006
> > >
> > >         3,695
> > >
> > >           70,474,041,999
> > >
> > >             974,374,765
> > >
> > >           4,186,692
> > >
> > > 19
> > >
> > > Sep-10
> > >
> > > 2006
> > >
> > >         3,774
> > >
> > >           70,694,879,544
> > >
> > >          1,012,985,077
> > >
> > >           4,311,543
> > >
> > > 20
> > >
> > > Nov-05
> > >
> > > 2006
> > >
> > >         3,919
> > >
> > >           72,679,681,505
> > >
> > >          1,061,797,276
> > >
> > >           4,567,569
> > >
> > > 21
> > >
> > > Jan-06
> > >
> > > 2007
> > >
> > >         4,079
> > >
> > >           73,864,990,566
> > >
> > >          1,144,795,927
> > >
> > >           4,742,335
> > >
> > > 22
> > >
> > > Mar-05
> > >
> > > 2007
> > >
> > >         4,187
> > >
> > >           82,441,128,546
> > >
> > >          1,215,085,694
> > >
> > >           5,207,865
> > >
> > > 23
> > >
> > > May-08
> > >
> > > 2007
> > >
> > >         4,300
> > >
> > >           83,148,327,110
> > >
> > >          1,291,050,995
> > >
> > >           5,503,385
> > >
> > > 24
> > >
> > > Jul-10
> > >
> > > 2007
> > >
> > >         4,511
> > >
> > >           89,856,995,521
> > >
> > >          1,365,916,222
> > >
> > >           6,073,814
> > >
> > > 25
> > >
> > > Sep-11
> > >
> > > 2007
> > >
> > >         4,646
> > >
> > >           91,265,840,843
> > >
> > >          1,470,475,398
> > >
> > >           6,515,132
> > >
> > > 26
> > >
> > > Nov-04
> > >
> > > 2007
> > >
> > >         4,737
> > >
> > >           99,105,705,485
> > >
> > >          1,495,032,507
> > >
> > >           6,698,250
> > >
> > > 27
> > >
> > > Jan-06
> > >
> > > 2008
> > >
> > >         4,926
> > >
> > >          101,059,552,113
> > >
> > >          1,556,356,987
> > >
> > >           7,025,715
> > >
> > > 28
> > >
> > > Mar-09
> > >
> > > 2008
> > >
> > >         5,059
> > >
> > >          102,051,350,525
> > >
> > >          1,770,627,427
> > >
> > >           7,914,560
> > >
> > > 29
> > >
> > > May-04
> > >
> > > 2008
> > >
> > >         5,168
> > >
> > >          104,671,101,150
> > >
> > >          1,870,214,220
> > >
> > >           8,376,141
> > >
> > > 30
> > >
> > > Jul-07
> > >
> > > 2008
> > >
> > >         5,395
> > >
> > >          105,074,486,709
> > >
> > >          1,913,447,691
> > >
> > >           8,572,852
> > >
> > > 31
> > >
> > > Aug-30
> > >
> > > 2008
> > >
> > >         5,513
> > >
> > >          109,214,348,591
> > >
> > >          2,026,768,719
> > >
> > >           9,145,702
> > >
> > > 32
> > >
> > > Nov-10
> > >
> > > 2008
> > >
> > >         5,726
> > >
> > >          111,122,203,221
> > >
> > >          2,089,596,746
> > >
> > >           9,501,764
> > >
> > > 33
> > >
> > > Jan-16
> > >
> > > 2009
> > >
> > >         7,773
> > >
> > >          116,001,583,818
> > >
> > >          2,204,073,443
> > >
> > >         10,325,282
> > >
> > > 34
> > >
> > > Mar-06
> > >
> > > 2009
> > >
> > >         8,054
> > >
> > >          111,792,574,830
> > >
> > >          2,299,682,138
> > >
> > >         10,021,870
> > >
> > > 35
> > >
> > > May-04
> > >
> > > 2009
> > >
> > >         8,393
> > >
> > >          113,210,655,336
> > >
> > >          2,565,199,170
> > >
> > >         10,993,891
> > >
> > > 36
> > >
> > > Jul-02
> > >
> > > 2009
> > >
> > >         8,665
> > >
> > >          117,013,741,530
> > >
> > >          2,756,884,219
> > >
> > >         12,141,825
> > >
> > > 37
> > >
> > > Sep-03
> > >
> > > 2009
> > >
> > >         9,005
> > >
> > >          119,151,229,820
> > >
> > >          2,965,450,333
> > >
> > >         12,941,750
> > >
> > > 38
> > >
> > > Nov-07
> > >
> > > 2009
> > >
> > >         9,166
> > >
> > >          119,196,622,435
> > >
> > >          3,115,246,540
> > >
> > >         13,436,447
> > >
> > >
> > >
> > > --Russell
> > >
> > >
> > > From: shalu sharma [mailto:sharmashalu.bio at gmail.com]
> > > Sent: Saturday, 6 February 2010 3:56 a.m.
> > > To: Smithies, Russell
> > > Cc: bioperl-l at lists.open-bio.org
> > > Subject: Re: [Bioperl-l] Refseq Version
> > >
> > > Hi Russell,
> > >                Thanks for your response.
> > > I am getting the number of sequence in the database but not the release
> > > number (like 38, 39).
> > > This is what i did:
> > >
> > > $ fastacmd -I -d /db/ncbiblast/refseq/refseq_protein
> > > Database: NCBI Protein Reference Sequences
> > >            7,585,993 sequences; 2,644,770,521 total letters
> > >
> > > File names:
> > > /db/ncbiblast/refseq/refseq_protein.00
> > >    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence:
> 36,805
> > > res
> > > /db/ncbiblast/refseq/refseq_protein.01
> > >    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence:
> 33,403
> > > res
> > > /db/ncbiblast/refseq/refseq_protein.02
> > >    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence:
> 15,830
> > > res
> > >
> > > I am still confuse that how i can get the release number. I know refseq
> > 39
> > > was released on Jan 30, 2010 but i don't know how to confirm this. I
> > also
> > > tried look refseq release file but was not able to get any thing.
> > >
> > > I would really appreciate if anyone can help me out with this.
> > >
> > > Thanks
> > > Shalu
> > >
> > > On Thu, Feb 4, 2010 at 6:39 PM, Smithies, Russell
> > >
> > <Russell.Smithies at agresearch.co.nz<mailto:
> Russell.Smithies at agresearch.co.n
> > > z>> wrote:
> > > If you have access to the blast database, use fastacmd -I -d
> > databasename
> > > Otherwise, it's usually at the bottom of your blast result.
> > >
> > > --Russell
> > >
> > > > -----Original Message-----
> > > > From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-
> > > bounces at lists.open-bio.org> [mailto:bioperl-l-<mailto:bioperl-l->
> > > > bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>] On
> > Behalf
> > > Of shalu sharma
> > > > Sent: Friday, 5 February 2010 11:02 a.m.
> > > > To: bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org
> >
> > > > Subject: [Bioperl-l] Refseq Version
> > > >
> > > > Hi All,
> > > >       This is not a bioperl query.
> > > > Is there any way to check refseq version (release). Actually i am
> > using
> > > > some
> > > > server to blast my sequences (blastall) against refseq. Is there any
> > way
> > > i
> > > > can get the version information on the refseq database (from the
> blast
> > > > file
> > > > or directly from the database)?
> > > >
> > > > Thanks
> > > > Shalu
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l at lists.open-bio.org<mailto:Bioperl-l at lists.open-bio.org>
> > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > > =======================================================================
> > > Attention: The information contained in this message and/or attachments
> > > from AgResearch Limited is intended only for the persons or entities
> > > to which it is addressed and may contain confidential and/or privileged
> > > material. Any review, retransmission, dissemination or other use of, or
> > > taking of any action in reliance upon, this information by persons or
> > > entities other than the intended recipients is prohibited by AgResearch
> > > Limited. If you have received this message in error, please notify the
> > > sender immediately.
> > > =======================================================================
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From MEC at stowers.org  Mon Feb  8 13:11:26 2010
From: MEC at stowers.org (Cook, Malcolm)
Date: Mon, 8 Feb 2010 12:11:26 -0600
Subject: [Bioperl-l] position announcement: Programmer Analyst /
 bioinformatics / next gen DNA sequencing
Message-ID: <BD62CBAC4395B94096109020651BE2EC12E0CA086F@EXCHMB-02.stowers-institute.org>


The Stowers Institute for Medical Research has two openings for Programmer Analysts to:

 * provide operational and data analysis support for Next-Generation DNA Sequencing Informatics processes. 

 * conduct bioinformatics/statistical analysis on a variety of data. 

Please see our postings at http://www.stowers-institute.org/ScientistsSought/ScientistsSought.asp


Malcolm Cook
Stowers Institute for Medical Research -  Bioinformatics
Kansas City, Missouri  USA
 



From scott at scottcain.net  Mon Feb  8 14:41:53 2010
From: scott at scottcain.net (Scott Cain)
Date: Mon, 8 Feb 2010 14:41:53 -0500
Subject: [Bioperl-l] Bio::Graphics inside PHP
In-Reply-To: <6dce9a0b1002080833o3ad29300kfcee727ed499e74e@mail.gmail.com>
References: <25c0f63d1002080820l60e9f9d2p837b9afd8bb1f90d@mail.gmail.com>
	<6dce9a0b1002080833o3ad29300kfcee727ed499e74e@mail.gmail.com>
Message-ID: <4536f7701002081141g251d761bnf4215df0bc82c95f@mail.gmail.com>

Lincoln,

Something I've been thinking about recently is whether it would be
possible to have gbrowse_img generate the image and the image map
separately so that they could be used in something like this (a php
page).  It could just return the image map if something like map=1
were supplied as an argument.  Could that be done?

Scott


On Mon, Feb 8, 2010 at 11:33 AM, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> There's an embeddable version of gbrowse_img that generates the imagemap so
> it is clickable. If you use an <iframe> the formatting usually works out
> pretty well.
>
> Lincoln
>
> On Mon, Feb 8, 2010 at 11:20 AM, Daniel Renfro <bluecurio at gmail.com> wrote:
>
>> I've been trying different ways to do this same thing. At EcoliWiki.net we
>> use GBrowse to show all the strains of Ecoli and assoc phage, plasmids,
>> etc.
>> so this is definitely something I think many other model-organism databases
>> could use.
>>
>> The final solution was to construct a link to gbrowse_img with all the
>> necessary variables coming in from $_REQUEST and throw it in the src=""
>> attribute of the <img> tag. This works pretty good for what we're doing.
>> Good luck.
>>
>> -Daniel Renfro
>>
>> Hu Lab Research Associate
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4055
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

From nml5566 at gmail.com  Mon Feb  8 20:25:59 2010
From: nml5566 at gmail.com (Nathan Liles)
Date: Mon, 08 Feb 2010 19:25:59 -0600
Subject: [Bioperl-l] Sheldon and genbank2gff converter testing
Message-ID: <4B70B9A7.2050603@gmail.com>

Sheldon,

     I have finished patching the converter. Since you are listed as the 
main author, I'm wondering if you'd be interested in taking it for a 
test drive. I can send you a file diff upon request. Also, if anyone 
else is interested, I'd be happy to oblige them.

-Nathan

From sharmashalu.bio at gmail.com  Tue Feb  9 10:55:14 2010
From: sharmashalu.bio at gmail.com (shalu sharma)
Date: Tue, 9 Feb 2010 10:55:14 -0500
Subject: [Bioperl-l] Installing Linux Binary
Message-ID: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>

Hi All,
         I know this is very basic query but i am stuck.
I am trying to install some program on my Mac (it contain Linux binary). I
tried "make" but its not working. I am not sure how i can install it.
Can anyone please guide me that how i can install linux binary on MAC?

I would really appreciate it.

Thanks
Shalu

From scott at scottcain.net  Tue Feb  9 10:59:33 2010
From: scott at scottcain.net (Scott Cain)
Date: Tue, 9 Feb 2010 10:59:33 -0500
Subject: [Bioperl-l] Installing Linux Binary
In-Reply-To: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
References: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
Message-ID: <4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>

Hi Shalu,

This is probably not the right mailing list for solving this problem.
What is the application you are trying to install?  When you say make
isn't working, what do you mean?  What are the error messages?  Have
you googled for hints on how to get it installed on a Mac?

Scott


On Tue, Feb 9, 2010 at 10:55 AM, shalu sharma <sharmashalu.bio at gmail.com> wrote:
> Hi All,
> ? ? ? ? I know this is very basic query but i am stuck.
> I am trying to install some program on my Mac (it contain Linux binary). I
> tried "make" but its not working. I am not sure how i can install it.
> Can anyone please guide me that how i can install linux binary on MAC?
>
> I would really appreciate it.
>
> Thanks
> Shalu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From sharmashalu.bio at gmail.com  Tue Feb  9 11:04:58 2010
From: sharmashalu.bio at gmail.com (shalu sharma)
Date: Tue, 9 Feb 2010 11:04:58 -0500
Subject: [Bioperl-l] Installing Linux Binary
In-Reply-To: <4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>
References: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
	<4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>
Message-ID: <465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>

I am really sorry for this. Actually i tried a lot but i am new to this. I
tried google it alos but couldn't find anything.
When i try to make , its saying " No target specified and no makefile found.

I am trying to install xipe.
http://phage.sdsu.edu/~brodrigu/xipe/

I am really sorry for the trouble.

Thanks
Shalu

On Tue, Feb 9, 2010 at 10:59 AM, Scott Cain <scott at scottcain.net> wrote:

> Hi Shalu,
>
> This is probably not the right mailing list for solving this problem.
> What is the application you are trying to install?  When you say make
> isn't working, what do you mean?  What are the error messages?  Have
> you googled for hints on how to get it installed on a Mac?
>
> Scott
>
>
> On Tue, Feb 9, 2010 at 10:55 AM, shalu sharma <sharmashalu.bio at gmail.com>
> wrote:
> > Hi All,
> >         I know this is very basic query but i am stuck.
> > I am trying to install some program on my Mac (it contain Linux binary).
> I
> > tried "make" but its not working. I am not sure how i can install it.
> > Can anyone please guide me that how i can install linux binary on MAC?
> >
> > I would really appreciate it.
> >
> > Thanks
> > Shalu
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

From Miquel.Ramia at uab.cat  Tue Feb  9 10:14:07 2010
From: Miquel.Ramia at uab.cat (Miquel Ramia)
Date: Tue, 09 Feb 2010 16:14:07 +0100
Subject: [Bioperl-l] Bio::Graphics inside PHP
In-Reply-To: <7E0F3ED7-682E-492B-99D7-45C77041F6F5@sgul.ac.uk>
References: <4B6C58B5.3080304@uab.cat>
	<7E0F3ED7-682E-492B-99D7-45C77041F6F5@sgul.ac.uk>
Message-ID: <4B717BBF.4020904@uab.cat>

Thanks! This solution worked perfectly!

The gbrowse_img option to add image maps seems very interesting, I'll 
try it in a near future.

thanks everybody

Miquel

Adam Witney wrote:
> you could output an <img ..> tag where the source is a perl script that generates the image. eg
>
> <img src="cgi-bin/biographics_script.cgi" />
>
> that perl script would then use Bio::Graphics to generate the image
>
> HTH
>
> adam
>
>
> On 5 Feb 2010, at 17:43, Miquel Ramia wrote:
>
>   
>> Hi,
>>
>> I'm working in a database with a web interface developed in php. I'm displaying Bio::Graphic images inside an IFrame, but doesn't look very well.
>>
>> Anybody knows if it's possible to include a Bio::Graphics image directly in a php page?
>>
>> Thank you
>>
>> Miquel R?mia
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>     
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   


From scott at scottcain.net  Tue Feb  9 12:02:40 2010
From: scott at scottcain.net (Scott Cain)
Date: Tue, 9 Feb 2010 12:02:40 -0500
Subject: [Bioperl-l] Installing Linux Binary
In-Reply-To: <465b5a661002090900h535a7014tb796541a636a6209@mail.gmail.com>
References: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
	<4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>
	<465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>
	<4536f7701002090850p466d6280qaa5f81065981daae@mail.gmail.com>
	<465b5a661002090900h535a7014tb796541a636a6209@mail.gmail.com>
Message-ID: <4536f7701002090902n30c30449pa68866aaf7103826@mail.gmail.com>

Hi Shalu,

I have no clue--it doesn't appear to have any documentation.  The name
having 2.4 after it suggests that you might need a 2.4 kernel, or it
may just be version 2.4.  I suggestion you contact the author.

Scott


On Tue, Feb 9, 2010 at 12:00 PM, shalu sharma <sharmashalu.bio at gmail.com> wrote:
> Thanks for the reply Scott, So i can install it only on Linux machine?
> I am really sorry again but then? also how i can install it (even on Linux
> machine)?
>
> Thanks
> Shalu
>
> On Tue, Feb 9, 2010 at 11:50 AM, Scott Cain <scott at scottcain.net> wrote:
>>
>> OK, I thought maybe you were misspeaking when you wrote it was a linux
>> binary, since you were trying to use make, but that really does appear
>> to be a linux binary, so you can't install it on a Mac.
>>
>> Scott
>>
>>
>> On Tue, Feb 9, 2010 at 11:04 AM, shalu sharma <sharmashalu.bio at gmail.com>
>> wrote:
>> > I am really sorry for this. Actually i tried a lot but i am new to this.
>> > I
>> > tried google it alos but couldn't find anything.
>> > When i try to make , its saying " No target specified and no makefile
>> > found.
>> >
>> > I am trying to install xipe.
>> > http://phage.sdsu.edu/~brodrigu/xipe/
>> >
>> > I am really sorry for the trouble.
>> >
>> > Thanks
>> > Shalu
>> >
>> > On Tue, Feb 9, 2010 at 10:59 AM, Scott Cain <scott at scottcain.net> wrote:
>> >>
>> >> Hi Shalu,
>> >>
>> >> This is probably not the right mailing list for solving this problem.
>> >> What is the application you are trying to install? ?When you say make
>> >> isn't working, what do you mean? ?What are the error messages? ?Have
>> >> you googled for hints on how to get it installed on a Mac?
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Tue, Feb 9, 2010 at 10:55 AM, shalu sharma
>> >> <sharmashalu.bio at gmail.com>
>> >> wrote:
>> >> > Hi All,
>> >> > ? ? ? ? I know this is very basic query but i am stuck.
>> >> > I am trying to install some program on my Mac (it contain Linux
>> >> > binary).
>> >> > I
>> >> > tried "make" but its not working. I am not sure how i can install it.
>> >> > Can anyone please guide me that how i can install linux binary on
>> >> > MAC?
>> >> >
>> >> > I would really appreciate it.
>> >> >
>> >> > Thanks
>> >> > Shalu
>> >> > _______________________________________________
>> >> > Bioperl-l mailing list
>> >> > Bioperl-l at lists.open-bio.org
>> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/) ? ? ? ? ? ? ? ? ? ? 216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/) ? ? ? ? ? ? ? ? ? ? 216-392-3087
>> Ontario Institute for Cancer Research
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From sharmashalu.bio at gmail.com  Tue Feb  9 12:32:48 2010
From: sharmashalu.bio at gmail.com (shalu sharma)
Date: Tue, 9 Feb 2010 12:32:48 -0500
Subject: [Bioperl-l] Installing Linux Binary
In-Reply-To: <4536f7701002090902n30c30449pa68866aaf7103826@mail.gmail.com>
References: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
	<4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>
	<465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>
	<4536f7701002090850p466d6280qaa5f81065981daae@mail.gmail.com>
	<465b5a661002090900h535a7014tb796541a636a6209@mail.gmail.com>
	<4536f7701002090902n30c30449pa68866aaf7103826@mail.gmail.com>
Message-ID: <465b5a661002090932g1e26a6dav98ec2030808aa440@mail.gmail.com>

Thanks a lot. Actually i have mailed the author but not getting any reply,
thats why i mailed in this list.
Just last thing, i know this is a version2.4 i already have version 1.0
installed on my MAC , will this help?

Thanks
Shalu

On Tue, Feb 9, 2010 at 12:02 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Shalu,
>
> I have no clue--it doesn't appear to have any documentation.  The name
> having 2.4 after it suggests that you might need a 2.4 kernel, or it
> may just be version 2.4.  I suggestion you contact the author.
>
> Scott
>
>
> On Tue, Feb 9, 2010 at 12:00 PM, shalu sharma <sharmashalu.bio at gmail.com>
> wrote:
> > Thanks for the reply Scott, So i can install it only on Linux machine?
> > I am really sorry again but then  also how i can install it (even on
> Linux
> > machine)?
> >
> > Thanks
> > Shalu
> >
> > On Tue, Feb 9, 2010 at 11:50 AM, Scott Cain <scott at scottcain.net> wrote:
> >>
> >> OK, I thought maybe you were misspeaking when you wrote it was a linux
> >> binary, since you were trying to use make, but that really does appear
> >> to be a linux binary, so you can't install it on a Mac.
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 9, 2010 at 11:04 AM, shalu sharma <
> sharmashalu.bio at gmail.com>
> >> wrote:
> >> > I am really sorry for this. Actually i tried a lot but i am new to
> this.
> >> > I
> >> > tried google it alos but couldn't find anything.
> >> > When i try to make , its saying " No target specified and no makefile
> >> > found.
> >> >
> >> > I am trying to install xipe.
> >> > http://phage.sdsu.edu/~brodrigu/xipe/<http://phage.sdsu.edu/%7Ebrodrigu/xipe/>
> >> >
> >> > I am really sorry for the trouble.
> >> >
> >> > Thanks
> >> > Shalu
> >> >
> >> > On Tue, Feb 9, 2010 at 10:59 AM, Scott Cain <scott at scottcain.net>
> wrote:
> >> >>
> >> >> Hi Shalu,
> >> >>
> >> >> This is probably not the right mailing list for solving this problem.
> >> >> What is the application you are trying to install?  When you say make
> >> >> isn't working, what do you mean?  What are the error messages?  Have
> >> >> you googled for hints on how to get it installed on a Mac?
> >> >>
> >> >> Scott
> >> >>
> >> >>
> >> >> On Tue, Feb 9, 2010 at 10:55 AM, shalu sharma
> >> >> <sharmashalu.bio at gmail.com>
> >> >> wrote:
> >> >> > Hi All,
> >> >> >         I know this is very basic query but i am stuck.
> >> >> > I am trying to install some program on my Mac (it contain Linux
> >> >> > binary).
> >> >> > I
> >> >> > tried "make" but its not working. I am not sure how i can install
> it.
> >> >> > Can anyone please guide me that how i can install linux binary on
> >> >> > MAC?
> >> >> >
> >> >> > I would really appreciate it.
> >> >> >
> >> >> > Thanks
> >> >> > Shalu
> >> >> > _______________________________________________
> >> >> > Bioperl-l mailing list
> >> >> > Bioperl-l at lists.open-bio.org
> >> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >>
> >> >>
> ------------------------------------------------------------------------
> >> >> Scott Cain, Ph. D.                                   scott at
> scottcain
> >> >> dot net
> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> >> Ontario Institute for Cancer Research
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> Ontario Institute for Cancer Research
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

From sharmashalu.bio at gmail.com  Tue Feb  9 12:44:17 2010
From: sharmashalu.bio at gmail.com (shalu sharma)
Date: Tue, 9 Feb 2010 12:44:17 -0500
Subject: [Bioperl-l] Installing Linux Binary
In-Reply-To: <4536f7701002090937m1feb77bfgfab1298e0f3fe551@mail.gmail.com>
References: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
	<4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>
	<465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>
	<4536f7701002090850p466d6280qaa5f81065981daae@mail.gmail.com>
	<465b5a661002090900h535a7014tb796541a636a6209@mail.gmail.com>
	<4536f7701002090902n30c30449pa68866aaf7103826@mail.gmail.com>
	<465b5a661002090932g1e26a6dav98ec2030808aa440@mail.gmail.com>
	<4536f7701002090937m1feb77bfgfab1298e0f3fe551@mail.gmail.com>
Message-ID: <465b5a661002090944v2d7717b1k10812dc64ae0c92f@mail.gmail.com>

Thanks a lot, i really appreciate your efforts.

Thanks
Shalu

On Tue, Feb 9, 2010 at 12:37 PM, Scott Cain <scott at scottcain.net> wrote:

> I don't know.
>
> On Tue, Feb 9, 2010 at 12:32 PM, shalu sharma <sharmashalu.bio at gmail.com>
> wrote:
> > Thanks a lot. Actually i have mailed the author but not getting any
> reply,
> > thats why i mailed in this list.
> > Just last thing, i know this is a version2.4 i already have version 1.0
> > installed on my MAC , will this help?
> >
> > Thanks
> > Shalu
> >
> > On Tue, Feb 9, 2010 at 12:02 PM, Scott Cain <scott at scottcain.net> wrote:
> >>
> >> Hi Shalu,
> >>
> >> I have no clue--it doesn't appear to have any documentation.  The name
> >> having 2.4 after it suggests that you might need a 2.4 kernel, or it
> >> may just be version 2.4.  I suggestion you contact the author.
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 9, 2010 at 12:00 PM, shalu sharma <
> sharmashalu.bio at gmail.com>
> >> wrote:
> >> > Thanks for the reply Scott, So i can install it only on Linux machine?
> >> > I am really sorry again but then  also how i can install it (even on
> >> > Linux
> >> > machine)?
> >> >
> >> > Thanks
> >> > Shalu
> >> >
> >> > On Tue, Feb 9, 2010 at 11:50 AM, Scott Cain <scott at scottcain.net>
> wrote:
> >> >>
> >> >> OK, I thought maybe you were misspeaking when you wrote it was a
> linux
> >> >> binary, since you were trying to use make, but that really does
> appear
> >> >> to be a linux binary, so you can't install it on a Mac.
> >> >>
> >> >> Scott
> >> >>
> >> >>
> >> >> On Tue, Feb 9, 2010 at 11:04 AM, shalu sharma
> >> >> <sharmashalu.bio at gmail.com>
> >> >> wrote:
> >> >> > I am really sorry for this. Actually i tried a lot but i am new to
> >> >> > this.
> >> >> > I
> >> >> > tried google it alos but couldn't find anything.
> >> >> > When i try to make , its saying " No target specified and no
> makefile
> >> >> > found.
> >> >> >
> >> >> > I am trying to install xipe.
> >> >> > http://phage.sdsu.edu/~brodrigu/xipe/<http://phage.sdsu.edu/%7Ebrodrigu/xipe/>
> >> >> >
> >> >> > I am really sorry for the trouble.
> >> >> >
> >> >> > Thanks
> >> >> > Shalu
> >> >> >
> >> >> > On Tue, Feb 9, 2010 at 10:59 AM, Scott Cain <scott at scottcain.net>
> >> >> > wrote:
> >> >> >>
> >> >> >> Hi Shalu,
> >> >> >>
> >> >> >> This is probably not the right mailing list for solving this
> >> >> >> problem.
> >> >> >> What is the application you are trying to install?  When you say
> >> >> >> make
> >> >> >> isn't working, what do you mean?  What are the error messages?
>  Have
> >> >> >> you googled for hints on how to get it installed on a Mac?
> >> >> >>
> >> >> >> Scott
> >> >> >>
> >> >> >>
> >> >> >> On Tue, Feb 9, 2010 at 10:55 AM, shalu sharma
> >> >> >> <sharmashalu.bio at gmail.com>
> >> >> >> wrote:
> >> >> >> > Hi All,
> >> >> >> >         I know this is very basic query but i am stuck.
> >> >> >> > I am trying to install some program on my Mac (it contain Linux
> >> >> >> > binary).
> >> >> >> > I
> >> >> >> > tried "make" but its not working. I am not sure how i can
> install
> >> >> >> > it.
> >> >> >> > Can anyone please guide me that how i can install linux binary
> on
> >> >> >> > MAC?
> >> >> >> >
> >> >> >> > I would really appreciate it.
> >> >> >> >
> >> >> >> > Thanks
> >> >> >> > Shalu
> >> >> >> > _______________________________________________
> >> >> >> > Bioperl-l mailing list
> >> >> >> > Bioperl-l at lists.open-bio.org
> >> >> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >>
> >> >> >>
> >> >> >>
> ------------------------------------------------------------------------
> >> >> >> Scott Cain, Ph. D.                                   scott at
> >> >> >> scottcain
> >> >> >> dot net
> >> >> >> GMOD Coordinator (http://gmod.org/)
> 216-392-3087
> >> >> >> Ontario Institute for Cancer Research
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >>
> >> >>
> ------------------------------------------------------------------------
> >> >> Scott Cain, Ph. D.                                   scott at
> scottcain
> >> >> dot net
> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> >> Ontario Institute for Cancer Research
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> Ontario Institute for Cancer Research
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

From scott at scottcain.net  Tue Feb  9 12:37:07 2010
From: scott at scottcain.net (Scott Cain)
Date: Tue, 9 Feb 2010 12:37:07 -0500
Subject: [Bioperl-l] Installing Linux Binary
In-Reply-To: <465b5a661002090932g1e26a6dav98ec2030808aa440@mail.gmail.com>
References: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
	<4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>
	<465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>
	<4536f7701002090850p466d6280qaa5f81065981daae@mail.gmail.com>
	<465b5a661002090900h535a7014tb796541a636a6209@mail.gmail.com>
	<4536f7701002090902n30c30449pa68866aaf7103826@mail.gmail.com>
	<465b5a661002090932g1e26a6dav98ec2030808aa440@mail.gmail.com>
Message-ID: <4536f7701002090937m1feb77bfgfab1298e0f3fe551@mail.gmail.com>

I don't know.

On Tue, Feb 9, 2010 at 12:32 PM, shalu sharma <sharmashalu.bio at gmail.com> wrote:
> Thanks a lot. Actually i have mailed the author but not getting any reply,
> thats why i mailed in this list.
> Just last thing, i know this is a version2.4 i already have version 1.0
> installed on my MAC , will this help?
>
> Thanks
> Shalu
>
> On Tue, Feb 9, 2010 at 12:02 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Shalu,
>>
>> I have no clue--it doesn't appear to have any documentation. ?The name
>> having 2.4 after it suggests that you might need a 2.4 kernel, or it
>> may just be version 2.4. ?I suggestion you contact the author.
>>
>> Scott
>>
>>
>> On Tue, Feb 9, 2010 at 12:00 PM, shalu sharma <sharmashalu.bio at gmail.com>
>> wrote:
>> > Thanks for the reply Scott, So i can install it only on Linux machine?
>> > I am really sorry again but then? also how i can install it (even on
>> > Linux
>> > machine)?
>> >
>> > Thanks
>> > Shalu
>> >
>> > On Tue, Feb 9, 2010 at 11:50 AM, Scott Cain <scott at scottcain.net> wrote:
>> >>
>> >> OK, I thought maybe you were misspeaking when you wrote it was a linux
>> >> binary, since you were trying to use make, but that really does appear
>> >> to be a linux binary, so you can't install it on a Mac.
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Tue, Feb 9, 2010 at 11:04 AM, shalu sharma
>> >> <sharmashalu.bio at gmail.com>
>> >> wrote:
>> >> > I am really sorry for this. Actually i tried a lot but i am new to
>> >> > this.
>> >> > I
>> >> > tried google it alos but couldn't find anything.
>> >> > When i try to make , its saying " No target specified and no makefile
>> >> > found.
>> >> >
>> >> > I am trying to install xipe.
>> >> > http://phage.sdsu.edu/~brodrigu/xipe/
>> >> >
>> >> > I am really sorry for the trouble.
>> >> >
>> >> > Thanks
>> >> > Shalu
>> >> >
>> >> > On Tue, Feb 9, 2010 at 10:59 AM, Scott Cain <scott at scottcain.net>
>> >> > wrote:
>> >> >>
>> >> >> Hi Shalu,
>> >> >>
>> >> >> This is probably not the right mailing list for solving this
>> >> >> problem.
>> >> >> What is the application you are trying to install? ?When you say
>> >> >> make
>> >> >> isn't working, what do you mean? ?What are the error messages? ?Have
>> >> >> you googled for hints on how to get it installed on a Mac?
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Tue, Feb 9, 2010 at 10:55 AM, shalu sharma
>> >> >> <sharmashalu.bio at gmail.com>
>> >> >> wrote:
>> >> >> > Hi All,
>> >> >> > ? ? ? ? I know this is very basic query but i am stuck.
>> >> >> > I am trying to install some program on my Mac (it contain Linux
>> >> >> > binary).
>> >> >> > I
>> >> >> > tried "make" but its not working. I am not sure how i can install
>> >> >> > it.
>> >> >> > Can anyone please guide me that how i can install linux binary on
>> >> >> > MAC?
>> >> >> >
>> >> >> > I would really appreciate it.
>> >> >> >
>> >> >> > Thanks
>> >> >> > Shalu
>> >> >> > _______________________________________________
>> >> >> > Bioperl-l mailing list
>> >> >> > Bioperl-l at lists.open-bio.org
>> >> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/) ? ? ? ? ? ? ? ? ? ? 216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/) ? ? ? ? ? ? ? ? ? ? 216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/) ? ? ? ? ? ? ? ? ? ? 216-392-3087
>> Ontario Institute for Cancer Research
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From cjfields at illinois.edu  Tue Feb  9 12:57:33 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Feb 2010 11:57:33 -0600
Subject: [Bioperl-l] Installing Linux Binary
In-Reply-To: <465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>
References: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
	<4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>
	<465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>
Message-ID: <4A75BCC9-FE53-4A0C-82F6-0B5B54B798A5@illinois.edu>

Shalu,

This really isn't the best place to ask; the list is specific for BioPerl.  You should contact the authors of the package in question.  

Note that the OS isn't really a limitation anymore, unless you are trying to run something specific for OS X from Windows/Linux (fortunately that's not too common).  If it's really important you could try installing Linux via a VM (VirtualBox is nice and free, VMWare is nice but $$), then install Xipe, or use Boot Camp and dual-boot into Linux.

chris

On Feb 9, 2010, at 10:04 AM, shalu sharma wrote:

> I am really sorry for this. Actually i tried a lot but i am new to this. I
> tried google it alos but couldn't find anything.
> When i try to make , its saying " No target specified and no makefile found.
> 
> I am trying to install xipe.
> http://phage.sdsu.edu/~brodrigu/xipe/
> 
> I am really sorry for the trouble.
> 
> Thanks
> Shalu
> 
> On Tue, Feb 9, 2010 at 10:59 AM, Scott Cain <scott at scottcain.net> wrote:
> 
>> Hi Shalu,
>> 
>> This is probably not the right mailing list for solving this problem.
>> What is the application you are trying to install?  When you say make
>> isn't working, what do you mean?  What are the error messages?  Have
>> you googled for hints on how to get it installed on a Mac?
>> 
>> Scott
>> 
>> 
>> On Tue, Feb 9, 2010 at 10:55 AM, shalu sharma <sharmashalu.bio at gmail.com>
>> wrote:
>>> Hi All,
>>>        I know this is very basic query but i am stuck.
>>> I am trying to install some program on my Mac (it contain Linux binary).
>> I
>>> tried "make" but its not working. I am not sure how i can install it.
>>> Can anyone please guide me that how i can install linux binary on MAC?
>>> 
>>> I would really appreciate it.
>>> 
>>> Thanks
>>> Shalu
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
>> 
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From scott at scottcain.net  Tue Feb  9 11:50:40 2010
From: scott at scottcain.net (Scott Cain)
Date: Tue, 9 Feb 2010 11:50:40 -0500
Subject: [Bioperl-l] Installing Linux Binary
In-Reply-To: <465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>
References: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
	<4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>
	<465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>
Message-ID: <4536f7701002090850p466d6280qaa5f81065981daae@mail.gmail.com>

OK, I thought maybe you were misspeaking when you wrote it was a linux
binary, since you were trying to use make, but that really does appear
to be a linux binary, so you can't install it on a Mac.

Scott


On Tue, Feb 9, 2010 at 11:04 AM, shalu sharma <sharmashalu.bio at gmail.com> wrote:
> I am really sorry for this. Actually i tried a lot but i am new to this. I
> tried google it alos but couldn't find anything.
> When i try to make , its saying " No target specified and no makefile found.
>
> I am trying to install xipe.
> http://phage.sdsu.edu/~brodrigu/xipe/
>
> I am really sorry for the trouble.
>
> Thanks
> Shalu
>
> On Tue, Feb 9, 2010 at 10:59 AM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Shalu,
>>
>> This is probably not the right mailing list for solving this problem.
>> What is the application you are trying to install? ?When you say make
>> isn't working, what do you mean? ?What are the error messages? ?Have
>> you googled for hints on how to get it installed on a Mac?
>>
>> Scott
>>
>>
>> On Tue, Feb 9, 2010 at 10:55 AM, shalu sharma <sharmashalu.bio at gmail.com>
>> wrote:
>> > Hi All,
>> > ? ? ? ? I know this is very basic query but i am stuck.
>> > I am trying to install some program on my Mac (it contain Linux binary).
>> > I
>> > tried "make" but its not working. I am not sure how i can install it.
>> > Can anyone please guide me that how i can install linux binary on MAC?
>> >
>> > I would really appreciate it.
>> >
>> > Thanks
>> > Shalu
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/) ? ? ? ? ? ? ? ? ? ? 216-392-3087
>> Ontario Institute for Cancer Research
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From lincoln.stein at gmail.com  Tue Feb  9 11:46:01 2010
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Tue, 9 Feb 2010 11:46:01 -0500
Subject: [Bioperl-l] Bio::Graphics inside PHP
In-Reply-To: <4536f7701002081141g251d761bnf4215df0bc82c95f@mail.gmail.com>
References: <25c0f63d1002080820l60e9f9d2p837b9afd8bb1f90d@mail.gmail.com>
	<6dce9a0b1002080833o3ad29300kfcee727ed499e74e@mail.gmail.com>
	<4536f7701002081141g251d761bnf4215df0bc82c95f@mail.gmail.com>
Message-ID: <6dce9a0b1002090846t14f42473p6572c8298bc27a6c@mail.gmail.com>

Actually this would be an easy feature to add.

Lincoln

On Mon, Feb 8, 2010 at 2:41 PM, Scott Cain <scott at scottcain.net> wrote:

> Lincoln,
>
> Something I've been thinking about recently is whether it would be
> possible to have gbrowse_img generate the image and the image map
> separately so that they could be used in something like this (a php
> page).  It could just return the image map if something like map=1
> were supplied as an argument.  Could that be done?
>
> Scott
>
>
> On Mon, Feb 8, 2010 at 11:33 AM, Lincoln Stein <lincoln.stein at gmail.com>
> wrote:
> > There's an embeddable version of gbrowse_img that generates the imagemap
> so
> > it is clickable. If you use an <iframe> the formatting usually works out
> > pretty well.
> >
> > Lincoln
> >
> > On Mon, Feb 8, 2010 at 11:20 AM, Daniel Renfro <bluecurio at gmail.com>
> wrote:
> >
> >> I've been trying different ways to do this same thing. At EcoliWiki.net
> we
> >> use GBrowse to show all the strains of Ecoli and assoc phage, plasmids,
> >> etc.
> >> so this is definitely something I think many other model-organism
> databases
> >> could use.
> >>
> >> The final solution was to construct a link to gbrowse_img with all the
> >> necessary variables coming in from $_REQUEST and throw it in the src=""
> >> attribute of the <img> tag. This works pretty good for what we're doing.
> >> Good luck.
> >>
> >> -Daniel Renfro
> >>
> >> Hu Lab Research Associate
> >> Dept. of Biochemistry and Biophysics
> >> 2128 TAMU
> >> Texas A&M Univ.
> >> College Station, TX 77843-2128
> >> 979-862-4055
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> >
> > --
> > Lincoln D. Stein
> > Director, Informatics and Biocomputing Platform
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>

From sharmashalu.bio at gmail.com  Tue Feb  9 12:00:55 2010
From: sharmashalu.bio at gmail.com (shalu sharma)
Date: Tue, 9 Feb 2010 12:00:55 -0500
Subject: [Bioperl-l] Installing Linux Binary
In-Reply-To: <4536f7701002090850p466d6280qaa5f81065981daae@mail.gmail.com>
References: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
	<4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>
	<465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>
	<4536f7701002090850p466d6280qaa5f81065981daae@mail.gmail.com>
Message-ID: <465b5a661002090900h535a7014tb796541a636a6209@mail.gmail.com>

Thanks for the reply Scott, So i can install it only on Linux machine?
I am really sorry again but then  also how i can install it (even on Linux
machine)?

Thanks
Shalu

On Tue, Feb 9, 2010 at 11:50 AM, Scott Cain <scott at scottcain.net> wrote:

> OK, I thought maybe you were misspeaking when you wrote it was a linux
> binary, since you were trying to use make, but that really does appear
> to be a linux binary, so you can't install it on a Mac.
>
> Scott
>
>
> On Tue, Feb 9, 2010 at 11:04 AM, shalu sharma <sharmashalu.bio at gmail.com>
> wrote:
> > I am really sorry for this. Actually i tried a lot but i am new to this.
> I
> > tried google it alos but couldn't find anything.
> > When i try to make , its saying " No target specified and no makefile
> found.
> >
> > I am trying to install xipe.
> > http://phage.sdsu.edu/~brodrigu/xipe/<http://phage.sdsu.edu/%7Ebrodrigu/xipe/>
> >
> > I am really sorry for the trouble.
> >
> > Thanks
> > Shalu
> >
> > On Tue, Feb 9, 2010 at 10:59 AM, Scott Cain <scott at scottcain.net> wrote:
> >>
> >> Hi Shalu,
> >>
> >> This is probably not the right mailing list for solving this problem.
> >> What is the application you are trying to install?  When you say make
> >> isn't working, what do you mean?  What are the error messages?  Have
> >> you googled for hints on how to get it installed on a Mac?
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 9, 2010 at 10:55 AM, shalu sharma <
> sharmashalu.bio at gmail.com>
> >> wrote:
> >> > Hi All,
> >> >         I know this is very basic query but i am stuck.
> >> > I am trying to install some program on my Mac (it contain Linux
> binary).
> >> > I
> >> > tried "make" but its not working. I am not sure how i can install it.
> >> > Can anyone please guide me that how i can install linux binary on MAC?
> >> >
> >> > I would really appreciate it.
> >> >
> >> > Thanks
> >> > Shalu
> >> > _______________________________________________
> >> > Bioperl-l mailing list
> >> > Bioperl-l at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> >
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> Ontario Institute for Cancer Research
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

From dan.kortschak at adelaide.edu.au  Tue Feb  9 15:51:55 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Wed, 10 Feb 2010 07:21:55 +1030
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
In-Reply-To: <4B71C533.7060705@cornell.edu>
References: <4B71C533.7060705@cornell.edu>
Message-ID: <1265748715.4660.13.camel@epistle>

Hi Rob,

Yes, I considered the problems involved in including B:A:IO:b in
bioperl-live because of that. Though I don't see it as a circularity
issue, just a straight dependency one.

>From memory (and a quick look at the .pm and .t files), in the absence
of bioperl-run the test should just be ignored (they currently are not
skipped - I will add that) and inclusion of the module in code should
fail informatively, so I don't really see that as a problem. If it is
seen as a problem though I think the best approach would be to migrate
it to bioperl-run, rather than placing it in it's own package -
bioperl-run already depends on bioperl-live, so all internal
dependencies would nominally be satisfied (samtools and other
executables are outside our control).

Other opinions?

cheers
Dan

On Tue, 2010-02-09 at 12:27 -0800, Robert Buels wrote:
> Bio::Assembly::IO::bowtie uses Bio::Tools::Run::Samtools, which is part 
> of bioperl-run.  Doesn't that introduce a circular dependency between 
> bioperl-live and bioperl-run?
> 
> Perhaps it should be split out into its own CPAN distribution that 
> depends on both bioperl-run and bioperl-live?  Or maybe some way can be 
> found for it to not use Bio::Tools::Run::Samtools?
> 
> Rob
> 
-- 
_____________________________________________________________   .`.`o
                                                         o| ,\__ `./`r
  Dr. Dan Kortschak  dan.kortschak at adelaide.edu.au    <\/    \_O> O
                                                          "|`...'.\
  Every time I see an adult on a bicycle, I no longer?      `      :\
  despair for the future of the human race.                       : \
    -- H. G. Wells, 1904

  By replying to this email you implicitly accept that your response
  may be forwarded to other recipients, unless otherwise specified.


From rmb32 at cornell.edu  Tue Feb  9 15:27:31 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 09 Feb 2010 12:27:31 -0800
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
Message-ID: <4B71C533.7060705@cornell.edu>

Bio::Assembly::IO::bowtie uses Bio::Tools::Run::Samtools, which is part 
of bioperl-run.  Doesn't that introduce a circular dependency between 
bioperl-live and bioperl-run?

Perhaps it should be split out into its own CPAN distribution that 
depends on both bioperl-run and bioperl-live?  Or maybe some way can be 
found for it to not use Bio::Tools::Run::Samtools?

Rob

-- 
Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu
http://www.sgn.cornell.edu

From Russell.Smithies at agresearch.co.nz  Tue Feb  9 16:12:27 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 10 Feb 2010 10:12:27 +1300
Subject: [Bioperl-l] Refseq Version
In-Reply-To: <465b5a661002080837v76b0215ctc7039c516bb0c82d@mail.gmail.com>
References: <465b5a661002041401u3b8ac5fdp483f7032ce35139b@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED520@exchsth.agresearch.co.nz>
	<465b5a661002050655u34ff94acwdf8fe72512dec4b3@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED76C@exchsth.agresearch.co.nz>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED78C@exchsth.agresearch.co.nz>
	<18DF7D20DFEC044098A1062202F5FFF32C61BED795@exchsth.agresearch.co.nz>
	<465b5a661002080837v76b0215ctc7039c516bb0c82d@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61BEDF26@exchsth.agresearch.co.nz>

At a rough guess, I'd say they've done some merging of sequences to remove redundancy i.e. where two or more sequences from different species are identical, they've only added a single sequence to the blast database and added all the IDs to the fasta header in the same fashion the NR database is done.
I don't have refseq_protein database at the moment but you could check by dumping it as fasta and grepping for the Ctrl-A fasta header description separator.

--Russell

From: shalu sharma [mailto:sharmashalu.bio at gmail.com]
Sent: Tuesday, 9 February 2010 5:38 a.m.
To: Smithies, Russell
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Refseq Version

Thanks a lot Russell.
But i am still confused. Actually i asked the server admin and he said that this is Refseq's latest vesrion (the one i am using).
But the number of sequences which i am getting from blast report are not matching with the refseq 38 release ( or i don't know which numbers to match).

Like from blast report i am getting :
$ fastacmd -I -d /db/ncbiblast/refseq/refseq_
protein
Database: NCBI Protein Reference Sequences
           7,585,993 sequences; 2,644,770,521 total letters

And when i am looking at refseq release notes , i don't understand that which numbers to match with because i don't see these numbers in release notes.

Thanks a lot, I really appreciate your help.

Thanks
Shalu


On Sun, Feb 7, 2010 at 4:05 PM, Smithies, Russell <Russell.Smithies at agresearch.co.nz<mailto:Russell.Smithies at agresearch.co.nz>> wrote:
AAArrrgg, what is it with Outlook this morning!!!
Formatting kaput again but I'm sure you can work it out from there!

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-bounces at lists.open-bio.org> [mailto:bioperl-l-<mailto:bioperl-l->
> bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>] On Behalf Of Smithies, Russell
> Sent: Monday, 8 February 2010 9:59 a.m.
> To: 'shalu sharma'
> Cc: 'bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>'
> Subject: Re: [Bioperl-l] Refseq Version
>
> I should have known it would break the formatting :-(
>
> Try this:
>
> Release 1:June 30, 2003;Release Size: 4672871949 bases, 263588685 amino
> acids, 1061675 records
> Release 2:October 21, 2003;Release Size: 2124 organisms, 7745398573
> nucleotide bases, 286957682 amino acids, 1097404 records
> Release 3:January 13, 2004;Release Size: 2218 organisms, 7992741222
> nucleotide bases, 294647847 amino acids, 1101244 records
> Release 4:March 24, 2004;Release Size: 2358 organisms, 8175128887
> nucleotide bases, 318253841 amino acids, 1193457 records
> Release 5:May 2 , 2004;Release Size: 2395 organisms, 8325515623 nucleotide
> bases, 337229387 amino acids, 1255613 records
> Release 6:July 5, 2004;Release Size: 2467 organisms, 8696371716 nucleotide
> bases, 365446682 amino acids, 1367206 records
> Release 7:September 12, 2004;Release Size: 2558 organisms, 21072808460
> nucleotide bases, 405233619 amino acids, 1579579 records
> Release 8:October 31, 2004;Release Size: 2645 organisms, 26814386658
> nucleotide bases, 430300369 amino acids, 1709723 records
> Release 9:January 9, 2005;Release Size:  2780 organisms, 36786975473
> nucleotide bases, 470534907 amino acids, 1843944 records
> Release 10:March 6, 2005;Release Size:2827 organisms, 36893741150
> nucleotide bases, 482862858 amino acids, 1893478 records
> Release 11:May 8, 2005;Release Size:2928 organisms, 39731702362 nucleotide
> bases, 507980644 amino acids, 2477893 records
> Release 12:July 10, 2005;Release Size:2969 organisms, 43043256058
> nucleotide bases, 608493108 amino acids, 2869675 records
> Release 13:September 11, 2005;Release Size:3060 organisms, 44727484853
> nucleotide bases, 686768902 amino acids, 3400773 records
> Release 14:November 20, 2005;Release Size:3198 organisms, 47364955367
> nucleotide bases, 763761075 amino acids, 3272776 records
> Release 15:January 1, 2006;Release Size:3244 organisms, 52645441913
> nucleotide bases, 810009733 amino acids, 3436263 records
> Release 16:March 11, 2006;Release Size:3397 organisms, 56175443059
> nucleotide bases, 887509001 amino acids, 3715260 records
> Release 17:May 1, 2006;Release Size:3497 organisms, 62130037371 nucleotide
> bases, 927587669 amino acids, 3999859 records
> Release 18:July 11, 2006;Release Size:3695 organisms, 70474041999
> nucleotide bases, 974374765 amino acids, 4186692 records
> Release 19:September 10, 2006;Release Size: 3774 organisms, 70694879544
> nucleotide bases, 1012985077 amino acids, 4311543 records
> Release 20:November 5, 2006;Release Size:3919 organisms, 72679681505
> nucleotide bases, 1061797276 amino acids, 4567569 records
> Release 21:January 6, 2007;Release Size:4079 organisms, 73864990566
> nucleotide bases, 1144795927 amino acids, 4742335 records
> Release 22:March 5, 2007;Release Size:4187 organisms, 82441128546
> nucleotide bases, 1215085694 amino acids, 5207865 records
> Release 23:May 8, 2007;Release Size:4300 organisms, 83148327110 nucleotide
> bases, 1291050995 amino acids, 5503385 records
> Release 24:July 10, 2007;Release Size:4511 organisms, 89856995521
> nucleotide bases, 1365916222 amino acids, 6073814 records
> Release 25:September 11, 2007;Release Size:4646 organisms, 91265840843
> nucleotide bases, 1470475398 amino acids, 6515132 records
> Release 26:November 4, 2007;Release Size:4737 organisms, 99105705485
> nucleotide bases, 1495032507 amino acids, 6698250 records
> Release 27:January 6, 2008;Release Size:4926 organisms, 101059552113
> nucleotide bases, 1556356987 amino acids, 7025715 records
> Release 28:March 9, 2008;Release Size: 5059 organisms, 102051350525
> nucleotide bases, 1770627427 amino acids, 7914560 records
> Release 29:May 4, 2008;Release Size:5168 organisms, 104671101150
> nucleotide bases, 1870214220 amino acids, 8376141 records
> Release 30:July 7, 2008;Release Size:5395 organisms, 105074486709
> nucleotide bases, 1913447691 amino acids, 8572852 records
> Release 31:August 30, 2008;Release Size: 5513 organisms, 109214348591
> nucleotide bases, 2026768719 amino acids, 9145702 records
> Release 32:November 10, 2008;Release Size: 5726 organisms, 111122203221
> nucleotide bases, 2089596746 amino acids, 9501764 records
> Release 33:January 16, 2009;Release Size:7773 organisms, 116001583818
> nucleotide bases, 2204073443 amino acids, 10325282 records
> Release 34:March 6, 2009;Release Size: 8054 organisms, 111792574830
> nucleotide bases, 2299682138 amino acids, 10021870 records
> Release 35:May 4, 2009;Release Size: 8393 organisms, 113210655336
> nucleotide bases, 2565199170 amino acids, 10993891 records
> Release 36:July 2, 2009;Release Size: 8665 organisms, 117013741530
> nucleotide bases, 2756884219 amino acids, 12141825 records
> Release 37:September 3, 2009;Release Size: 9005 organisms, 119151229820
> nucleotide bases, 2965450333 amino acids, 12941750 records
> Release 38:November 7, 2009;Release Size: 9166 organisms, 119196622435
> nucleotide bases, 3115246540 amino acids, 13436447 records
>
>
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-bounces at lists.open-bio.org> [mailto:bioperl-l-<mailto:bioperl-l->
> > bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>] On Behalf Of Smithies, Russell
> > Sent: Monday, 8 February 2010 9:47 a.m.
> > To: 'shalu sharma'
> > Cc: 'bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>'
> > Subject: Re: [Bioperl-l] Refseq Version
> >
> > Release 39 was Jan 30 and according to the README releases only come out
> > in odd months (January, March, May, July, September, November)
> > The stats file is here: ftp://ftp.ncbi.nih.gov/refseq/release/release-
> > statistics/RefSeq-release39.01232010.stats.txt
> >
> > The numbers of sequences between the fasta release and the pre-build
> blast
> > databases seem to differ but I guess only NCBI can explain that.
> > I can't see any way of extracting the release number from the pre-build
> > blast databases (apart from the build date) but it might be worth asking
> > NCBI if they'd include the information in future releases.
> >
> >
> > FYI, here's the old release stats.
> > (I wget'ed and grep'ed all the stats files)
> >
> > Release
> >
> > Date
> >
> > Year
> >
> > Organisms
> >
> > Nucleotide Bases
> >
> > Amino Acids
> >
> > Records
> >
> > 1
> >
> > Jun-30
> >
> > 2003
> >
> >             4,672,871,949
> >
> >             263,588,685
> >
> >           1,061,675
> >
> > 2
> >
> > Oct-21
> >
> > 2003
> >
> >         2,124
> >
> >             7,745,398,573
> >
> >             286,957,682
> >
> >           1,097,404
> >
> > 3
> >
> > Jan-13
> >
> > 2004
> >
> >         2,218
> >
> >             7,992,741,222
> >
> >             294,647,847
> >
> >           1,101,244
> >
> > 4
> >
> > Mar-24
> >
> > 2004
> >
> >         2,358
> >
> >             8,175,128,887
> >
> >             318,253,841
> >
> >           1,193,457
> >
> > 5
> >
> > May-02
> >
> > 2004
> >
> >         2,395
> >
> >             8,325,515,623
> >
> >             337,229,387
> >
> >           1,255,613
> >
> > 6
> >
> > Jul-05
> >
> > 2004
> >
> >         2,467
> >
> >             8,696,371,716
> >
> >             365,446,682
> >
> >           1,367,206
> >
> > 7
> >
> > Sep-12
> >
> > 2004
> >
> >         2,558
> >
> >           21,072,808,460
> >
> >             405,233,619
> >
> >           1,579,579
> >
> > 8
> >
> > Oct-31
> >
> > 2004
> >
> >         2,645
> >
> >           26,814,386,658
> >
> >             430,300,369
> >
> >           1,709,723
> >
> > 9
> >
> > Jan-09
> >
> > 2005
> >
> >         2,780
> >
> >           36,786,975,473
> >
> >             470,534,907
> >
> >           1,843,944
> >
> > 10
> >
> > Mar-06
> >
> > 2005
> >
> >         2,827
> >
> >           36,893,741,150
> >
> >             482,862,858
> >
> >           1,893,478
> >
> > 11
> >
> > May-08
> >
> > 2005
> >
> >         2,928
> >
> >           39,731,702,362
> >
> >             507,980,644
> >
> >           2,477,893
> >
> > 12
> >
> > Jul-10
> >
> > 2005
> >
> >         2,969
> >
> >           43,043,256,058
> >
> >             608,493,108
> >
> >           2,869,675
> >
> > 13
> >
> > Sep-11
> >
> > 2005
> >
> >         3,060
> >
> >           44,727,484,853
> >
> >             686,768,902
> >
> >           3,400,773
> >
> > 14
> >
> > Nov-20
> >
> > 2005
> >
> >         3,198
> >
> >           47,364,955,367
> >
> >             763,761,075
> >
> >           3,272,776
> >
> > 15
> >
> > Jan-01
> >
> > 2006
> >
> >         3,244
> >
> >           52,645,441,913
> >
> >             810,009,733
> >
> >           3,436,263
> >
> > 16
> >
> > Mar-11
> >
> > 2006
> >
> >         3,397
> >
> >           56,175,443,059
> >
> >             887,509,001
> >
> >           3,715,260
> >
> > 17
> >
> > May-01
> >
> > 2006
> >
> >         3,497
> >
> >           62,130,037,371
> >
> >             927,587,669
> >
> >           3,999,859
> >
> > 18
> >
> > Jul-11
> >
> > 2006
> >
> >         3,695
> >
> >           70,474,041,999
> >
> >             974,374,765
> >
> >           4,186,692
> >
> > 19
> >
> > Sep-10
> >
> > 2006
> >
> >         3,774
> >
> >           70,694,879,544
> >
> >          1,012,985,077
> >
> >           4,311,543
> >
> > 20
> >
> > Nov-05
> >
> > 2006
> >
> >         3,919
> >
> >           72,679,681,505
> >
> >          1,061,797,276
> >
> >           4,567,569
> >
> > 21
> >
> > Jan-06
> >
> > 2007
> >
> >         4,079
> >
> >           73,864,990,566
> >
> >          1,144,795,927
> >
> >           4,742,335
> >
> > 22
> >
> > Mar-05
> >
> > 2007
> >
> >         4,187
> >
> >           82,441,128,546
> >
> >          1,215,085,694
> >
> >           5,207,865
> >
> > 23
> >
> > May-08
> >
> > 2007
> >
> >         4,300
> >
> >           83,148,327,110
> >
> >          1,291,050,995
> >
> >           5,503,385
> >
> > 24
> >
> > Jul-10
> >
> > 2007
> >
> >         4,511
> >
> >           89,856,995,521
> >
> >          1,365,916,222
> >
> >           6,073,814
> >
> > 25
> >
> > Sep-11
> >
> > 2007
> >
> >         4,646
> >
> >           91,265,840,843
> >
> >          1,470,475,398
> >
> >           6,515,132
> >
> > 26
> >
> > Nov-04
> >
> > 2007
> >
> >         4,737
> >
> >           99,105,705,485
> >
> >          1,495,032,507
> >
> >           6,698,250
> >
> > 27
> >
> > Jan-06
> >
> > 2008
> >
> >         4,926
> >
> >          101,059,552,113
> >
> >          1,556,356,987
> >
> >           7,025,715
> >
> > 28
> >
> > Mar-09
> >
> > 2008
> >
> >         5,059
> >
> >          102,051,350,525
> >
> >          1,770,627,427
> >
> >           7,914,560
> >
> > 29
> >
> > May-04
> >
> > 2008
> >
> >         5,168
> >
> >          104,671,101,150
> >
> >          1,870,214,220
> >
> >           8,376,141
> >
> > 30
> >
> > Jul-07
> >
> > 2008
> >
> >         5,395
> >
> >          105,074,486,709
> >
> >          1,913,447,691
> >
> >           8,572,852
> >
> > 31
> >
> > Aug-30
> >
> > 2008
> >
> >         5,513
> >
> >          109,214,348,591
> >
> >          2,026,768,719
> >
> >           9,145,702
> >
> > 32
> >
> > Nov-10
> >
> > 2008
> >
> >         5,726
> >
> >          111,122,203,221
> >
> >          2,089,596,746
> >
> >           9,501,764
> >
> > 33
> >
> > Jan-16
> >
> > 2009
> >
> >         7,773
> >
> >          116,001,583,818
> >
> >          2,204,073,443
> >
> >         10,325,282
> >
> > 34
> >
> > Mar-06
> >
> > 2009
> >
> >         8,054
> >
> >          111,792,574,830
> >
> >          2,299,682,138
> >
> >         10,021,870
> >
> > 35
> >
> > May-04
> >
> > 2009
> >
> >         8,393
> >
> >          113,210,655,336
> >
> >          2,565,199,170
> >
> >         10,993,891
> >
> > 36
> >
> > Jul-02
> >
> > 2009
> >
> >         8,665
> >
> >          117,013,741,530
> >
> >          2,756,884,219
> >
> >         12,141,825
> >
> > 37
> >
> > Sep-03
> >
> > 2009
> >
> >         9,005
> >
> >          119,151,229,820
> >
> >          2,965,450,333
> >
> >         12,941,750
> >
> > 38
> >
> > Nov-07
> >
> > 2009
> >
> >         9,166
> >
> >          119,196,622,435
> >
> >          3,115,246,540
> >
> >         13,436,447
> >
> >
> >
> > --Russell
> >
> >
> > From: shalu sharma [mailto:sharmashalu.bio at gmail.com<mailto:sharmashalu.bio at gmail.com>]
> > Sent: Saturday, 6 February 2010 3:56 a.m.
> > To: Smithies, Russell
> > Cc: bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>
> > Subject: Re: [Bioperl-l] Refseq Version
> >
> > Hi Russell,
> >                Thanks for your response.
> > I am getting the number of sequence in the database but not the release
> > number (like 38, 39).
> > This is what i did:
> >
> > $ fastacmd -I -d /db/ncbiblast/refseq/refseq_protein
> > Database: NCBI Protein Reference Sequences
> >            7,585,993 sequences; 2,644,770,521 total letters
> >
> > File names:
> > /db/ncbiblast/refseq/refseq_protein.00
> >    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 36,805
> > res
> > /db/ncbiblast/refseq/refseq_protein.01
> >    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 33,403
> > res
> > /db/ncbiblast/refseq/refseq_protein.02
> >    Date: Jan 30, 2010  8:34 PM    Version: 4    Longest sequence: 15,830
> > res
> >
> > I am still confuse that how i can get the release number. I know refseq
> 39
> > was released on Jan 30, 2010 but i don't know how to confirm this. I
> also
> > tried look refseq release file but was not able to get any thing.
> >
> > I would really appreciate if anyone can help me out with this.
> >
> > Thanks
> > Shalu
> >
> > On Thu, Feb 4, 2010 at 6:39 PM, Smithies, Russell
> >
> <Russell.Smithies at agresearch.co.nz<mailto:Russell.Smithies at agresearch.co.nz><mailto:Russell.Smithies at agresearch.co.n<mailto:Russell.Smithies at agresearch.co.n>
> > z>> wrote:
> > If you have access to the blast database, use fastacmd -I -d
> databasename
> > Otherwise, it's usually at the bottom of your blast result.
> >
> > --Russell
> >
> > > -----Original Message-----
> > > From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-bounces at lists.open-bio.org><mailto:bioperl-l-<mailto:bioperl-l->
> > bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>> [mailto:bioperl-l-<mailto:bioperl-l-><mailto:bioperl-l-<mailto:bioperl-l->>
> > > bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org><mailto:bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>>] On
> Behalf
> > Of shalu sharma
> > > Sent: Friday, 5 February 2010 11:02 a.m.
> > > To: bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org><mailto:bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>>
> > > Subject: [Bioperl-l] Refseq Version
> > >
> > > Hi All,
> > >       This is not a bioperl query.
> > > Is there any way to check refseq version (release). Actually i am
> using
> > > some
> > > server to blast my sequences (blastall) against refseq. Is there any
> way
> > i
> > > can get the version information on the refseq database (from the blast
> > > file
> > > or directly from the database)?
> > >
> > > Thanks
> > > Shalu
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org<mailto:Bioperl-l at lists.open-bio.org><mailto:Bioperl-l at lists.open-bio.org<mailto:Bioperl-l at lists.open-bio.org>>
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > =======================================================================
> > Attention: The information contained in this message and/or attachments
> > from AgResearch Limited is intended only for the persons or entities
> > to which it is addressed and may contain confidential and/or privileged
> > material. Any review, retransmission, dissemination or other use of, or
> > taking of any action in reliance upon, this information by persons or
> > entities other than the intended recipients is prohibited by AgResearch
> > Limited. If you have received this message in error, please notify the
> > sender immediately.
> > =======================================================================
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org<mailto:Bioperl-l at lists.open-bio.org>
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
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> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From maj at fortinbras.us  Tue Feb  9 16:21:21 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Tue, 9 Feb 2010 16:21:21 -0500
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
In-Reply-To: <4B71C533.7060705@cornell.edu>
References: <4B71C533.7060705@cornell.edu>
Message-ID: <46B2F24717394AB79664BB4732E18E77@NewLife>

Yeah, this is getting kinda hairy-- B:T:R:Samtools is
a basic wrapper for anything that wants to use
Bio::DB::Samtools ( lstein's samtools library wrapper,
a CPAN and not a BioPerl module. Savvy?). Because
its likely that other parser-like modules will want to
use samtools ( as well as wrapper-like modules), I
would vote for moving Samtools and Samtools::Config
into the bioperl-live version of Bio::Tools::Run.
(A question for another day is, should we/can we
coalesce the two instances of Bio::Tools:Run,
and where?)
MAJ


----- Original Message ----- 
From: "Robert Buels" <rmb32 at cornell.edu>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>; "Dan Kortschak" 
<dan.kortschak at adelaide.edu.au>
Sent: Tuesday, February 09, 2010 3:27 PM
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?


> Bio::Assembly::IO::bowtie uses Bio::Tools::Run::Samtools, which is part of 
> bioperl-run.  Doesn't that introduce a circular dependency between 
> bioperl-live and bioperl-run?
>
> Perhaps it should be split out into its own CPAN distribution that depends on 
> both bioperl-run and bioperl-live?  Or maybe some way can be found for it to 
> not use Bio::Tools::Run::Samtools?
>
> Rob
>
> -- 
> Robert Buels
> Bioinformatics Analyst, Sol Genomics Network
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From cjfields at illinois.edu  Tue Feb  9 17:54:52 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Feb 2010 16:54:52 -0600
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
In-Reply-To: <1265748715.4660.13.camel@epistle>
References: <4B71C533.7060705@cornell.edu> <1265748715.4660.13.camel@epistle>
Message-ID: <E01ACF36-2E6F-4647-AB08-C02817B4A42F@illinois.edu>

Dan,

It does introduce circularity, in that Bio::Assembly::IO::bowtie requires Bio::Tools::Run::Samtools in bioperl-run, but bioperl-run itself requires Bio::Root::Root.  So we'll need to decide on something...

Re: Rob's proposal: one of the long-term goals we have is to make the bioperl installations more modular and focused.  This will probably start up after I push out a 1.6.2 release and will involve splitting up and focusing modules into separate releases.  Reasons being:

(1) allowing bug fixes and updates to be pushed to CPAN faster, 
(2) reducing the overhead of donating code (it can go straight into CPAN, just declare the proper deps), 
(3) reduce the issue where the bulk of module maintenance is placed on bioperl devs (particularly core devs),
(4) start breaking the reliance many have had of using svn checkouts for bug fixes.

We can focus on specific problematic areas (for instance, FeatureIO) w/o hampering the release of other unrelated modules (SearchIO, etc).   The current set of modules will likely remain under the 'BioPerl' aegis, in that they will be maintained by the current devs and released under the BIOPERLML cpan account, with a cabal of devs/maintainers all capable of pushing a CPAN release.  This is essentially how Moose is set up, and I believe the dev and 5.12 releases of perl will also follow this route.

With that in mind, creating either a focused BowTie-specific package, or a focused next-gen specific one, does make sense.  Nothing prevents a dev from using the same general directory structure (Bio::Assembly, Bio::Tools::Run, Bio::Search::*, etc).  That would enable you to develop the code and make CPAN releases on your own timetable, instead of being bound to the (very slow) current release cycle.  

chris

On Feb 9, 2010, at 2:51 PM, Dan Kortschak wrote:

> Hi Rob,
> 
> Yes, I considered the problems involved in including B:A:IO:b in
> bioperl-live because of that. Though I don't see it as a circularity
> issue, just a straight dependency one.
> 
>> From memory (and a quick look at the .pm and .t files), in the absence
> of bioperl-run the test should just be ignored (they currently are not
> skipped - I will add that) and inclusion of the module in code should
> fail informatively, so I don't really see that as a problem. If it is
> seen as a problem though I think the best approach would be to migrate
> it to bioperl-run, rather than placing it in it's own package -
> bioperl-run already depends on bioperl-live, so all internal
> dependencies would nominally be satisfied (samtools and other
> executables are outside our control).
> 
> Other opinions?
> 
> cheers
> Dan
> 
> On Tue, 2010-02-09 at 12:27 -0800, Robert Buels wrote:
>> Bio::Assembly::IO::bowtie uses Bio::Tools::Run::Samtools, which is part 
>> of bioperl-run.  Doesn't that introduce a circular dependency between 
>> bioperl-live and bioperl-run?
>> 
>> Perhaps it should be split out into its own CPAN distribution that 
>> depends on both bioperl-run and bioperl-live?  Or maybe some way can be 
>> found for it to not use Bio::Tools::Run::Samtools?
>> 
>> Rob
>> 
> -- 
> _____________________________________________________________   .`.`o
>                                                         o| ,\__ `./`r
>  Dr. Dan Kortschak  dan.kortschak at adelaide.edu.au    <\/    \_O> O
>                                                          "|`...'.\
>  Every time I see an adult on a bicycle, I no longer?      `      :\
>  despair for the future of the human race.                       : \
>    -- H. G. Wells, 1904
> 
>  By replying to this email you implicitly accept that your response
>  may be forwarded to other recipients, unless otherwise specified.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From dan.kortschak at adelaide.edu.au  Tue Feb  9 17:58:45 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Wed, 10 Feb 2010 09:28:45 +1030
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
In-Reply-To: <46B2F24717394AB79664BB4732E18E77@NewLife>
References: <4B71C533.7060705@cornell.edu>
	<46B2F24717394AB79664BB4732E18E77@NewLife>
Message-ID: <1265756325.12397.6.camel@zoidberg.mbs.adelaide.edu.au>

Given the general utility of samtools, I'd go with that approach. But in
the meantime, I've added a SKIP to the bowtie tests so that they depend
on B:T:R:Samtools and the samtools executable in addition to B:DB:Sam
(as they were previously piggy backing on with the B:A:IO:sam).

BTW MAJ, there are a number of useless void arrays in the sam tests and
test failures from, I think, having the wrong expectations of the
results from B:DB:Sam. I left them when I was doing the bowtie tests as
I wasn't sure exactly what you were getting - the results seem correct
to me, but what do I know :)

This should probably be in guts, so if we continue this can we jump over
there?

cheers
Dan

On Tue, 2010-02-09 at 16:21 -0500, Mark A. Jensen wrote: 
> Yeah, this is getting kinda hairy-- B:T:R:Samtools is
> a basic wrapper for anything that wants to use
> Bio::DB::Samtools ( lstein's samtools library wrapper,
> a CPAN and not a BioPerl module. Savvy?). Because
> its likely that other parser-like modules will want to
> use samtools ( as well as wrapper-like modules), I
> would vote for moving Samtools and Samtools::Config
> into the bioperl-live version of Bio::Tools::Run.



From cjfields at illinois.edu  Tue Feb  9 18:07:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Feb 2010 17:07:17 -0600
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
In-Reply-To: <46B2F24717394AB79664BB4732E18E77@NewLife>
References: <4B71C533.7060705@cornell.edu>
	<46B2F24717394AB79664BB4732E18E77@NewLife>
Message-ID: <F75B7ED2-9F61-4CBE-ABCC-7353F3D4A3CB@illinois.edu>

Mark,

If I've learned anything from the 1.6 release series, I would rather it not be bound to the bioperl core release cycle, particularly if we are progressing towards splitting up bioperl anyway.  In that light it makes more sense (at least to me) to move this into either a focused set of modules for next-gen analysis, or as focused packages based on the specific functionality (e.g. all BowTie modules bundled together, all bioperl-related Samtools bundled together, etc).  

Bascially, we would set up both you and Dan as co-maintainers, and push all related code under the BIOPERLML CPAN mantle as primary maintainer.  This way any of the co-maintainers can step in and push out new releases if needed.  

chris

On Feb 9, 2010, at 3:21 PM, Mark A. Jensen wrote:

> Yeah, this is getting kinda hairy-- B:T:R:Samtools is
> a basic wrapper for anything that wants to use
> Bio::DB::Samtools ( lstein's samtools library wrapper,
> a CPAN and not a BioPerl module. Savvy?). Because
> its likely that other parser-like modules will want to
> use samtools ( as well as wrapper-like modules), I
> would vote for moving Samtools and Samtools::Config
> into the bioperl-live version of Bio::Tools::Run.
> (A question for another day is, should we/can we
> coalesce the two instances of Bio::Tools:Run,
> and where?)
> MAJ
> 
> ----- Original Message ----- From: "Robert Buels" <rmb32 at cornell.edu>
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>; "Dan Kortschak" <dan.kortschak at adelaide.edu.au>
> Sent: Tuesday, February 09, 2010 3:27 PM
> Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
> 
> 
>> Bio::Assembly::IO::bowtie uses Bio::Tools::Run::Samtools, which is part of bioperl-run.  Doesn't that introduce a circular dependency between bioperl-live and bioperl-run?
>> 
>> Perhaps it should be split out into its own CPAN distribution that depends on both bioperl-run and bioperl-live?  Or maybe some way can be found for it to not use Bio::Tools::Run::Samtools?
>> 
>> Rob
>> 
>> -- 
>> Robert Buels
>> Bioinformatics Analyst, Sol Genomics Network
>> Boyce Thompson Institute for Plant Research
>> Tower Rd
>> Ithaca, NY  14853
>> Tel: 503-889-8539
>> rmb32 at cornell.edu
>> http://www.sgn.cornell.edu
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From maj at fortinbras.us  Tue Feb  9 18:30:50 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Tue, 9 Feb 2010 18:30:50 -0500
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
In-Reply-To: <F75B7ED2-9F61-4CBE-ABCC-7353F3D4A3CB@illinois.edu>
References: <4B71C533.7060705@cornell.edu>
	<46B2F24717394AB79664BB4732E18E77@NewLife>
	<F75B7ED2-9F61-4CBE-ABCC-7353F3D4A3CB@illinois.edu>
Message-ID: <9A27087FAAD34DA6BD5493F18D527BF4@NewLife>

I'm game-- it sounds like the right direction to go-

----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Robert Buels" <rmb32 at cornell.edu>; "BioPerl List" 
<bioperl-l at lists.open-bio.org>; "Dan Kortschak" <dan.kortschak at adelaide.edu.au>
Sent: Tuesday, February 09, 2010 6:07 PM
Subject: Re: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?


Mark,

If I've learned anything from the 1.6 release series, I would rather it not be 
bound to the bioperl core release cycle, particularly if we are progressing 
towards splitting up bioperl anyway.  In that light it makes more sense (at 
least to me) to move this into either a focused set of modules for next-gen 
analysis, or as focused packages based on the specific functionality (e.g. all 
BowTie modules bundled together, all bioperl-related Samtools bundled together, 
etc).

Bascially, we would set up both you and Dan as co-maintainers, and push all 
related code under the BIOPERLML CPAN mantle as primary maintainer.  This way 
any of the co-maintainers can step in and push out new releases if needed.

chris

On Feb 9, 2010, at 3:21 PM, Mark A. Jensen wrote:

> Yeah, this is getting kinda hairy-- B:T:R:Samtools is
> a basic wrapper for anything that wants to use
> Bio::DB::Samtools ( lstein's samtools library wrapper,
> a CPAN and not a BioPerl module. Savvy?). Because
> its likely that other parser-like modules will want to
> use samtools ( as well as wrapper-like modules), I
> would vote for moving Samtools and Samtools::Config
> into the bioperl-live version of Bio::Tools::Run.
> (A question for another day is, should we/can we
> coalesce the two instances of Bio::Tools:Run,
> and where?)
> MAJ
>
> ----- Original Message ----- From: "Robert Buels" <rmb32 at cornell.edu>
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>; "Dan Kortschak" 
> <dan.kortschak at adelaide.edu.au>
> Sent: Tuesday, February 09, 2010 3:27 PM
> Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
>
>
>> Bio::Assembly::IO::bowtie uses Bio::Tools::Run::Samtools, which is part of 
>> bioperl-run.  Doesn't that introduce a circular dependency between 
>> bioperl-live and bioperl-run?
>>
>> Perhaps it should be split out into its own CPAN distribution that depends on 
>> both bioperl-run and bioperl-live?  Or maybe some way can be found for it to 
>> not use Bio::Tools::Run::Samtools?
>>
>> Rob
>>
>> -- 
>> Robert Buels
>> Bioinformatics Analyst, Sol Genomics Network
>> Boyce Thompson Institute for Plant Research
>> Tower Rd
>> Ithaca, NY  14853
>> Tel: 503-889-8539
>> rmb32 at cornell.edu
>> http://www.sgn.cornell.edu
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dan.kortschak at adelaide.edu.au  Tue Feb  9 18:37:08 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Wed, 10 Feb 2010 10:07:08 +1030
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
In-Reply-To: <9A27087FAAD34DA6BD5493F18D527BF4@NewLife>
References: <4B71C533.7060705@cornell.edu>
	<46B2F24717394AB79664BB4732E18E77@NewLife>
	<F75B7ED2-9F61-4CBE-ABCC-7353F3D4A3CB@illinois.edu>
	<9A27087FAAD34DA6BD5493F18D527BF4@NewLife>
Message-ID: <1265758628.12397.12.camel@zoidberg.mbs.adelaide.edu.au>

I'm happy to take this on with Mark.

On Tue, 2010-02-09 at 18:30 -0500, Mark A. Jensen wrote:
> I'm game-- it sounds like the right direction to go-
> 


From maj at fortinbras.us  Tue Feb  9 22:56:36 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Tue, 9 Feb 2010 22:56:36 -0500
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
In-Reply-To: <46B2F24717394AB79664BB4732E18E77@NewLife>
References: <4B71C533.7060705@cornell.edu>
	<46B2F24717394AB79664BB4732E18E77@NewLife>
Message-ID: <466C8637A0E1498483C046DC400A6AC5@NewLife>

( btw, je ne savvy pas: that should be Bio::DB::Sam (in the Bio-SamTools 
distribution) -- ugh MAJ)
----- Original Message ----- 
From: "Mark A. Jensen" <maj at fortinbras.us>
To: "Robert Buels" <rmb32 at cornell.edu>; "BioPerl List" 
<bioperl-l at lists.open-bio.org>; "Dan Kortschak" <dan.kortschak at adelaide.edu.au>
Sent: Tuesday, February 09, 2010 4:21 PM
Subject: Re: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?


> Yeah, this is getting kinda hairy-- B:T:R:Samtools is
> a basic wrapper for anything that wants to use
> Bio::DB::Samtools ( lstein's samtools library wrapper,
> a CPAN and not a BioPerl module. Savvy?). Because
> its likely that other parser-like modules will want to
> use samtools ( as well as wrapper-like modules), I
> would vote for moving Samtools and Samtools::Config
> into the bioperl-live version of Bio::Tools::Run.
> (A question for another day is, should we/can we
> coalesce the two instances of Bio::Tools:Run,
> and where?)
> MAJ
>
>
> ----- Original Message ----- 
> From: "Robert Buels" <rmb32 at cornell.edu>
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>; "Dan Kortschak" 
> <dan.kortschak at adelaide.edu.au>
> Sent: Tuesday, February 09, 2010 3:27 PM
> Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?
>
>
>> Bio::Assembly::IO::bowtie uses Bio::Tools::Run::Samtools, which is part of 
>> bioperl-run.  Doesn't that introduce a circular dependency between 
>> bioperl-live and bioperl-run?
>>
>> Perhaps it should be split out into its own CPAN distribution that depends on 
>> both bioperl-run and bioperl-live?  Or maybe some way can be found for it to 
>> not use Bio::Tools::Run::Samtools?
>>
>> Rob
>>
>> -- 
>> Robert Buels
>> Bioinformatics Analyst, Sol Genomics Network
>> Boyce Thompson Institute for Plant Research
>> Tower Rd
>> Ithaca, NY  14853
>> Tel: 503-889-8539
>> rmb32 at cornell.edu
>> http://www.sgn.cornell.edu
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From bluecurio at gmail.com  Wed Feb 10 02:44:59 2010
From: bluecurio at gmail.com (Daniel Renfro)
Date: Wed, 10 Feb 2010 01:44:59 -0600
Subject: [Bioperl-l] writing GFF3
Message-ID: <25c0f63d1002092344h4c11bf62la5765f5446de05b2@mail.gmail.com>

I'm working on a class to compare two Seq objects (tentatively called
"SeqDiff" for now.) It works great, but as of now just spits out hashes of
differences. Instead of printing these differences to the screen (which is
fine for my test genome of 9 features) I would like to create some GFF3 that
I can load into GBrowse. I could just print the 9 columns, but I'm sure
there is something that could do this better/already. I found two packages
in BioPerl, which one should I be using?

Bio::FeatureIO::gff
Bio::Tools::gff

Also, I vaguely recall something being said about deprecating Bio::FeatureIO
at the BioPerl meeting in San Diego (prior to the GMOD meeting.) -- or I
could be mixing things up.

-Daniel Renfro

http://ecoliwiki.net/User:DanielRenfro
Hu Lab Research Associate
979-862-4055

From cjfields at illinois.edu  Wed Feb 10 08:27:35 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 10 Feb 2010 07:27:35 -0600
Subject: [Bioperl-l] writing GFF3
In-Reply-To: <25c0f63d1002092344h4c11bf62la5765f5446de05b2@mail.gmail.com>
References: <25c0f63d1002092344h4c11bf62la5765f5446de05b2@mail.gmail.com>
Message-ID: <D8B89167-750F-4D5D-B113-1D94DE024ADD@illinois.edu>

Daniel,

I'm in the process of refactoring Bio::FeatureIO to remove Bio::SeqFeature::Annotated and work with Bio::DB::SeqFeature::Store, which may take a little time (I've started on the gff/gtf stuff already, just need to build the handler for the information and standardize a few things).  I would suggest going with Bio::DB::SeqFeature::Store's memory implementation if the features are few, or you could also try Bio::Tools::GFF.

chris

On Feb 10, 2010, at 1:44 AM, Daniel Renfro wrote:

> I'm working on a class to compare two Seq objects (tentatively called
> "SeqDiff" for now.) It works great, but as of now just spits out hashes of
> differences. Instead of printing these differences to the screen (which is
> fine for my test genome of 9 features) I would like to create some GFF3 that
> I can load into GBrowse. I could just print the 9 columns, but I'm sure
> there is something that could do this better/already. I found two packages
> in BioPerl, which one should I be using?
> 
> Bio::FeatureIO::gff
> Bio::Tools::gff
> 
> Also, I vaguely recall something being said about deprecating Bio::FeatureIO
> at the BioPerl meeting in San Diego (prior to the GMOD meeting.) -- or I
> could be mixing things up.
> 
> -Daniel Renfro
> 
> http://ecoliwiki.net/User:DanielRenfro
> Hu Lab Research Associate
> 979-862-4055
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From awitney at sgul.ac.uk  Wed Feb 10 09:30:10 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Wed, 10 Feb 2010 14:30:10 +0000
Subject: [Bioperl-l] Adding namespace support to
	Bio::DB::SeqFeature::Store::DBI::Pg
Message-ID: <4A885CF2-8E39-443F-A6DE-6E03CF05BB86@sgul.ac.uk>


I noticed that namespace's didn't work with Bio::DB::SeqFeature::Store::DBI::Pg because when creating the database the CREATE INDEX statements didn't pass through _qualify to add the namespace prefix, thus giving a "relation "typelist_tab" already exists" error.

The patch below fixes this, but the question is does this seem like a good approach?

thanks

adam


Index: Pg.pm
===================================================================
--- Pg.pm	(revision 16551)
+++ Pg.pm	(working copy)
@@ -256,22 +256,20 @@
   indexed  int default 1,
   object     bytea not null
 );
-  CREATE INDEX feature_stuff ON feature(seqid,tier,bin,typeid);
-  CREATE INDEX feature_typeid ON feature(typeid);
 END
 
 	  locationlist => <<END,
 (
   id         serial primary key,
   seqname    varchar(256)   not null
-); CREATE INDEX locationlist_seqname ON locationlist(seqname);
+);
 END
 
 	  typelist => <<END,
 (
   id       serial primary key,
   tag      varchar(256)  not null
-); CREATE INDEX typelist_tab ON typelist(tag);
+);
 END
 	  name => <<END,
 (
@@ -279,8 +277,6 @@
   name         varchar(256)  not null,
   display_name int       default 0
 );
-  CREATE INDEX name_id ON name(id);
-  CREATE INDEX name_name ON name(name);
 END
 
 	  attribute => <<END,
@@ -289,8 +285,6 @@
   attribute_id     int   not null,
   attribute_value  text
 );
-  CREATE INDEX attribute_id ON attribute(id);
-  CREATE INDEX attribute_id_val ON attribute(attribute_id,SUBSTR(attribute_value, 1, 10));
 END
 
 	  attributelist => <<END,
@@ -298,14 +292,12 @@
   id       serial primary key,
   tag      varchar(256)  not null
 );
-  CREATE INDEX attributelist_tag ON attributelist(tag);
 END
 	  parent2child => <<END,
 (
   id               int       not null,
   child            int       not null
 );
-  CREATE INDEX parent2child_id_child ON parent2child(id,child);
 END
 
 	  meta => <<END,
@@ -325,6 +317,22 @@
 	 };
 }
 
+sub index_definitions {
+  my $self = shift;
+  return {
+	  feature_stuff  => "feature(seqid,tier,bin,typeid)",
+	  feature_typeid => "feature(typeid)",
+	  locationlist_seqname => "locationlist(seqname)",
+      typelist_tab => "typelist(tag)",
+      name_id => "name(id)",
+      name_name => "name(name)",
+      attribute_id => "attribute(id)",
+      attribute_id_val => "attribute(attribute_id,SUBSTR(attribute_value, 1, 10))",
+      attributelist_tag =>  "attributelist(tag)",
+      parent2child_id_child => "parent2child(id,child)",
+	 };
+}
+
 sub schema {
   my ($self, $schema) = @_;
   $self->{'schema'} = $schema if defined($schema);
@@ -354,6 +362,18 @@
 			$dbh->do($query) or $self->throw($dbh->errstr);
 		}
   }
+  
+  my $indexes = $self->index_definitions;
+  foreach (keys %$indexes) {
+    my $index = $self->_qualify($_);
+    my $index_def = $self->_qualify($indexes->{$_});
+    $dbh->do("DROP INDEX IF EXISTS $index") if $erase;
+    my @index_exists = $dbh->selectrow_array("SELECT * FROM pg_indexes WHERE indexname = '$index'");
+		if (!scalar(@index_exists)) {
+			my $query = "CREATE INDEX $index ON $index_def";
+			$dbh->do($query) or $self->throw($dbh->errstr);
+		}
+  }
   $self->subfeatures_are_indexed(1) if $erase;
   1;
 }





From scott at scottcain.net  Wed Feb 10 10:16:07 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 10 Feb 2010 10:16:07 -0500
Subject: [Bioperl-l] writing GFF3
In-Reply-To: <25c0f63d1002092344h4c11bf62la5765f5446de05b2@mail.gmail.com>
References: <25c0f63d1002092344h4c11bf62la5765f5446de05b2@mail.gmail.com>
Message-ID: <4536f7701002100716m3d874e70g49c134bf29072a52@mail.gmail.com>

Hi Daniel,

What I would do depends on how complicated your features are.  If
there are not parent child relationships, it would probably be easiest
to just print the GFF yourself rather than going through a module.
The beauty of GFF3 is that it is pretty easy to write (at least for
the simple stuff).  If it is more complicated, you could look at using
one of the BioPerl modules.

Scott

On Wed, Feb 10, 2010 at 2:44 AM, Daniel Renfro <bluecurio at gmail.com> wrote:
> I'm working on a class to compare two Seq objects (tentatively called
> "SeqDiff" for now.) It works great, but as of now just spits out hashes of
> differences. Instead of printing these differences to the screen (which is
> fine for my test genome of 9 features) I would like to create some GFF3 that
> I can load into GBrowse. I could just print the 9 columns, but I'm sure
> there is something that could do this better/already. I found two packages
> in BioPerl, which one should I be using?
>
> Bio::FeatureIO::gff
> Bio::Tools::gff
>
> Also, I vaguely recall something being said about deprecating Bio::FeatureIO
> at the BioPerl meeting in San Diego (prior to the GMOD meeting.) -- or I
> could be mixing things up.
>
> -Daniel Renfro
>
> http://ecoliwiki.net/User:DanielRenfro
> Hu Lab Research Associate
> 979-862-4055
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

From sherisim at gmail.com  Mon Feb  8 18:31:51 2010
From: sherisim at gmail.com (Sheri Simmons)
Date: Mon, 8 Feb 2010 18:31:51 -0500 (EST)
Subject: [Bioperl-l] issues with installation in home directory
Message-ID: <10560647.761265671907371.JavaMail.GREIGITE$@Greigite>

hi,
Apologies for the stupid question, but I think I am missing something basic. I installed Bioperl 1.6.1 in my home directory on a shared system and wrote a simple fastq converter script with headers as follows:

#!/usr/bin/perl -w
#use strict;
# program to convert FASTQ files generated with Illumina pipeline 1.3+ to Sanger format FASTQ files

use lib "/home/perl_modules/";
use Bio::Perl;
use Bio::SeqIO;

However, when I run the script I get this error:

Can't locate object method "FASTQ" via package "parser" (perhaps you forgot to load "parser"?)


What is the parser package referred to here? I have written lots of Bioperl scripts and never seen this before, but I always used to use a system installation of Bioperl.


From maj at fortinbras.us  Wed Feb 10 11:55:43 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 10 Feb 2010 11:55:43 -0500
Subject: [Bioperl-l] issues with installation in home directory
In-Reply-To: <10560647.761265671907371.JavaMail.GREIGITE$@Greigite>
References: <10560647.761265671907371.JavaMail.GREIGITE$@Greigite>
Message-ID: <2B53762E213A485C96E9B106CB58BDF4@NewLife>

Hi Sheri-- better send the whole script; error is
reminiscent of a typo bug.
MAJ
----- Original Message ----- 
From: "Sheri Simmons" <sherisim at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Monday, February 08, 2010 6:31 PM
Subject: [Bioperl-l] issues with installation in home directory


> hi,
> Apologies for the stupid question, but I think I am missing something basic. I 
> installed Bioperl 1.6.1 in my home directory on a shared system and wrote a 
> simple fastq converter script with headers as follows:
>
> #!/usr/bin/perl -w
> #use strict;
> # program to convert FASTQ files generated with Illumina pipeline 1.3+ to 
> Sanger format FASTQ files
>
> use lib "/home/perl_modules/";
> use Bio::Perl;
> use Bio::SeqIO;
>
> However, when I run the script I get this error:
>
> Can't locate object method "FASTQ" via package "parser" (perhaps you forgot to 
> load "parser"?)
>
>
> What is the parser package referred to here? I have written lots of Bioperl 
> scripts and never seen this before, but I always used to use a system 
> installation of Bioperl.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From rvos at interchange.ubc.ca  Wed Feb 10 11:55:58 2010
From: rvos at interchange.ubc.ca (Rutger Vos)
Date: Wed, 10 Feb 2010 16:55:58 +0000
Subject: [Bioperl-l] issues with installation in home directory
In-Reply-To: <5763_1265820717_1265820717_4924_1265820715_1265820715_10560647.761265671907371.JavaMail.GREIGITE$@Greigite>
References: <5763_1265820717_1265820717_4924_1265820715_1265820715_10560647.761265671907371.JavaMail.GREIGITE$@Greigite>
Message-ID: <2bb9b24a1002100855s66a3aee7jf25011990c3f112@mail.gmail.com>

There must be something wrong elsewhere in the script, is it possible
there's a typo further down the line? What you have here looks ok to
me.

On Mon, Feb 8, 2010 at 11:31 PM, Sheri Simmons <sherisim at gmail.com> wrote:
> hi,
> Apologies for the stupid question, but I think I am missing something basic. I installed Bioperl 1.6.1 in my home directory on a shared system and wrote a simple fastq converter script with headers as follows:
>
> #!/usr/bin/perl -w
> #use strict;
> # program to convert FASTQ files generated with Illumina pipeline 1.3+ to Sanger format FASTQ files
>
> use lib "/home/perl_modules/";
> use Bio::Perl;
> use Bio::SeqIO;
>
> However, when I run the script I get this error:
>
> Can't locate object method "FASTQ" via package "parser" (perhaps you forgot to load "parser"?)
>
>
> What is the parser package referred to here? I have written lots of Bioperl scripts and never seen this before, but I always used to use a system installation of Bioperl.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

From scott at scottcain.net  Wed Feb 10 14:35:48 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 10 Feb 2010 14:35:48 -0500
Subject: [Bioperl-l] Adding namespace support to
	Bio::DB::SeqFeature::Store::DBI::Pg
In-Reply-To: <4A885CF2-8E39-443F-A6DE-6E03CF05BB86@sgul.ac.uk>
References: <4A885CF2-8E39-443F-A6DE-6E03CF05BB86@sgul.ac.uk>
Message-ID: <4536f7701002101135s4694ff9bpb4232ac8b7eb0e21@mail.gmail.com>

Hi Adam,

I don't have a problem with this approach. Can you verify that this
patch still passes the Pg SFS tests? I don't generally use
schemas/name spaces (same thing,right?) much, so I wouldn't feel
comfortable evaluting it completely.  And, even better, could you add
to the tests that exercise this behavior?

Thanks,
Scott


On Wednesday, February 10, 2010, Adam Witney <awitney at sgul.ac.uk> wrote:
>
> I noticed that namespace's didn't work with Bio::DB::SeqFeature::Store::DBI::Pg because when creating the database the CREATE INDEX statements didn't pass through _qualify to add the namespace prefix, thus giving a "relation "typelist_tab" already exists" error.
>
> The patch below fixes this, but the question is does this seem like a good approach?
>
> thanks
>
> adam
>
>
> Index: Pg.pm
> ===================================================================
> --- Pg.pm ? ? ? (revision 16551)
> +++ Pg.pm ? ? ? (working copy)
> @@ -256,22 +256,20 @@
>  ? indexed ?int default 1,
>  ? object ? ? bytea not null
> ?);
> - ?CREATE INDEX feature_stuff ON feature(seqid,tier,bin,typeid);
> - ?CREATE INDEX feature_typeid ON feature(typeid);
> ?END
>
>  ? ? ? ? ?locationlist => <<END,
> ?(
>  ? id ? ? ? ? serial primary key,
>  ? seqname ? ?varchar(256) ? not null
> -); CREATE INDEX locationlist_seqname ON locationlist(seqname);
> +);
> ?END
>
>  ? ? ? ? ?typelist => <<END,
> ?(
>  ? id ? ? ? serial primary key,
>  ? tag ? ? ?varchar(256) ?not null
> -); CREATE INDEX typelist_tab ON typelist(tag);
> +);
> ?END
>  ? ? ? ? ?name => <<END,
> ?(
> @@ -279,8 +277,6 @@
>  ? name ? ? ? ? varchar(256) ?not null,
>  ? display_name int ? ? ? default 0
> ?);
> - ?CREATE INDEX name_id ON name(id);
> - ?CREATE INDEX name_name ON name(name);
> ?END
>
>  ? ? ? ? ?attribute => <<END,
> @@ -289,8 +285,6 @@
>  ? attribute_id ? ? int ? not null,
>  ? attribute_value ?text
> ?);
> - ?CREATE INDEX attribute_id ON attribute(id);
> - ?CREATE INDEX attribute_id_val ON attribute(attribute_id,SUBSTR(attribute_value, 1, 10));
> ?END
>
>  ? ? ? ? ?attributelist => <<END,
> @@ -298,14 +292,12 @@
>  ? id ? ? ? serial primary key,
>  ? tag ? ? ?varchar(256) ?not null
> ?);
> - ?CREATE INDEX attributelist_tag ON attributelist(tag);
> ?END
>  ? ? ? ? ?parent2child => <<END,
> ?(
>  ? id ? ? ? ? ? ? ? int ? ? ? not null,
>  ? child ? ? ? ? ? ?int ? ? ? not null
> ?);
> - ?CREATE INDEX parent2child_id_child ON parent2child(id,child);
> ?END
>
>  ? ? ? ? ?meta => <<END,
> @@ -325,6 +317,22 @@
>  ? ? ? ? };
> ?}
>
> +sub index_definitions {
> + ?my $self = shift;
> + ?return {
> + ? ? ? ? feature_stuff ?=> "feature(seqid,tier,bin,typeid)",
> + ? ? ? ? feature_typeid => "feature(typeid)",
> + ? ? ? ? locationlist_seqname => "locationlist(seqname)",
> + ? ? ?typelist_tab => "typelist(tag)",
> + ? ? ?name_id => "name(id)",
> + ? ? ?name_name => "name(name)",
> + ? ? ?attribute_id => "attribute(id)",
> + ? ? ?attribute_id_val => "attribute(attribute_id,SUBSTR(attribute_value, 1, 10))",
> + ? ? ?attributelist_tag => ?"attributelist(tag)",
> + ? ? ?parent2child_id_child => "parent2child(id,child)",
> + ? ? ? ?};
> +}
> +
> ?sub schema {
>  ? my ($self, $schema) = @_;
>  ? $self->{'schema'} = $schema if defined($schema);
> @@ -354,6 +362,18 @@
>  ? ? ? ? ? ? ? ? ? ? ? ?$dbh->do($query) or $self->throw($dbh->errstr);
>  ? ? ? ? ? ? ? ?}
>  ? }
> +
> + ?my $indexes = $self->index_definitions;
> + ?foreach (keys %$indexes) {
> + ? ?my $index = $self->_qualify($_);
> + ? ?my $index_def = $self->_qualify($indexes->{$_});
> + ? ?$dbh->do("DROP INDEX IF EXISTS $index") if $erase;
> + ? ?my @index_exists = $dbh->selectrow_array("SELECT * FROM pg_indexes WHERE indexname = '$index'");
> + ? ? ? ? ? ? ? if (!scalar(@index_exists)) {
> + ? ? ? ? ? ? ? ? ? ? ? my $query = "CREATE INDEX $index ON $index_def";
> + ? ? ? ? ? ? ? ? ? ? ? $dbh->do($query) or $self->throw($dbh->errstr);
> + ? ? ? ? ? ? ? }
> + ?}
>  ? $self->subfeatures_are_indexed(1) if $erase;
>  ? 1;
> ?}
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


From bhakti.dwivedi at gmail.com  Wed Feb 10 23:35:52 2010
From: bhakti.dwivedi at gmail.com (Bhakti Dwivedi)
Date: Wed, 10 Feb 2010 23:35:52 -0500
Subject: [Bioperl-l] how to retrieve classification from a taxon name or
	taxon id?
Message-ID: <b643abd21002102035qaa72e94t3115849c89336404@mail.gmail.com>

Hi,

For a given taxon name (or taxon ID), how can I retrieve the classification
(Family in specific)?

Thanks!

From shalabh.sharma7 at gmail.com  Wed Feb 10 23:56:42 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 10 Feb 2010 23:56:42 -0500
Subject: [Bioperl-l] how to retrieve classification from a taxon name or
	taxon id?
In-Reply-To: <b643abd21002102035qaa72e94t3115849c89336404@mail.gmail.com>
References: <b643abd21002102035qaa72e94t3115849c89336404@mail.gmail.com>
Message-ID: <9fcc48c71002102056l21c12814ycd877118da004a65@mail.gmail.com>

Bhakti,
          This is can done by using Bio::taxon

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html

<http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html>-Shalabh
Sharma


On Wed, Feb 10, 2010 at 11:35 PM, Bhakti Dwivedi
<bhakti.dwivedi at gmail.com>wrote:

> Hi,
>
> For a given taxon name (or taxon ID), how can I retrieve the classification
> (Family in specific)?
>
> Thanks!
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From bhakti.dwivedi at gmail.com  Wed Feb 10 23:57:34 2010
From: bhakti.dwivedi at gmail.com (Bhakti Dwivedi)
Date: Wed, 10 Feb 2010 23:57:34 -0500
Subject: [Bioperl-l] how to get consensus_iupac from dna alignment that has
	lot of iupac ambiguity codes?
Message-ID: <b643abd21002102057v66a4887dv10867c2ae37239dd@mail.gmail.com>

Hi,

I am trying to make a consensus for the nucleotide sequence alignment.
 The alignment sequences, however contain a lot of
IUPAC ambiquity codes.  And this seems to throw off an error message
(indicating that it is a protein sequence) when I use
consensus_iupac().
How can I fix this?  Do I have to manually define the dna iupac alphabets?

I will appreciate any kind of help. Thanks!

Bhakti

From awitney at sgul.ac.uk  Thu Feb 11 06:35:14 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 11 Feb 2010 11:35:14 +0000
Subject: [Bioperl-l] Adding namespace support to
	Bio::DB::SeqFeature::Store::DBI::Pg
In-Reply-To: <4536f7701002101135s4694ff9bpb4232ac8b7eb0e21@mail.gmail.com>
References: <4A885CF2-8E39-443F-A6DE-6E03CF05BB86@sgul.ac.uk>
	<4536f7701002101135s4694ff9bpb4232ac8b7eb0e21@mail.gmail.com>
Message-ID: <9B5BDE90-FA5F-42B4-BE6B-3B86CCE8D7F5@sgul.ac.uk>


Hi Scott,

This actually only implements it in the same way as it does for the mysql version and does not make use of PostgeSQL schemas. That is it adds a namespace prefix with an underscore to the table names.

I think it should be workable using PostgreSQL schemas, but this will then work differently to the mysql version, is that a problem?

thanks

adam

On 10 Feb 2010, at 19:35, Scott Cain wrote:

> Hi Adam,
> 
> I don't have a problem with this approach. Can you verify that this
> patch still passes the Pg SFS tests? I don't generally use
> schemas/name spaces (same thing,right?) much, so I wouldn't feel
> comfortable evaluting it completely.  And, even better, could you add
> to the tests that exercise this behavior?
> 
> Thanks,
> Scott
> 
> 
> On Wednesday, February 10, 2010, Adam Witney <awitney at sgul.ac.uk> wrote:
>> 
>> I noticed that namespace's didn't work with Bio::DB::SeqFeature::Store::DBI::Pg because when creating the database the CREATE INDEX statements didn't pass through _qualify to add the namespace prefix, thus giving a "relation "typelist_tab" already exists" error.
>> 
>> The patch below fixes this, but the question is does this seem like a good approach?
>> 
>> thanks
>> 
>> adam
>> 
>> 
>> Index: Pg.pm
>> ===================================================================
>> --- Pg.pm       (revision 16551)
>> +++ Pg.pm       (working copy)
>> @@ -256,22 +256,20 @@
>>   indexed  int default 1,
>>   object     bytea not null
>>  );
>> -  CREATE INDEX feature_stuff ON feature(seqid,tier,bin,typeid);
>> -  CREATE INDEX feature_typeid ON feature(typeid);
>>  END
>> 
>>          locationlist => <<END,
>>  (
>>   id         serial primary key,
>>   seqname    varchar(256)   not null
>> -); CREATE INDEX locationlist_seqname ON locationlist(seqname);
>> +);
>>  END
>> 
>>          typelist => <<END,
>>  (
>>   id       serial primary key,
>>   tag      varchar(256)  not null
>> -); CREATE INDEX typelist_tab ON typelist(tag);
>> +);
>>  END
>>          name => <<END,
>>  (
>> @@ -279,8 +277,6 @@
>>   name         varchar(256)  not null,
>>   display_name int       default 0
>>  );
>> -  CREATE INDEX name_id ON name(id);
>> -  CREATE INDEX name_name ON name(name);
>>  END
>> 
>>          attribute => <<END,
>> @@ -289,8 +285,6 @@
>>   attribute_id     int   not null,
>>   attribute_value  text
>>  );
>> -  CREATE INDEX attribute_id ON attribute(id);
>> -  CREATE INDEX attribute_id_val ON attribute(attribute_id,SUBSTR(attribute_value, 1, 10));
>>  END
>> 
>>          attributelist => <<END,
>> @@ -298,14 +292,12 @@
>>   id       serial primary key,
>>   tag      varchar(256)  not null
>>  );
>> -  CREATE INDEX attributelist_tag ON attributelist(tag);
>>  END
>>          parent2child => <<END,
>>  (
>>   id               int       not null,
>>   child            int       not null
>>  );
>> -  CREATE INDEX parent2child_id_child ON parent2child(id,child);
>>  END
>> 
>>          meta => <<END,
>> @@ -325,6 +317,22 @@
>>         };
>>  }
>> 
>> +sub index_definitions {
>> +  my $self = shift;
>> +  return {
>> +         feature_stuff  => "feature(seqid,tier,bin,typeid)",
>> +         feature_typeid => "feature(typeid)",
>> +         locationlist_seqname => "locationlist(seqname)",
>> +      typelist_tab => "typelist(tag)",
>> +      name_id => "name(id)",
>> +      name_name => "name(name)",
>> +      attribute_id => "attribute(id)",
>> +      attribute_id_val => "attribute(attribute_id,SUBSTR(attribute_value, 1, 10))",
>> +      attributelist_tag =>  "attributelist(tag)",
>> +      parent2child_id_child => "parent2child(id,child)",
>> +        };
>> +}
>> +
>>  sub schema {
>>   my ($self, $schema) = @_;
>>   $self->{'schema'} = $schema if defined($schema);
>> @@ -354,6 +362,18 @@
>>                        $dbh->do($query) or $self->throw($dbh->errstr);
>>                }
>>   }
>> +
>> +  my $indexes = $self->index_definitions;
>> +  foreach (keys %$indexes) {
>> +    my $index = $self->_qualify($_);
>> +    my $index_def = $self->_qualify($indexes->{$_});
>> +    $dbh->do("DROP INDEX IF EXISTS $index") if $erase;
>> +    my @index_exists = $dbh->selectrow_array("SELECT * FROM pg_indexes WHERE indexname = '$index'");
>> +               if (!scalar(@index_exists)) {
>> +                       my $query = "CREATE INDEX $index ON $index_def";
>> +                       $dbh->do($query) or $self->throw($dbh->errstr);
>> +               }
>> +  }
>>   $self->subfeatures_are_indexed(1) if $erase;
>>   1;
>>  }
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research



From torsten.seemann at infotech.monash.edu.au  Thu Feb 11 06:43:04 2010
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Thu, 11 Feb 2010 22:43:04 +1100
Subject: [Bioperl-l] writing GFF3
In-Reply-To: <25c0f63d1002092344h4c11bf62la5765f5446de05b2@mail.gmail.com>
References: <25c0f63d1002092344h4c11bf62la5765f5446de05b2@mail.gmail.com>
Message-ID: <a79f6a4b1002110343ha9b3f7di2d3efec2456a451d@mail.gmail.com>

> I would like to create some GFF3 that
> I can load into GBrowse. I could just print the 9 columns, but I'm sure
> there is something that could do this better/already. I found two packages
> in BioPerl, which one should I be using?
> Bio::FeatureIO::gff
> Bio::Tools::gff
> Also, I vaguely recall something being said about deprecating Bio::FeatureIO
> at the BioPerl meeting in San Diego (prior to the GMOD meeting.) -- or I
> could be mixing things up.

I have done similar things to you, and here is the skeleton code I use
based on Bio::Tools::GFF. (FeatureIO::GFF is problematic). Just fill
in the ? with values from your %diff hash.

use Bio::Tools::GFF;
use Bio::SeqFeature::Generic;

my $gff_factory = Bio::Tools::GFF->new(-gff_version=>3);

print "##gff-version 3\n";

for my $diff (keys %diff) {
  my $feature = Bio::SeqFeature::Generic->new(
    -seq_id     => ?,    -source_tag => ?,    -primary    => ?,
    -start      => ?,    -end        => ?,    -strand     => ?,
    -tag        => {      'name' => ?,      'name' =>  ?   }
  );
  print $feature->gff_string($gff_factory), "\n";
}


--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
University, AUSTRALIA

From torsten.seemann at infotech.monash.edu.au  Thu Feb 11 06:52:12 2010
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Thu, 11 Feb 2010 22:52:12 +1100
Subject: [Bioperl-l] string comparision mismatches and matches
In-Reply-To: <DD9E6B53DD0A4B3BBB650B89E73D4DCB@NewLife>
References: <c7cac1601002030550g7b356f47s42d97de2c6168830@mail.gmail.com> 
	<DD9E6B53DD0A4B3BBB650B89E73D4DCB@NewLife>
Message-ID: <a79f6a4b1002110352l539215cbn95151e6c13f5490d@mail.gmail.com>

> $in = 'ACCTCCTCCTCGAGTATGTG';
> $tgt = 'TATCTTGCGCCGGAGATAAT';
> $mask = pack("A*",$in)^pack("A*",$tgt);
> $matches = $mask =~ tr/"\x0"/"\x0"/;

Impressive! Not often you see pack() let alone exclusive-or with a
scalar context tr// thrown in for good measure!

For those who don't follow what it is doing, here is my (possibly
wrong) interpretation: The pack() is converting each of the two (equal
length) strings into a byte set. A bit-wise exclusive-or (XOR) is
performed between these two byte sets. This will create bytes of value
zero (0) where they were the same, and non-zero where they were
different. The tr// then counts how many of the bytes were zero (\x0
is ascii zero).

I'll just assume it is more efficient than for/substr/eq :-)

--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
University, AUSTRALIA

From maj at fortinbras.us  Thu Feb 11 08:43:37 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 11 Feb 2010 08:43:37 -0500
Subject: [Bioperl-l] string comparision mismatches and matches
In-Reply-To: <a79f6a4b1002110352l539215cbn95151e6c13f5490d@mail.gmail.com>
References: <c7cac1601002030550g7b356f47s42d97de2c6168830@mail.gmail.com>
	<DD9E6B53DD0A4B3BBB650B89E73D4DCB@NewLife>
	<a79f6a4b1002110352l539215cbn95151e6c13f5490d@mail.gmail.com>
Message-ID: <7666500BA717407FA55C0D5221E24282@NewLife>

Perfectly described, Torsten. Yes, I confess a certain pride in this hack....
Roopa reports that it sped up her script 3X. cheers MAJ
----- Original Message ----- 
From: "Torsten Seemann" <torsten.seemann at infotech.monash.edu.au>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Roopa Raghuveer" <rtbio.2009 at gmail.com>; <bioperl-l at lists.open-bio.org>
Sent: Thursday, February 11, 2010 6:52 AM
Subject: Re: [Bioperl-l] string comparision mismatches and matches


>> $in = 'ACCTCCTCCTCGAGTATGTG';
>> $tgt = 'TATCTTGCGCCGGAGATAAT';
>> $mask = pack("A*",$in)^pack("A*",$tgt);
>> $matches = $mask =~ tr/"\x0"/"\x0"/;
> 
> Impressive! Not often you see pack() let alone exclusive-or with a
> scalar context tr// thrown in for good measure!
> 
> For those who don't follow what it is doing, here is my (possibly
> wrong) interpretation: The pack() is converting each of the two (equal
> length) strings into a byte set. A bit-wise exclusive-or (XOR) is
> performed between these two byte sets. This will create bytes of value
> zero (0) where they were the same, and non-zero where they were
> different. The tr// then counts how many of the bytes were zero (\x0
> is ascii zero).
> 
> I'll just assume it is more efficient than for/substr/eq :-)
> 
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
> University, AUSTRALIA
> 
>

From bernd.web at gmail.com  Thu Feb 11 08:59:53 2010
From: bernd.web at gmail.com (Bernd Web)
Date: Thu, 11 Feb 2010 14:59:53 +0100
Subject: [Bioperl-l] string comparision mismatches and matches
In-Reply-To: <7666500BA717407FA55C0D5221E24282@NewLife>
References: <c7cac1601002030550g7b356f47s42d97de2c6168830@mail.gmail.com>
	<DD9E6B53DD0A4B3BBB650B89E73D4DCB@NewLife>
	<a79f6a4b1002110352l539215cbn95151e6c13f5490d@mail.gmail.com>
	<7666500BA717407FA55C0D5221E24282@NewLife>
Message-ID: <716af09c1002110559h7b8d538es4364537e4d2864c4@mail.gmail.com>

Hi Mark,

Indeed nice.
Just one question
Why is pack used? It is faster? ^ works on strings too.

$mask = $in ^ $tgt;
$matches = $mask =~ tr/\x0/\x0/;

(btw I had to remove the "" around \x01 in tr)

Regards.

On Thu, Feb 11, 2010 at 2:43 PM, Mark A. Jensen <maj at fortinbras.us> wrote:
> Perfectly described, Torsten. Yes, I confess a certain pride in this
> hack....
> Roopa reports that it sped up her script 3X. cheers MAJ
> ----- Original Message ----- From: "Torsten Seemann"
> <torsten.seemann at infotech.monash.edu.au>
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: "Roopa Raghuveer" <rtbio.2009 at gmail.com>; <bioperl-l at lists.open-bio.org>
> Sent: Thursday, February 11, 2010 6:52 AM
> Subject: Re: [Bioperl-l] string comparision mismatches and matches
>
>
>>> $in = 'ACCTCCTCCTCGAGTATGTG';
>>> $tgt = 'TATCTTGCGCCGGAGATAAT';
>>> $mask = pack("A*",$in)^pack("A*",$tgt);
>>> $matches = $mask =~ tr/"\x0"/"\x0"/;
>>
>> Impressive! Not often you see pack() let alone exclusive-or with a
>> scalar context tr// thrown in for good measure!
>>
>> For those who don't follow what it is doing, here is my (possibly
>> wrong) interpretation: The pack() is converting each of the two (equal
>> length) strings into a byte set. A bit-wise exclusive-or (XOR) is
>> performed between these two byte sets. This will create bytes of value
>> zero (0) where they were the same, and non-zero where they were
>> different. The tr// then counts how many of the bytes were zero (\x0
>> is ascii zero).
>>
>> I'll just assume it is more efficient than for/substr/eq :-)
>>
>> --Torsten Seemann
>> --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
>> University, AUSTRALIA
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From awitney at sgul.ac.uk  Thu Feb 11 09:21:52 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 11 Feb 2010 14:21:52 +0000
Subject: [Bioperl-l] Adding namespace support to
	Bio::DB::SeqFeature::Store::DBI::Pg
In-Reply-To: <4536f7701002101135s4694ff9bpb4232ac8b7eb0e21@mail.gmail.com>
References: <4A885CF2-8E39-443F-A6DE-6E03CF05BB86@sgul.ac.uk>
	<4536f7701002101135s4694ff9bpb4232ac8b7eb0e21@mail.gmail.com>
Message-ID: <18F52839-7085-4AF8-ACDC-10432475F1F1@sgul.ac.uk>


Hi Scott,

ok I now have a version working with PostgreSQL schemas.

I was looking for the SFS tests, but can only find SeqFeature.t which only tests the "memory" adaptor. Are there any tests for the mysql/Pg adaptors?

thanks

adam

On 10 Feb 2010, at 19:35, Scott Cain wrote:

> Hi Adam,
> 
> I don't have a problem with this approach. Can you verify that this
> patch still passes the Pg SFS tests? I don't generally use
> schemas/name spaces (same thing,right?) much, so I wouldn't feel
> comfortable evaluting it completely.  And, even better, could you add
> to the tests that exercise this behavior?
> 
> Thanks,
> Scott
> 
> 
> On Wednesday, February 10, 2010, Adam Witney <awitney at sgul.ac.uk> wrote:
>> 
>> I noticed that namespace's didn't work with Bio::DB::SeqFeature::Store::DBI::Pg because when creating the database the CREATE INDEX statements didn't pass through _qualify to add the namespace prefix, thus giving a "relation "typelist_tab" already exists" error.
>> 
>> The patch below fixes this, but the question is does this seem like a good approach?
>> 
>> thanks
>> 
>> adam
>> 
>> 
>> Index: Pg.pm
>> ===================================================================
>> --- Pg.pm       (revision 16551)
>> +++ Pg.pm       (working copy)
>> @@ -256,22 +256,20 @@
>>   indexed  int default 1,
>>   object     bytea not null
>>  );
>> -  CREATE INDEX feature_stuff ON feature(seqid,tier,bin,typeid);
>> -  CREATE INDEX feature_typeid ON feature(typeid);
>>  END
>> 
>>          locationlist => <<END,
>>  (
>>   id         serial primary key,
>>   seqname    varchar(256)   not null
>> -); CREATE INDEX locationlist_seqname ON locationlist(seqname);
>> +);
>>  END
>> 
>>          typelist => <<END,
>>  (
>>   id       serial primary key,
>>   tag      varchar(256)  not null
>> -); CREATE INDEX typelist_tab ON typelist(tag);
>> +);
>>  END
>>          name => <<END,
>>  (
>> @@ -279,8 +277,6 @@
>>   name         varchar(256)  not null,
>>   display_name int       default 0
>>  );
>> -  CREATE INDEX name_id ON name(id);
>> -  CREATE INDEX name_name ON name(name);
>>  END
>> 
>>          attribute => <<END,
>> @@ -289,8 +285,6 @@
>>   attribute_id     int   not null,
>>   attribute_value  text
>>  );
>> -  CREATE INDEX attribute_id ON attribute(id);
>> -  CREATE INDEX attribute_id_val ON attribute(attribute_id,SUBSTR(attribute_value, 1, 10));
>>  END
>> 
>>          attributelist => <<END,
>> @@ -298,14 +292,12 @@
>>   id       serial primary key,
>>   tag      varchar(256)  not null
>>  );
>> -  CREATE INDEX attributelist_tag ON attributelist(tag);
>>  END
>>          parent2child => <<END,
>>  (
>>   id               int       not null,
>>   child            int       not null
>>  );
>> -  CREATE INDEX parent2child_id_child ON parent2child(id,child);
>>  END
>> 
>>          meta => <<END,
>> @@ -325,6 +317,22 @@
>>         };
>>  }
>> 
>> +sub index_definitions {
>> +  my $self = shift;
>> +  return {
>> +         feature_stuff  => "feature(seqid,tier,bin,typeid)",
>> +         feature_typeid => "feature(typeid)",
>> +         locationlist_seqname => "locationlist(seqname)",
>> +      typelist_tab => "typelist(tag)",
>> +      name_id => "name(id)",
>> +      name_name => "name(name)",
>> +      attribute_id => "attribute(id)",
>> +      attribute_id_val => "attribute(attribute_id,SUBSTR(attribute_value, 1, 10))",
>> +      attributelist_tag =>  "attributelist(tag)",
>> +      parent2child_id_child => "parent2child(id,child)",
>> +        };
>> +}
>> +
>>  sub schema {
>>   my ($self, $schema) = @_;
>>   $self->{'schema'} = $schema if defined($schema);
>> @@ -354,6 +362,18 @@
>>                        $dbh->do($query) or $self->throw($dbh->errstr);
>>                }
>>   }
>> +
>> +  my $indexes = $self->index_definitions;
>> +  foreach (keys %$indexes) {
>> +    my $index = $self->_qualify($_);
>> +    my $index_def = $self->_qualify($indexes->{$_});
>> +    $dbh->do("DROP INDEX IF EXISTS $index") if $erase;
>> +    my @index_exists = $dbh->selectrow_array("SELECT * FROM pg_indexes WHERE indexname = '$index'");
>> +               if (!scalar(@index_exists)) {
>> +                       my $query = "CREATE INDEX $index ON $index_def";
>> +                       $dbh->do($query) or $self->throw($dbh->errstr);
>> +               }
>> +  }
>>   $self->subfeatures_are_indexed(1) if $erase;
>>   1;
>>  }
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From maj at fortinbras.us  Thu Feb 11 09:22:07 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 11 Feb 2010 09:22:07 -0500
Subject: [Bioperl-l] string comparision mismatches and matches
In-Reply-To: <716af09c1002110559h7b8d538es4364537e4d2864c4@mail.gmail.com>
References: <c7cac1601002030550g7b356f47s42d97de2c6168830@mail.gmail.com>
	<DD9E6B53DD0A4B3BBB650B89E73D4DCB@NewLife>
	<a79f6a4b1002110352l539215cbn95151e6c13f5490d@mail.gmail.com>
	<7666500BA717407FA55C0D5221E24282@NewLife>
	<716af09c1002110559h7b8d538es4364537e4d2864c4@mail.gmail.com>
Message-ID: <2667CC0A4DC5407AA384B45DC37841AA@NewLife>

You are right Bernd-- I have used this without pack before,
and I'm sure that's faster that a call to pack(),
but for some strange reason my perl was not behaving;
I was getting $mask == 0 for $in ^ $tgt, as if the operation
were logical and not bitwise.
...further investigation reveals that my cygwin perl (5.10) is
evidently buggy in this regard, for ActiveState perl performs
the bitwise xor directly on the strings as you describe.

(yes, I know...the solution is to get a real operating system....)
Thanks! MAJ

----- Original Message ----- 
From: "Bernd Web" <bernd.web at gmail.com>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Torsten Seemann" <torsten.seemann at infotech.monash.edu.au>; 
<bioperl-l at lists.open-bio.org>; "Roopa Raghuveer" <rtbio.2009 at gmail.com>
Sent: Thursday, February 11, 2010 8:59 AM
Subject: Re: [Bioperl-l] string comparision mismatches and matches


> Hi Mark,
>
> Indeed nice.
> Just one question
> Why is pack used? It is faster? ^ works on strings too.
>
> $mask = $in ^ $tgt;
> $matches = $mask =~ tr/\x0/\x0/;
>
> (btw I had to remove the "" around \x01 in tr)
>
> Regards.
>
> On Thu, Feb 11, 2010 at 2:43 PM, Mark A. Jensen <maj at fortinbras.us> wrote:
>> Perfectly described, Torsten. Yes, I confess a certain pride in this
>> hack....
>> Roopa reports that it sped up her script 3X. cheers MAJ
>> ----- Original Message ----- From: "Torsten Seemann"
>> <torsten.seemann at infotech.monash.edu.au>
>> To: "Mark A. Jensen" <maj at fortinbras.us>
>> Cc: "Roopa Raghuveer" <rtbio.2009 at gmail.com>; <bioperl-l at lists.open-bio.org>
>> Sent: Thursday, February 11, 2010 6:52 AM
>> Subject: Re: [Bioperl-l] string comparision mismatches and matches
>>
>>
>>>> $in = 'ACCTCCTCCTCGAGTATGTG';
>>>> $tgt = 'TATCTTGCGCCGGAGATAAT';
>>>> $mask = pack("A*",$in)^pack("A*",$tgt);
>>>> $matches = $mask =~ tr/"\x0"/"\x0"/;
>>>
>>> Impressive! Not often you see pack() let alone exclusive-or with a
>>> scalar context tr// thrown in for good measure!
>>>
>>> For those who don't follow what it is doing, here is my (possibly
>>> wrong) interpretation: The pack() is converting each of the two (equal
>>> length) strings into a byte set. A bit-wise exclusive-or (XOR) is
>>> performed between these two byte sets. This will create bytes of value
>>> zero (0) where they were the same, and non-zero where they were
>>> different. The tr// then counts how many of the bytes were zero (\x0
>>> is ascii zero).
>>>
>>> I'll just assume it is more efficient than for/substr/eq :-)
>>>
>>> --Torsten Seemann
>>> --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
>>> University, AUSTRALIA
>>>
>>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> 


From maj at fortinbras.us  Thu Feb 11 09:34:27 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 11 Feb 2010 09:34:27 -0500
Subject: [Bioperl-l] Adding namespace support
	toBio::DB::SeqFeature::Store::DBI::Pg
In-Reply-To: <18F52839-7085-4AF8-ACDC-10432475F1F1@sgul.ac.uk>
References: <4A885CF2-8E39-443F-A6DE-6E03CF05BB86@sgul.ac.uk><4536f7701002101135s4694ff9bpb4232ac8b7eb0e21@mail.gmail.com>
	<18F52839-7085-4AF8-ACDC-10432475F1F1@sgul.ac.uk>
Message-ID: <8FD6B9FA50144F15A34EFF2541B1C885@NewLife>

Hey Adam,
The SeqFeature tests are slightly complex in the Build-- during Build.PL 
execution,
the user specifies the DBMS, which is dynamically incorporated during the test.
So, any new tests you want to make, you can probably just add to SeqFeature.t,
and the Build script will make sure these are routed to the right handler. 
Jason/Chris
will certainly correct me if I'm wrong....
cheers MAJ
----- Original Message ----- 
From: "Adam Witney" <awitney at sgul.ac.uk>
To: "Scott Cain" <scott at scottcain.net>
Cc: "BioPerl" <bioperl-l at lists.open-bio.org>
Sent: Thursday, February 11, 2010 9:21 AM
Subject: Re: [Bioperl-l] Adding namespace support 
toBio::DB::SeqFeature::Store::DBI::Pg


>
> Hi Scott,
>
> ok I now have a version working with PostgreSQL schemas.
>
> I was looking for the SFS tests, but can only find SeqFeature.t which only 
> tests the "memory" adaptor. Are there any tests for the mysql/Pg adaptors?
>
> thanks
>
> adam
>
> On 10 Feb 2010, at 19:35, Scott Cain wrote:
>
>> Hi Adam,
>>
>> I don't have a problem with this approach. Can you verify that this
>> patch still passes the Pg SFS tests? I don't generally use
>> schemas/name spaces (same thing,right?) much, so I wouldn't feel
>> comfortable evaluting it completely.  And, even better, could you add
>> to the tests that exercise this behavior?
>>
>> Thanks,
>> Scott
>>
>>
>> On Wednesday, February 10, 2010, Adam Witney <awitney at sgul.ac.uk> wrote:
>>>
>>> I noticed that namespace's didn't work with 
>>> Bio::DB::SeqFeature::Store::DBI::Pg because when creating the database the 
>>> CREATE INDEX statements didn't pass through _qualify to add the namespace 
>>> prefix, thus giving a "relation "typelist_tab" already exists" error.
>>>
>>> The patch below fixes this, but the question is does this seem like a good 
>>> approach?
>>>
>>> thanks
>>>
>>> adam
>>>
>>>
>>> Index: Pg.pm
>>> ===================================================================
>>> --- Pg.pm       (revision 16551)
>>> +++ Pg.pm       (working copy)
>>> @@ -256,22 +256,20 @@
>>>   indexed  int default 1,
>>>   object     bytea not null
>>>  );
>>> -  CREATE INDEX feature_stuff ON feature(seqid,tier,bin,typeid);
>>> -  CREATE INDEX feature_typeid ON feature(typeid);
>>>  END
>>>
>>>          locationlist => <<END,
>>>  (
>>>   id         serial primary key,
>>>   seqname    varchar(256)   not null
>>> -); CREATE INDEX locationlist_seqname ON locationlist(seqname);
>>> +);
>>>  END
>>>
>>>          typelist => <<END,
>>>  (
>>>   id       serial primary key,
>>>   tag      varchar(256)  not null
>>> -); CREATE INDEX typelist_tab ON typelist(tag);
>>> +);
>>>  END
>>>          name => <<END,
>>>  (
>>> @@ -279,8 +277,6 @@
>>>   name         varchar(256)  not null,
>>>   display_name int       default 0
>>>  );
>>> -  CREATE INDEX name_id ON name(id);
>>> -  CREATE INDEX name_name ON name(name);
>>>  END
>>>
>>>          attribute => <<END,
>>> @@ -289,8 +285,6 @@
>>>   attribute_id     int   not null,
>>>   attribute_value  text
>>>  );
>>> -  CREATE INDEX attribute_id ON attribute(id);
>>> -  CREATE INDEX attribute_id_val ON 
>>> attribute(attribute_id,SUBSTR(attribute_value, 1, 10));
>>>  END
>>>
>>>          attributelist => <<END,
>>> @@ -298,14 +292,12 @@
>>>   id       serial primary key,
>>>   tag      varchar(256)  not null
>>>  );
>>> -  CREATE INDEX attributelist_tag ON attributelist(tag);
>>>  END
>>>          parent2child => <<END,
>>>  (
>>>   id               int       not null,
>>>   child            int       not null
>>>  );
>>> -  CREATE INDEX parent2child_id_child ON parent2child(id,child);
>>>  END
>>>
>>>          meta => <<END,
>>> @@ -325,6 +317,22 @@
>>>         };
>>>  }
>>>
>>> +sub index_definitions {
>>> +  my $self = shift;
>>> +  return {
>>> +         feature_stuff  => "feature(seqid,tier,bin,typeid)",
>>> +         feature_typeid => "feature(typeid)",
>>> +         locationlist_seqname => "locationlist(seqname)",
>>> +      typelist_tab => "typelist(tag)",
>>> +      name_id => "name(id)",
>>> +      name_name => "name(name)",
>>> +      attribute_id => "attribute(id)",
>>> +      attribute_id_val => "attribute(attribute_id,SUBSTR(attribute_value, 
>>> 1, 10))",
>>> +      attributelist_tag =>  "attributelist(tag)",
>>> +      parent2child_id_child => "parent2child(id,child)",
>>> +        };
>>> +}
>>> +
>>>  sub schema {
>>>   my ($self, $schema) = @_;
>>>   $self->{'schema'} = $schema if defined($schema);
>>> @@ -354,6 +362,18 @@
>>>                        $dbh->do($query) or $self->throw($dbh->errstr);
>>>                }
>>>   }
>>> +
>>> +  my $indexes = $self->index_definitions;
>>> +  foreach (keys %$indexes) {
>>> +    my $index = $self->_qualify($_);
>>> +    my $index_def = $self->_qualify($indexes->{$_});
>>> +    $dbh->do("DROP INDEX IF EXISTS $index") if $erase;
>>> +    my @index_exists = $dbh->selectrow_array("SELECT * FROM pg_indexes 
>>> WHERE indexname = '$index'");
>>> +               if (!scalar(@index_exists)) {
>>> +                       my $query = "CREATE INDEX $index ON $index_def";
>>> +                       $dbh->do($query) or $self->throw($dbh->errstr);
>>> +               }
>>> +  }
>>>   $self->subfeatures_are_indexed(1) if $erase;
>>>   1;
>>>  }
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot 
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From jonas_schaer at gmx.de  Thu Feb 11 10:05:12 2010
From: jonas_schaer at gmx.de (jonas s)
Date: Thu, 11 Feb 2010 16:05:12 +0100
Subject: [Bioperl-l] Fwd: Problem with using blast and blastp in one single
	program
Message-ID: <4B741CA8.2000006@gmx.de>

Hi,

I have a problem using the online blast applications.
I wrote two scripts in PERL (with your help btw, thanks again :) ).
One of these calls at some point a subroutine that submitts blast requests
and stores the recieved reports.
parameters:


########################################################################################################
my $prog = 'blastp';
my $db = 'nr';
my $e_val= '1e-10';
my @params = ( '-prog' =>  $prog,
'-data' =>  $db,
'-expect' =>  $e_val,
'-readmethod' =>  'SearchIO' );
my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

$Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '11 1';
$Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
$Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
$Bio::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATISTICS'} = '2';

my %put = (
WORD_SIZE =>  3,
HITLIST_SIZE =>  100,
THRESHOLD =>  11,
FILTER =>  'R', #''L'' for Low Complexity, ''R'' for Human Repeats, ''m''
for Mask for Lookup
GENETIC_CODE =>  1
);
########################################################################################################

The other one does almost the same thing, except it uses blastp to
search for conserved domains:
parameters:

########################################################################################################
my $cddprog = 'blastp';
my $cdddb = 'cdsearch/cdd';
my $cdde_val= '0.010';

my @cddparams = ( '-prog' =>  $cddprog,
'-data' =>  $cdddb,
'-expect' =>  $cdde_val,
'-readmethod' =>  'SearchIO' );
my $cddfactory = Bio::Tools::Run::RemoteBlast->new(@cddparams);

$Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '11 1';
$Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
$Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
$Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast';



my %cddput = (
WORD_SIZE =>  3,
HITLIST_SIZE =>  100,
THRESHOLD =>  11,
FILTER =>  'R', #''L'' for Low Complexity, ''R'' for Human Repeats, ''m''
for Mask for Lookup
GENETIC_CODE =>  1
);
########################################################################################################

Both skripts work fine, but i need to combine them to one single
programm and if i do that the first subroutine works but the second one
doesn't (it doesn't matter which one is called first, its always the
second one that crashes instead submitting the requests). Instead of submitting the same sequences again
to recieve the other blast_reports, there is some output one my screen,
the end of it is this:


url=http%3A//blast.ncbi.nlm.nih.gov/Blast.cgi%3FALIGNMENTS%3D50%26ALIGNMENT%5FVI
EW%3DPairwise%26CMD%3DPut%26COMPOSITION%5FBASED%5FSTATISTICS%3D2%26DATABASE%3Dnr
%26DESCRIPTIONS%3D100%26ERROR%3D%26EXPECT%3D10%26FILTER%3DR%26FORMAT%5FOBJECT%3D
Alignment%26FORMAT%5FTYPE%3DText%26GAPCOSTS%3D11%2B1%26GENETIC%5FCODE%3D1%26HITL
IST%5FSIZE%3D100%26MAX%5FNUM%5FSEQ%3D100%26MYNCBI%5FUSER%3D%2D1%26PROGRAM%3Dblas
tp%26QUERY%3D%253Ejgi%257CChlre4%257C522274%257Cau5.g11876%5Ft1%2B%250AMASLLAGKP
LMGGLKLQRSAKMAVPAVAVPRVATAAAARVGLKGGLGERPFAPKPVEKKPLAPAPQAASGDAPAPEPKKFLGFEPITWA
KILPLGAMFFCILFNYTILRDTKDVLVVTAPGSGAEIIPFLKTWVNLPMAIGFTIMYSALSNRLSSEALFYTCIIPFIAF
FGAFAALMYPMRDALHPTEFCQNLLEQMGPRFAGPIAILRNWTFCLFYVMAELWGSVVVSVLFWGFANQITTVEEASQFY
PLFGLGANVALIFSGQAVKYFSQVRAGLPPDVDGWGVSLNGLMGMVVIGGLLIIGIYFSLQRLVVPKLKSLREGKKKKNK
TKMSVGESFAFLAQSSYIRDMATLVVAYGISINLVEVTWKGKLKAQFPNPNDYSSFMGEFSTATGTVTFTMMILSRWIFK
QFGWGVAALITPIMLLITGLLFFTLVLAGDTVKPALAAWGMTPLYAAVLVGAAQNVFSKSSKYSLFDPCKEMAYIPLEDE
VKTKGKAAIDVICNPLGKSGGALIQQFMIIGLGSLAASTPYLGAILCVIIVAWINAAASLNKQFTALQEETGMYITGEKP
ANKSEKKD%2A%26SERVICE%3Drpsblast%26THRESHOLD%3D11%26USER%5FTYPE%3D0%26WORD%5FSIZ
E%3D3" title="Click to register for an
account"onclick="MyNCBI_auto_submit('http
://www.ncbi.nlm.nih.gov/sites/myncbi/register/?back_url=http%3A//blast.ncbi.nlm.
nih.gov/Blast.cgi%3FALIGNMENTS%3D50%26ALIGNMENT%5FVIEW%3DPairwise%26CMD%3DPut%26
COMPOSITION%5FBASED%5FSTATISTICS%3D2%26DATABASE%3Dnr%26DESCRIPTIONS%3D100%26ERRO
R%3D%26EXPECT%3D10%26FILTER%3DR%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3D
Text%26GAPCOSTS%3D11%2B1%26GENETIC%5FCODE%3D1%26HITLIST%5FSIZE%3D100%26MAX%5FNUM
%5FSEQ%3D100%26MYNCBI%5FUSER%3D%2D1%26PROGRAM%3Dblastp%26QUERY%3D%253Ejgi%257CCh
lre4%257C522274%257Cau5.g11876%5Ft1%2B%250AMASLLAGKPLMGGLKLQRSAKMAVPAVAVPRVATAAA
ARVGLKGGLGERPFAPKPVEKKPLAPAPQAASGDAPAPEPKKFLGFEPITWAKILPLGAMFFCILFNYTILRDTKDVLVV
TAPGSGAEIIPFLKTWVNLPMAIGFTIMYSALSNRLSSEALFYTCIIPFIAFFGAFAALMYPMRDALHPTEFCQNLLEQM
GPRFAGPIAILRNWTFCLFYVMAELWGSVVVSVLFWGFANQITTVEEASQFYPLFGLGANVALIFSGQAVKYFSQVRAGL
PPDVDGWGVSLNGLMGMVVIGGLLIIGIYFSLQRLVVPKLKSLREGKKKKNKTKMSVGESFAFLAQSSYIRDMATLVVAY
GISINLVEVTWKGKLKAQFPNPNDYSSFMGEFSTATGTVTFTMMILSRWIFKQFGWGVAALITPIMLLITGLLFFTLVLA
GDTVKPALAAWGMTPLYAAVLVGAAQNVFSKSSKYSLFDPCKEMAYIPLEDEVKTKGKAAIDVICNPLGKSGGALIQQFM
IIGLGSLAASTPYLGAILCVIIVAWINAAASLNKQFTALQEETGMYITGEKPANKSEKKD%2A%26SERVICE%3Drpsb
last%26THRESHOLD%3D11%26USER%5FTYPE%3D0%26WORD%5FSIZE%3D3');return
false;">[Regi
ster]</a></td></tr></table></div>  </div>
<ul id="nav">  <li class="first "><a href="Blast.cgi?CMD=Web&amp;
PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>  <li class=
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d BLAST jobs">Recent Results</a></li>  <li class=
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search para
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">  <a href="Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs" title="BLAST
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on">Help</a></li>  </ul>  </div>  <div id=
"content-wrap">  <!-- %%% Add breadcrumb text -->  <
div id="breadcrumb">  <a href="http://www.ncbi.nlm.nih.gov/">NC
BI</a>/<a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST<
/a>/<strong>Format Request</strong>
</div>  <!-- Do errors t
his way -->  <!--<ul
class="msg"><li class="error"><p></p></li></ul>-->
<ul id="msgR" class="msg"><li class="error"><div class="error
msInf">Message ID#
35 Error: Cannot validate the Blast options: Compositional adjustments
are only
supported with blastp or tblastn<a class="helplink hiding shown
errorHelp error
" title="help" href="#" id="errorHelp0"><span>[?]</span></a><div
toggle="errorHe
lp0" class="helpbox hidden">This error message indicates that the
combination of
options for this Blast search is inconsistent or invalid. This can
happen when
the selected Blast program does not support one of the options provided,
when tw
o or more options have conflicting values, etc. If you are using URL
API, please
check the options mentioned in the error message string and re-submit
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ch. Please note that the current version of the Blast CGI application is
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sts, please, contact<a
href="mailto:blast-help at ncbi.nlm.nih.gov">Blast-help at ncb
i.nlm.nih.gov</a>  for more help.</div></div></li></ul>  <div id="c
ontent">  <form action="Blast.cgi" enctype="applic
ation/x-www-form-urlencoded" method="post" name="FormatForm"
id="FormatForm">
<script language="JavaScript">  <!--//document.images['Bl
astHeaderGif'].src = 'html/head_formating.gif';// --></script><!--
<p class='info'><strong>Job submitted.</strong>We estimate that results
will b
e ready in 16 seconds or less.</p>--><div class="fbtn"><!--<a
href="javascript:d
ocument.forms[0].submit();"><img align="middle" alt="Format button"
border="0" s
rc="FormatPage_files/format_but.gif"></a>--></div><dl class="summary
db"><dd></
dd><!--<span class=" db">--><!--<span class="hidden
query"><dt>Query</dt><dd>
</dd></span>  --><dt class="hidden query">Query</dt><dd class="hidden
query"></dd
><dt class="hidden db">Database</dt><dd class="hidden db">nr</dd><dt
class="hidd
en title">Job title</dt><dd class="hidden title"></dd><dt class="hidden
entrez">
Entrez Query</dt><dd class="hidden entrez"><span class="note
entrez">Note: Your
search is limited to records matching this Entrez query</span></dd><!--
</span>
--><dt><label for="rid">Request ID</label></dt><dd><input name="RID"
size="50" t
ype="text" value="" id="rid" /><input type="submit" value="View report"
name="Vi
ewReport" class="button" /><!--<img border="0" id="viewRpButton"
src="images/ve
iwRpButton.jpg" class="viewReport" alt="View report"
mouseovImg="images/veiwRp
ButtonOver.jpg" mouseoutImg="images/veiwRpButton.jpg"
mousedownImg="images/veiwR
pButtonDown.jpg" mouseupImg="images/veiwRpButtonOver.jpg" />--><input
type="che
ckbox" name="NEWWINRES" form="FormatForm" winType="const" id="nw"
class="newwin
" /><label for="nw">Show results in a new
window</label></dd><dt>Format<br/><!-
-<a class='help' href="#">[Help]</a></dt>  --><dd><table class="options
blastp ">
<tr class="paramSet xgl"><td class="hd"><label
for="FORMAT_OBJECT">Show</label><
/td><td><div class="fi"><select id="FORMAT_OBJECT" class="reset"
name="FORMAT_OB
JECT" defVal="Alignment"><option value="Alignment"
selected="selected">Alignment
</option><option value="PSSM">PSSM</option><option
value="PSSM_Scoremat">PssmW
ithParameters</option><option value="Bioseq"
>Bioseq</option></select><label fo
r="FORMAT_TYPE">as</label><select name="FORMAT_TYPE" id="FORMAT_TYPE"
class="res
et" defVal="HTML"><option value="HTML">HTML</option><option
value="Text" selec
ted="selected">Plain text</option><option value="ASN.1"
>ASN.1</option><option
value="XML">XML</option></select><input name="PSSM_FORMAT_TYPE"
value="Text"
size="3" id="pssmFormat" type="text" class="hidden dispType" /><input
name="BIOS
EQ_FORMAT_TYPE" value="ASN.1" size="3" id="bioseqFormat" type="text"
class="hidd
en dispType" /><input name="PSSM_SC_FORMAT_TYPE" value="ASN.1" size="3"
id="pssm
ScFormat" type="text" class="hidden dispType" /><span id="advView"
class=""><inp
ut name="NEW_VIEW" id="NEW_VIEW" type="checkbox" class="cb reset"
defVal="checke
d" /><label for="NEW_VIEW">Advanced View</label><span class=""><input
name="OLD
_BLAST" id="OLD_BLAST" type="checkbox" class="cb reset"
defVal="unchecked" /><l
abel for="OLD_BLAST">Use old BLAST report format</label></span></span><a
class="
resetAll" id="resetAll">Reset form to defaults</a><a class="helplink
hiding" ti
tle="Alignments object formatting help" id="formatHelp"
href="#"><span>[?]</span
></a><p toggle="formatHelp" class="helpbox hidden" id="hlp1">These
options contr
ol formatting of alignments in results pages. Thedefault is HTML, but
other form
ats (including plain text) are available.PSSM and PssmWithParameters are
represe
ntations of Position Specific Scoring Matrices and are only available
for PSI-BL
AST. The Advanced view option allows the database descriptions to be
sorted by v
arious indices in a table.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihel
p.shtml#format_object" target="helpWin" title="Additional alignments
object form
atting help">more...</a></p></div></td></tr><tr class="odd paramSet"><td
class="
hd"><label for="ALIGNMENT_VIEW">Alignment View</label></td><td><div
class="fi"><
select name="ALIGNMENT_VIEW" id="ALIGNMENT_VIEW" defVal="Pairwise"
class="reset"
><option value="Pairwise" selected="selected">Pairwise</option><option
value="P
airwiseWithIdentities">Pairwise with dots for
identities</option><option value
="QueryAnchored">Query-anchored with dots for
identities</option><option value
="QueryAnchoredNoIdentities">Query-anchored with letters for
identities</optio
n><option value="FlatQueryAnchored">Flat query-anchored with dots for
identiti
es</option><option value="FlatQueryAnchoredNoIdentities">Flat
query-anchored w
ith letters for identities</option><option value="Tabular">Hit
Table</option><
/select><a class="helplink hiding" title="Alignments view options help"
id="alnV
iewHelp" href="#"><span>[?]</span></a><p toggle="alnViewHelp"
class="helpbox hid
den" id="hlp2">Choose how to view alignments.The default "pairwise" view
shows h
ow each subject sequence alignsindividually to the query sequence. The
"query-an
chored" view shows howall subject sequences align to the query sequence.
For eac
h view type,you can choose to show "identities" (matching residues) as
letters o
rdots.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#alignment_vi
ew" target="helpWin" title="Additional alignments view options
help">more...</a>
</p></div></td></tr><tr class="paramSet"><td
class="hd"><label>Display</label></
td><td class="cb"><div class="fi"><input name="SHOW_OVERVIEW"
id="SHOW_OVERVIEW"
type="checkbox" class="cb reset" defVal="checked" checked="checked"
/><label cl
ass="rb" for="SHOW_OVERVIEW">Graphical Overview</label><input
name="SHOW_LINKOUT
" id="SHOW_LINKOUT" type="checkbox" class="cb reset" defVal="checked"
checked="c
hecked" /><label class="rb" for="SHOW_LINKOUT">Linkout</label><input
name="GET_S
EQUENCE" id="GET_SEQUENCE" type="checkbox" class="cb reset"
defVal="checked" che
cked="checked" /><label class="rb" for="GET_SEQUENCE">Sequence
Retrieval</label>
<input name="NCBI_GI" id="NCBI_GI" type="checkbox" class="cb reset"
defVal="unch
ecked" /><label class="rb" for="NCBI_GI">NCBI-gi</label><input
name="SHOW_CDS_F
EATURE" id="SHOW_CDS_FEATURE" type="checkbox" class="cb reset blastn"
defVal="un
checked" /><label for="SHOW_CDS_FEATURE" class="blastn">CDS
feature</label><a c
lass="helplink hiding" title="Alignments display options help"
id="displayHelp"
href="#"><span>[?]</span></a><ul toggle="displayHelp" class="helpbox
hidden" id=
"hlp3"><li>Graphical Overview: Graphical Overview: Show graph of similar
sequenc
e regions aligned to query.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgih
elp.shtml#show_overview" target="helpWin" title="Graphical Overview
help">more..
.</a></li><li>Database LinkOuts: Show links from matching sequences to
entries i
n specialized NCBI databases.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgi
help.shtml#show_linkout" title="LinkOut help" target="helpWin"
>more...</a></li>
<li>Sequence Retrieval: Show buttons to download matching sequences.<a
href="htt
p://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#get_sequence"
title="Sequence
Retrieval help" target="helpWin">more...</a></li><li>NCBI-gi: Show NCBI
gi iden
tifiers.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#ncbi_gi" t
itle="NCBI-gi help" target="helpWin">more...</a></li><li>CDS feature:
Show anno
tated coding region and translation.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/b
lastcgihelp.shtml#show_cds_feature" title="CDS feature help"
target="helpWin">m
ore...</a></li></ul></div></td></tr><tr class="paramSet odd xgl"><td
class="hd">
<label>Masking</label></td><td><div class="fi"><label for="MASK_CHAR">
Character
:</label><select name="MASK_CHAR" id="MASK_CHAR" class="reset"
defVal="2"><opt
ion value="0">X for protein, n for nucleotide</option><option value="2"
select
ed="selected">Lower Case</option></select><label for="MASK_COLOR">
Color:</labe
l><select name="MASK_COLOR" id="MASK_COLOR" class="reset"
defVal="1"><option val
ue="0">Black</option><option value="1" selected="selected"
>Grey</option><opti
on value="2">Red</option></select><a class="helplink hiding"
title="Alignments
masking help" id="maskingHelp" href="#"><span>[?]</span></a><ul
toggle="masking
Help" class="helpbox hidden" id="hlp4"><li>Masking Character: Display
masked (fi
ltered) sequence regions as lower-case or as specific letters (N for
nucleotide,
P for protein).</li><li>Masking Color: Display masked sequence regions
in the g
iven color.</li></ul></div></td></tr><tr class="paramSet xgl"><td
class="hd"><la
bel>Limit results</label></td><td><div class="fi"><label
for="FRM_DESCRIPTIONS">
Descriptions:</label><select name="DESCRIPTIONS" id="FRM_DESCRIPTIONS"
class="re
set" defVal="100"><option value="0">0</option><option value="10">10</
option><option value="50">50</option><option value="100" selected="select
ed">100</option><option value="250">250</option><option value="500">500
</option><option value="1000">1000</option><option value="5000">5000</opti
on><option value="10000">10000</option><option value="20000"
>20000</option><
/select><label for="FRM_NUM_OVERVIEW">Graphical overview:</label><select
name="N
UM_OVERVIEW" id="FRM_NUM_OVERVIEW" class="reset" defVal="100"><option
value="0"
>0</option><option value="10">10</option><option value="50">50</opti
on><option value="100" selected="selected">100</option><option
value="250">
250</option><option value="500">500</option><option value="1000"
>1000</optio
n></select><label for="FRM_ALIGNMENTS">Alignments:</label><select
name="ALIGNMEN
TS" id="FRM_ALIGNMENTS" class="reset" defVal="100"><option value="0">0</op
tion><option value="10">10</option><option value="50" selected="selected
">50</option><option value="100">100</option><option value="250">250</o
ption><option value="500">500</option><option value="1000">1000</option><
option value="5000">5000</option><option value="10000"
>10000</option><optio
n value="20000">20000</option></select><a class="helplink hiding"
title="Limit
number of descriptions/alignments help" id="numHelp"
href="#"><span>[?]</span><
/a><ul toggle="numHelp" class="helpbox hidden"
id="hlp5"><li>Descriptions: Show
short descriptions for up to the given number of sequences.</li>
<li>Alignments
: Show alignments for up to the given number of sequences, in order of
statisti
cal significance.</li></ul></div></td></tr><tr class="paramSet odd
xgl"><td clas
s="hd"></td><td><div class="fi"><label
for="qorganism">Organism</label><span cla
ss="instr">Type common name, binomial, taxid, or group name. Only 20 top
taxa wi
ll be shown.</span><input name="FORMAT_ORGANISM" size="55"
id="qorganism" sgDic
t="taxids_sg" value="" sgStyle="SG_green" class="reset" /><a
class="helplink hi
ding" title="Limit results by organism help" id="organismHelp"
href="#"><span>[?
]</span></a><p toggle="organismHelp" class="helpbox hidden"
id="hlp6">Show only
sequences from the given organism.</p></div></td></tr><tr
class="paramSet xgl"><
td class="hd"></td><td><div class="fi"><label
for="FORMAT_EQ_TEXT">Entrez query:
</label><input name="FORMAT_EQ_TEXT" id="FORMAT_EQ_TEXT" size="60"
type="text" v
alue="" class="reset" /><a class="helplink hiding" title="Limit results
by Entre
z query help" id="entrezHelp" href="#"><span>[?]</span></a><p
toggle="entrezHelp
" class="helpbox hidden" id="hlp7">Show only those sequences that match
the give
n Entrez query.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#lim
it_result" target="helpWin" title="Additional limit results by Entrez
query help
" target="helpWin">more...</a></p></div></td></tr><tr class="paramSet
odd xgl">
<td class="hd"></td><td><div class="fi"><label for="EXPECT_LOW">Expect
Min:</lab
el>  <input name="EXPECT_LOW" id="EXPECT_LOW" size="10" type="text"
value="" clas
s="reset"/><label for="EXPECT_HIGH">Expect Max:</label>  <input
name="EXPECT_HIGH
" id="EXPECT_HIGH" size="10" type="text" value="" class="reset" /><a
class="help
link hiding" title="Limit results by expect value range help"
id="expectHelp" hr
ef="#"><span>[?]</span></a><p toggle="expectHelp" class="helpbox hidden"
id="hlp
8">Show only sequences with expect values in the given range.<a
href="http://www
.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect_range"
target="helpWin" title=
"Additional limit results by expect value range
help">more...</a></p></div></td>
</tr><tr class="psiBlast paramSet xgl"><td class="hd"><label>Format
for</label><
/td><td><div class="fi"><input name="RUN_PSIBLAST_FORM"
id="RUN_PSIBLAST" type="
checkbox" class="cb psiBlast" /><label class="rb psiBlast"
for="RUN_PSIBLAST">P
SI-BLAST</label><label for="I_THRESH">with inclusion
threshold:</label><input na
me="I_THRESH" id="I_THRESH" size="10" type="text" value=""
defVal="0.005" /><a c
lass="helplink hiding" title="PSI BLAST formatting help" id="psiHelp"
href="#"><
span>[?]</span></a><ul toggle="psiHelp" class="helpbox hidden"
id="hlp9"><li>For
mat for PSI-BLAST: The Position-Specific Iterated BLAST (PSI-BLAST)
program perf
orms iterative searches with a protein query, in which sequences found
in one ro
und of search are used to build a custom score model for the next
round.</li><a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#psiblast"
target="hel
pWin" title="Additional PSI BLAST formatting
help">more...</a><li>Inclusion Thre
shold: This sets the statistical significance threshold for including a
sequence
in the model used by PSI-BLAST to create the PSSM on the next
iteration.</li>  <
/ul></div></td></tr></table></dd></dl><input name="RID" value=""
type="hidden" /
><input name="CDD_RID" value="" type="hidden" /><input
name="CDD_SEARCH_STATE" t
ype="hidden" value="" /><input name="STEP_NUMBER" value=""
id="stepNumber" type=
"hidden" /><input name="CMD" value="Get" type="hidden" /><input
name="FORMAT_EQ_
OP" value="AND" type="hidden" /><input name="RESULTS_PAGE_TARGET"
type="hidden"
id="resPageTarget" value="Blast_Results_for_1661104373" /><input
name="QUERY_INF
O" type="hidden" value="" />  <input name="ENTREZ_QUER
Y" type="hidden" value="" /><input name="QUERY_INDEX" type="hidden"
value="0"/><
!-- Those params are set in the template (blastn.dat, blastp.dat etc.
--><input
name="BLAST_PROGRAMS" type="hidden" value="blastp"/><input name="PAGE"
type="hid
den" value="Proteins"/><input name="PROGRAM" type="hidden"
value="blastp"/><inpu
t name="MEGABLAST" type="hidden" value="" /><input name="RUN_PSIBLAST"
type="hid
den" value="" /><input name="BLAST_SPEC" id="blastSpec" type="hidden"
value=""/>
<input name="QUERY" type="hidden"
value=">jgi|Chlre4|522274|au5.g11876_t1 MASLLA
GKPLMGGLKLQRSAKMAVPAVAVPRVATAAAARVGLKGGLGERPFAPKPVEKKPLAPAPQAASGDAPAPEPKKFLGFEPI
TWAKILPLGAMFFCILFNYTILRDTKDVLVVTAPGSGAEIIPFLKTWVNLPMAIGFTIMYSALSNRLSSEALFYTCIIPF
IAFFGAFAALMYPMRDALHPTEFCQNLLEQMGPRFAGPIAILRNWTFCLFYVMAELWGSVVVSVLFWGFANQITTVEEAS
QFYPLFGLGANVALIFSGQAVKYFSQVRAGLPPDVDGWGVSLNGLMGMVVIGGLLIIGIYFSLQRLVVPKLKSLREGKKK
KNKTKMSVGESFAFLAQSSYIRDMATLVVAYGISINLVEVTWKGKLKAQFPNPNDYSSFMGEFSTATGTVTFTMMILSRW
IFKQFGWGVAALITPIMLLITGLLFFTLVLAGDTVKPALAAWGMTPLYAAVLVGAAQNVFSKSSKYSLFDPCKEMAYIPL
EDEVKTKGKAAIDVICNPLGKSGGALIQQFMIIGLGSLAASTPYLGAILCVIIVAWINAAASLNKQFTALQEETGMYITG
EKPANKSEKKD*"/><input name="JOB_TITLE" type="hidden" value=""/><input
name="QUER
Y_TO" type="hidden" value=""/><input name="QUERY_FROM" type="hidden"
value=""/><
input name="EQ_TEXT" type="hidden" value=""/><input name="ORGN"
type="hidden" va
lue=""/><input name="EQ_MENU" type="hidden" value=""/><input
name="ORG_EXCLUDE"
type="hidden" value=""/><input name="PHI_PATTERN" type="hidden"
value=""/><input
name="EXPECT" type="hidden" value="10"/>
<input name="DATABASE" type="hidden" value="nr"/
><input name="DB_GROUP" type="hidden" value=""/><input
name="SUBGROUP_NAME" type
="hidden" value=""/><input name="GENETIC_CODE" type="hidden"
value="1"/><input n
ame="WORD_SIZE" type="hidden" value="3"/><input name="MATCH_SCORES"
type="hidden
" value=""/>  <input name="MATRIX_NAME" type="hidden" value=""
/>  <input name="GAPCOSTS" type="hidden" value="11 1
"/><input name="MAX_NUM_SEQ" id="maxNumSeq" type="hidden" value="100"/>
<input name="COMPOSITION_BASED_STATISTICS" type="hidden"
value="2"/>  <input name="NEWWIN" type="hidden" value=""/><in
put name="SHORT_QUERY_ADJUST" type="hidden" value=""/><input
name="FILTER" type=
"hidden" value="R;"/><input name="REPEATS" type="hidden"
value=""/><input name="
ID_FOR_PSSM" type="hidden" value=""/><input name="EXCLUDE_MODELS"
type="hidden"
value=""/><input name="EXCLUDE_SEQ_UNCULT" type="hidden"
value=""/><input name="
NUM_ORG" type="hidden" value = "1" /><!-- PSSM --><input
name="LCASE_MASK" type=
"hidden" value=""/><input name="TEMPLATE_TYPE" type="hidden"
value=""/><input na
me="TEMPLATE_LENGTH" type="hidden" value=""/><input name="I_THRESH"
type="hidden
" value=""/><input name="ADJUSTED_FOR_SHORT_QUERY" type="hidden"
value=""/><inpu
t name="MIXED_QUERIES" type="hidden" value=""/><!--QBlastInfoBegin RID =
RTOE = QBlastInfoEnd--></form>
</div><!-- /#con
tent -->  </div><!-- /#content-wrap -->  <div id="footer"
>  <p id="orgns">  <a href="http://www.ncbi.nlm.nih.gov/" title="National C
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---------------------------------------------------
########################################################################################################


After printing that text the program continues normally, so it actually
doesnt "crash", but submitting the requests for a second time is abortet.
Again: both skripts work fine individually, but as soon as they are combined there is this problem...
I really need to put theses two subroutines in one single program.
Can you please tell me why this doesn?t work?

Thanks in advance, Jonas Schaer


From awitney at sgul.ac.uk  Thu Feb 11 10:55:03 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 11 Feb 2010 15:55:03 +0000
Subject: [Bioperl-l] Adding namespace support
	toBio::DB::SeqFeature::Store::DBI::Pg
In-Reply-To: <8FD6B9FA50144F15A34EFF2541B1C885@NewLife>
References: <4A885CF2-8E39-443F-A6DE-6E03CF05BB86@sgul.ac.uk>
	<4536f7701002101135s4694ff9bpb4232ac8b7eb0e21@mail.gmail.com>
	<18F52839-7085-4AF8-ACDC-10432475F1F1@sgul.ac.uk>
	<8FD6B9FA50144F15A34EFF2541B1C885@NewLife>
Message-ID: <F6DF9153-4A8F-4705-9F01-6ACC2C53642F@sgul.ac.uk>


Thanks Mark, that makes sense and I've got SeqFeature.t running now with the Pg adaptor.

However, I have just noticed that Bio::DB::SeqFeature::Store::DBI::Pg did have some partial code to support "schema" as well as "namespace" (the latter by inheriting this from the mysql version). 

I have only just started using this code so unless i am not quite understanding what the namespace concept is trying to do here then they should both equate to the same thing? I can remove the redundancy and use just one term; which would be preferred, schema or namespace? it would make sense to use namespace as it would then use the same options as the mysql adaptor. I'll go ahead and do that unless anyone has any objections?

thanks

adam

On 11 Feb 2010, at 14:34, Mark A. Jensen wrote:

> Hey Adam,
> The SeqFeature tests are slightly complex in the Build-- during Build.PL execution,
> the user specifies the DBMS, which is dynamically incorporated during the test.
> So, any new tests you want to make, you can probably just add to SeqFeature.t,
> and the Build script will make sure these are routed to the right handler. Jason/Chris
> will certainly correct me if I'm wrong....
> cheers MAJ
> ----- Original Message ----- From: "Adam Witney" <awitney at sgul.ac.uk>
> To: "Scott Cain" <scott at scottcain.net>
> Cc: "BioPerl" <bioperl-l at lists.open-bio.org>
> Sent: Thursday, February 11, 2010 9:21 AM
> Subject: Re: [Bioperl-l] Adding namespace support toBio::DB::SeqFeature::Store::DBI::Pg
> 
> 
>> 
>> Hi Scott,
>> 
>> ok I now have a version working with PostgreSQL schemas.
>> 
>> I was looking for the SFS tests, but can only find SeqFeature.t which only tests the "memory" adaptor. Are there any tests for the mysql/Pg adaptors?
>> 
>> thanks
>> 
>> adam
>> 
>> On 10 Feb 2010, at 19:35, Scott Cain wrote:
>> 
>>> Hi Adam,
>>> 
>>> I don't have a problem with this approach. Can you verify that this
>>> patch still passes the Pg SFS tests? I don't generally use
>>> schemas/name spaces (same thing,right?) much, so I wouldn't feel
>>> comfortable evaluting it completely.  And, even better, could you add
>>> to the tests that exercise this behavior?
>>> 
>>> Thanks,
>>> Scott
>>> 
>>> 
>>> On Wednesday, February 10, 2010, Adam Witney <awitney at sgul.ac.uk> wrote:
>>>> 
>>>> I noticed that namespace's didn't work with Bio::DB::SeqFeature::Store::DBI::Pg because when creating the database the CREATE INDEX statements didn't pass through _qualify to add the namespace prefix, thus giving a "relation "typelist_tab" already exists" error.
>>>> 
>>>> The patch below fixes this, but the question is does this seem like a good approach?
>>>> 
>>>> thanks
>>>> 
>>>> adam
>>>> 
>>>> 
>>>> Index: Pg.pm
>>>> ===================================================================
>>>> --- Pg.pm       (revision 16551)
>>>> +++ Pg.pm       (working copy)
>>>> @@ -256,22 +256,20 @@
>>>>  indexed  int default 1,
>>>>  object     bytea not null
>>>> );
>>>> -  CREATE INDEX feature_stuff ON feature(seqid,tier,bin,typeid);
>>>> -  CREATE INDEX feature_typeid ON feature(typeid);
>>>> END
>>>> 
>>>>         locationlist => <<END,
>>>> (
>>>>  id         serial primary key,
>>>>  seqname    varchar(256)   not null
>>>> -); CREATE INDEX locationlist_seqname ON locationlist(seqname);
>>>> +);
>>>> END
>>>> 
>>>>         typelist => <<END,
>>>> (
>>>>  id       serial primary key,
>>>>  tag      varchar(256)  not null
>>>> -); CREATE INDEX typelist_tab ON typelist(tag);
>>>> +);
>>>> END
>>>>         name => <<END,
>>>> (
>>>> @@ -279,8 +277,6 @@
>>>>  name         varchar(256)  not null,
>>>>  display_name int       default 0
>>>> );
>>>> -  CREATE INDEX name_id ON name(id);
>>>> -  CREATE INDEX name_name ON name(name);
>>>> END
>>>> 
>>>>         attribute => <<END,
>>>> @@ -289,8 +285,6 @@
>>>>  attribute_id     int   not null,
>>>>  attribute_value  text
>>>> );
>>>> -  CREATE INDEX attribute_id ON attribute(id);
>>>> -  CREATE INDEX attribute_id_val ON attribute(attribute_id,SUBSTR(attribute_value, 1, 10));
>>>> END
>>>> 
>>>>         attributelist => <<END,
>>>> @@ -298,14 +292,12 @@
>>>>  id       serial primary key,
>>>>  tag      varchar(256)  not null
>>>> );
>>>> -  CREATE INDEX attributelist_tag ON attributelist(tag);
>>>> END
>>>>         parent2child => <<END,
>>>> (
>>>>  id               int       not null,
>>>>  child            int       not null
>>>> );
>>>> -  CREATE INDEX parent2child_id_child ON parent2child(id,child);
>>>> END
>>>> 
>>>>         meta => <<END,
>>>> @@ -325,6 +317,22 @@
>>>>        };
>>>> }
>>>> 
>>>> +sub index_definitions {
>>>> +  my $self = shift;
>>>> +  return {
>>>> +         feature_stuff  => "feature(seqid,tier,bin,typeid)",
>>>> +         feature_typeid => "feature(typeid)",
>>>> +         locationlist_seqname => "locationlist(seqname)",
>>>> +      typelist_tab => "typelist(tag)",
>>>> +      name_id => "name(id)",
>>>> +      name_name => "name(name)",
>>>> +      attribute_id => "attribute(id)",
>>>> +      attribute_id_val => "attribute(attribute_id,SUBSTR(attribute_value, 1, 10))",
>>>> +      attributelist_tag =>  "attributelist(tag)",
>>>> +      parent2child_id_child => "parent2child(id,child)",
>>>> +        };
>>>> +}
>>>> +
>>>> sub schema {
>>>>  my ($self, $schema) = @_;
>>>>  $self->{'schema'} = $schema if defined($schema);
>>>> @@ -354,6 +362,18 @@
>>>>                       $dbh->do($query) or $self->throw($dbh->errstr);
>>>>               }
>>>>  }
>>>> +
>>>> +  my $indexes = $self->index_definitions;
>>>> +  foreach (keys %$indexes) {
>>>> +    my $index = $self->_qualify($_);
>>>> +    my $index_def = $self->_qualify($indexes->{$_});
>>>> +    $dbh->do("DROP INDEX IF EXISTS $index") if $erase;
>>>> +    my @index_exists = $dbh->selectrow_array("SELECT * FROM pg_indexes WHERE indexname = '$index'");
>>>> +               if (!scalar(@index_exists)) {
>>>> +                       my $query = "CREATE INDEX $index ON $index_def";
>>>> +                       $dbh->do($query) or $self->throw($dbh->errstr);
>>>> +               }
>>>> +  }
>>>>  $self->subfeatures_are_indexed(1) if $erase;
>>>>  1;
>>>> }
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 



From ferdinand.marletaz at gmail.com  Thu Feb 11 11:41:01 2010
From: ferdinand.marletaz at gmail.com (Ferdi)
Date: Thu, 11 Feb 2010 08:41:01 -0800 (PST)
Subject: [Bioperl-l] Bio::TreeIO: Problem rerooting with a leaf
Message-ID: <fac99fe3-ce8c-49d5-a501-3b84b20af302@g27g2000yqh.googlegroups.com>

Hi-
I am an enthusiastic user of Bio::TreeIO module, and I got some
problems with it after a recent reinstall of bioperl on my new mac
(10.6, previous was 10.5).  Particularly, when attempting to reroot
($tree->reroot($leaf))  a tree with a leaf node, it doesn't seem to
consider ianymore t as an outgroup but as the root itself... For
example, with the example provided on Howto bioperl page:
(((A,B),(C,D)),E);
what I get when reroot with A:
((B,((C,D),(E))))A;
while I should get something like:
(A,((E,(C,D)),B));
with A considered as outgroup instead of the root node itself.
Thanks for your help!
Ferdi

From maj at fortinbras.us  Thu Feb 11 12:20:00 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 11 Feb 2010 12:20:00 -0500
Subject: [Bioperl-l] Bio::TreeIO: Problem rerooting with a leaf
In-Reply-To: <fac99fe3-ce8c-49d5-a501-3b84b20af302@g27g2000yqh.googlegroups.com>
References: <fac99fe3-ce8c-49d5-a501-3b84b20af302@g27g2000yqh.googlegroups.com>
Message-ID: <70691285F9CA4AB3A3FB5E25849142D5@NewLife>

Hi Ferdi-
I'm afraid I caused your trouble. The new reroot 
makes the the node you provide the root, rather than
creating a new (and arbitrary) node. Now, the 
user specifies that node, and so has more control.
Sometime one wants to take an existing polytomic
node an make it itself the root; now reroot does this
transparently. (It also fixes some other things, I think.)
Try this:

# put a midpoint node on the ancestral branch of the leaf:
# this is a new method...
$new_root = $leaf->create_node_on_branch(-fraction => 0.5);
# reroot 
$tree->reroot($new_root);

(this is what reroot actually did before, essentially secretly
changing the tree)--
HTH -MAJ

----- Original Message ----- 
From: "Ferdi" <ferdinand.marletaz at gmail.com>
To: <bioperl-l at bioperl.org>
Sent: Thursday, February 11, 2010 11:41 AM
Subject: [Bioperl-l] Bio::TreeIO: Problem rerooting with a leaf


> Hi-
> I am an enthusiastic user of Bio::TreeIO module, and I got some
> problems with it after a recent reinstall of bioperl on my new mac
> (10.6, previous was 10.5).  Particularly, when attempting to reroot
> ($tree->reroot($leaf))  a tree with a leaf node, it doesn't seem to
> consider ianymore t as an outgroup but as the root itself... For
> example, with the example provided on Howto bioperl page:
> (((A,B),(C,D)),E);
> what I get when reroot with A:
> ((B,((C,D),(E))))A;
> while I should get something like:
> (A,((E,(C,D)),B));
> with A considered as outgroup instead of the root node itself.
> Thanks for your help!
> Ferdi
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
>

From bhakti.dwivedi at gmail.com  Thu Feb 11 16:17:17 2010
From: bhakti.dwivedi at gmail.com (Bhakti Dwivedi)
Date: Thu, 11 Feb 2010 16:17:17 -0500
Subject: [Bioperl-l] how to retrieve classification from a taxon
	name(id) using Bio::Taxon?
Message-ID: <b643abd21002111317s79a91b77sd7bcf6865f5d9a0c@mail.gmail.com>

I am having a hard time to work with Bio::Taxon to get the taxon
classification (based on the documentation provided online).  I was familiar
with objects as Bio::Taxonomy (now deprecated) to get the same thing, which
to me were quite straightforward.  This one I am not sure.  May be it is
something that I am not getting?

I simply need classification for a given taxon name (or id).  Can anyone
help me please here..

Thanks!

Bhakti


On Wed, Feb 10, 2010 at 11:56 PM, shalabh sharma
<shalabh.sharma7 at gmail.com>wrote:

> Bhakti,
>           This is can done by using Bio::taxon
>
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html
>
>
> <http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html>-Shalabh
> Sharma
>
>
> On Wed, Feb 10, 2010 at 11:35 PM, Bhakti Dwivedi <bhakti.dwivedi at gmail.com
> > wrote:
>
>> Hi,
>>
>> For a given taxon name (or taxon ID), how can I retrieve the
>> classification
>> (Family in specific)?
>>
>> Thanks!
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>

From rmb32 at cornell.edu  Thu Feb 11 18:13:45 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Thu, 11 Feb 2010 15:13:45 -0800
Subject: [Bioperl-l] string comparision mismatches and matches
In-Reply-To: <2667CC0A4DC5407AA384B45DC37841AA@NewLife>
References: <c7cac1601002030550g7b356f47s42d97de2c6168830@mail.gmail.com>	<DD9E6B53DD0A4B3BBB650B89E73D4DCB@NewLife>	<a79f6a4b1002110352l539215cbn95151e6c13f5490d@mail.gmail.com>	<7666500BA717407FA55C0D5221E24282@NewLife>	<716af09c1002110559h7b8d538es4364537e4d2864c4@mail.gmail.com>
	<2667CC0A4DC5407AA384B45DC37841AA@NewLife>
Message-ID: <4B748F29.7070704@cornell.edu>

Mark A. Jensen wrote:
> (yes, I know...the solution is to get a real operating system....)
> Thanks! MAJ

Nonono!  That might be good for *your* sanity, but Bioperl needs windows 
devs!

Let's get our priorities straight here!

R

From maj at fortinbras.us  Thu Feb 11 21:33:24 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 11 Feb 2010 21:33:24 -0500
Subject: [Bioperl-l] string comparision mismatches and matches
In-Reply-To: <4B748F29.7070704@cornell.edu>
References: <c7cac1601002030550g7b356f47s42d97de2c6168830@mail.gmail.com>	<DD9E6B53DD0A4B3BBB650B89E73D4DCB@NewLife>	<a79f6a4b1002110352l539215cbn95151e6c13f5490d@mail.gmail.com>	<7666500BA717407FA55C0D5221E24282@NewLife>	<716af09c1002110559h7b8d538es4364537e4d2864c4@mail.gmail.com>
	<2667CC0A4DC5407AA384B45DC37841AA@NewLife>
	<4B748F29.7070704@cornell.edu>
Message-ID: <542E487E63A14571AB01239DAB8B7A95@NewLife>

Ah! Thanks for that, Rob--I thought I was gonna hafta go straight after all...
----- Original Message ----- 
From: "Robert Buels" <rmb32 at cornell.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Bernd Web" <bernd.web at gmail.com>; <bioperl-l at lists.open-bio.org>; "Roopa 
Raghuveer" <rtbio.2009 at gmail.com>; "Torsten Seemann" 
<torsten.seemann at infotech.monash.edu.au>
Sent: Thursday, February 11, 2010 6:13 PM
Subject: Re: [Bioperl-l] string comparision mismatches and matches


> Mark A. Jensen wrote:
>> (yes, I know...the solution is to get a real operating system....)
>> Thanks! MAJ
>
> Nonono!  That might be good for *your* sanity, but Bioperl needs windows devs!
>
> Let's get our priorities straight here!
>
> R
>
> 


From giles.weaver at googlemail.com  Fri Feb 12 06:13:09 2010
From: giles.weaver at googlemail.com (Giles Weaver)
Date: Fri, 12 Feb 2010 11:13:09 +0000
Subject: [Bioperl-l] Installing Linux Binary
In-Reply-To: <4A75BCC9-FE53-4A0C-82F6-0B5B54B798A5@illinois.edu>
References: <465b5a661002090755r2a54dd39w391b4d60acd92512@mail.gmail.com>
	<4536f7701002090759l6be70c36n7d6e5554e25d4410@mail.gmail.com>
	<465b5a661002090804k10ab1bd5k585d2bf05485e09a@mail.gmail.com>
	<4A75BCC9-FE53-4A0C-82F6-0B5B54B798A5@illinois.edu>
Message-ID: <1d06cd5d1002120313m3f67f410g110fef3ce5b23e8f@mail.gmail.com>

 I just misread the subject line as "Installing Ewan Birney"!
Imagine having Ewan Birney in your computer, now that would be useful.
Perhaps someone can make an AMI?

I must get my prescription checked...

Giles

On 09/02/10 17:57, Chris Fields wrote:

Shalu,

This really isn't the best place to ask; the list is specific for
BioPerl.  You should contact the authors of the package in question.

Note that the OS isn't really a limitation anymore, unless you are
trying to run something specific for OS X from Windows/Linux
(fortunately that's not too common).  If it's really important you
could try installing Linux via a VM (VirtualBox is nice and free,
VMWare is nice but $$), then install Xipe, or use Boot Camp and
dual-boot into Linux.

chris

On Feb 9, 2010, at 10:04 AM, shalu sharma wrote:



 I am really sorry for this. Actually i tried a lot but i am new to this. I
tried google it alos but couldn't find anything.
When i try to make , its saying " No target specified and no makefile found.

I am trying to install xipe.http://phage.sdsu.edu/~brodrigu/xipe/

I am really sorry for the trouble.

Thanks
Shalu

On Tue, Feb 9, 2010 at 10:59 AM, Scott Cain <scott at scottcain.net>
<scott at scottcain.net> wrote:



 Hi Shalu,

This is probably not the right mailing list for solving this problem.
What is the application you are trying to install?  When you say make
isn't working, what do you mean?  What are the error messages?  Have
you googled for hints on how to get it installed on a Mac?

Scott


On Tue, Feb 9, 2010 at 10:55 AM, shalu sharma
<sharmashalu.bio at gmail.com> <sharmashalu.bio at gmail.com>
wrote:


 Hi All,
       I know this is very basic query but i am stuck.
I am trying to install some program on my Mac (it contain Linux binary).


 I


 tried "make" but its not working. I am not sure how i can install it.
Can anyone please guide me that how i can install linux binary on MAC?

I would really appreciate it.

Thanks
Shalu
_______________________________________________
Bioperl-l mailing
listBioperl-l at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



 _______________________________________________
Bioperl-l mailing
listBioperl-l at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l

 _______________________________________________
Bioperl-l mailing
listBioperl-l at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l

From awitney at sgul.ac.uk  Fri Feb 12 08:25:42 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Fri, 12 Feb 2010 13:25:42 +0000
Subject: [Bioperl-l] Adding namespace support
	toBio::DB::SeqFeature::Store::DBI::Pg
In-Reply-To: <8FD6B9FA50144F15A34EFF2541B1C885@NewLife>
References: <4A885CF2-8E39-443F-A6DE-6E03CF05BB86@sgul.ac.uk>
	<4536f7701002101135s4694ff9bpb4232ac8b7eb0e21@mail.gmail.com>
	<18F52839-7085-4AF8-ACDC-10432475F1F1@sgul.ac.uk>
	<8FD6B9FA50144F15A34EFF2541B1C885@NewLife>
Message-ID: <781858E3-E639-4B5F-A5DD-C9277F29CB6F@sgul.ac.uk>


Hi Mark,

What is the general approach for creating a database in the tests and where does that test database then get deleted? My test runs, but it leaves the database in place.

thanks

adam


On 11 Feb 2010, at 14:34, Mark A. Jensen wrote:

> Hey Adam,
> The SeqFeature tests are slightly complex in the Build-- during Build.PL execution,
> the user specifies the DBMS, which is dynamically incorporated during the test.
> So, any new tests you want to make, you can probably just add to SeqFeature.t,
> and the Build script will make sure these are routed to the right handler. Jason/Chris
> will certainly correct me if I'm wrong....
> cheers MAJ
> ----- Original Message ----- From: "Adam Witney" <awitney at sgul.ac.uk>
> To: "Scott Cain" <scott at scottcain.net>
> Cc: "BioPerl" <bioperl-l at lists.open-bio.org>
> Sent: Thursday, February 11, 2010 9:21 AM
> Subject: Re: [Bioperl-l] Adding namespace support toBio::DB::SeqFeature::Store::DBI::Pg
> 
> 
>> 
>> Hi Scott,
>> 
>> ok I now have a version working with PostgreSQL schemas.
>> 
>> I was looking for the SFS tests, but can only find SeqFeature.t which only tests the "memory" adaptor. Are there any tests for the mysql/Pg adaptors?
>> 
>> thanks
>> 
>> adam
>> 
>> On 10 Feb 2010, at 19:35, Scott Cain wrote:
>> 
>>> Hi Adam,
>>> 
>>> I don't have a problem with this approach. Can you verify that this
>>> patch still passes the Pg SFS tests? I don't generally use
>>> schemas/name spaces (same thing,right?) much, so I wouldn't feel
>>> comfortable evaluting it completely.  And, even better, could you add
>>> to the tests that exercise this behavior?
>>> 
>>> Thanks,
>>> Scott
>>> 
>>> 
>>> On Wednesday, February 10, 2010, Adam Witney <awitney at sgul.ac.uk> wrote:
>>>> 
>>>> I noticed that namespace's didn't work with Bio::DB::SeqFeature::Store::DBI::Pg because when creating the database the CREATE INDEX statements didn't pass through _qualify to add the namespace prefix, thus giving a "relation "typelist_tab" already exists" error.
>>>> 
>>>> The patch below fixes this, but the question is does this seem like a good approach?
>>>> 
>>>> thanks
>>>> 
>>>> adam
>>>> 
>>>> 
>>>> Index: Pg.pm
>>>> ===================================================================
>>>> --- Pg.pm       (revision 16551)
>>>> +++ Pg.pm       (working copy)
>>>> @@ -256,22 +256,20 @@
>>>>  indexed  int default 1,
>>>>  object     bytea not null
>>>> );
>>>> -  CREATE INDEX feature_stuff ON feature(seqid,tier,bin,typeid);
>>>> -  CREATE INDEX feature_typeid ON feature(typeid);
>>>> END
>>>> 
>>>>         locationlist => <<END,
>>>> (
>>>>  id         serial primary key,
>>>>  seqname    varchar(256)   not null
>>>> -); CREATE INDEX locationlist_seqname ON locationlist(seqname);
>>>> +);
>>>> END
>>>> 
>>>>         typelist => <<END,
>>>> (
>>>>  id       serial primary key,
>>>>  tag      varchar(256)  not null
>>>> -); CREATE INDEX typelist_tab ON typelist(tag);
>>>> +);
>>>> END
>>>>         name => <<END,
>>>> (
>>>> @@ -279,8 +277,6 @@
>>>>  name         varchar(256)  not null,
>>>>  display_name int       default 0
>>>> );
>>>> -  CREATE INDEX name_id ON name(id);
>>>> -  CREATE INDEX name_name ON name(name);
>>>> END
>>>> 
>>>>         attribute => <<END,
>>>> @@ -289,8 +285,6 @@
>>>>  attribute_id     int   not null,
>>>>  attribute_value  text
>>>> );
>>>> -  CREATE INDEX attribute_id ON attribute(id);
>>>> -  CREATE INDEX attribute_id_val ON attribute(attribute_id,SUBSTR(attribute_value, 1, 10));
>>>> END
>>>> 
>>>>         attributelist => <<END,
>>>> @@ -298,14 +292,12 @@
>>>>  id       serial primary key,
>>>>  tag      varchar(256)  not null
>>>> );
>>>> -  CREATE INDEX attributelist_tag ON attributelist(tag);
>>>> END
>>>>         parent2child => <<END,
>>>> (
>>>>  id               int       not null,
>>>>  child            int       not null
>>>> );
>>>> -  CREATE INDEX parent2child_id_child ON parent2child(id,child);
>>>> END
>>>> 
>>>>         meta => <<END,
>>>> @@ -325,6 +317,22 @@
>>>>        };
>>>> }
>>>> 
>>>> +sub index_definitions {
>>>> +  my $self = shift;
>>>> +  return {
>>>> +         feature_stuff  => "feature(seqid,tier,bin,typeid)",
>>>> +         feature_typeid => "feature(typeid)",
>>>> +         locationlist_seqname => "locationlist(seqname)",
>>>> +      typelist_tab => "typelist(tag)",
>>>> +      name_id => "name(id)",
>>>> +      name_name => "name(name)",
>>>> +      attribute_id => "attribute(id)",
>>>> +      attribute_id_val => "attribute(attribute_id,SUBSTR(attribute_value, 1, 10))",
>>>> +      attributelist_tag =>  "attributelist(tag)",
>>>> +      parent2child_id_child => "parent2child(id,child)",
>>>> +        };
>>>> +}
>>>> +
>>>> sub schema {
>>>>  my ($self, $schema) = @_;
>>>>  $self->{'schema'} = $schema if defined($schema);
>>>> @@ -354,6 +362,18 @@
>>>>                       $dbh->do($query) or $self->throw($dbh->errstr);
>>>>               }
>>>>  }
>>>> +
>>>> +  my $indexes = $self->index_definitions;
>>>> +  foreach (keys %$indexes) {
>>>> +    my $index = $self->_qualify($_);
>>>> +    my $index_def = $self->_qualify($indexes->{$_});
>>>> +    $dbh->do("DROP INDEX IF EXISTS $index") if $erase;
>>>> +    my @index_exists = $dbh->selectrow_array("SELECT * FROM pg_indexes WHERE indexname = '$index'");
>>>> +               if (!scalar(@index_exists)) {
>>>> +                       my $query = "CREATE INDEX $index ON $index_def";
>>>> +                       $dbh->do($query) or $self->throw($dbh->errstr);
>>>> +               }
>>>> +  }
>>>>  $self->subfeatures_are_indexed(1) if $erase;
>>>>  1;
>>>> }
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 



From cjfields at illinois.edu  Fri Feb 12 08:38:19 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 12 Feb 2010 07:38:19 -0600
Subject: [Bioperl-l] Adding namespace support
	toBio::DB::SeqFeature::Store::DBI::Pg
In-Reply-To: <781858E3-E639-4B5F-A5DD-C9277F29CB6F@sgul.ac.uk>
References: <4A885CF2-8E39-443F-A6DE-6E03CF05BB86@sgul.ac.uk>
	<4536f7701002101135s4694ff9bpb4232ac8b7eb0e21@mail.gmail.com>
	<18F52839-7085-4AF8-ACDC-10432475F1F1@sgul.ac.uk>
	<8FD6B9FA50144F15A34EFF2541B1C885@NewLife>
	<781858E3-E639-4B5F-A5DD-C9277F29CB6F@sgul.ac.uk>
Message-ID: <54069B42-9785-4D88-80C8-AC24777D9ED6@illinois.edu>

Code for post-test cleanup is found in Build.PL file; look for the code re: Bio::DB::Seqfeature::Store tests for BDB, Pg, MySQL, etc.

chris

On Feb 12, 2010, at 7:25 AM, Adam Witney wrote:

> 
> Hi Mark,
> 
> What is the general approach for creating a database in the tests and where does that test database then get deleted? My test runs, but it leaves the database in place.
> 
> thanks
> 
> adam
> 
> 
> On 11 Feb 2010, at 14:34, Mark A. Jensen wrote:
> 
>> Hey Adam,
>> The SeqFeature tests are slightly complex in the Build-- during Build.PL execution,
>> the user specifies the DBMS, which is dynamically incorporated during the test.
>> So, any new tests you want to make, you can probably just add to SeqFeature.t,
>> and the Build script will make sure these are routed to the right handler. Jason/Chris
>> will certainly correct me if I'm wrong....
>> cheers MAJ
>> ----- Original Message ----- From: "Adam Witney" <awitney at sgul.ac.uk>
>> To: "Scott Cain" <scott at scottcain.net>
>> Cc: "BioPerl" <bioperl-l at lists.open-bio.org>
>> Sent: Thursday, February 11, 2010 9:21 AM
>> Subject: Re: [Bioperl-l] Adding namespace support toBio::DB::SeqFeature::Store::DBI::Pg
>> 
>> 
>>> 
>>> Hi Scott,
>>> 
>>> ok I now have a version working with PostgreSQL schemas.
>>> 
>>> I was looking for the SFS tests, but can only find SeqFeature.t which only tests the "memory" adaptor. Are there any tests for the mysql/Pg adaptors?
>>> 
>>> thanks
>>> 
>>> adam
>>> 
>>> On 10 Feb 2010, at 19:35, Scott Cain wrote:
>>> 
>>>> Hi Adam,
>>>> 
>>>> I don't have a problem with this approach. Can you verify that this
>>>> patch still passes the Pg SFS tests? I don't generally use
>>>> schemas/name spaces (same thing,right?) much, so I wouldn't feel
>>>> comfortable evaluting it completely.  And, even better, could you add
>>>> to the tests that exercise this behavior?
>>>> 
>>>> Thanks,
>>>> Scott
>>>> 
>>>> 
>>>> On Wednesday, February 10, 2010, Adam Witney <awitney at sgul.ac.uk> wrote:
>>>>> 
>>>>> I noticed that namespace's didn't work with Bio::DB::SeqFeature::Store::DBI::Pg because when creating the database the CREATE INDEX statements didn't pass through _qualify to add the namespace prefix, thus giving a "relation "typelist_tab" already exists" error.
>>>>> 
>>>>> The patch below fixes this, but the question is does this seem like a good approach?
>>>>> 
>>>>> thanks
>>>>> 
>>>>> adam
>>>>> 
>>>>> 
>>>>> Index: Pg.pm
>>>>> ===================================================================
>>>>> --- Pg.pm       (revision 16551)
>>>>> +++ Pg.pm       (working copy)
>>>>> @@ -256,22 +256,20 @@
>>>>> indexed  int default 1,
>>>>> object     bytea not null
>>>>> );
>>>>> -  CREATE INDEX feature_stuff ON feature(seqid,tier,bin,typeid);
>>>>> -  CREATE INDEX feature_typeid ON feature(typeid);
>>>>> END
>>>>> 
>>>>>        locationlist => <<END,
>>>>> (
>>>>> id         serial primary key,
>>>>> seqname    varchar(256)   not null
>>>>> -); CREATE INDEX locationlist_seqname ON locationlist(seqname);
>>>>> +);
>>>>> END
>>>>> 
>>>>>        typelist => <<END,
>>>>> (
>>>>> id       serial primary key,
>>>>> tag      varchar(256)  not null
>>>>> -); CREATE INDEX typelist_tab ON typelist(tag);
>>>>> +);
>>>>> END
>>>>>        name => <<END,
>>>>> (
>>>>> @@ -279,8 +277,6 @@
>>>>> name         varchar(256)  not null,
>>>>> display_name int       default 0
>>>>> );
>>>>> -  CREATE INDEX name_id ON name(id);
>>>>> -  CREATE INDEX name_name ON name(name);
>>>>> END
>>>>> 
>>>>>        attribute => <<END,
>>>>> @@ -289,8 +285,6 @@
>>>>> attribute_id     int   not null,
>>>>> attribute_value  text
>>>>> );
>>>>> -  CREATE INDEX attribute_id ON attribute(id);
>>>>> -  CREATE INDEX attribute_id_val ON attribute(attribute_id,SUBSTR(attribute_value, 1, 10));
>>>>> END
>>>>> 
>>>>>        attributelist => <<END,
>>>>> @@ -298,14 +292,12 @@
>>>>> id       serial primary key,
>>>>> tag      varchar(256)  not null
>>>>> );
>>>>> -  CREATE INDEX attributelist_tag ON attributelist(tag);
>>>>> END
>>>>>        parent2child => <<END,
>>>>> (
>>>>> id               int       not null,
>>>>> child            int       not null
>>>>> );
>>>>> -  CREATE INDEX parent2child_id_child ON parent2child(id,child);
>>>>> END
>>>>> 
>>>>>        meta => <<END,
>>>>> @@ -325,6 +317,22 @@
>>>>>       };
>>>>> }
>>>>> 
>>>>> +sub index_definitions {
>>>>> +  my $self = shift;
>>>>> +  return {
>>>>> +         feature_stuff  => "feature(seqid,tier,bin,typeid)",
>>>>> +         feature_typeid => "feature(typeid)",
>>>>> +         locationlist_seqname => "locationlist(seqname)",
>>>>> +      typelist_tab => "typelist(tag)",
>>>>> +      name_id => "name(id)",
>>>>> +      name_name => "name(name)",
>>>>> +      attribute_id => "attribute(id)",
>>>>> +      attribute_id_val => "attribute(attribute_id,SUBSTR(attribute_value, 1, 10))",
>>>>> +      attributelist_tag =>  "attributelist(tag)",
>>>>> +      parent2child_id_child => "parent2child(id,child)",
>>>>> +        };
>>>>> +}
>>>>> +
>>>>> sub schema {
>>>>> my ($self, $schema) = @_;
>>>>> $self->{'schema'} = $schema if defined($schema);
>>>>> @@ -354,6 +362,18 @@
>>>>>                      $dbh->do($query) or $self->throw($dbh->errstr);
>>>>>              }
>>>>> }
>>>>> +
>>>>> +  my $indexes = $self->index_definitions;
>>>>> +  foreach (keys %$indexes) {
>>>>> +    my $index = $self->_qualify($_);
>>>>> +    my $index_def = $self->_qualify($indexes->{$_});
>>>>> +    $dbh->do("DROP INDEX IF EXISTS $index") if $erase;
>>>>> +    my @index_exists = $dbh->selectrow_array("SELECT * FROM pg_indexes WHERE indexname = '$index'");
>>>>> +               if (!scalar(@index_exists)) {
>>>>> +                       my $query = "CREATE INDEX $index ON $index_def";
>>>>> +                       $dbh->do($query) or $self->throw($dbh->errstr);
>>>>> +               }
>>>>> +  }
>>>>> $self->subfeatures_are_indexed(1) if $erase;
>>>>> 1;
>>>>> }
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>> 
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From bhakti.dwivedi at gmail.com  Fri Feb 12 11:22:32 2010
From: bhakti.dwivedi at gmail.com (Bhakti Dwivedi)
Date: Fri, 12 Feb 2010 11:22:32 -0500
Subject: [Bioperl-l] Current Genbank sequence version from the previous
	version GI number?
Message-ID: <b643abd21002120822j26e484dah6918637f70be8d0f@mail.gmail.com>

I have a file with a list of gi numbers.  I have to obtain the genbank files
for each of these.  For some of the gi's, the sequence has been updated on
ncbi and therefore has the new version with a different gi number.

For example, sequence with 'GI: 126070' has been updated and is now
'GI: 1170742'.
The particular genbank file for the old and the new version is quite
different and has more updated information.  When I retrieve the genbank
file with Bio::DB::Genbank, I am getting the older version.  Is there a way
I can retrieve the updated versions directly from the old gi numbers in
bioperl?

Thanks

Bhakti

From maj at fortinbras.us  Fri Feb 12 13:48:09 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Fri, 12 Feb 2010 13:48:09 -0500
Subject: [Bioperl-l] BlastPlus proactive fix
Message-ID: <A2620BFEA4444954B49A02CF6B3A623D@NewLife>

All-
With revision 16384, your StandAloneBlastPlus object
will retrieve additional blast results using

 $result = $bp_factory->blastn( -query => [$this_seq, $that_seq], -db => 'mydb' );
 # do something with this_seq result
 $result = $bp_factory->next_result;
 # do something with that_seq result

and you may also

 $bp_factory->rewind_results;
 while (my $result = $bp_factory->next_result) {
   ..
 }

happy coding, MAJ

From ferdi.marletaz at me.com  Fri Feb 12 04:07:44 2010
From: ferdi.marletaz at me.com (=?iso-8859-1?Q?Ferdinand_Marl=E9taz?=)
Date: Fri, 12 Feb 2010 10:07:44 +0100
Subject: [Bioperl-l] Bio::TreeIO: Problem rerooting with a leaf
In-Reply-To: <70691285F9CA4AB3A3FB5E25849142D5@NewLife>
References: <fac99fe3-ce8c-49d5-a501-3b84b20af302@g27g2000yqh.googlegroups.com>
	<70691285F9CA4AB3A3FB5E25849142D5@NewLife>
Message-ID: <90E1B16E-101A-492B-AFB1-6509DCBDD166@me.com>

Hi Mark
 this definitely makes sense to me, and your suggestions works fine!
Thank you for your help!
Ferdi


Le 11 f?vr. 2010 ? 18:20, Mark A. Jensen a ?crit :

> Hi Ferdi-
> I'm afraid I caused your trouble. The new reroot makes the the node you provide the root, rather than
> creating a new (and arbitrary) node. Now, the user specifies that node, and so has more control.
> Sometime one wants to take an existing polytomic
> node an make it itself the root; now reroot does this
> transparently. (It also fixes some other things, I think.)
> Try this:
> 
> # put a midpoint node on the ancestral branch of the leaf:
> # this is a new method...
> $new_root = $leaf->create_node_on_branch(-fraction => 0.5);
> # reroot $tree->reroot($new_root);
> 
> (this is what reroot actually did before, essentially secretly
> changing the tree)--
> HTH -MAJ
> 
> ----- Original Message ----- From: "Ferdi" <ferdinand.marletaz at gmail.com>
> To: <bioperl-l at bioperl.org>
> Sent: Thursday, February 11, 2010 11:41 AM
> Subject: [Bioperl-l] Bio::TreeIO: Problem rerooting with a leaf
> 
> 
>> Hi-
>> I am an enthusiastic user of Bio::TreeIO module, and I got some
>> problems with it after a recent reinstall of bioperl on my new mac
>> (10.6, previous was 10.5).  Particularly, when attempting to reroot
>> ($tree->reroot($leaf))  a tree with a leaf node, it doesn't seem to
>> consider ianymore t as an outgroup but as the root itself... For
>> example, with the example provided on Howto bioperl page:
>> (((A,B),(C,D)),E);
>> what I get when reroot with A:
>> ((B,((C,D),(E))))A;
>> while I should get something like:
>> (A,((E,(C,D)),B));
>> with A considered as outgroup instead of the root node itself.
>> Thanks for your help!
>> Ferdi
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 



From asekhar at dow.com  Fri Feb 12 16:25:35 2010
From: asekhar at dow.com (ThirumalaiswamySekhar, Arvind (A))
Date: Fri, 12 Feb 2010 16:25:35 -0500
Subject: [Bioperl-l] Blastxml parser not parsing multiple hits
Message-ID: <EED991CA19FFA64BBD60DD12A5B39FEC36E523@USMDLMDOWX031.dow.com>

Hello

I have been using the blastxml parser and based on what I see as output,
the parser does not move the result object correctly when there are
muliple sequence results in one file.

All hits and their hsps always appear with the same query name which
should not be the case. Is this a bug?


From cjfields at illinois.edu  Fri Feb 12 17:24:52 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 12 Feb 2010 16:24:52 -0600
Subject: [Bioperl-l] Blastxml parser not parsing multiple hits
In-Reply-To: <EED991CA19FFA64BBD60DD12A5B39FEC36E523@USMDLMDOWX031.dow.com>
References: <EED991CA19FFA64BBD60DD12A5B39FEC36E523@USMDLMDOWX031.dow.com>
Message-ID: <7AB89085-8E85-4FA8-93CD-1D92C9587FEB@illinois.edu>

This sounds like a bug, but I believe there are tests in the test suite that cover this.  So, you'll definitely have to be more explicit.  Can you submit a bug report, containing code and an example file?

chris

On Feb 12, 2010, at 3:25 PM, ThirumalaiswamySekhar, Arvind (A) wrote:

> Hello
> 
> I have been using the blastxml parser and based on what I see as output,
> the parser does not move the result object correctly when there are
> muliple sequence results in one file.
> 
> All hits and their hsps always appear with the same query name which
> should not be the case. Is this a bug?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jessica.sun at gmail.com  Fri Feb 12 20:44:30 2010
From: jessica.sun at gmail.com (Jessica Sun)
Date: Fri, 12 Feb 2010 20:44:30 -0500
Subject: [Bioperl-l] one more question
Message-ID: <9adc0e9b1002121744v6093c524hcc6b72379de15c3@mail.gmail.com>

Does anyone knows how to get genomic(dna) sequences(with right sub regions)
in gbk format when you only have NM_(mRNA) accession numbers.

Thanks,


-- 
Jessica Jingping Sun

From awitney at sgul.ac.uk  Sat Feb 13 11:43:08 2010
From: awitney at sgul.ac.uk (Adam Witney)
Date: Sat, 13 Feb 2010 16:43:08 +0000
Subject: [Bioperl-l] Adding namespace support to
	Bio::DB::SeqFeature::Store::DBI::Pg
In-Reply-To: <54069B42-9785-4D88-80C8-AC24777D9ED6@illinois.edu>
References: <4A885CF2-8E39-443F-A6DE-6E03CF05BB86@sgul.ac.uk>
	<4536f7701002101135s4694ff9bpb4232ac8b7eb0e21@mail.gmail.com>
	<18F52839-7085-4AF8-ACDC-10432475F1F1@sgul.ac.uk>
	<8FD6B9FA50144F15A34EFF2541B1C885@NewLife>
	<781858E3-E639-4B5F-A5DD-C9277F29CB6F@sgul.ac.uk>
	<54069B42-9785-4D88-80C8-AC24777D9ED6@illinois.edu>
Message-ID: <4ECF9AC9-9319-403B-A07B-A86E07412D01@sgul.ac.uk>


Hi guys,

I have this working now using PostgreSQL schema support. I have filed a patch on bugzilla (ID: 3011), which includes some extra tests in SeqFeature.t for the DBI::mysql and DBI::Pg adaptors.

let me know if there are any questions or anything you want me to change.

thanks 

adam




On 12 Feb 2010, at 13:38, Chris Fields wrote:

> Code for post-test cleanup is found in Build.PL file; look for the code re: Bio::DB::Seqfeature::Store tests for BDB, Pg, MySQL, etc.
> 
> chris
> 
> On Feb 12, 2010, at 7:25 AM, Adam Witney wrote:
> 
>> 
>> Hi Mark,
>> 
>> What is the general approach for creating a database in the tests and where does that test database then get deleted? My test runs, but it leaves the database in place.
>> 
>> thanks
>> 
>> adam
>> 
>> 
>> On 11 Feb 2010, at 14:34, Mark A. Jensen wrote:
>> 
>>> Hey Adam,
>>> The SeqFeature tests are slightly complex in the Build-- during Build.PL execution,
>>> the user specifies the DBMS, which is dynamically incorporated during the test.
>>> So, any new tests you want to make, you can probably just add to SeqFeature.t,
>>> and the Build script will make sure these are routed to the right handler. Jason/Chris
>>> will certainly correct me if I'm wrong....
>>> cheers MAJ
>>> ----- Original Message ----- From: "Adam Witney" <awitney at sgul.ac.uk>
>>> To: "Scott Cain" <scott at scottcain.net>
>>> Cc: "BioPerl" <bioperl-l at lists.open-bio.org>
>>> Sent: Thursday, February 11, 2010 9:21 AM
>>> Subject: Re: [Bioperl-l] Adding namespace support toBio::DB::SeqFeature::Store::DBI::Pg
>>> 
>>> 
>>>> 
>>>> Hi Scott,
>>>> 
>>>> ok I now have a version working with PostgreSQL schemas.
>>>> 
>>>> I was looking for the SFS tests, but can only find SeqFeature.t which only tests the "memory" adaptor. Are there any tests for the mysql/Pg adaptors?
>>>> 
>>>> thanks
>>>> 
>>>> adam
>>>> 
>>>> On 10 Feb 2010, at 19:35, Scott Cain wrote:
>>>> 
>>>>> Hi Adam,
>>>>> 
>>>>> I don't have a problem with this approach. Can you verify that this
>>>>> patch still passes the Pg SFS tests? I don't generally use
>>>>> schemas/name spaces (same thing,right?) much, so I wouldn't feel
>>>>> comfortable evaluting it completely.  And, even better, could you add
>>>>> to the tests that exercise this behavior?
>>>>> 
>>>>> Thanks,
>>>>> Scott
>>>>> 
>>>>> 
>>>>> On Wednesday, February 10, 2010, Adam Witney <awitney at sgul.ac.uk> wrote:
>>>>>> 
>>>>>> I noticed that namespace's didn't work with Bio::DB::SeqFeature::Store::DBI::Pg because when creating the database the CREATE INDEX statements didn't pass through _qualify to add the namespace prefix, thus giving a "relation "typelist_tab" already exists" error.
>>>>>> 
>>>>>> The patch below fixes this, but the question is does this seem like a good approach?
>>>>>> 
>>>>>> thanks
>>>>>> 
>>>>>> adam
>>>>>> 
>>>>>> 
>>>>>> Index: Pg.pm
>>>>>> ===================================================================
>>>>>> --- Pg.pm       (revision 16551)
>>>>>> +++ Pg.pm       (working copy)
>>>>>> @@ -256,22 +256,20 @@
>>>>>> indexed  int default 1,
>>>>>> object     bytea not null
>>>>>> );
>>>>>> -  CREATE INDEX feature_stuff ON feature(seqid,tier,bin,typeid);
>>>>>> -  CREATE INDEX feature_typeid ON feature(typeid);
>>>>>> END
>>>>>> 
>>>>>>       locationlist => <<END,
>>>>>> (
>>>>>> id         serial primary key,
>>>>>> seqname    varchar(256)   not null
>>>>>> -); CREATE INDEX locationlist_seqname ON locationlist(seqname);
>>>>>> +);
>>>>>> END
>>>>>> 
>>>>>>       typelist => <<END,
>>>>>> (
>>>>>> id       serial primary key,
>>>>>> tag      varchar(256)  not null
>>>>>> -); CREATE INDEX typelist_tab ON typelist(tag);
>>>>>> +);
>>>>>> END
>>>>>>       name => <<END,
>>>>>> (
>>>>>> @@ -279,8 +277,6 @@
>>>>>> name         varchar(256)  not null,
>>>>>> display_name int       default 0
>>>>>> );
>>>>>> -  CREATE INDEX name_id ON name(id);
>>>>>> -  CREATE INDEX name_name ON name(name);
>>>>>> END
>>>>>> 
>>>>>>       attribute => <<END,
>>>>>> @@ -289,8 +285,6 @@
>>>>>> attribute_id     int   not null,
>>>>>> attribute_value  text
>>>>>> );
>>>>>> -  CREATE INDEX attribute_id ON attribute(id);
>>>>>> -  CREATE INDEX attribute_id_val ON attribute(attribute_id,SUBSTR(attribute_value, 1, 10));
>>>>>> END
>>>>>> 
>>>>>>       attributelist => <<END,
>>>>>> @@ -298,14 +292,12 @@
>>>>>> id       serial primary key,
>>>>>> tag      varchar(256)  not null
>>>>>> );
>>>>>> -  CREATE INDEX attributelist_tag ON attributelist(tag);
>>>>>> END
>>>>>>       parent2child => <<END,
>>>>>> (
>>>>>> id               int       not null,
>>>>>> child            int       not null
>>>>>> );
>>>>>> -  CREATE INDEX parent2child_id_child ON parent2child(id,child);
>>>>>> END
>>>>>> 
>>>>>>       meta => <<END,
>>>>>> @@ -325,6 +317,22 @@
>>>>>>      };
>>>>>> }
>>>>>> 
>>>>>> +sub index_definitions {
>>>>>> +  my $self = shift;
>>>>>> +  return {
>>>>>> +         feature_stuff  => "feature(seqid,tier,bin,typeid)",
>>>>>> +         feature_typeid => "feature(typeid)",
>>>>>> +         locationlist_seqname => "locationlist(seqname)",
>>>>>> +      typelist_tab => "typelist(tag)",
>>>>>> +      name_id => "name(id)",
>>>>>> +      name_name => "name(name)",
>>>>>> +      attribute_id => "attribute(id)",
>>>>>> +      attribute_id_val => "attribute(attribute_id,SUBSTR(attribute_value, 1, 10))",
>>>>>> +      attributelist_tag =>  "attributelist(tag)",
>>>>>> +      parent2child_id_child => "parent2child(id,child)",
>>>>>> +        };
>>>>>> +}
>>>>>> +
>>>>>> sub schema {
>>>>>> my ($self, $schema) = @_;
>>>>>> $self->{'schema'} = $schema if defined($schema);
>>>>>> @@ -354,6 +362,18 @@
>>>>>>                     $dbh->do($query) or $self->throw($dbh->errstr);
>>>>>>             }
>>>>>> }
>>>>>> +
>>>>>> +  my $indexes = $self->index_definitions;
>>>>>> +  foreach (keys %$indexes) {
>>>>>> +    my $index = $self->_qualify($_);
>>>>>> +    my $index_def = $self->_qualify($indexes->{$_});
>>>>>> +    $dbh->do("DROP INDEX IF EXISTS $index") if $erase;
>>>>>> +    my @index_exists = $dbh->selectrow_array("SELECT * FROM pg_indexes WHERE indexname = '$index'");
>>>>>> +               if (!scalar(@index_exists)) {
>>>>>> +                       my $query = "CREATE INDEX $index ON $index_def";
>>>>>> +                       $dbh->do($query) or $self->throw($dbh->errstr);
>>>>>> +               }
>>>>>> +  }
>>>>>> $self->subfeatures_are_indexed(1) if $erase;
>>>>>> 1;
>>>>>> }
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> -- 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From adam at ali.as  Sat Feb 13 21:22:07 2010
From: adam at ali.as (Adam Kennedy)
Date: Sun, 14 Feb 2010 13:22:07 +1100
Subject: [Bioperl-l] Recommendations for BioPerl-related packages to include
	in Strawberry Perl Professional
Message-ID: <255d58531002131822j5991a575ke666a19b6921ba76@mail.gmail.com>

Greetings BioPerl'ers

The Strawberry Perl team is beginning to put together our new (and
still free) Strawberry Professional distribution.

Unlike the core product (which has a mandate to be like the Unix Perl,
and provide the means to install as much of CPAN as possible) the new
distribution has the goal of pre-installing as many useful, important,
or essential modules in advance as possible. The aim is to get users
up and running with simple common tasks quickly, delaying the need to
navigate the CPAN and the module installation process until after they
are convinced they can create useful programs.

As part of this, we plan to include BioPerl and a Perl IDE in the
default installation, so that BioPeople on Windows can just install a
single program and then be up and running fast. At the moment,
Strawberry supports the installation of the BioPerl package with the
default options (a number of options that add more pieces still fail
at the present time).

My question to this list is, what are the packages that are not in the
default option install of BioPerl that you feel are the most
important, and the most often needed.

And are there any complementary packages you would like us to include
to make life easier for newbie Windows BioPeople?

Best Regards

Adam K

From cjfields at illinois.edu  Sun Feb 14 00:05:24 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sat, 13 Feb 2010 23:05:24 -0600
Subject: [Bioperl-l] Recommendations for BioPerl-related packages to
	include in Strawberry Perl Professional
In-Reply-To: <255d58531002131822j5991a575ke666a19b6921ba76@mail.gmail.com>
References: <255d58531002131822j5991a575ke666a19b6921ba76@mail.gmail.com>
Message-ID: <A0E17A05-53B3-4366-95F0-64FFF73D085B@illinois.edu>

On Feb 13, 2010, at 8:22 PM, Adam Kennedy wrote:

> Greetings BioPerl'ers
> 
> The Strawberry Perl team is beginning to put together our new (and
> still free) Strawberry Professional distribution.
> 
> Unlike the core product (which has a mandate to be like the Unix Perl,
> and provide the means to install as much of CPAN as possible) the new
> distribution has the goal of pre-installing as many useful, important,
> or essential modules in advance as possible. The aim is to get users
> up and running with simple common tasks quickly, delaying the need to
> navigate the CPAN and the module installation process until after they
> are convinced they can create useful programs.
> 
> As part of this, we plan to include BioPerl and a Perl IDE in the
> default installation, so that BioPeople on Windows can just install a
> single program and then be up and running fast. At the moment,
> Strawberry supports the installation of the BioPerl package with the
> default options (a number of options that add more pieces still fail
> at the present time).

I suppose the Perl IDE would be Padre? ;> 

> My question to this list is, what are the packages that are not in the
> default option install of BioPerl that you feel are the most
> important, and the most often needed.

In order:

1) BioPerl-Run is a good runner up.  
2) BioPerl-Network is easy as well (pure perl).  
3) BioPerl-DB, but it requires a DBI adaptor for mysql, Pg, Oracle.  

These should all install on Windows (have tested with ActiveState before).  I has actually pushed alpha releases out for the above three to CPAN, this following the core 1.6.1 release, but never got around to pushing out newer alphas.  I could possibly rectify that this coming week, with the final release soon after.  The previous releases already in CPAN might also suffice.

> And are there any complementary packages you would like us to include
> to make life easier for newbie Windows BioPeople?

Related to BioPerl:

Bio::Graphics.  Very important module!

> Best Regards
> 
> Adam K

No prob.  

chris

From Russell.Smithies at agresearch.co.nz  Sun Feb 14 14:43:56 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 15 Feb 2010 08:43:56 +1300
Subject: [Bioperl-l] Hello
In-Reply-To: <3cf6e5271002130216l5d6263ej5d7dcce39bc445e5@mail.gmail.com>
References: <3cf6e5271002130216l5d6263ej5d7dcce39bc445e5@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61C81F35@exchsth.agresearch.co.nz>

Hi,
One of these should get you most of the way to what you need.
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#How_do_I_retrieve_a_long_list_of_sequences_using_a_query.3F
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#How_do_I_retrieve_the_DNA_sequence_using_EntrezGene_IDs.3F
http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service

You may find it easier if you have the gene id numbers rather than just the gene names.


Hope this helps,

Russell

From: chirag matkar [mailto:chirag.matkar at gmail.com]
Sent: Saturday, 13 February 2010 11:16 p.m.
To: Smithies, Russell
Subject: Hello

Hello Sir,
i am working on Bioperl and have a doubt.
I have aList of gene names of Mtb H37Rv and i want to retrieve FASTA format of all sequences
How can i do that?

--
Regards,
Chirag Matkar,
BTech Bioinformatics,
Dr.D.Y.Patil Biotechnology and Bioinformatics Institute,
http://www.dypbbi.edu.in
Pune.

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From michael.watson at bbsrc.ac.uk  Sun Feb 14 14:51:15 2010
From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C))
Date: Sun, 14 Feb 2010 19:51:15 +0000
Subject: [Bioperl-l] Hello
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32C61C81F35@exchsth.agresearch.co.nz>
References: <3cf6e5271002130216l5d6263ej5d7dcce39bc445e5@mail.gmail.com>,
	<18DF7D20DFEC044098A1062202F5FFF32C61C81F35@exchsth.agresearch.co.nz>
Message-ID: <8D08960C647E64438CE5740657CBBDC501F91060EA@iahcexch1.iah.bbsrc.ac.uk>

If I was going to do this, I wouldn't use BioPerl.

I'd download the RefSeq entry for the genome (Mtb)
Then I would use the EMBOSS extractfeat program to extract fasta sequences of the gene features.

Simples.
________________________________________
From: bioperl-l-bounces at lists.open-bio.org [bioperl-l-bounces at lists.open-bio.org] On Behalf Of Smithies, Russell [Russell.Smithies at agresearch.co.nz]
Sent: 14 February 2010 19:43
To: 'chirag matkar'
Cc: 'bioperl-l at lists.open-bio.org'
Subject: Re: [Bioperl-l] Hello

Hi,
One of these should get you most of the way to what you need.
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#How_do_I_retrieve_a_long_list_of_sequences_using_a_query.3F
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#How_do_I_retrieve_the_DNA_sequence_using_EntrezGene_IDs.3F
http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service

You may find it easier if you have the gene id numbers rather than just the gene names.


Hope this helps,

Russell

From: chirag matkar [mailto:chirag.matkar at gmail.com]
Sent: Saturday, 13 February 2010 11:16 p.m.
To: Smithies, Russell
Subject: Hello

Hello Sir,
i am working on Bioperl and have a doubt.
I have aList of gene names of Mtb H37Rv and i want to retrieve FASTA format of all sequences
How can i do that?

--
Regards,
Chirag Matkar,
BTech Bioinformatics,
Dr.D.Y.Patil Biotechnology and Bioinformatics Institute,
http://www.dypbbi.edu.in
Pune.

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l


From rmb32 at cornell.edu  Sun Feb 14 15:21:49 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Sun, 14 Feb 2010 12:21:49 -0800
Subject: [Bioperl-l] Recommendations for BioPerl-related packages to
 include in Strawberry Perl Professional
In-Reply-To: <255d58531002131822j5991a575ke666a19b6921ba76@mail.gmail.com>
References: <255d58531002131822j5991a575ke666a19b6921ba76@mail.gmail.com>
Message-ID: <4B785B5D.1010403@cornell.edu>

Thank you for doing this Adam, it's very important work.

Is there a similar concept for newbie BioPeople running OS X or perhaps 
SSHing into shared unix accounts?

Rob

Adam Kennedy wrote:
> Greetings BioPerl'ers
> 
> The Strawberry Perl team is beginning to put together our new (and
> still free) Strawberry Professional distribution.
> 
> Unlike the core product (which has a mandate to be like the Unix Perl,
> and provide the means to install as much of CPAN as possible) the new
> distribution has the goal of pre-installing as many useful, important,
> or essential modules in advance as possible. The aim is to get users
> up and running with simple common tasks quickly, delaying the need to
> navigate the CPAN and the module installation process until after they
> are convinced they can create useful programs.
> 
> As part of this, we plan to include BioPerl and a Perl IDE in the
> default installation, so that BioPeople on Windows can just install a
> single program and then be up and running fast. At the moment,
> Strawberry supports the installation of the BioPerl package with the
> default options (a number of options that add more pieces still fail
> at the present time).
> 
> My question to this list is, what are the packages that are not in the
> default option install of BioPerl that you feel are the most
> important, and the most often needed.
> 
> And are there any complementary packages you would like us to include
> to make life easier for newbie Windows BioPeople?
> 
> Best Regards
> 
> Adam K
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From Russell.Smithies at agresearch.co.nz  Sun Feb 14 15:45:01 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 15 Feb 2010 09:45:01 +1300
Subject: [Bioperl-l] Hello
In-Reply-To: <8D08960C647E64438CE5740657CBBDC501F91060EA@iahcexch1.iah.bbsrc.ac.uk>
References: <3cf6e5271002130216l5d6263ej5d7dcce39bc445e5@mail.gmail.com>,
	<18DF7D20DFEC044098A1062202F5FFF32C61C81F35@exchsth.agresearch.co.nz>
	<8D08960C647E64438CE5740657CBBDC501F91060EA@iahcexch1.iah.bbsrc.ac.uk>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61C81FD3@exchsth.agresearch.co.nz>

Or as Michael suggests, you could download the Genbank file for the genome http://www.ncbi.nlm.nih.gov/nuccore/NC_000962  as it's fairly small and pull the gene annotations from that.
Of course, I'd recommend reading this:
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Getting_the_Annotations


--Russell

> -----Original Message-----
> From: michael watson (IAH-C) [mailto:michael.watson at bbsrc.ac.uk]
> Sent: Monday, 15 February 2010 8:51 a.m.
> To: Smithies, Russell; 'chirag matkar'
> Cc: 'bioperl-l at lists.open-bio.org'
> Subject: RE: Hello
> 
> If I was going to do this, I wouldn't use BioPerl.
> 
> I'd download the RefSeq entry for the genome (Mtb)
> Then I would use the EMBOSS extractfeat program to extract fasta sequences
> of the gene features.
> 
> Simples.
> ________________________________________
> From: bioperl-l-bounces at lists.open-bio.org [bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of Smithies, Russell
> [Russell.Smithies at agresearch.co.nz]
> Sent: 14 February 2010 19:43
> To: 'chirag matkar'
> Cc: 'bioperl-l at lists.open-bio.org'
> Subject: Re: [Bioperl-l] Hello
> 
> Hi,
> One of these should get you most of the way to what you need.
> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#How_do_I_retrieve_a_
> long_list_of_sequences_using_a_query.3F
> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#How_do_I_retrieve_th
> e_DNA_sequence_using_EntrezGene_IDs.3F
> http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service
> 
> You may find it easier if you have the gene id numbers rather than just
> the gene names.
> 
> 
> Hope this helps,
> 
> Russell
> 
> From: chirag matkar [mailto:chirag.matkar at gmail.com]
> Sent: Saturday, 13 February 2010 11:16 p.m.
> To: Smithies, Russell
> Subject: Hello
> 
> Hello Sir,
> i am working on Bioperl and have a doubt.
> I have aList of gene names of Mtb H37Rv and i want to retrieve FASTA
> format of all sequences
> How can i do that?
> 
> --
> Regards,
> Chirag Matkar,
> BTech Bioinformatics,
> Dr.D.Y.Patil Biotechnology and Bioinformatics Institute,
> http://www.dypbbi.edu.in
> Pune.
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From avilella at gmail.com  Mon Feb 15 08:45:10 2010
From: avilella at gmail.com (Albert Vilella)
Date: Mon, 15 Feb 2010 13:45:10 +0000
Subject: [Bioperl-l] Simulate fragment and read-pair reads from sample
	sequence
Message-ID: <358f4d651002150545h7d4f58aewd0e3cbbbd38c453f@mail.gmail.com>

Hi,

This may have been asked before but I couldn't find any similar
question by searching the archives.
I want to simulate substr's from a sequence of a given (read) length.

If I have a starting sequence of 10,000bp, the way I understand it is
that a standard Solexa (or 454) library
preparation will give me random $read_length=75 (or 450) reads along
the 10k sequence.
So I want to do a random substr on the sequence itself.

But if I am simulating read-pairs of a 10,000bp sequence, given a
defined $insert_size length, how would I
do the random substr pairs?

Cheers,

Albert.

From asekhar at dow.com  Sat Feb 13 11:31:28 2010
From: asekhar at dow.com (ThirumalaiswamySekhar, Arvind (A))
Date: Sat, 13 Feb 2010 11:31:28 -0500
Subject: [Bioperl-l] Blastxml parser not parsing multiple hits
In-Reply-To: <7AB89085-8E85-4FA8-93CD-1D92C9587FEB@illinois.edu>
References: <EED991CA19FFA64BBD60DD12A5B39FEC36E523@USMDLMDOWX031.dow.com>
	<7AB89085-8E85-4FA8-93CD-1D92C9587FEB@illinois.edu>
Message-ID: <EED991CA19FFA64BBD60DD12A5B39FEC36E525@USMDLMDOWX031.dow.com>

Sure Chris

I will. 

-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu] 
Sent: Friday, February 12, 2010 5:25 PM
To: ThirumalaiswamySekhar, Arvind (A)
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Blastxml parser not parsing multiple hits

This sounds like a bug, but I believe there are tests in the test suite
that cover this.  So, you'll definitely have to be more explicit.  Can
you submit a bug report, containing code and an example file?

chris

On Feb 12, 2010, at 3:25 PM, ThirumalaiswamySekhar, Arvind (A) wrote:

> Hello
> 
> I have been using the blastxml parser and based on what I see as
output,
> the parser does not move the result object correctly when there are
> muliple sequence results in one file.
> 
> All hits and their hsps always appear with the same query name which
> should not be the case. Is this a bug?
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From janine.arloth at googlemail.com  Sat Feb 13 15:58:11 2010
From: janine.arloth at googlemail.com (Janine Arloth)
Date: Sat, 13 Feb 2010 21:58:11 +0100
Subject: [Bioperl-l] BlastPlus and Bio::Graphics
Message-ID: <EB3B3684-6A54-4549-BAAA-6AED15F1C8C8@gmail.com>

Hello,

I am a new user of bioperl and use blast (+). 
I want to get a graphic output so I use the example described on web http://www.bioperl.org/wiki/HOWTO:Graphics .

I have installed all required Modules.
But the output looks like:

??PNG

IHDR4)?????=PLTE?Q?????.??Wk??#????????K????2???????H???????????????????????????????????H=???????F??????????????G?@?????????/OO??????????????Uk/e????r??????????=??????????????????????????????w? ???????????????`"??"p??2f????????e??????????????????????????????????cG?????jZ?????
......

Do you have an idea, what I make wrong?

Best regards
Janine









From janine.arloth at googlemail.com  Sat Feb 13 16:46:15 2010
From: janine.arloth at googlemail.com (Janine Arloth)
Date: Sat, 13 Feb 2010 22:46:15 +0100
Subject: [Bioperl-l] Distribution of Blast Hits on the Query Sequence
Message-ID: <93409F51-2B24-4808-A8A7-B31025119B33@gmail.com>

Hello,


is possible to produce a graphic from the blast (+) output of the distribution of Blast Hits on the Query Sequence?
(As it is on the blast website)
Thanks and regards



From jessica.sun at gmail.com  Mon Feb 15 09:35:16 2010
From: jessica.sun at gmail.com (Jessica Sun)
Date: Mon, 15 Feb 2010 09:35:16 -0500
Subject: [Bioperl-l] Fwd: get gene bank file
Message-ID: <9adc0e9b1002150635w23054bdar4b9515ffe1267dc@mail.gmail.com>

---------- Forwarded message ----------
From: Jessica Sun <jessica.sun at gmail.com>
Date: Fri, Feb 12, 2010 at 8:44 PM
Subject: one more question
To: bioperl-l at lists.open-bio.org


Does anyone knows how to get genomic(dna) sequences(with right sub regions)
in gbk format when you only have NM_(mRNA) accession numbers.

Thanks,


-- 
Jessica Jingping Sun



-- 
Jessica Jingping Sun

From bhakti.dwivedi at gmail.com  Mon Feb 15 09:37:38 2010
From: bhakti.dwivedi at gmail.com (Bhakti Dwivedi)
Date: Mon, 15 Feb 2010 09:37:38 -0500
Subject: [Bioperl-l] Distribution of Blast Hits on the Query Sequence
In-Reply-To: <93409F51-2B24-4808-A8A7-B31025119B33@gmail.com>
References: <93409F51-2B24-4808-A8A7-B31025119B33@gmail.com>
Message-ID: <b643abd21002150637k7dec9436m102406e9911e6697@mail.gmail.com>

You can use Bio::Graphics.


There is a HOWTO doc on:
http://stein.cshl.org/genome_informatics/BioGraphics/Graphics-HOWTO.html

and another Bio::Graphics tutorial doc on:
http://bio-graphics.rubyforge.org/

You can also search through cpan http://search.cpan.org/dist/Bio-Graphics/


I hope it helps.


Bhakti




On Sat, Feb 13, 2010 at 4:46 PM, Janine Arloth <janine.arloth at googlemail.com
> wrote:

> Hello,
>
>
> is possible to produce a graphic from the blast (+) output of the
> distribution of Blast Hits on the Query Sequence?
> (As it is on the blast website)
> Thanks and regards
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From cjfields at illinois.edu  Mon Feb 15 09:47:11 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 15 Feb 2010 08:47:11 -0600
Subject: [Bioperl-l] BlastPlus and Bio::Graphics
In-Reply-To: <EB3B3684-6A54-4549-BAAA-6AED15F1C8C8@gmail.com>
References: <EB3B3684-6A54-4549-BAAA-6AED15F1C8C8@gmail.com>
Message-ID: <AE077B66-BA45-4E03-AEA6-6E96D1CB0E48@illinois.edu>

Hard to say w/o seeing the code.  My first thought is you either haven't set binmode() for the file handle (essential for Windows), or you are attempting to open the binary PNG file as text.  The binmode issue is covered in the Bio::Graphics HOWTO.

chris

On Feb 13, 2010, at 2:58 PM, Janine Arloth wrote:

> Hello,
> 
> I am a new user of bioperl and use blast (+). 
> I want to get a graphic output so I use the example described on web http://www.bioperl.org/wiki/HOWTO:Graphics .
> 
> I have installed all required Modules.
> But the output looks like:
> 
> ??PNG
> 
> IHDR4)?????=PLTE?Q?????.??Wk??#????????K????2???????H???????????????????????????????????H=???????F??????????????G?@?????????/OO??????????????Uk/e????r??????????=??????????????????????????????w? ???????????????`"??"p??2f????????e??????????????????????????????????cG?????jZ?????
> ......
> 
> Do you have an idea, what I make wrong?
> 
> Best regards
> Janine
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From shalabh.sharma7 at gmail.com  Mon Feb 15 10:06:29 2010
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Mon, 15 Feb 2010 10:06:29 -0500
Subject: [Bioperl-l] BlastPlus and Bio::Graphics
In-Reply-To: <AE077B66-BA45-4E03-AEA6-6E96D1CB0E48@illinois.edu>
References: <EB3B3684-6A54-4549-BAAA-6AED15F1C8C8@gmail.com>
	<AE077B66-BA45-4E03-AEA6-6E96D1CB0E48@illinois.edu>
Message-ID: <9fcc48c71002150706v45668c05l21cb3176b3796e91@mail.gmail.com>

I think you are trying to open the png fine as text , or directly taking the
output  ( i tried the same and i am getting a same kind of output).
Try to save the output as png file first then open it.

-Shalabh Sharma

On Mon, Feb 15, 2010 at 9:47 AM, Chris Fields <cjfields at illinois.edu> wrote:

> Hard to say w/o seeing the code.  My first thought is you either haven't
> set binmode() for the file handle (essential for Windows), or you are
> attempting to open the binary PNG file as text.  The binmode issue is
> covered in the Bio::Graphics HOWTO.
>
> chris
>
> On Feb 13, 2010, at 2:58 PM, Janine Arloth wrote:
>
> > Hello,
> >
> > I am a new user of bioperl and use blast (+).
> > I want to get a graphic output so I use the example described on web
> http://www.bioperl.org/wiki/HOWTO:Graphics .
> >
> > I have installed all required Modules.
> > But the output looks like:
> >
> > ??PNG
> >
> > IHDR4)?????=PLTE?Q?????.??Wk??#????????K????2??
> ?????H???????????????????????????????????H=???????F??????????????G?@?????????/OO??????????????Uk/e????r??????????=??????????????????????????????w?
> ???????????????`"??"p??2f????????e??????????????????????????????????cG?????jZ?????
> > ......
> >
> > Do you have an idea, what I make wrong?
> >
> > Best regards
> > Janine
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From ajmackey at gmail.com  Mon Feb 15 12:25:15 2010
From: ajmackey at gmail.com (Aaron Mackey)
Date: Mon, 15 Feb 2010 12:25:15 -0500
Subject: [Bioperl-l] Simulate fragment and read-pair reads from sample
	sequence
In-Reply-To: <358f4d651002150545h7d4f58aewd0e3cbbbd38c453f@mail.gmail.com>
References: <358f4d651002150545h7d4f58aewd0e3cbbbd38c453f@mail.gmail.com>
Message-ID: <24c96eca1002150925m7037eafbna1a48b1eae55735b@mail.gmail.com>

Hi Albert,

There are some tools out there that already do a good job of this, and
take into consideration platform-specific error models, paired end
fragment length distributions, etc.  maq has an Illumina read
simulator that also simulates quality scores, and MetaSim has a nice
454 read simulator (and Illumina as well, though unfortunately doesn't
do quality scores for either).

But to answer your question, you'd first select a random fragment of
length $insert_length, and then take the two reads from the left and
right ends of the fragment (reading from 5' and 3'/revcomp
respectively).

Note that in a real-world DNA capture experiment targeting 10 kb,
you'd get some fragments that extend past the boundaries.

-Aaron

On Mon, Feb 15, 2010 at 8:45 AM, Albert Vilella <avilella at gmail.com> wrote:
> Hi,
>
> This may have been asked before but I couldn't find any similar
> question by searching the archives.
> I want to simulate substr's from a sequence of a given (read) length.
>
> If I have a starting sequence of 10,000bp, the way I understand it is
> that a standard Solexa (or 454) library
> preparation will give me random $read_length=75 (or 450) reads along
> the 10k sequence.
> So I want to do a random substr on the sequence itself.
>
> But if I am simulating read-pairs of a 10,000bp sequence, given a
> defined $insert_size length, how would I
> do the random substr pairs?
>
> Cheers,
>
> Albert.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From florent.angly at gmail.com  Mon Feb 15 17:13:42 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Tue, 16 Feb 2010 08:13:42 +1000
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
Message-ID: <4B79C716.90405@gmail.com>

Hi all,

I am trying to reduce memory usage and speedup reading FASTA files using 
the facilities provided by BioPerl.

The first thing I noticed is that when using Bio::SeqIO::fasta, the 
objects returned are Bio::Seq, not Bio::PrimarySeq objects. 
Bio::PrimarySeq sequences are lighter than Bio::Seq sequences, so it's 
what I need. See code below:
> use warnings;
> use strict;
> use Data::Dumper;
> use Bio::SeqIO;
> my $in = Bio::SeqIO->new(-fh=>\*DATA);
> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
> print "The factory is a ".ref($seqfactory)."\n";
> $seqfactory->type('Bio::PrimarySeq'); # gives an error
> my $seq = $in->next_seq;
> print Dumper($seq);
> __END__
> >seq1 a small test sequence
> ACGTACGACTACGACTAGCGCCATCAGC
It returns:
> $VAR1 = bless( {
>                  'primary_id' => 'seq1',
>                  'primary_seq' => bless( {
>                                            'display_id' => 'seq1',
>                                            'primary_id' => 'seq1',
>                                            'desc' => 'a small test 
> sequence',
>                                            'seq' => 
> 'ACGTACGACTACGACTAGCGCCATCAGC',
>                                            'alphabet' => 'dna'
>                                          }, 'Bio::PrimarySeq' )
>                }, 'Bio::Seq' );

Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I really only 
need the Bio::PrimarySeq. Looking at the documentation for Bio::SeqIO I 
found that I could in theory adjust the sequence factory and sequence 
builder to my liking... I tried this:
> use warnings;
> use strict;
> use Data::Dumper;
> use Bio::SeqIO;
> my $in = Bio::SeqIO->new(-fh=>\*DATA);
> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
> print "The factory is a ".ref($seqfactory)."\n";
> $seqfactory->type('Bio::PrimarySeq'); # gives an error
> my $seq = $in->next_seq;
> print Dumper($seq);
> __END__
> >seq1 a small test sequence
> ACGTACGACTACGACTAGCGCCATCAGC
This returns:
> The factory is a Bio::Seq::SeqFastaSpeedFactory
> Can't locate object method "type" via package 
> "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl line 12, 
> <DATA> line 1.

According to Bio::Seq::FastaSpeedFactory's documentation:
> If you want the factory to create Bio::Seq objects instead
> of the default Bio::PrimarySeq objects, use the -type parameter
So, PrimarySeq should be the default type, even though in my case it 
seems not to be. Second, I can't seem to use the -type method to change 
what the return type is... It errors.

Any ideas??? Thanks,

Florent




From wkretzsch at gmail.com  Mon Feb 15 17:34:36 2010
From: wkretzsch at gmail.com (Warren W. Kretzschmar)
Date: Mon, 15 Feb 2010 17:34:36 -0500
Subject: [Bioperl-l] Using Bio::PopGen::Statistics with missing data
Message-ID: <5d2ac05c1002151434x292ae342w1addfe7b1f36ba7f@mail.gmail.com>

Hi,
I have two questions:
Will the Bio::PopGen::Stastistcis module functions all work with
missing data in the ingroup as well as the outgroup populations?

Here is some sample data in csv format

Ingroup:

SAMPLE,chr6_24659643,chr6_24659708,chr6_24664915,chr6_24667221,chr6_24667260,chr6_24672519,chr6_24672523,chr6_24677020,chr6_24684610,chr6_24684764,chr6_24684785,chr6_24686388,chr6_24686434,chr6_24691838,chr6_24696805,chr6_24696863,chr6_24696878,chr6_24704356,chr6_24704412,chr6_24704457,chr6_24704515,chr6_24704652,chr6_24704721,chr6_24704742,fchr1_35673249,fchr1_35673250,fchr1_35679239,fchr1_35679296,fchr1_35689919,fchr1_35698567,fchr1_35700870,fchr1_35744884,fchr1_35744941,fchr1_35792606,fchr6_24659713,fchr6_24664917,fchr6_24667334,fchr6_24671655,fchr6_24672514,fchr6_24672523,fchr6_24684620,fchr6_24684674,fchr6_24686387,fchr6_24688078,fchr6_24690529,fchr6_24691897,fchr6_24696850,fchr6_24696911,fchr6_24696963,fchr6_24704111,fchr6_24704285,fchr6_24704362,fchr6_24704817
NA20856,T T,T T,C C,T T,A A,A A,T T,C C,C C,T T,C C,T T,G G,C C,C C,T
T,T T,C C,A A,G G,G G,A A,C C,G G,A A,A A,T T,C C,A A,T T,A A,G G,A
A,G G,T T,A A,T T,C C,G G,T T,C C,G G,C C,G G,T T,G G,T T,C C,C C,T
T,A A,C C,G G
NA20853,T T,T T,C C,T T,A A,A A,T T,C C,C C,T T,C C,T T,G G,C C,C C,C
C,T T,C C,A A,G G,G G,A A,C C,G G,A A,A A,T T,C C,A A,T T,A A,G G,A
A,G G,T T,A A,T T,C C,G G,T T,C C,G G,C C,G G,T T,G G,T T,C C,C C,T
T,A A,C C,G G
NA20849,C T,C T,C C,T T,A G,A A,T T,C C,C C,T T,C C,C T,G G,C C,C C,T
T,T T,C C,A A,G G,G G,A A,C C,G G,A A,A A,T T,C C,A A,T T,A A,G G,A
A,G G,T T,A A,T T,C C,G G,T T,C C,G G,C C,G G,T T,G G,T T,C C,C C,T
T,A A,C C,G G


Outgroup:

SAMPLE,chr6_24659643,chr6_24659708,chr6_24664915,chr6_24667221,chr6_24667260,chr6_24672519,chr6_24672523,chr6_24677020,chr6_24684610,chr6_24684764,chr6_24684785,chr6_24686388,chr6_24686434,chr6_24691838,chr6_24696805,chr6_24696863,chr6_24696878,chr6_24704356,chr6_24704412,chr6_24704457,chr6_24704515,chr6_24704652,chr6_24704721,chr6_24704742,fchr1_35673249,fchr1_35673250,fchr1_35679239,fchr1_35679296,fchr1_35689919,fchr1_35698567,fchr1_35700870,fchr1_35744884,fchr1_35744941,fchr1_35792606,fchr6_24659713,fchr6_24664917,fchr6_24667334,fchr6_24671655,fchr6_24672514,fchr6_24672523,fchr6_24684620,fchr6_24684674,fchr6_24686387,fchr6_24688078,fchr6_24690529,fchr6_24691897,fchr6_24696850,fchr6_24696911,fchr6_24696963,fchr6_24704111,fchr6_24704285,fchr6_24704362,fchr6_24704817
OUT0000,T T,,C C,T T,A A,G G,,C C,C C,T T,C C,T T,G G,C C,C C,C C,T
T,C C,A A,G G,G G,A A,C C,G G,C C,C C,C C,T T,G G,C C,G G,T T,G G,A
A,G G,G G,C C,T T,A A,C C,A A,A A,T T,A A,C C,A A,C C,A A,T T,C C,G
G,T T,A A


The second question is this: If I pass the outgroup in as a population
(i.e. a population of a single homozygous diploid individual), then I
get a completely different fu_and_li_F value than when I only pass in
a haploid individual as the outgroup.  (In the former case I also get
a 'missing value' error emanating from the fact that
Bio::PopGen::Statistics->derived_mutations($ingroup_pop,$outgroup_pop)
returns no external mutations).  Because I get no errors when I pass
in a haploid individual as the outgroup, I'm assuming that that is the
correct way to use fu_and_li_F. If so, it would be helpful to put this
information in the Bio::PopGen::Statistics POD file.  The way it is
currently written, one could assume that fu_and_li_F will deal with a
homozygous diploid individual the same way it deals with a haploid
individual, which I don't think is the case.

Thanks,
Warren Kretzschmar


From jason at bioperl.org  Mon Feb 15 19:03:36 2010
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 15 Feb 2010 16:03:36 -0800
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <4B79C716.90405@gmail.com>
References: <4B79C716.90405@gmail.com>
Message-ID: <4B79E0D8.3060806@bioperl.org>

I don't think that aspect of the documentation vs interface was ever 
implemented - the interface object doesn't specify a type method or init 
argument even though the documentation says so. Not really sure why not, 
this was ages ago unfortunately.

This particular factory definitely assumes you are building Bio::Seq 
objects - you can try and subclass and build your own to see if it makes 
much of a difference in speed/memory - I would posit it won't make a 
significant difference but be interested to see what you find.

Just make your own Bio::Seq::PrimarySeqFactory object based on 
Bio::Seq::FastaSpeedFactory and simplify that code so it doesn't build 
Bio::Seq object wrapper around the Bio::PrimarySeq and do some perf 
tests so we'll know if it makes any difference here.

-jason
Florent Angly wrote:
> Hi all,
>
> I am trying to reduce memory usage and speedup reading FASTA files 
> using the facilities provided by BioPerl.
>
> The first thing I noticed is that when using Bio::SeqIO::fasta, the 
> objects returned are Bio::Seq, not Bio::PrimarySeq objects. 
> Bio::PrimarySeq sequences are lighter than Bio::Seq sequences, so it's 
> what I need. See code below:
>> use warnings;
>> use strict;
>> use Data::Dumper;
>> use Bio::SeqIO;
>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>> print "The factory is a ".ref($seqfactory)."\n";
>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>> my $seq = $in->next_seq;
>> print Dumper($seq);
>> __END__
>> >seq1 a small test sequence q
>> ACGTACGACTACGACTAGCGCCATCAGC 
> It returns:
>> $VAR1 = bless( {
>>                  'primary_id' => 'seq1',
>>                  'primary_seq' => bless( {
>>                                            'display_id' => 'seq1',
>>                                            'primary_id' => 'seq1',
>>                                            'desc' => 'a small test 
>> sequence',
>>                                            'seq' => 
>> 'ACGTACGACTACGACTAGCGCCATCAGC',
>>                                            'alphabet' => 'dna'
>>                                          }, 'Bio::PrimarySeq' )
>>                }, 'Bio::Seq' ); 
>
> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I really 
> only need the Bio::PrimarySeq. Looking at the documentation for 
> Bio::SeqIO I found that I could in theory adjust the sequence factory 
> and sequence builder to my liking... I tried this:
>> use warnings;
>> use strict;
>> use Data::Dumper;
>> use Bio::SeqIO;
>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>> print "The factory is a ".ref($seqfactory)."\n";
>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>> my $seq = $in->next_seq;
>> print Dumper($seq);
>> __END__
>> >seq1 a small test sequence
>> ACGTACGACTACGACTAGCGCCATCAGC 
> This returns:
>> The factory is a Bio::Seq::SeqFastaSpeedFactory
>> Can't locate object method "type" via package 
>> "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl line 12, 
>> <DATA> line 1. 
>
> According to Bio::Seq::FastaSpeedFactory's documentation:
>> If you want the factory to create Bio::Seq objects instead
>> of the default Bio::PrimarySeq objects, use the -type parameter 
> So, PrimarySeq should be the default type, even though in my case it 
> seems not to be. Second, I can't seem to use the -type method to 
> change what the return type is... It errors.
>
> Any ideas??? Thanks,
>
> Florent
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 

From florent.angly at gmail.com  Mon Feb 15 20:19:37 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Tue, 16 Feb 2010 11:19:37 +1000
Subject: [Bioperl-l] Simulate fragment and read-pair reads from sample
 sequence
In-Reply-To: <24c96eca1002150925m7037eafbna1a48b1eae55735b@mail.gmail.com>
References: <358f4d651002150545h7d4f58aewd0e3cbbbd38c453f@mail.gmail.com>
	<24c96eca1002150925m7037eafbna1a48b1eae55735b@mail.gmail.com>
Message-ID: <4B79F2A9.3080300@gmail.com>


Self-promotion here, but I could not do the things I needed with MetaSim 
and it's not open-source, so I had to roll my own random shotgun library 
simulator: Grinder (http://sourceforge.net/projects/biogrinder/).

Grinder has worked well for my purpose but there's room for 
improvements. Albert, I'd be happy to work with you on adding new 
features in Grinder, for example the mate-pair feature you were mentioning.

Cheers,

Florent


On 16/02/10 03:25, Aaron Mackey wrote:
> There are some tools out there that already do a good job of this, and
> take into consideration platform-specific error models, paired end
> fragment length distributions, etc.  maq has an Illumina read
> simulator that also simulates quality scores, and MetaSim has a nice
> 454 read simulator (and Illumina as well, though unfortunately doesn't
> do quality scores for either).
>    


From florent.angly at gmail.com  Tue Feb 16 01:18:16 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Tue, 16 Feb 2010 16:18:16 +1000
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <4B79E0D8.3060806@bioperl.org>
References: <4B79C716.90405@gmail.com> <4B79E0D8.3060806@bioperl.org>
Message-ID: <4B7A38A8.80702@gmail.com>

Thanks for your reply Jason. It's very valuable since you coded the 
modules in question!

Now that I understand the purpose of these modules, I did a little bit 
of documentation clarification. I also figured out that I should 
implement the 'type' method in Bio::Seq::SeqFastaSpeedFactory and made 
it support creating Bio::PrimarySeq. This is all committed to SVN.

When sequences are large, you are right that it does not make much 
difference in time or memory resource to use one sequence type over the 
other. However, that's different for short sequences. I took a FASTA 
file weighting 39.3 MB and containing 360,000 sequences of 106 bp on 
average.

CASE 1:
   Requested factory Bio::Seq::SeqFactory
   Requested sequence type is Bio::Seq
   Memory used: 329 MB
   Time spent: 1m8.522s

CASE 2:
   Requested factory Bio::Seq::SeqFactory
   Requested sequence type is Bio::PrimarySeq
   Memory used: 246 MB
   Time spent: 0m52.663s

CASE 3:
   Requested factory Bio::Seq::SeqFastaSpeedFactory
   Requested sequence type is Bio::Seq
   Memory used: 298 MB
   Time spent: 0m31.292s

CASE 4:
   Requested factory Bio::Seq::SeqFastaSpeedFactory
   Requested sequence type is Bio::PrimarySeq
   Memory used: 231 MB
   Time spent: 0m28.500s

Clearly, when only simple sequence attributes are needed or FASTA files 
are used, it's fast and memory efficient to use the SeqFastaSpeedFactory 
with PrimarySeq.

Florent


On 16/02/10 10:03, Jason Stajich wrote:
> I don't think that aspect of the documentation vs interface was ever 
> implemented - the interface object doesn't specify a type method or 
> init argument even though the documentation says so. Not really sure 
> why not, this was ages ago unfortunately.
>
> This particular factory definitely assumes you are building Bio::Seq 
> objects - you can try and subclass and build your own to see if it 
> makes much of a difference in speed/memory - I would posit it won't 
> make a significant difference but be interested to see what you find.
>
> Just make your own Bio::Seq::PrimarySeqFactory object based on 
> Bio::Seq::FastaSpeedFactory and simplify that code so it doesn't build 
> Bio::Seq object wrapper around the Bio::PrimarySeq and do some perf 
> tests so we'll know if it makes any difference here.
>
> -jason
> Florent Angly wrote:
>> Hi all,
>>
>> I am trying to reduce memory usage and speedup reading FASTA files 
>> using the facilities provided by BioPerl.
>>
>> The first thing I noticed is that when using Bio::SeqIO::fasta, the 
>> objects returned are Bio::Seq, not Bio::PrimarySeq objects. 
>> Bio::PrimarySeq sequences are lighter than Bio::Seq sequences, so 
>> it's what I need. See code below:
>>> use warnings;
>>> use strict;
>>> use Data::Dumper;
>>> use Bio::SeqIO;
>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>>> print "The factory is a ".ref($seqfactory)."\n";
>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>> my $seq = $in->next_seq;
>>> print Dumper($seq);
>>> __END__
>>> >seq1 a small test sequence q
>>> ACGTACGACTACGACTAGCGCCATCAGC 
>> It returns:
>>> $VAR1 = bless( {
>>>                  'primary_id' => 'seq1',
>>>                  'primary_seq' => bless( {
>>>                                            'display_id' => 'seq1',
>>>                                            'primary_id' => 'seq1',
>>>                                            'desc' => 'a small test 
>>> sequence',
>>>                                            'seq' => 
>>> 'ACGTACGACTACGACTAGCGCCATCAGC',
>>>                                            'alphabet' => 'dna'
>>>                                          }, 'Bio::PrimarySeq' )
>>>                }, 'Bio::Seq' ); 
>>
>> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I really 
>> only need the Bio::PrimarySeq. Looking at the documentation for 
>> Bio::SeqIO I found that I could in theory adjust the sequence factory 
>> and sequence builder to my liking... I tried this:
>>> use warnings;
>>> use strict;
>>> use Data::Dumper;
>>> use Bio::SeqIO;
>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>>> print "The factory is a ".ref($seqfactory)."\n";
>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>> my $seq = $in->next_seq;
>>> print Dumper($seq);
>>> __END__
>>> >seq1 a small test sequence
>>> ACGTACGACTACGACTAGCGCCATCAGC 
>> This returns:
>>> The factory is a Bio::Seq::SeqFastaSpeedFactory
>>> Can't locate object method "type" via package 
>>> "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl line 12, 
>>> <DATA> line 1. 
>>
>> According to Bio::Seq::FastaSpeedFactory's documentation:
>>> If you want the factory to create Bio::Seq objects instead
>>> of the default Bio::PrimarySeq objects, use the -type parameter 
>> So, PrimarySeq should be the default type, even though in my case it 
>> seems not to be. Second, I can't seem to use the -type method to 
>> change what the return type is... It errors.
>>
>> Any ideas??? Thanks,
>>
>> Florent
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l 


From jessica.sun at gmail.com  Tue Feb 16 09:26:31 2010
From: jessica.sun at gmail.com (Jessica Sun)
Date: Tue, 16 Feb 2010 09:26:31 -0500
Subject: [Bioperl-l] display sequence alignment
Message-ID: <9adc0e9b1002160626k3bf8d66w8c9889daa72713c4@mail.gmail.com>

Do any one know how to display protein/peptide alignments in color using
bioperl.

thx

On Mon, Feb 15, 2010 at 9:35 AM, Jessica Sun <jessica.sun at gmail.com> wrote:

>
>
> ---------- Forwarded message ----------
> From: Jessica Sun <jessica.sun at gmail.com>
> Date: Fri, Feb 12, 2010 at 8:44 PM
> Subject: one more question
> To: bioperl-l at lists.open-bio.org
>
>
> Does anyone knows how to get genomic(dna) sequences(with right sub regions)
> in gbk format when you only have NM_(mRNA) accession numbers.
>
> Thanks,
>
>
> --
> Jessica Jingping Sun
>
>
>
> --
> Jessica Jingping Sun
>



-- 
Jessica Jingping Sun

From bhakti.dwivedi at gmail.com  Tue Feb 16 10:17:48 2010
From: bhakti.dwivedi at gmail.com (Bhakti Dwivedi)
Date: Tue, 16 Feb 2010 10:17:48 -0500
Subject: [Bioperl-l] Grouping the sequences in the alignment based on
	similarity?
Message-ID: <b643abd21002160717i5bf960e0p6a617a60445248aa@mail.gmail.com>

I have nucleotide sequence alignments of closely related and distantly
related sequences.  I wish to produce new sequence alignment(s) based on the
presence of conserved regions among the sequences in the alignment.  So that
the new alignment (s) will be subgroups of the original alignment based on
the degree of similarity.

For example:(may not be the perfect example, but just to show the point)
seq1    ATGGCAR
seq2    ATGGCAR
seq3    GCGCTAN
seq4    GCCGTAY

will produce the following
seq 1  ATGGCAR              seq3  GCGCTAN
seq 2  ATGGCAR              seq4  GCCGTAY


This is a manual process, where I select/de-select the sequences in the
alignment based on how similar they look to each other to obtain a better
consensus conserved sequence for each group.  I know that there are
techniques like clustering algorithm to group the sequences in the multiple
alignment, but wondering if there is a way to automate this in bioperl?

Thanks!

Bhakti

From avilella at gmail.com  Tue Feb 16 11:41:12 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 16 Feb 2010 16:41:12 +0000
Subject: [Bioperl-l] display sequence alignment
In-Reply-To: <9adc0e9b1002160626k3bf8d66w8c9889daa72713c4@mail.gmail.com>
References: <9adc0e9b1002160626k3bf8d66w8c9889daa72713c4@mail.gmail.com>
Message-ID: <358f4d651002160841r5629f3absa71e6d0f563aed5e@mail.gmail.com>

I am actually also interested in this :-)

My requirements are to be able to define an image size, like 1200x800
pixels, and then have a representation of the alignment produced
through a script, with the clustalw or nucleotide colour palette like
in Jalview.

Anyone?

On Tue, Feb 16, 2010 at 2:26 PM, Jessica Sun <jessica.sun at gmail.com> wrote:
> Do any one know how to display protein/peptide alignments in color using
> bioperl.
>
> thx
>
> On Mon, Feb 15, 2010 at 9:35 AM, Jessica Sun <jessica.sun at gmail.com> wrote:
>
>>
>>
>> ---------- Forwarded message ----------
>> From: Jessica Sun <jessica.sun at gmail.com>
>> Date: Fri, Feb 12, 2010 at 8:44 PM
>> Subject: one more question
>> To: bioperl-l at lists.open-bio.org
>>
>>
>> Does anyone knows how to get genomic(dna) sequences(with right sub regions)
>> in gbk format when you only have NM_(mRNA) accession numbers.
>>
>> Thanks,
>>
>>
>> --
>> Jessica Jingping Sun
>>
>>
>>
>> --
>> Jessica Jingping Sun
>>
>
>
>
> --
> Jessica Jingping Sun
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From jason at bioperl.org  Tue Feb 16 11:57:14 2010
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 16 Feb 2010 08:57:14 -0800
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <4B7A38A8.80702@gmail.com>
References: <4B79C716.90405@gmail.com> <4B79E0D8.3060806@bioperl.org>
	<4B7A38A8.80702@gmail.com>
Message-ID: <4B7ACE6A.3000402@bioperl.org>

Great!  thanks for committing it.

Florent Angly wrote:
> Thanks for your reply Jason. It's very valuable since you coded the 
> modules in question!
>
> Now that I understand the purpose of these modules, I did a little bit 
> of documentation clarification. I also figured out that I should 
> implement the 'type' method in Bio::Seq::SeqFastaSpeedFactory and made 
> it support creating Bio::PrimarySeq. This is all committed to SVN.
>
> When sequences are large, you are right that it does not make much 
> difference in time or memory resource to use one sequence type over 
> the other. However, that's different for short sequences. I took a 
> FASTA file weighting 39.3 MB and containing 360,000 sequences of 106 
> bp on average.
>
> CASE 1:
>   Requested factory Bio::Seq::SeqFactory
>   Requested sequence type is Bio::Seq
>   Memory used: 329 MB
>   Time spent: 1m8.522s
>
> CASE 2:
>   Requested factory Bio::Seq::SeqFactory
>   Requested sequence type is Bio::PrimarySeq
>   Memory used: 246 MB
>   Time spent: 0m52.663s
>
> CASE 3:
>   Requested factory Bio::Seq::SeqFastaSpeedFactory
>   Requested sequence type is Bio::Seq
>   Memory used: 298 MB
>   Time spent: 0m31.292s
>
> CASE 4:
>   Requested factory Bio::Seq::SeqFastaSpeedFactory
>   Requested sequence type is Bio::PrimarySeq
>   Memory used: 231 MB
>   Time spent: 0m28.500s
>
> Clearly, when only simple sequence attributes are needed or FASTA 
> files are used, it's fast and memory efficient to use the 
> SeqFastaSpeedFactory with PrimarySeq.
>
> Florent
>
>
> On 16/02/10 10:03, Jason Stajich wrote:
>> I don't think that aspect of the documentation vs interface was ever 
>> implemented - the interface object doesn't specify a type method or 
>> init argument even though the documentation says so. Not really sure 
>> why not, this was ages ago unfortunately.
>>
>> This particular factory definitely assumes you are building Bio::Seq 
>> objects - you can try and subclass and build your own to see if it 
>> makes much of a difference in speed/memory - I would posit it won't 
>> make a significant difference but be interested to see what you find.
>>
>> Just make your own Bio::Seq::PrimarySeqFactory object based on 
>> Bio::Seq::FastaSpeedFactory and simplify that code so it doesn't 
>> build Bio::Seq object wrapper around the Bio::PrimarySeq and do some 
>> perf tests so we'll know if it makes any difference here.
>>
>> -jason
>> Florent Angly wrote:
>>> Hi all,
>>>
>>> I am trying to reduce memory usage and speedup reading FASTA files 
>>> using the facilities provided by BioPerl.
>>>
>>> The first thing I noticed is that when using Bio::SeqIO::fasta, the 
>>> objects returned are Bio::Seq, not Bio::PrimarySeq objects. 
>>> Bio::PrimarySeq sequences are lighter than Bio::Seq sequences, so 
>>> it's what I need. See code below:
>>>> use warnings;
>>>> use strict;
>>>> use Data::Dumper;
>>>> use Bio::SeqIO;
>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>> my $seq = $in->next_seq;
>>>> print Dumper($seq);
>>>> __END__
>>>> >seq1 a small test sequence q
>>>> ACGTACGACTACGACTAGCGCCATCAGC 
>>> It returns:
>>>> $VAR1 = bless( {
>>>>                  'primary_id' => 'seq1',
>>>>                  'primary_seq' => bless( {
>>>>                                            'display_id' => 'seq1',
>>>>                                            'primary_id' => 'seq1',
>>>>                                            'desc' => 'a small test 
>>>> sequence',
>>>>                                            'seq' => 
>>>> 'ACGTACGACTACGACTAGCGCCATCAGC',
>>>>                                            'alphabet' => 'dna'
>>>>                                          }, 'Bio::PrimarySeq' )
>>>>                }, 'Bio::Seq' ); 
>>>
>>> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I really 
>>> only need the Bio::PrimarySeq. Looking at the documentation for 
>>> Bio::SeqIO I found that I could in theory adjust the sequence 
>>> factory and sequence builder to my liking... I tried this:
>>>> use warnings;
>>>> use strict;
>>>> use Data::Dumper;
>>>> use Bio::SeqIO;
>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>> my $seq = $in->next_seq;
>>>> print Dumper($seq);
>>>> __END__
>>>> >seq1 a small test sequence
>>>> ACGTACGACTACGACTAGCGCCATCAGC 
>>> This returns:
>>>> The factory is a Bio::Seq::SeqFastaSpeedFactory
>>>> Can't locate object method "type" via package 
>>>> "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl line 12, 
>>>> <DATA> line 1. 
>>>
>>> According to Bio::Seq::FastaSpeedFactory's documentation:
>>>> If you want the factory to create Bio::Seq objects instead
>>>> of the default Bio::PrimarySeq objects, use the -type parameter 
>>> So, PrimarySeq should be the default type, even though in my case it 
>>> seems not to be. Second, I can't seem to use the -type method to 
>>> change what the return type is... It errors.
>>>
>>> Any ideas??? Thanks,
>>>
>>> Florent
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l 

From jason.stajich at gmail.com  Tue Feb 16 11:59:11 2010
From: jason.stajich at gmail.com (Jason Stajich)
Date: Tue, 16 Feb 2010 08:59:11 -0800
Subject: [Bioperl-l] display sequence alignment
In-Reply-To: <358f4d651002160841r5629f3absa71e6d0f563aed5e@mail.gmail.com>
References: <9adc0e9b1002160626k3bf8d66w8c9889daa72713c4@mail.gmail.com>
	<358f4d651002160841r5629f3absa71e6d0f563aed5e@mail.gmail.com>
Message-ID: <4B7ACEDF.2090808@gmail.com>

I've done this by marking it up an alignment into HTML with colors, but 
no bioperl module for it that I know of. My way was pretty heavy 
(producing large files) but maybe a more compact CSS approach could 
produce smaller files.

How else were you thinking of seeing this - in a PNG ?

-jason

Albert Vilella wrote:
> I am actually also interested in this :-)
>
> My requirements are to be able to define an image size, like 1200x800
> pixels, and then have a representation of the alignment produced
> through a script, with the clustalw or nucleotide colour palette like
> in Jalview.
>
> Anyone?
>
> On Tue, Feb 16, 2010 at 2:26 PM, Jessica Sun<jessica.sun at gmail.com>  wrote:
>    
>> Do any one know how to display protein/peptide alignments in color using
>> bioperl.
>>
>> thx
>>
>> On Mon, Feb 15, 2010 at 9:35 AM, Jessica Sun<jessica.sun at gmail.com>  wrote:
>>
>>      
>>> ---------- Forwarded message ----------
>>> From: Jessica Sun<jessica.sun at gmail.com>
>>> Date: Fri, Feb 12, 2010 at 8:44 PM
>>> Subject: one more question
>>> To: bioperl-l at lists.open-bio.org
>>>
>>>
>>> Does anyone knows how to get genomic(dna) sequences(with right sub regions)
>>> in gbk format when you only have NM_(mRNA) accession numbers.
>>>
>>> Thanks,
>>>
>>>
>>> --
>>> Jessica Jingping Sun
>>>
>>>
>>>
>>> --
>>> Jessica Jingping Sun
>>>
>>>        
>>
>> --
>> Jessica Jingping Sun
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>      
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>    

From cjfields at illinois.edu  Tue Feb 16 11:50:24 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 16 Feb 2010 10:50:24 -0600
Subject: [Bioperl-l] Tons of test failing in bioperl-live
Message-ID: <812CC488-05C8-4B53-9988-D39DDED7CD9F@illinois.edu>

All,

Just updated to the latest live today (both Mac OS X and Ubuntu 9.10) and found a ton of tests failing due to recent commits.  This isn't to say the commits were wrong or bad, as failures could just as easily indicate bad regression tests, but they do indicate *something* needs to be addressed.  We still have a lot of users unfortunately pulling from svn due to GBrowse2 bug fixes. Please make sure to run tests prior to committing to trunk, particularly if you are making changes to commonly used modules (SeqIO, LocatableSeq, etc), and address problems if they pop up.  If tests are failing, having a discussion on list as to the reasons why is a good thing.

Also, with this in mind, please make sure to retain the previous API as much as possible.  The recent commits to SeqIO re: optionally returning a PrimarySeq now fundamentally change the returned object to a Bio::PrimarySeq by default (i.e. is-not-a Bio::SeqI).  A significant subset of the trunk failures are due to this fundamental change in behavior.  Running tests prior to the commit would have caught this out, and we could have discussed it more on list.  

These, and other failed tests, should be addressed in some way so tests pass accordingly (and new tests for the optional Bio::PrimarySeq behavior would be a good thing too).  I'll do my best to dig in and fix a few as well.

chris

Latest test run on bioperl-live (Mac OS X):

Test Summary Report
-------------------
t/Assembly/Assembly.t                      (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: No plan found in TAP output
t/Assembly/ContigSpectrum.t                (Wstat: 1024 Tests: 188 Failed: 4)
  Failed tests:  153, 155, 168, 170
  Non-zero exit status: 4
t/LocalDB/Flat.t                           (Wstat: 6400 Tests: 4 Failed: 1)
  Failed test:  4
  Non-zero exit status: 25
  Parse errors: Bad plan.  You planned 24 tests but ran 4.
t/LocalDB/Index/Index.t                    (Wstat: 1024 Tests: 64 Failed: 4)
  Failed tests:  10, 12, 14, 20
  Non-zero exit status: 4
t/LocalDB/Registry.t                       (Wstat: 2304 Tests: 13 Failed: 1)
  Failed test:  13
  Non-zero exit status: 9
  Parse errors: Bad plan.  You planned 14 tests but ran 13.
t/LocalDB/transfac_pro.t                   (Wstat: 65280 Tests: 67 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 115 tests but ran 67.
t/Map/Map.t                                (Wstat: 1536 Tests: 267 Failed: 6)
  Failed tests:  249, 262-264, 266-267
  Non-zero exit status: 6
t/Perl.t                                   (Wstat: 768 Tests: 29 Failed: 3)
  Failed tests:  3, 7-8
  Non-zero exit status: 3
t/RemoteDB/BioFetch.t                      (Wstat: 1024 Tests: 36 Failed: 4)
  Failed tests:  18, 21-23
  Non-zero exit status: 4
t/RemoteDB/HIV/HIVQuery.t                  (Wstat: 2304 Tests: 35 Failed: 0)
  Non-zero exit status: 9
  Parse errors: Bad plan.  You planned 41 tests but ran 35.
t/SearchIO/SimilarityPair.t                (Wstat: 65280 Tests: 10 Failed: 1)
  Failed test:  4
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 12 tests but ran 10.
t/SearchIO/Tiling.t                        (Wstat: 256 Tests: 1097 Failed: 1)
  Failed test:  1095
  Non-zero exit status: 1
t/Seq/PrimedSeq.t                          (Wstat: 65280 Tests: 2 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 10 tests but ran 2.
t/SeqFeature/SeqAnalysisParser.t           (Wstat: 2304 Tests: 5 Failed: 0)
  Non-zero exit status: 9
  Parse errors: Bad plan.  You planned 14 tests but ran 5.
t/SeqFeature/SeqFeature.t                  (Wstat: 256 Tests: 222 Failed: 1)
  Failed test:  86
  Non-zero exit status: 1
t/SeqIO/seqxml.t                           (Wstat: 2304 Tests: 45 Failed: 2)
  Failed tests:  15, 36
  Non-zero exit status: 9
  Parse errors: Bad plan.  You planned 58 tests but ran 45.
t/SeqTools/GuessSeqFormat.t                (Wstat: 256 Tests: 52 Failed: 1)
  Failed test:  12
  Non-zero exit status: 1
t/Tools/Run/WBCommandExts.t                (Wstat: 256 Tests: 22 Failed: 1)
  Failed test:  22
  Non-zero exit status: 1
t/Tools/ePCR.t                             (Wstat: 2304 Tests: 7 Failed: 0)
  Non-zero exit status: 9
  Parse errors: Bad plan.  You planned 27 tests but ran 7.
Files=341, Tests=21416, 439 wallclock secs ( 3.52 usr  1.67 sys + 133.53 cusr 16.14 csys = 154.86 CPU)
Result: FAIL
Failed 19/341 test programs. 30/21416 subtests failed.




From cjfields at illinois.edu  Tue Feb 16 11:52:56 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 16 Feb 2010 10:52:56 -0600
Subject: [Bioperl-l] display sequence alignment
In-Reply-To: <358f4d651002160841r5629f3absa71e6d0f563aed5e@mail.gmail.com>
References: <9adc0e9b1002160626k3bf8d66w8c9889daa72713c4@mail.gmail.com>
	<358f4d651002160841r5629f3absa71e6d0f563aed5e@mail.gmail.com>
Message-ID: <0FDE37FC-F98D-42F8-B2F1-83C0ED9046A3@illinois.edu>

How about something like this:

http://www.bioperl.org/wiki/Simple_graphical_alignment_overview

chris

On Feb 16, 2010, at 10:41 AM, Albert Vilella wrote:

> I am actually also interested in this :-)
> 
> My requirements are to be able to define an image size, like 1200x800
> pixels, and then have a representation of the alignment produced
> through a script, with the clustalw or nucleotide colour palette like
> in Jalview.
> 
> Anyone?
> 
> On Tue, Feb 16, 2010 at 2:26 PM, Jessica Sun <jessica.sun at gmail.com> wrote:
>> Do any one know how to display protein/peptide alignments in color using
>> bioperl.
>> 
>> thx
>> 
>> On Mon, Feb 15, 2010 at 9:35 AM, Jessica Sun <jessica.sun at gmail.com> wrote:
>> 
>>> 
>>> 
>>> ---------- Forwarded message ----------
>>> From: Jessica Sun <jessica.sun at gmail.com>
>>> Date: Fri, Feb 12, 2010 at 8:44 PM
>>> Subject: one more question
>>> To: bioperl-l at lists.open-bio.org
>>> 
>>> 
>>> Does anyone knows how to get genomic(dna) sequences(with right sub regions)
>>> in gbk format when you only have NM_(mRNA) accession numbers.
>>> 
>>> Thanks,
>>> 
>>> 
>>> --
>>> Jessica Jingping Sun
>>> 
>>> 
>>> 
>>> --
>>> Jessica Jingping Sun
>>> 
>> 
>> 
>> 
>> --
>> Jessica Jingping Sun
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Tue Feb 16 12:11:16 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 16 Feb 2010 11:11:16 -0600
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <4B7ACE6A.3000402@bioperl.org>
References: <4B79C716.90405@gmail.com> <4B79E0D8.3060806@bioperl.org>
	<4B7A38A8.80702@gmail.com> <4B7ACE6A.3000402@bioperl.org>
Message-ID: <AF001D8E-3B3C-4405-9D31-E0BE358C9559@illinois.edu>

Yes, except that tests are now failing on live.  Bio::PrimarySeq isn't a Bio::SeqI, so it's a bit of an API change in a lot of places expecting a Bio::SeqI.  We should make this optional for the time being, until we discuss it more on list.

chris

On Feb 16, 2010, at 10:57 AM, Jason Stajich wrote:

> Great!  thanks for committing it.
> 
> Florent Angly wrote:
>> Thanks for your reply Jason. It's very valuable since you coded the modules in question!
>> 
>> Now that I understand the purpose of these modules, I did a little bit of documentation clarification. I also figured out that I should implement the 'type' method in Bio::Seq::SeqFastaSpeedFactory and made it support creating Bio::PrimarySeq. This is all committed to SVN.
>> 
>> When sequences are large, you are right that it does not make much difference in time or memory resource to use one sequence type over the other. However, that's different for short sequences. I took a FASTA file weighting 39.3 MB and containing 360,000 sequences of 106 bp on average.
>> 
>> CASE 1:
>>  Requested factory Bio::Seq::SeqFactory
>>  Requested sequence type is Bio::Seq
>>  Memory used: 329 MB
>>  Time spent: 1m8.522s
>> 
>> CASE 2:
>>  Requested factory Bio::Seq::SeqFactory
>>  Requested sequence type is Bio::PrimarySeq
>>  Memory used: 246 MB
>>  Time spent: 0m52.663s
>> 
>> CASE 3:
>>  Requested factory Bio::Seq::SeqFastaSpeedFactory
>>  Requested sequence type is Bio::Seq
>>  Memory used: 298 MB
>>  Time spent: 0m31.292s
>> 
>> CASE 4:
>>  Requested factory Bio::Seq::SeqFastaSpeedFactory
>>  Requested sequence type is Bio::PrimarySeq
>>  Memory used: 231 MB
>>  Time spent: 0m28.500s
>> 
>> Clearly, when only simple sequence attributes are needed or FASTA files are used, it's fast and memory efficient to use the SeqFastaSpeedFactory with PrimarySeq.
>> 
>> Florent
>> 
>> 
>> On 16/02/10 10:03, Jason Stajich wrote:
>>> I don't think that aspect of the documentation vs interface was ever implemented - the interface object doesn't specify a type method or init argument even though the documentation says so. Not really sure why not, this was ages ago unfortunately.
>>> 
>>> This particular factory definitely assumes you are building Bio::Seq objects - you can try and subclass and build your own to see if it makes much of a difference in speed/memory - I would posit it won't make a significant difference but be interested to see what you find.
>>> 
>>> Just make your own Bio::Seq::PrimarySeqFactory object based on Bio::Seq::FastaSpeedFactory and simplify that code so it doesn't build Bio::Seq object wrapper around the Bio::PrimarySeq and do some perf tests so we'll know if it makes any difference here.
>>> 
>>> -jason
>>> Florent Angly wrote:
>>>> Hi all,
>>>> 
>>>> I am trying to reduce memory usage and speedup reading FASTA files using the facilities provided by BioPerl.
>>>> 
>>>> The first thing I noticed is that when using Bio::SeqIO::fasta, the objects returned are Bio::Seq, not Bio::PrimarySeq objects. Bio::PrimarySeq sequences are lighter than Bio::Seq sequences, so it's what I need. See code below:
>>>>> use warnings;
>>>>> use strict;
>>>>> use Data::Dumper;
>>>>> use Bio::SeqIO;
>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>> my $seq = $in->next_seq;
>>>>> print Dumper($seq);
>>>>> __END__
>>>>> >seq1 a small test sequence q
>>>>> ACGTACGACTACGACTAGCGCCATCAGC 
>>>> It returns:
>>>>> $VAR1 = bless( {
>>>>>                 'primary_id' => 'seq1',
>>>>>                 'primary_seq' => bless( {
>>>>>                                           'display_id' => 'seq1',
>>>>>                                           'primary_id' => 'seq1',
>>>>>                                           'desc' => 'a small test sequence',
>>>>>                                           'seq' => 'ACGTACGACTACGACTAGCGCCATCAGC',
>>>>>                                           'alphabet' => 'dna'
>>>>>                                         }, 'Bio::PrimarySeq' )
>>>>>               }, 'Bio::Seq' ); 
>>>> 
>>>> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I really only need the Bio::PrimarySeq. Looking at the documentation for Bio::SeqIO I found that I could in theory adjust the sequence factory and sequence builder to my liking... I tried this:
>>>>> use warnings;
>>>>> use strict;
>>>>> use Data::Dumper;
>>>>> use Bio::SeqIO;
>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>> my $seq = $in->next_seq;
>>>>> print Dumper($seq);
>>>>> __END__
>>>>> >seq1 a small test sequence
>>>>> ACGTACGACTACGACTAGCGCCATCAGC 
>>>> This returns:
>>>>> The factory is a Bio::Seq::SeqFastaSpeedFactory
>>>>> Can't locate object method "type" via package "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl line 12, <DATA> line 1. 
>>>> 
>>>> According to Bio::Seq::FastaSpeedFactory's documentation:
>>>>> If you want the factory to create Bio::Seq objects instead
>>>>> of the default Bio::PrimarySeq objects, use the -type parameter 
>>>> So, PrimarySeq should be the default type, even though in my case it seems not to be. Second, I can't seem to use the -type method to change what the return type is... It errors.
>>>> 
>>>> Any ideas??? Thanks,
>>>> 
>>>> Florent
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From Kevin.M.Brown at asu.edu  Tue Feb 16 12:02:59 2010
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Tue, 16 Feb 2010 10:02:59 -0700
Subject: [Bioperl-l] display sequence alignment
In-Reply-To: <358f4d651002160841r5629f3absa71e6d0f563aed5e@mail.gmail.com>
References: <9adc0e9b1002160626k3bf8d66w8c9889daa72713c4@mail.gmail.com>
	<358f4d651002160841r5629f3absa71e6d0f563aed5e@mail.gmail.com>
Message-ID: <1A4207F8295607498283FE9E93B775B406942BBA@EX02.asurite.ad.asu.edu>

http://search.cpan.org/~lds/Bio-Graphics-2.00/lib/Bio/Graphics.pm

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Albert Vilella
> Sent: Tuesday, February 16, 2010 9:41 AM
> To: Jessica Sun
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] display sequence alignment
> 
> I am actually also interested in this :-)
> 
> My requirements are to be able to define an image size, like 1200x800
> pixels, and then have a representation of the alignment produced
> through a script, with the clustalw or nucleotide colour palette like
> in Jalview.
> 
> Anyone?
> 
> On Tue, Feb 16, 2010 at 2:26 PM, Jessica Sun 
> <jessica.sun at gmail.com> wrote:
> > Do any one know how to display protein/peptide alignments 
> in color using
> > bioperl.
> >
> > thx
> >
> > On Mon, Feb 15, 2010 at 9:35 AM, Jessica Sun 
> <jessica.sun at gmail.com> wrote:
> >
> >>
> >>
> >> ---------- Forwarded message ----------
> >> From: Jessica Sun <jessica.sun at gmail.com>
> >> Date: Fri, Feb 12, 2010 at 8:44 PM
> >> Subject: one more question
> >> To: bioperl-l at lists.open-bio.org
> >>
> >>
> >> Does anyone knows how to get genomic(dna) sequences(with 
> right sub regions)
> >> in gbk format when you only have NM_(mRNA) accession numbers.
> >>
> >> Thanks,
> >>
> >>
> >> --
> >> Jessica Jingping Sun
> >>
> >>
> >>
> >> --
> >> Jessica Jingping Sun
> >>
> >
> >
> >
> > --
> > Jessica Jingping Sun
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From rmb32 at cornell.edu  Tue Feb 16 12:49:40 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Tue, 16 Feb 2010 09:49:40 -0800
Subject: [Bioperl-l] Tons of test failing in bioperl-live
In-Reply-To: <812CC488-05C8-4B53-9988-D39DDED7CD9F@illinois.edu>
References: <812CC488-05C8-4B53-9988-D39DDED7CD9F@illinois.edu>
Message-ID: <4B7ADAB4.9060602@cornell.edu>

To second Chris's comments:  before committing to trunk, you must run 
the entire test suite, and what's more, all tests should pass.

If you are working on changes that may be disruptive (such as causing 
these kinds of test failures), you must make a branch.

If you need help with something, make a branch, and email the list to 
ask for help with whatever test failures you are seeing.

Rob



From David.Messina at sbc.su.se  Tue Feb 16 13:39:33 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 16 Feb 2010 19:39:33 +0100
Subject: [Bioperl-l] Tons of test failing in bioperl-live
In-Reply-To: <812CC488-05C8-4B53-9988-D39DDED7CD9F@illinois.edu>
References: <812CC488-05C8-4B53-9988-D39DDED7CD9F@illinois.edu>
Message-ID: <7FF3AA30-25BB-464A-A3FE-A8AD5323C2D5@sbc.su.se>

These are mine:

> t/SeqIO/seqxml.t                           (Wstat: 2304 Tests: 45 Failed: 2)
>  Failed tests:  15, 36
>  Non-zero exit status: 9
>  Parse errors: Bad plan.  You planned 58 tests but ran 45.


Sorry about that -- thought I had tested the last change, but clearly not.

I'll get a fix out ASAP.


-Dave



From jason at bioperl.org  Tue Feb 16 15:18:31 2010
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 16 Feb 2010 12:18:31 -0800
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <AF001D8E-3B3C-4405-9D31-E0BE358C9559@illinois.edu>
References: <4B79C716.90405@gmail.com> <4B79E0D8.3060806@bioperl.org>
	<4B7A38A8.80702@gmail.com> <4B7ACE6A.3000402@bioperl.org>
	<AF001D8E-3B3C-4405-9D31-E0BE358C9559@illinois.edu>
Message-ID: <4B7AFD97.5050003@bioperl.org>

hmm yes. Let's roll back those Florent.

I guess we need to also discuss the concept of branches again here for 
major changes like this. The speed fix is helpful for short read but 
probably not for all systems so just having the ability to provide the 
right type when you use your scripts focused on short-reads might be the 
best way to go forward and preserve backwards compatibility.

-jason

Chris Fields wrote:
> Yes, except that tests are now failing on live.  Bio::PrimarySeq isn't a Bio::SeqI, so it's a bit of an API change in a lot of places expecting a Bio::SeqI.  We should make this optional for the time being, until we discuss it more on list.
>
> chris
>
> On Feb 16, 2010, at 10:57 AM, Jason Stajich wrote:
>
>    
>> Great!  thanks for committing it.
>>
>> Florent Angly wrote:
>>      
>>> Thanks for your reply Jason. It's very valuable since you coded the modules in question!
>>>
>>> Now that I understand the purpose of these modules, I did a little bit of documentation clarification. I also figured out that I should implement the 'type' method in Bio::Seq::SeqFastaSpeedFactory and made it support creating Bio::PrimarySeq. This is all committed to SVN.
>>>
>>> When sequences are large, you are right that it does not make much difference in time or memory resource to use one sequence type over the other. However, that's different for short sequences. I took a FASTA file weighting 39.3 MB and containing 360,000 sequences of 106 bp on average.
>>>
>>> CASE 1:
>>>   Requested factory Bio::Seq::SeqFactory
>>>   Requested sequence type is Bio::Seq
>>>   Memory used: 329 MB
>>>   Time spent: 1m8.522s
>>>
>>> CASE 2:
>>>   Requested factory Bio::Seq::SeqFactory
>>>   Requested sequence type is Bio::PrimarySeq
>>>   Memory used: 246 MB
>>>   Time spent: 0m52.663s
>>>
>>> CASE 3:
>>>   Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>   Requested sequence type is Bio::Seq
>>>   Memory used: 298 MB
>>>   Time spent: 0m31.292s
>>>
>>> CASE 4:
>>>   Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>   Requested sequence type is Bio::PrimarySeq
>>>   Memory used: 231 MB
>>>   Time spent: 0m28.500s
>>>
>>> Clearly, when only simple sequence attributes are needed or FASTA files are used, it's fast and memory efficient to use the SeqFastaSpeedFactory with PrimarySeq.
>>>
>>> Florent
>>>
>>>
>>> On 16/02/10 10:03, Jason Stajich wrote:
>>>        
>>>> I don't think that aspect of the documentation vs interface was ever implemented - the interface object doesn't specify a type method or init argument even though the documentation says so. Not really sure why not, this was ages ago unfortunately.
>>>>
>>>> This particular factory definitely assumes you are building Bio::Seq objects - you can try and subclass and build your own to see if it makes much of a difference in speed/memory - I would posit it won't make a significant difference but be interested to see what you find.
>>>>
>>>> Just make your own Bio::Seq::PrimarySeqFactory object based on Bio::Seq::FastaSpeedFactory and simplify that code so it doesn't build Bio::Seq object wrapper around the Bio::PrimarySeq and do some perf tests so we'll know if it makes any difference here.
>>>>
>>>> -jason
>>>> Florent Angly wrote:
>>>>          
>>>>> Hi all,
>>>>>
>>>>> I am trying to reduce memory usage and speedup reading FASTA files using the facilities provided by BioPerl.
>>>>>
>>>>> The first thing I noticed is that when using Bio::SeqIO::fasta, the objects returned are Bio::Seq, not Bio::PrimarySeq objects. Bio::PrimarySeq sequences are lighter than Bio::Seq sequences, so it's what I need. See code below:
>>>>>            
>>>>>> use warnings;
>>>>>> use strict;
>>>>>> use Data::Dumper;
>>>>>> use Bio::SeqIO;
>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>> my $seq = $in->next_seq;
>>>>>> print Dumper($seq);
>>>>>> __END__
>>>>>>              
>>>>>>> seq1 a small test sequence q
>>>>>>>                
>>>>>> ACGTACGACTACGACTAGCGCCATCAGC
>>>>>>              
>>>>> It returns:
>>>>>            
>>>>>> $VAR1 = bless( {
>>>>>>                  'primary_id' =>  'seq1',
>>>>>>                  'primary_seq' =>  bless( {
>>>>>>                                            'display_id' =>  'seq1',
>>>>>>                                            'primary_id' =>  'seq1',
>>>>>>                                            'desc' =>  'a small test sequence',
>>>>>>                                            'seq' =>  'ACGTACGACTACGACTAGCGCCATCAGC',
>>>>>>                                            'alphabet' =>  'dna'
>>>>>>                                          }, 'Bio::PrimarySeq' )
>>>>>>                }, 'Bio::Seq' );
>>>>>>              
>>>>> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I really only need the Bio::PrimarySeq. Looking at the documentation for Bio::SeqIO I found that I could in theory adjust the sequence factory and sequence builder to my liking... I tried this:
>>>>>            
>>>>>> use warnings;
>>>>>> use strict;
>>>>>> use Data::Dumper;
>>>>>> use Bio::SeqIO;
>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>> my $seq = $in->next_seq;
>>>>>> print Dumper($seq);
>>>>>> __END__
>>>>>>              
>>>>>>> seq1 a small test sequence
>>>>>>>                
>>>>>> ACGTACGACTACGACTAGCGCCATCAGC
>>>>>>              
>>>>> This returns:
>>>>>            
>>>>>> The factory is a Bio::Seq::SeqFastaSpeedFactory
>>>>>> Can't locate object method "type" via package "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl line 12,<DATA>  line 1.
>>>>>>              
>>>>> According to Bio::Seq::FastaSpeedFactory's documentation:
>>>>>            
>>>>>> If you want the factory to create Bio::Seq objects instead
>>>>>> of the default Bio::PrimarySeq objects, use the -type parameter
>>>>>>              
>>>>> So, PrimarySeq should be the default type, even though in my case it seems not to be. Second, I can't seem to use the -type method to change what the return type is... It errors.
>>>>>
>>>>> Any ideas??? Thanks,
>>>>>
>>>>> Florent
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>            
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>      
>
>    

From help at gmod.org  Tue Feb 16 17:58:45 2010
From: help at gmod.org (Dave Clements, GMOD Help Desk)
Date: Tue, 16 Feb 2010 14:58:45 -0800
Subject: [Bioperl-l] 2010 GMOD Summer School - Americas
In-Reply-To: <71ee57c71001291403s19be18f3s3a1d5a314c74def@mail.gmail.com>
References: <71ee57c71001291351q47994b82w10dffb390dbf2837@mail.gmail.com>
	<71ee57c71001291356p5e7f1aadi2bf437c93014a393@mail.gmail.com>
	<71ee57c71001291357h67112e2fkcf835687e59f66ae@mail.gmail.com>
	<71ee57c71001291358k74781b08n232534d8895c5ec1@mail.gmail.com>
	<71ee57c71001291400y28e40eb6i112ea91df977dc67@mail.gmail.com>
	<71ee57c71001291400n6133982eh3a02293ff741900b@mail.gmail.com>
	<71ee57c71001291401y505b56baic61c11754d88a444@mail.gmail.com>
	<71ee57c71001291402s23e3f2e9w2562d6acf85bd4ae@mail.gmail.com>
	<71ee57c71001291402h2ec67300r4fc7a3b2375f4080@mail.gmail.com>
	<71ee57c71001291403s19be18f3s3a1d5a314c74def@mail.gmail.com>
Message-ID: <71ee57c71002161458t828500bqfc1bdb038d80c73a@mail.gmail.com>

Hello all,

This is a reminder that the deadline for applying to the 2010 GMOD
Summer School - Americas is the end of the day on Monday, February 22,
which is now less than a week away.  Any applications received after
that will automatically be placed on the waiting list.

Admission is competitive and is based on the strength of the
application, especially the statement of interest.  See
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas for additional
information.

Thanks,

Dave Clements

On Fri, Jan 29, 2010 at 2:03 PM, Dave Clements, GMOD Help Desk
<help at gmod.org> wrote:
> Hello all,
>
> I am pleased to announce that we are now accepting applications for:
>
> ? 2010 GMOD Summer School - Americas
> ? ? 6-9 May 2010
> ? ? NESCent, Durham, NC, USA
> ? ? http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
>
> This will be a hands-on multi-day course aimed at teaching new GMOD
> users/administrators how to get GMOD Components up and running. The
> course will introduce participants to the GMOD project and then focus
> on installation, configuration and integration of popular GMOD
> Components. The course will be held May 6-9, at NESCent in Durham, NC.
>
> These components will be covered:
> ? ?* Apollo - genome annotation editor
> ? ?* Chado - a modular and extensible database schema
> ? ?* Galaxy - workflow system
> ? ?* GBrowse - the Generic Genome Browser
> ? ?* GBrowse_syn - A generic synteny browser
> ? ?* JBrowse - genome browser
> ? ?* MAKER - genome annotation pipeline
> ? ?* Tripal - web front end for Chado
>
> The deadline for applying is the end of Friday, February 22. Admission
> is competitive and is based on the strength of the application
> (especially the statement of interest). In 2009 there were over 50
> applications for the 25 slots. Any applications received after the
> deadline will be placed on the waiting list.
>
> See the course page for details and an application link:
> ?http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
>
> Thanks,
>
> Dave Clements
> GMOD Help Desk
>
> PS: We are also investigating holding a GMOD course in the
> Asia/Pacific region, sometime this fall. Watch the GMOD mailing lists
> and the GMOD News page/RSS feed for updates.
> --
> Please keep responses on the list!
> http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
> http://gmod.org/wiki/GMOD_News
> Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
>



-- 
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
http://gmod.org/wiki/GMOD_Logo_Program
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback


From alex at bioinf.uni-leipzig.de  Mon Feb 15 09:33:32 2010
From: alex at bioinf.uni-leipzig.de (Alexander Donath)
Date: Mon, 15 Feb 2010 15:33:32 +0100 (CET)
Subject: [Bioperl-l] BlastPlus and Bio::Graphics
In-Reply-To: <EB3B3684-6A54-4549-BAAA-6AED15F1C8C8@gmail.com>
References: <EB3B3684-6A54-4549-BAAA-6AED15F1C8C8@gmail.com>
Message-ID: <alpine.LFD.2.00.1002151530561.26475@bierdepot.bioinf.uni-leipzig.de>

Janine,

the first line tells you that you're producing a PNG image. everything is 
alright. you just need to write the output in a file. try something 
like

./your-bioperl-script > image.png

then open image.png with your favourite image viewer.

so long,
alex


On Sat, 13 Feb 2010, Janine Arloth wrote:

> Hello,
>
> I am a new user of bioperl and use blast (+). 
> I want to get a graphic output so I use the example described on web http://www.bioperl.org/wiki/HOWTO:Graphics .
>
> I have installed all required Modules.
> But the output looks like:
>
> ??PNG
>
> IHDR4)?????=PLTE?Q?????.??Wk??#????????K????2???????H???????????????????????????????????H=???????F??????????????G?@?????????/OO??????????????Uk/e????r??????????=??????????????????????????????w? ???????????????`"??"p??2f????????e??????????????????????????????????cG?????jZ?????
> ......
>
> Do you have an idea, what I make wrong?
>
> Best regards
> Janine
>
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
By the time you've read this, you've already read it!

From mysarapa at cyf-kr.edu.pl  Tue Feb 16 12:03:25 2010
From: mysarapa at cyf-kr.edu.pl (Krzysztof Sarapata)
Date: Tue, 16 Feb 2010 18:03:25 +0100
Subject: [Bioperl-l] load_seqdatabase.pl
Message-ID: <007501caaf29$f4565920$2f0c9c95@rubin>

Hi



I've loaded GenBank file into bioSQL structure with "load_seqdatabase.pl" script. 

Is it correct that each entity (qualifier) from FEATURES even "db_xref"  e.g.

 

FEATURES             Location/Qualifiers

     source          1..257719

                     /organism="Homo sapiens"

                     /mol_type="genomic DNA"

                     /db_xref="taxon:9606"

                     /chromosome="1"

                     .....

                    /db_xref="GeneID:100287102"

 

is put into  "Seqfeature Qualifier Value" table, if we have exactly table "Dbxref"?

Why value of this qualifier (db_xref) isn't put into "Dbxref" table?



With regards

Krzysztof Sarapata


From avilella at gmail.com  Tue Feb 16 15:38:30 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 16 Feb 2010 20:38:30 +0000
Subject: [Bioperl-l] display sequence alignment
In-Reply-To: <4B7ACEDF.2090808@gmail.com>
References: <9adc0e9b1002160626k3bf8d66w8c9889daa72713c4@mail.gmail.com>
	<358f4d651002160841r5629f3absa71e6d0f563aed5e@mail.gmail.com>
	<4B7ACEDF.2090808@gmail.com>
Message-ID: <358f4d651002161238o198df131xdf95113a6329a394@mail.gmail.com>

Yes, a PNG. Something as close as possible to the one attached, which
is a snapshot for the overview of a Jalview session. Jalview cannot be
scripted, so being able to programmatically produce this would be very
useful.

On Tue, Feb 16, 2010 at 4:59 PM, Jason Stajich <jason.stajich at gmail.com> wrote:
> I've done this by marking it up an alignment into HTML with colors, but no
> bioperl module for it that I know of. My way was pretty heavy (producing
> large files) but maybe a more compact CSS approach could produce smaller
> files.
>
> How else were you thinking of seeing this - in a PNG ?
>
> -jason
>
> Albert Vilella wrote:
>
> I am actually also interested in this :-)
>
> My requirements are to be able to define an image size, like 1200x800
> pixels, and then have a representation of the alignment produced
> through a script, with the clustalw or nucleotide colour palette like
> in Jalview.
>
> Anyone?
>
> On Tue, Feb 16, 2010 at 2:26 PM, Jessica Sun <jessica.sun at gmail.com> wrote:
>
>
> Do any one know how to display protein/peptide alignments in color using
> bioperl.
>
> thx
>
> On Mon, Feb 15, 2010 at 9:35 AM, Jessica Sun <jessica.sun at gmail.com> wrote:
>
>
>
> ---------- Forwarded message ----------
> From: Jessica Sun <jessica.sun at gmail.com>
> Date: Fri, Feb 12, 2010 at 8:44 PM
> Subject: one more question
> To: bioperl-l at lists.open-bio.org
>
>
> Does anyone knows how to get genomic(dna) sequences(with right sub regions)
> in gbk format when you only have NM_(mRNA) accession numbers.
>
> Thanks,
>
>
> --
> Jessica Jingping Sun
>
>
>
> --
> Jessica Jingping Sun
>
>
>
> --
> Jessica Jingping Sun
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
-------------- next part --------------
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From roy.chaudhuri at gmail.com  Wed Feb 17 11:29:08 2010
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 17 Feb 2010 16:29:08 +0000
Subject: [Bioperl-l] load_seqdatabase.pl
In-Reply-To: <007501caaf29$f4565920$2f0c9c95@rubin>
References: <007501caaf29$f4565920$2f0c9c95@rubin>
Message-ID: <4B7C1954.1050507@gmail.com>

Hi Krzysztof,

The reasons for this are discussed in this post on the BioSQL list:
http://lists.open-bio.org/pipermail/biosql-l/2005-March/000751.html

In short - BioPerl does not perform any magic to insert the db_xref 
feature tags where you might expect (ie. the seqfeature_dbxref table). 
It should be possible to write a SeqProcessor to do so, although it's 
pretty easy to access them where they are with a query like:
SELECT * FROM seqfeature_qualifier_value s JOIN term t USING(term_id) 
WHERE t.name='db_xref'

Roy.

On 16/02/2010 17:03, Krzysztof Sarapata wrote:
> Hi
>
>
>
> I've loaded GenBank file into bioSQL structure with
> "load_seqdatabase.pl" script.
>
> Is it correct that each entity (qualifier) from FEATURES even
> "db_xref"  e.g.
>
>
>
> FEATURES             Location/Qualifiers
>
> source          1..257719
>
> /organism="Homo sapiens"
>
> /mol_type="genomic DNA"
>
> /db_xref="taxon:9606"
>
> /chromosome="1"
>
> .....
>
> /db_xref="GeneID:100287102"
>
>
>
> is put into  "Seqfeature Qualifier Value" table, if we have exactly
> table "Dbxref"?
>
> Why value of this qualifier (db_xref) isn't put into "Dbxref" table?
>
>
>
> With regards
>
> Krzysztof Sarapata

From rmb32 at cornell.edu  Wed Feb 17 12:52:00 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 17 Feb 2010 09:52:00 -0800
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <4B7AFD97.5050003@bioperl.org>
References: <4B79C716.90405@gmail.com>
	<4B79E0D8.3060806@bioperl.org>	<4B7A38A8.80702@gmail.com>
	<4B7ACE6A.3000402@bioperl.org>	<AF001D8E-3B3C-4405-9D31-E0BE358C9559@illinois.edu>
	<4B7AFD97.5050003@bioperl.org>
Message-ID: <4B7C2CC0.1060108@cornell.edu>

OK, well are you guys going to roll them back and do a branch?  Broken 
trunk is not good.

R

Jason Stajich wrote:
> hmm yes. Let's roll back those Florent.
> 
> I guess we need to also discuss the concept of branches again here for 
> major changes like this. The speed fix is helpful for short read but 
> probably not for all systems so just having the ability to provide the 
> right type when you use your scripts focused on short-reads might be the 
> best way to go forward and preserve backwards compatibility.
> 
> -jason
> 
> Chris Fields wrote:
>> Yes, except that tests are now failing on live.  Bio::PrimarySeq isn't 
>> a Bio::SeqI, so it's a bit of an API change in a lot of places 
>> expecting a Bio::SeqI.  We should make this optional for the time 
>> being, until we discuss it more on list.
>>
>> chris
>>
>> On Feb 16, 2010, at 10:57 AM, Jason Stajich wrote:
>>
>>   
>>> Great!  thanks for committing it.
>>>
>>> Florent Angly wrote:
>>>     
>>>> Thanks for your reply Jason. It's very valuable since you coded the 
>>>> modules in question!
>>>>
>>>> Now that I understand the purpose of these modules, I did a little 
>>>> bit of documentation clarification. I also figured out that I should 
>>>> implement the 'type' method in Bio::Seq::SeqFastaSpeedFactory and 
>>>> made it support creating Bio::PrimarySeq. This is all committed to SVN.
>>>>
>>>> When sequences are large, you are right that it does not make much 
>>>> difference in time or memory resource to use one sequence type over 
>>>> the other. However, that's different for short sequences. I took a 
>>>> FASTA file weighting 39.3 MB and containing 360,000 sequences of 106 
>>>> bp on average.
>>>>
>>>> CASE 1:
>>>>   Requested factory Bio::Seq::SeqFactory
>>>>   Requested sequence type is Bio::Seq
>>>>   Memory used: 329 MB
>>>>   Time spent: 1m8.522s
>>>>
>>>> CASE 2:
>>>>   Requested factory Bio::Seq::SeqFactory
>>>>   Requested sequence type is Bio::PrimarySeq
>>>>   Memory used: 246 MB
>>>>   Time spent: 0m52.663s
>>>>
>>>> CASE 3:
>>>>   Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>>   Requested sequence type is Bio::Seq
>>>>   Memory used: 298 MB
>>>>   Time spent: 0m31.292s
>>>>
>>>> CASE 4:
>>>>   Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>>   Requested sequence type is Bio::PrimarySeq
>>>>   Memory used: 231 MB
>>>>   Time spent: 0m28.500s
>>>>
>>>> Clearly, when only simple sequence attributes are needed or FASTA 
>>>> files are used, it's fast and memory efficient to use the 
>>>> SeqFastaSpeedFactory with PrimarySeq.
>>>>
>>>> Florent
>>>>
>>>>
>>>> On 16/02/10 10:03, Jason Stajich wrote:
>>>>       
>>>>> I don't think that aspect of the documentation vs interface was 
>>>>> ever implemented - the interface object doesn't specify a type 
>>>>> method or init argument even though the documentation says so. Not 
>>>>> really sure why not, this was ages ago unfortunately.
>>>>>
>>>>> This particular factory definitely assumes you are building 
>>>>> Bio::Seq objects - you can try and subclass and build your own to 
>>>>> see if it makes much of a difference in speed/memory - I would 
>>>>> posit it won't make a significant difference but be interested to 
>>>>> see what you find.
>>>>>
>>>>> Just make your own Bio::Seq::PrimarySeqFactory object based on 
>>>>> Bio::Seq::FastaSpeedFactory and simplify that code so it doesn't 
>>>>> build Bio::Seq object wrapper around the Bio::PrimarySeq and do 
>>>>> some perf tests so we'll know if it makes any difference here.
>>>>>
>>>>> -jason
>>>>> Florent Angly wrote:
>>>>>         
>>>>>> Hi all,
>>>>>>
>>>>>> I am trying to reduce memory usage and speedup reading FASTA files 
>>>>>> using the facilities provided by BioPerl.
>>>>>>
>>>>>> The first thing I noticed is that when using Bio::SeqIO::fasta, 
>>>>>> the objects returned are Bio::Seq, not Bio::PrimarySeq objects. 
>>>>>> Bio::PrimarySeq sequences are lighter than Bio::Seq sequences, so 
>>>>>> it's what I need. See code below:
>>>>>>           
>>>>>>> use warnings;
>>>>>>> use strict;
>>>>>>> use Data::Dumper;
>>>>>>> use Bio::SeqIO;
>>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>>> my $seqfactory = $in->sequence_factory; # 
>>>>>>> Bio::Factory::ObjectBuilderI
>>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>>> my $seq = $in->next_seq;
>>>>>>> print Dumper($seq);
>>>>>>> __END__
>>>>>>>             
>>>>>>>> seq1 a small test sequence q
>>>>>>>>                
>>>>>>> ACGTACGACTACGACTAGCGCCATCAGC
>>>>>>>              
>>>>>> It returns:
>>>>>>           
>>>>>>> $VAR1 = bless( {
>>>>>>>                  'primary_id' =>  'seq1',
>>>>>>>                  'primary_seq' =>  bless( {
>>>>>>>                                            'display_id' =>  'seq1',
>>>>>>>                                            'primary_id' =>  'seq1',
>>>>>>>                                            'desc' =>  'a small 
>>>>>>> test sequence',
>>>>>>>                                            'seq' =>  
>>>>>>> 'ACGTACGACTACGACTAGCGCCATCAGC',
>>>>>>>                                            'alphabet' =>  'dna'
>>>>>>>                                          }, 'Bio::PrimarySeq' )
>>>>>>>                }, 'Bio::Seq' );
>>>>>>>              
>>>>>> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I 
>>>>>> really only need the Bio::PrimarySeq. Looking at the documentation 
>>>>>> for Bio::SeqIO I found that I could in theory adjust the sequence 
>>>>>> factory and sequence builder to my liking... I tried this:
>>>>>>           
>>>>>>> use warnings;
>>>>>>> use strict;
>>>>>>> use Data::Dumper;
>>>>>>> use Bio::SeqIO;
>>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>>> my $seqfactory = $in->sequence_factory; # 
>>>>>>> Bio::Factory::ObjectBuilderI
>>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>>> my $seq = $in->next_seq;
>>>>>>> print Dumper($seq);
>>>>>>> __END__
>>>>>>>             
>>>>>>>> seq1 a small test sequence
>>>>>>>>                
>>>>>>> ACGTACGACTACGACTAGCGCCATCAGC
>>>>>>>              
>>>>>> This returns:
>>>>>>           
>>>>>>> The factory is a Bio::Seq::SeqFastaSpeedFactory
>>>>>>> Can't locate object method "type" via package 
>>>>>>> "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl line 
>>>>>>> 12,<DATA>  line 1.
>>>>>>>              
>>>>>> According to Bio::Seq::FastaSpeedFactory's documentation:
>>>>>>           
>>>>>>> If you want the factory to create Bio::Seq objects instead
>>>>>>> of the default Bio::PrimarySeq objects, use the -type parameter
>>>>>>>              
>>>>>> So, PrimarySeq should be the default type, even though in my case 
>>>>>> it seems not to be. Second, I can't seem to use the -type method 
>>>>>> to change what the return type is... It errors.
>>>>>>
>>>>>> Any ideas??? Thanks,
>>>>>>
>>>>>> Florent
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>            
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>      
>>
>>    
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


-- 
Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu
http://www.sgn.cornell.edu

From jcline at ieee.org  Wed Feb 17 16:39:43 2010
From: jcline at ieee.org (Jonathan Cline)
Date: Wed, 17 Feb 2010 13:39:43 -0800
Subject: [Bioperl-l] Lab Instrumentation common interface standards fyi
Message-ID: <f5f256441002171339l38b280bfr39c3d429827629df@mail.gmail.com>

Amazingly, a huge issue in bio/chem labs is all the instrumentation
which is: uniquely designed, non-networked, uses custom data formats,
has proprietary software controls, etc.  Briefly, an
organization/consortium called SiLA is attempting to unify lab
equipment vendors under a common set of computer interface (data
communication) standards.  They seem to be making regular progress.
This standard is open to $$$ members $$$, and currently does not allow
open source implementations although this possibility is under
discussion - and basically comes down to $$$.   My own perl open
source lab automation software won't support SiLA until SiLA allows
the implementation to become more open.

The SiLA Device Interface Standard for example ( http://www.sila.coop
), defines what operations a centrifuge performs and what data it
sends back to a host.  The specified data comm stack is
IP/TCP/HTTP/SOAP/XML over wired ethernet.  Yes, SOAP.  Using HTTPS for
security is optional.

A benefit to the choices in their standard is that Perl would support
the entire stack quite easily.


-- 
## Jonathan Cline
## jcline at ieee.org
## Mobile: +1-805-617-0223
########################

From cjfields at illinois.edu  Wed Feb 17 17:03:39 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 17 Feb 2010 16:03:39 -0600
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <4B7C2CC0.1060108@cornell.edu>
References: <4B79C716.90405@gmail.com> <4B79E0D8.3060806@bioperl.org>
	<4B7A38A8.80702@gmail.com> <4B7ACE6A.3000402@bioperl.org>
	<AF001D8E-3B3C-4405-9D31-E0BE358C9559@illinois.edu>
	<4B7AFD97.5050003@bioperl.org>  <4B7C2CC0.1060108@cornell.edu>
Message-ID: <1266444219.3370.0.camel@pyrimidine.igb.uiuc.edu>

Rob, 

Looks like Jason took care of it.  There are likely more tests still
failing on trunk, but hopefully much fewer of them than before ;>

chris

On Wed, 2010-02-17 at 09:52 -0800, Robert Buels wrote:
> OK, well are you guys going to roll them back and do a branch?  Broken 
> trunk is not good.
> 
> R
> 
> Jason Stajich wrote:
> > hmm yes. Let's roll back those Florent.
> > 
> > I guess we need to also discuss the concept of branches again here for 
> > major changes like this. The speed fix is helpful for short read but 
> > probably not for all systems so just having the ability to provide the 
> > right type when you use your scripts focused on short-reads might be the 
> > best way to go forward and preserve backwards compatibility.
> > 
> > -jason
> > 
> > Chris Fields wrote:
> >> Yes, except that tests are now failing on live.  Bio::PrimarySeq isn't 
> >> a Bio::SeqI, so it's a bit of an API change in a lot of places 
> >> expecting a Bio::SeqI.  We should make this optional for the time 
> >> being, until we discuss it more on list.
> >>
> >> chris
> >>
> >> On Feb 16, 2010, at 10:57 AM, Jason Stajich wrote:
> >>
> >>   
> >>> Great!  thanks for committing it.
> >>>
> >>> Florent Angly wrote:
> >>>     
> >>>> Thanks for your reply Jason. It's very valuable since you coded the 
> >>>> modules in question!
> >>>>
> >>>> Now that I understand the purpose of these modules, I did a little 
> >>>> bit of documentation clarification. I also figured out that I should 
> >>>> implement the 'type' method in Bio::Seq::SeqFastaSpeedFactory and 
> >>>> made it support creating Bio::PrimarySeq. This is all committed to SVN.
> >>>>
> >>>> When sequences are large, you are right that it does not make much 
> >>>> difference in time or memory resource to use one sequence type over 
> >>>> the other. However, that's different for short sequences. I took a 
> >>>> FASTA file weighting 39.3 MB and containing 360,000 sequences of 106 
> >>>> bp on average.
> >>>>
> >>>> CASE 1:
> >>>>   Requested factory Bio::Seq::SeqFactory
> >>>>   Requested sequence type is Bio::Seq
> >>>>   Memory used: 329 MB
> >>>>   Time spent: 1m8.522s
> >>>>
> >>>> CASE 2:
> >>>>   Requested factory Bio::Seq::SeqFactory
> >>>>   Requested sequence type is Bio::PrimarySeq
> >>>>   Memory used: 246 MB
> >>>>   Time spent: 0m52.663s
> >>>>
> >>>> CASE 3:
> >>>>   Requested factory Bio::Seq::SeqFastaSpeedFactory
> >>>>   Requested sequence type is Bio::Seq
> >>>>   Memory used: 298 MB
> >>>>   Time spent: 0m31.292s
> >>>>
> >>>> CASE 4:
> >>>>   Requested factory Bio::Seq::SeqFastaSpeedFactory
> >>>>   Requested sequence type is Bio::PrimarySeq
> >>>>   Memory used: 231 MB
> >>>>   Time spent: 0m28.500s
> >>>>
> >>>> Clearly, when only simple sequence attributes are needed or FASTA 
> >>>> files are used, it's fast and memory efficient to use the 
> >>>> SeqFastaSpeedFactory with PrimarySeq.
> >>>>
> >>>> Florent
> >>>>
> >>>>
> >>>> On 16/02/10 10:03, Jason Stajich wrote:
> >>>>       
> >>>>> I don't think that aspect of the documentation vs interface was 
> >>>>> ever implemented - the interface object doesn't specify a type 
> >>>>> method or init argument even though the documentation says so. Not 
> >>>>> really sure why not, this was ages ago unfortunately.
> >>>>>
> >>>>> This particular factory definitely assumes you are building 
> >>>>> Bio::Seq objects - you can try and subclass and build your own to 
> >>>>> see if it makes much of a difference in speed/memory - I would 
> >>>>> posit it won't make a significant difference but be interested to 
> >>>>> see what you find.
> >>>>>
> >>>>> Just make your own Bio::Seq::PrimarySeqFactory object based on 
> >>>>> Bio::Seq::FastaSpeedFactory and simplify that code so it doesn't 
> >>>>> build Bio::Seq object wrapper around the Bio::PrimarySeq and do 
> >>>>> some perf tests so we'll know if it makes any difference here.
> >>>>>
> >>>>> -jason
> >>>>> Florent Angly wrote:
> >>>>>         
> >>>>>> Hi all,
> >>>>>>
> >>>>>> I am trying to reduce memory usage and speedup reading FASTA files 
> >>>>>> using the facilities provided by BioPerl.
> >>>>>>
> >>>>>> The first thing I noticed is that when using Bio::SeqIO::fasta, 
> >>>>>> the objects returned are Bio::Seq, not Bio::PrimarySeq objects. 
> >>>>>> Bio::PrimarySeq sequences are lighter than Bio::Seq sequences, so 
> >>>>>> it's what I need. See code below:
> >>>>>>           
> >>>>>>> use warnings;
> >>>>>>> use strict;
> >>>>>>> use Data::Dumper;
> >>>>>>> use Bio::SeqIO;
> >>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
> >>>>>>> my $seqfactory = $in->sequence_factory; # 
> >>>>>>> Bio::Factory::ObjectBuilderI
> >>>>>>> print "The factory is a ".ref($seqfactory)."\n";
> >>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
> >>>>>>> my $seq = $in->next_seq;
> >>>>>>> print Dumper($seq);
> >>>>>>> __END__
> >>>>>>>             
> >>>>>>>> seq1 a small test sequence q
> >>>>>>>>                
> >>>>>>> ACGTACGACTACGACTAGCGCCATCAGC
> >>>>>>>              
> >>>>>> It returns:
> >>>>>>           
> >>>>>>> $VAR1 = bless( {
> >>>>>>>                  'primary_id' =>  'seq1',
> >>>>>>>                  'primary_seq' =>  bless( {
> >>>>>>>                                            'display_id' =>  'seq1',
> >>>>>>>                                            'primary_id' =>  'seq1',
> >>>>>>>                                            'desc' =>  'a small 
> >>>>>>> test sequence',
> >>>>>>>                                            'seq' =>  
> >>>>>>> 'ACGTACGACTACGACTAGCGCCATCAGC',
> >>>>>>>                                            'alphabet' =>  'dna'
> >>>>>>>                                          }, 'Bio::PrimarySeq' )
> >>>>>>>                }, 'Bio::Seq' );
> >>>>>>>              
> >>>>>> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I 
> >>>>>> really only need the Bio::PrimarySeq. Looking at the documentation 
> >>>>>> for Bio::SeqIO I found that I could in theory adjust the sequence 
> >>>>>> factory and sequence builder to my liking... I tried this:
> >>>>>>           
> >>>>>>> use warnings;
> >>>>>>> use strict;
> >>>>>>> use Data::Dumper;
> >>>>>>> use Bio::SeqIO;
> >>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
> >>>>>>> my $seqfactory = $in->sequence_factory; # 
> >>>>>>> Bio::Factory::ObjectBuilderI
> >>>>>>> print "The factory is a ".ref($seqfactory)."\n";
> >>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
> >>>>>>> my $seq = $in->next_seq;
> >>>>>>> print Dumper($seq);
> >>>>>>> __END__
> >>>>>>>             
> >>>>>>>> seq1 a small test sequence
> >>>>>>>>                
> >>>>>>> ACGTACGACTACGACTAGCGCCATCAGC
> >>>>>>>              
> >>>>>> This returns:
> >>>>>>           
> >>>>>>> The factory is a Bio::Seq::SeqFastaSpeedFactory
> >>>>>>> Can't locate object method "type" via package 
> >>>>>>> "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl line 
> >>>>>>> 12,<DATA>  line 1.
> >>>>>>>              
> >>>>>> According to Bio::Seq::FastaSpeedFactory's documentation:
> >>>>>>           
> >>>>>>> If you want the factory to create Bio::Seq objects instead
> >>>>>>> of the default Bio::PrimarySeq objects, use the -type parameter
> >>>>>>>              
> >>>>>> So, PrimarySeq should be the default type, even though in my case 
> >>>>>> it seems not to be. Second, I can't seem to use the -type method 
> >>>>>> to change what the return type is... It errors.
> >>>>>>
> >>>>>> Any ideas??? Thanks,
> >>>>>>
> >>>>>> Florent
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Bioperl-l mailing list
> >>>>>> Bioperl-l at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>            
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>      
> >>
> >>    
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 



From jason at bioperl.org  Wed Feb 17 18:22:56 2010
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 17 Feb 2010 15:22:56 -0800
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <4B7C2CC0.1060108@cornell.edu>
References: <4B79C716.90405@gmail.com>
	<4B79E0D8.3060806@bioperl.org>	<4B7A38A8.80702@gmail.com>
	<4B7ACE6A.3000402@bioperl.org>	<AF001D8E-3B3C-4405-9D31-E0BE358C9559@illinois.edu>
	<4B7AFD97.5050003@bioperl.org> <4B7C2CC0.1060108@cornell.edu>
Message-ID: <4B7C7A50.3000505@bioperl.org>

I rolled back.
The fix seems to just be to make the default Bio::Seq not 
Bio::PrimarySeq in terms of what the factory return and undo some of the 
explicit expectations in the code.  I think this speedup is a special 
case and Bio::Seq still needs to be the default but you override it when 
you want Bio::PrimarySeq objects only.

Florent for your purposes you need to just set the type in your scripts.

And in the future - you must run tests before committing something, 
especially one that touches so many files!

I think I've unrolled most of the defaults while keeping the new type 
method intact.

There are still warnings and few failed tests to followup.

Okay - I am really now in favor of breaking the modules into packages 
test running taking forever and this is way unwieldy. I am looking 
forward to seeing things in smaller pieces somehow.

-jason
Robert Buels wrote:
> OK, well are you guys going to roll them back and do a branch?  Broken 
> trunk is not good.
>
> R
>
> Jason Stajich wrote:
>> hmm yes. Let's roll back those Florent.
>>
>> I guess we need to also discuss the concept of branches again here 
>> for major changes like this. The speed fix is helpful for short read 
>> but probably not for all systems so just having the ability to 
>> provide the right type when you use your scripts focused on 
>> short-reads might be the best way to go forward and preserve 
>> backwards compatibility.
>>
>> -jason
>>
>> Chris Fields wrote:
>>> Yes, except that tests are now failing on live.  Bio::PrimarySeq 
>>> isn't a Bio::SeqI, so it's a bit of an API change in a lot of places 
>>> expecting a Bio::SeqI.  We should make this optional for the time 
>>> being, until we discuss it more on list.
>>>
>>> chris
>>>
>>> On Feb 16, 2010, at 10:57 AM, Jason Stajich wrote:
>>>
>>>> Great!  thanks for committing it.
>>>>
>>>> Florent Angly wrote:
>>>>> Thanks for your reply Jason. It's very valuable since you coded 
>>>>> the modules in question!
>>>>>
>>>>> Now that I understand the purpose of these modules, I did a little 
>>>>> bit of documentation clarification. I also figured out that I 
>>>>> should implement the 'type' method in 
>>>>> Bio::Seq::SeqFastaSpeedFactory and made it support creating 
>>>>> Bio::PrimarySeq. This is all committed to SVN.
>>>>>
>>>>> When sequences are large, you are right that it does not make much 
>>>>> difference in time or memory resource to use one sequence type 
>>>>> over the other. However, that's different for short sequences. I 
>>>>> took a FASTA file weighting 39.3 MB and containing 360,000 
>>>>> sequences of 106 bp on average.
>>>>>
>>>>> CASE 1:
>>>>>   Requested factory Bio::Seq::SeqFactory
>>>>>   Requested sequence type is Bio::Seq
>>>>>   Memory used: 329 MB
>>>>>   Time spent: 1m8.522s
>>>>>
>>>>> CASE 2:
>>>>>   Requested factory Bio::Seq::SeqFactory
>>>>>   Requested sequence type is Bio::PrimarySeq
>>>>>   Memory used: 246 MB
>>>>>   Time spent: 0m52.663s
>>>>>
>>>>> CASE 3:
>>>>>   Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>>>   Requested sequence type is Bio::Seq
>>>>>   Memory used: 298 MB
>>>>>   Time spent: 0m31.292s
>>>>>
>>>>> CASE 4:
>>>>>   Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>>>   Requested sequence type is Bio::PrimarySeq
>>>>>   Memory used: 231 MB
>>>>>   Time spent: 0m28.500s
>>>>>
>>>>> Clearly, when only simple sequence attributes are needed or FASTA 
>>>>> files are used, it's fast and memory efficient to use the 
>>>>> SeqFastaSpeedFactory with PrimarySeq.
>>>>>
>>>>> Florent
>>>>>
>>>>>
>>>>> On 16/02/10 10:03, Jason Stajich wrote:
>>>>>> I don't think that aspect of the documentation vs interface was 
>>>>>> ever implemented - the interface object doesn't specify a type 
>>>>>> method or init argument even though the documentation says so. 
>>>>>> Not really sure why not, this was ages ago unfortunately.
>>>>>>
>>>>>> This particular factory definitely assumes you are building 
>>>>>> Bio::Seq objects - you can try and subclass and build your own to 
>>>>>> see if it makes much of a difference in speed/memory - I would 
>>>>>> posit it won't make a significant difference but be interested to 
>>>>>> see what you find.
>>>>>>
>>>>>> Just make your own Bio::Seq::PrimarySeqFactory object based on 
>>>>>> Bio::Seq::FastaSpeedFactory and simplify that code so it doesn't 
>>>>>> build Bio::Seq object wrapper around the Bio::PrimarySeq and do 
>>>>>> some perf tests so we'll know if it makes any difference here.
>>>>>>
>>>>>> -jason
>>>>>> Florent Angly wrote:
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I am trying to reduce memory usage and speedup reading FASTA 
>>>>>>> files using the facilities provided by BioPerl.
>>>>>>>
>>>>>>> The first thing I noticed is that when using Bio::SeqIO::fasta, 
>>>>>>> the objects returned are Bio::Seq, not Bio::PrimarySeq objects. 
>>>>>>> Bio::PrimarySeq sequences are lighter than Bio::Seq sequences, 
>>>>>>> so it's what I need. See code below:
>>>>>>>> use warnings;
>>>>>>>> use strict;
>>>>>>>> use Data::Dumper;
>>>>>>>> use Bio::SeqIO;
>>>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>>>> my $seqfactory = $in->sequence_factory; # 
>>>>>>>> Bio::Factory::ObjectBuilderI
>>>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>>>> my $seq = $in->next_seq;
>>>>>>>> print Dumper($seq);
>>>>>>>> __END__
>>>>>>>>> seq1 a small test sequence q 
>>>>>>>> ACGTACGACTACGACTAGCGCCATCAGC 
>>>>>>> It returns:
>>>>>>>> $VAR1 = bless( {
>>>>>>>>                  'primary_id' =>  'seq1',
>>>>>>>>                  'primary_seq' =>  bless( {
>>>>>>>>                                            'display_id' =>  
>>>>>>>> 'seq1',
>>>>>>>>                                            'primary_id' =>  
>>>>>>>> 'seq1',
>>>>>>>>                                            'desc' =>  'a small 
>>>>>>>> test sequence',
>>>>>>>>                                            'seq' =>  
>>>>>>>> 'ACGTACGACTACGACTAGCGCCATCAGC',
>>>>>>>>                                            'alphabet' =>  'dna'
>>>>>>>>                                          }, 'Bio::PrimarySeq' )
>>>>>>>>                }, 'Bio::Seq' ); 
>>>>>>> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I 
>>>>>>> really only need the Bio::PrimarySeq. Looking at the 
>>>>>>> documentation for Bio::SeqIO I found that I could in theory 
>>>>>>> adjust the sequence factory and sequence builder to my liking... 
>>>>>>> I tried this:
>>>>>>>> use warnings;
>>>>>>>> use strict;
>>>>>>>> use Data::Dumper;
>>>>>>>> use Bio::SeqIO;
>>>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>>>> my $seqfactory = $in->sequence_factory; # 
>>>>>>>> Bio::Factory::ObjectBuilderI
>>>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>>>> my $seq = $in->next_seq;
>>>>>>>> print Dumper($seq);
>>>>>>>> __END__
>>>>>>>>> seq1 a small test sequence 
>>>>>>>> ACGTACGACTACGACTAGCGCCATCAGC 
>>>>>>> This returns:
>>>>>>>> The factory is a Bio::Seq::SeqFastaSpeedFactory
>>>>>>>> Can't locate object method "type" via package 
>>>>>>>> "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl line 
>>>>>>>> 12,<DATA>  line 1. 
>>>>>>> According to Bio::Seq::FastaSpeedFactory's documentation:
>>>>>>>> If you want the factory to create Bio::Seq objects instead
>>>>>>>> of the default Bio::PrimarySeq objects, use the -type parameter 
>>>>>>> So, PrimarySeq should be the default type, even though in my 
>>>>>>> case it seems not to be. Second, I can't seem to use the -type 
>>>>>>> method to change what the return type is... It errors.
>>>>>>>
>>>>>>> Any ideas??? Thanks,
>>>>>>>
>>>>>>> Florent
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From cjfields at illinois.edu  Wed Feb 17 20:33:05 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 17 Feb 2010 19:33:05 -0600
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <4B7C7A50.3000505@bioperl.org>
References: <4B79C716.90405@gmail.com>
	<4B79E0D8.3060806@bioperl.org>	<4B7A38A8.80702@gmail.com>
	<4B7ACE6A.3000402@bioperl.org>	<AF001D8E-3B3C-4405-9D31-E0BE358C9559@illinois.edu>
	<4B7AFD97.5050003@bioperl.org> <4B7C2CC0.1060108@cornell.edu>
	<4B7C7A50.3000505@bioperl.org>
Message-ID: <0D08C9A4-FCE9-477D-B7B8-108952426052@illinois.edu>

I can work on pushing out another 1.6 point release (1.6.2), then we should work on breaking things up.  

chris

On Feb 17, 2010, at 5:22 PM, Jason Stajich wrote:

> I rolled back.
> The fix seems to just be to make the default Bio::Seq not Bio::PrimarySeq in terms of what the factory return and undo some of the explicit expectations in the code.  I think this speedup is a special case and Bio::Seq still needs to be the default but you override it when you want Bio::PrimarySeq objects only.
> 
> Florent for your purposes you need to just set the type in your scripts.
> 
> And in the future - you must run tests before committing something, especially one that touches so many files!
> 
> I think I've unrolled most of the defaults while keeping the new type method intact.
> 
> There are still warnings and few failed tests to followup.
> 
> Okay - I am really now in favor of breaking the modules into packages test running taking forever and this is way unwieldy. I am looking forward to seeing things in smaller pieces somehow.
> 
> -jason
> Robert Buels wrote:
>> OK, well are you guys going to roll them back and do a branch?  Broken trunk is not good.
>> 
>> R
>> 
>> Jason Stajich wrote:
>>> hmm yes. Let's roll back those Florent.
>>> 
>>> I guess we need to also discuss the concept of branches again here for major changes like this. The speed fix is helpful for short read but probably not for all systems so just having the ability to provide the right type when you use your scripts focused on short-reads might be the best way to go forward and preserve backwards compatibility.
>>> 
>>> -jason
>>> 
>>> Chris Fields wrote:
>>>> Yes, except that tests are now failing on live.  Bio::PrimarySeq isn't a Bio::SeqI, so it's a bit of an API change in a lot of places expecting a Bio::SeqI.  We should make this optional for the time being, until we discuss it more on list.
>>>> 
>>>> chris
>>>> 
>>>> On Feb 16, 2010, at 10:57 AM, Jason Stajich wrote:
>>>> 
>>>>> Great!  thanks for committing it.
>>>>> 
>>>>> Florent Angly wrote:
>>>>>> Thanks for your reply Jason. It's very valuable since you coded the modules in question!
>>>>>> 
>>>>>> Now that I understand the purpose of these modules, I did a little bit of documentation clarification. I also figured out that I should implement the 'type' method in Bio::Seq::SeqFastaSpeedFactory and made it support creating Bio::PrimarySeq. This is all committed to SVN.
>>>>>> 
>>>>>> When sequences are large, you are right that it does not make much difference in time or memory resource to use one sequence type over the other. However, that's different for short sequences. I took a FASTA file weighting 39.3 MB and containing 360,000 sequences of 106 bp on average.
>>>>>> 
>>>>>> CASE 1:
>>>>>>  Requested factory Bio::Seq::SeqFactory
>>>>>>  Requested sequence type is Bio::Seq
>>>>>>  Memory used: 329 MB
>>>>>>  Time spent: 1m8.522s
>>>>>> 
>>>>>> CASE 2:
>>>>>>  Requested factory Bio::Seq::SeqFactory
>>>>>>  Requested sequence type is Bio::PrimarySeq
>>>>>>  Memory used: 246 MB
>>>>>>  Time spent: 0m52.663s
>>>>>> 
>>>>>> CASE 3:
>>>>>>  Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>>>>  Requested sequence type is Bio::Seq
>>>>>>  Memory used: 298 MB
>>>>>>  Time spent: 0m31.292s
>>>>>> 
>>>>>> CASE 4:
>>>>>>  Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>>>>  Requested sequence type is Bio::PrimarySeq
>>>>>>  Memory used: 231 MB
>>>>>>  Time spent: 0m28.500s
>>>>>> 
>>>>>> Clearly, when only simple sequence attributes are needed or FASTA files are used, it's fast and memory efficient to use the SeqFastaSpeedFactory with PrimarySeq.
>>>>>> 
>>>>>> Florent
>>>>>> 
>>>>>> 
>>>>>> On 16/02/10 10:03, Jason Stajich wrote:
>>>>>>> I don't think that aspect of the documentation vs interface was ever implemented - the interface object doesn't specify a type method or init argument even though the documentation says so. Not really sure why not, this was ages ago unfortunately.
>>>>>>> 
>>>>>>> This particular factory definitely assumes you are building Bio::Seq objects - you can try and subclass and build your own to see if it makes much of a difference in speed/memory - I would posit it won't make a significant difference but be interested to see what you find.
>>>>>>> 
>>>>>>> Just make your own Bio::Seq::PrimarySeqFactory object based on Bio::Seq::FastaSpeedFactory and simplify that code so it doesn't build Bio::Seq object wrapper around the Bio::PrimarySeq and do some perf tests so we'll know if it makes any difference here.
>>>>>>> 
>>>>>>> -jason
>>>>>>> Florent Angly wrote:
>>>>>>>> Hi all,
>>>>>>>> 
>>>>>>>> I am trying to reduce memory usage and speedup reading FASTA files using the facilities provided by BioPerl.
>>>>>>>> 
>>>>>>>> The first thing I noticed is that when using Bio::SeqIO::fasta, the objects returned are Bio::Seq, not Bio::PrimarySeq objects. Bio::PrimarySeq sequences are lighter than Bio::Seq sequences, so it's what I need. See code below:
>>>>>>>>> use warnings;
>>>>>>>>> use strict;
>>>>>>>>> use Data::Dumper;
>>>>>>>>> use Bio::SeqIO;
>>>>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>>>>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>>>>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>>>>> my $seq = $in->next_seq;
>>>>>>>>> print Dumper($seq);
>>>>>>>>> __END__
>>>>>>>>>> seq1 a small test sequence q 
>>>>>>>>> ACGTACGACTACGACTAGCGCCATCAGC 
>>>>>>>> It returns:
>>>>>>>>> $VAR1 = bless( {
>>>>>>>>>                 'primary_id' =>  'seq1',
>>>>>>>>>                 'primary_seq' =>  bless( {
>>>>>>>>>                                           'display_id' =>  'seq1',
>>>>>>>>>                                           'primary_id' =>  'seq1',
>>>>>>>>>                                           'desc' =>  'a small test sequence',
>>>>>>>>>                                           'seq' =>  'ACGTACGACTACGACTAGCGCCATCAGC',
>>>>>>>>>                                           'alphabet' =>  'dna'
>>>>>>>>>                                         }, 'Bio::PrimarySeq' )
>>>>>>>>>               }, 'Bio::Seq' ); 
>>>>>>>> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I really only need the Bio::PrimarySeq. Looking at the documentation for Bio::SeqIO I found that I could in theory adjust the sequence factory and sequence builder to my liking... I tried this:
>>>>>>>>> use warnings;
>>>>>>>>> use strict;
>>>>>>>>> use Data::Dumper;
>>>>>>>>> use Bio::SeqIO;
>>>>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>>>>> my $seqfactory = $in->sequence_factory; # Bio::Factory::ObjectBuilderI
>>>>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>>>>> my $seq = $in->next_seq;
>>>>>>>>> print Dumper($seq);
>>>>>>>>> __END__
>>>>>>>>>> seq1 a small test sequence 
>>>>>>>>> ACGTACGACTACGACTAGCGCCATCAGC 
>>>>>>>> This returns:
>>>>>>>>> The factory is a Bio::Seq::SeqFastaSpeedFactory
>>>>>>>>> Can't locate object method "type" via package "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl line 12,<DATA>  line 1. 
>>>>>>>> According to Bio::Seq::FastaSpeedFactory's documentation:
>>>>>>>>> If you want the factory to create Bio::Seq objects instead
>>>>>>>>> of the default Bio::PrimarySeq objects, use the -type parameter 
>>>>>>>> So, PrimarySeq should be the default type, even though in my case it seems not to be. Second, I can't seem to use the -type method to change what the return type is... It errors.
>>>>>>>> 
>>>>>>>> Any ideas??? Thanks,
>>>>>>>> 
>>>>>>>> Florent
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From sclantw at hotmail.com  Wed Feb 17 21:10:32 2010
From: sclantw at hotmail.com (teetee)
Date: Wed, 17 Feb 2010 18:10:32 -0800 (PST)
Subject: [Bioperl-l] primer candidates validation by comparing the wgs blast
 results between fwd and rev.
Message-ID: <27633496.post@talk.nabble.com>


I am totally new to bioperl.

I would like to see if anyone could give me a hint or clue for tackling this
problem I am trying to solve:
Use bioperl/perl script and CGI to create a primer quality control web
interface

the steps I would like to be automated:
I design many primer pairs (~500+) flanking intron regions of silkworm wgs
sequences close to cDNA/mRNA/EST/molecular anchor loci selected. After the
primers are generated (I wish this step could be automated but it really
can't), I have to blast each and every of them against the wgs database of
the same organism to make sure there is no common hits in terms of the same
contig number result between the forward and the reverse primers blastn hits
to avoid the non-target amplification except for the target intron region.
The steps I take to validate the primers are as follows:
1. At NCBI blastn webpage, put in the forward primer sequence in the search
field, label it ("job title"), choose the wgs database and the organism, and
click "submit" to start search.
2. Open another browser tab and go to NCBI blastn webpage, put in the
reverse primer sequence in the search field, label it ("job title"), choose
the wgs database and the organism, and click "submit" to start search.
3. On the forward primer blastn result page, write down the top 20 wgs
sequence that was from build 2 genomic sequencing project (the title of each
hit has a text string with certain format like
"Bm_scaf<number>_contig<number>"). 
4. On the reverse primer blastn result page, write down the top 20 wgs
sequence that was from build 2 genomic sequencing project (the title of each
hit has a text string with certain format like
"Bm_scaf<number>_contig<number>"). 
5. compare the recorded blast hits from step 3 and step 4 and list the
common hit(s) between the two primer sequences (with the same scaffold and
contig number)
6. show a warning if there is more than one common hit since there should be
only one target hit.

Example:
I have these two primer sequences:
GCATCGGTGAACGAGCTA
CGCCTGCAAACGAGAATA

First I blast each of the above primer sequences against wgs database bombyx
mori (organismid:7091) on blast website
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome
After I get the results in two different browser tabs, I record down the
results. For example, from the forward primer result page(only the first
several hits are listed):
=================== first few hits from forward primer blast result
==================
BABH01015134.1
Bombyx mori DNA, contig: Bm_scaf21_contig15134,
strain: p50T/Dazao, build 2, whole genome shotgun
sequence
34.2 34.2 94% 0.12 100%

BABH01038273.1
Bombyx mori DNA, contig: Bm_scaf121_contig38273,
strain: p50T/Dazao, build 2, whole genome shotgun
sequence
34.2 34.2 94% 0.12 100%

AADK01021213.1
Bombyx mori strain Dazao Ctg021213, whole genome
shotgun sequence
34.2 34.2 94% 0.12 100%

BAAB01106839.1
Bombyx mori DNA, contig477862, whole genome shotgun
sequence
34.2 34.2 94% 0.12 100%

BAAB01154920.1
Bombyx mori DNA, contig585939, whole genome shotgun
sequence
34.2 34.2 94% 0.12 100%

BABH01007204.1
Bombyx mori DNA, contig: Bm_scaf8_contig7204,
strain: p50T/Dazao, build 2, whole genome shotgun
sequence
32.2 32.2 88% 0.48 100%

BABH01020379.1
Bombyx mori DNA, contig: Bm_scaf33_contig20379,
strain: p50T/Dazao, build 2, whole genome shotgun
sequence
32.2 32.2 88% 0.48 100%
================================ end of the forward blast result
================================ first few hits from reverse primer blast
result ==================
BABH01015134.1
Bombyx mori DNA, contig:
Bm_scaf21_contig15134, strain: p50T/Dazao,
build 2, whole genome shotgun sequence
36.2 36.2 100% 0.031 100%

AADK01021213.1
Bombyx mori strain Dazao Ctg021213, whole
genome shotgun sequence
36.2 36.2 100% 0.031 100%

AADK01032592.1
Bombyx mori strain Dazao Ctg032592, whole
genome shotgun sequence
36.2 36.2 100% 0.031 100%

BAAB01106839.1
Bombyx mori DNA, contig477862, whole genome
shotgun sequence
36.2 36.2 100% 0.031 100%

BABH01028024.1
Bombyx mori DNA, contig:
Bm_scaf56_contig28024, strain: p50T/Dazao,
build 2, whole genome shotgun sequence
30.2 30.2 83% 1.9 100%

AADK01039561.1
Bombyx mori strain Dazao Ctg039561, whole
genome shotgun sequence
30.2 30.2 83% 1.9 100%

AADK01056852.1
Bombyx mori strain Dazao Ctg063892, whole
genome shotgun sequence
30.2 30.2 83% 1.9 100%

BABH01001710.1
Bombyx mori DNA, contig: Bm_scaf2_contig1710,
strain: p50T/Dazao, build 2, whole genome
shotgun sequence
===============================end of the reverse result

>From the list, I would record down the ones with "Bm_scaf#_contig#"(ex.
Bm_scaf21_contig15134) since that's the string pattern I would like to
compare with the hits from reverse primer blast results.
After I record down the first 20 qualified blast hits(hopefully with blast
paser program I can use more than 20), I compare them with the ones from the
reverse primer search result and see if there is any common result other
than the target.

I am OK to go through this validation process manually if there are only
tens of primers I have to design. However with 500 and maybe more primers to
come I believe there is an easier way.


I imagine the code will have the following functions:
input: user's primer pairs, multiple entry capatability
output: compare the blastn results between both fwd and reverse primer and
generate a list of common blastn hits (w/ same scaf# and contig# from build
2 wgs sequences - naming convention: Bm_scaf#_contig#) on the wgs (accept
the blast search parameters through the web and pass to the blast command)
background record-keeping mechanism: create records of the blast report for
each primer vs wgs blastn results and properly name the files.

I guess my question is:
What would be the most stright-forward approach? (I know you probably think
I already know the method since I post the question here, but more
suggestions the better) and where should I start?

My background: 
1. I've written codes for retrieving PDB file upon user's PDB 4-letter
protein ID entry and atom-atom distance measurement with the same setup(perl
script+web CGI interface)
2. I've used command-line megablast to batch blast multiple sequences
however my impression is that it's not intend to do short sequence
blast(primers are usually around 20-24bp long).
ref.:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
3. I can modify simple perl codes and do some text string menupilation in
perl
4. I have my own linux box and have apache/perl/bioperl/cgi ready.

-- 
View this message in context: http://old.nabble.com/primer-candidates-validation-by-comparing-the-wgs-blast-results-between-fwd-and-rev.-tp27633496p27633496.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From hlapp at drycafe.net  Wed Feb 17 22:48:00 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 17 Feb 2010 22:48:00 -0500
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <4B7C7A50.3000505@bioperl.org>
References: <4B79C716.90405@gmail.com> <4B79E0D8.3060806@bioperl.org>
	<4B7A38A8.80702@gmail.com> <4B7ACE6A.3000402@bioperl.org>
	<AF001D8E-3B3C-4405-9D31-E0BE358C9559@illinois.edu>
	<4B7AFD97.5050003@bioperl.org> <4B7C2CC0.1060108@cornell.edu>
	<4B7C7A50.3000505@bioperl.org>
Message-ID: <4ADC962A-3118-40EE-B117-7D02E095579E@drycafe.net>

Thanks Jason - your help is hugely appreciated.

-hilmar

Sent from away

On Feb 17, 2010, at 6:22 PM, Jason Stajich <jason at bioperl.org> wrote:

> I rolled back.
> The fix seems to just be to make the default Bio::Seq not  
> Bio::PrimarySeq in terms of what the factory return and undo some of  
> the explicit expectations in the code.  I think this speedup is a  
> special case and Bio::Seq still needs to be the default but you  
> override it when you want Bio::PrimarySeq objects only.
>
> Florent for your purposes you need to just set the type in your  
> scripts.
>
> And in the future - you must run tests before committing something,  
> especially one that touches so many files!
>
> I think I've unrolled most of the defaults while keeping the new  
> type method intact.
>
> There are still warnings and few failed tests to followup.
>
> Okay - I am really now in favor of breaking the modules into  
> packages test running taking forever and this is way unwieldy. I am  
> looking forward to seeing things in smaller pieces somehow.
>
> -jason
> Robert Buels wrote:
>> OK, well are you guys going to roll them back and do a branch?   
>> Broken trunk is not good.
>>
>> R
>>
>> Jason Stajich wrote:
>>> hmm yes. Let's roll back those Florent.
>>>
>>> I guess we need to also discuss the concept of branches again here  
>>> for major changes like this. The speed fix is helpful for short  
>>> read but probably not for all systems so just having the ability  
>>> to provide the right type when you use your scripts focused on  
>>> short-reads might be the best way to go forward and preserve  
>>> backwards compatibility.
>>>
>>> -jason
>>>
>>> Chris Fields wrote:
>>>> Yes, except that tests are now failing on live.  Bio::PrimarySeq  
>>>> isn't a Bio::SeqI, so it's a bit of an API change in a lot of  
>>>> places expecting a Bio::SeqI.  We should make this optional for  
>>>> the time being, until we discuss it more on list.
>>>>
>>>> chris
>>>>
>>>> On Feb 16, 2010, at 10:57 AM, Jason Stajich wrote:
>>>>
>>>>> Great!  thanks for committing it.
>>>>>
>>>>> Florent Angly wrote:
>>>>>> Thanks for your reply Jason. It's very valuable since you coded  
>>>>>> the modules in question!
>>>>>>
>>>>>> Now that I understand the purpose of these modules, I did a  
>>>>>> little bit of documentation clarification. I also figured out  
>>>>>> that I should implement the 'type' method in  
>>>>>> Bio::Seq::SeqFastaSpeedFactory and made it support creating  
>>>>>> Bio::PrimarySeq. This is all committed to SVN.
>>>>>>
>>>>>> When sequences are large, you are right that it does not make  
>>>>>> much difference in time or memory resource to use one sequence  
>>>>>> type over the other. However, that's different for short  
>>>>>> sequences. I took a FASTA file weighting 39.3 MB and containing  
>>>>>> 360,000 sequences of 106 bp on average.
>>>>>>
>>>>>> CASE 1:
>>>>>>  Requested factory Bio::Seq::SeqFactory
>>>>>>  Requested sequence type is Bio::Seq
>>>>>>  Memory used: 329 MB
>>>>>>  Time spent: 1m8.522s
>>>>>>
>>>>>> CASE 2:
>>>>>>  Requested factory Bio::Seq::SeqFactory
>>>>>>  Requested sequence type is Bio::PrimarySeq
>>>>>>  Memory used: 246 MB
>>>>>>  Time spent: 0m52.663s
>>>>>>
>>>>>> CASE 3:
>>>>>>  Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>>>>  Requested sequence type is Bio::Seq
>>>>>>  Memory used: 298 MB
>>>>>>  Time spent: 0m31.292s
>>>>>>
>>>>>> CASE 4:
>>>>>>  Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>>>>  Requested sequence type is Bio::PrimarySeq
>>>>>>  Memory used: 231 MB
>>>>>>  Time spent: 0m28.500s
>>>>>>
>>>>>> Clearly, when only simple sequence attributes are needed or  
>>>>>> FASTA files are used, it's fast and memory efficient to use the  
>>>>>> SeqFastaSpeedFactory with PrimarySeq.
>>>>>>
>>>>>> Florent
>>>>>>
>>>>>>
>>>>>> On 16/02/10 10:03, Jason Stajich wrote:
>>>>>>> I don't think that aspect of the documentation vs interface  
>>>>>>> was ever implemented - the interface object doesn't specify a  
>>>>>>> type method or init argument even though the documentation  
>>>>>>> says so. Not really sure why not, this was ages ago  
>>>>>>> unfortunately.
>>>>>>>
>>>>>>> This particular factory definitely assumes you are building  
>>>>>>> Bio::Seq objects - you can try and subclass and build your own  
>>>>>>> to see if it makes much of a difference in speed/memory - I  
>>>>>>> would posit it won't make a significant difference but be  
>>>>>>> interested to see what you find.
>>>>>>>
>>>>>>> Just make your own Bio::Seq::PrimarySeqFactory object based on  
>>>>>>> Bio::Seq::FastaSpeedFactory and simplify that code so it  
>>>>>>> doesn't build Bio::Seq object wrapper around the  
>>>>>>> Bio::PrimarySeq and do some perf tests so we'll know if it  
>>>>>>> makes any difference here.
>>>>>>>
>>>>>>> -jason
>>>>>>> Florent Angly wrote:
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I am trying to reduce memory usage and speedup reading FASTA  
>>>>>>>> files using the facilities provided by BioPerl.
>>>>>>>>
>>>>>>>> The first thing I noticed is that when using  
>>>>>>>> Bio::SeqIO::fasta, the objects returned are Bio::Seq, not  
>>>>>>>> Bio::PrimarySeq objects. Bio::PrimarySeq sequences are  
>>>>>>>> lighter than Bio::Seq sequences, so it's what I need. See  
>>>>>>>> code below:
>>>>>>>>> use warnings;
>>>>>>>>> use strict;
>>>>>>>>> use Data::Dumper;
>>>>>>>>> use Bio::SeqIO;
>>>>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>>>>> my $seqfactory = $in->sequence_factory; #  
>>>>>>>>> Bio::Factory::ObjectBuilderI
>>>>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>>>>> my $seq = $in->next_seq;
>>>>>>>>> print Dumper($seq);
>>>>>>>>> __END__
>>>>>>>>>> seq1 a small test sequence q
>>>>>>>>> ACGTACGACTACGACTAGCGCCATCAGC
>>>>>>>> It returns:
>>>>>>>>> $VAR1 = bless( {
>>>>>>>>>                 'primary_id' =>  'seq1',
>>>>>>>>>                 'primary_seq' =>  bless( {
>>>>>>>>>                                           'display_id' =>   
>>>>>>>>> 'seq1',
>>>>>>>>>                                           'primary_id' =>   
>>>>>>>>> 'seq1',
>>>>>>>>>                                           'desc' =>  'a  
>>>>>>>>> small test sequence',
>>>>>>>>>                                           'seq' =>   
>>>>>>>>> 'ACGTACGACTACGACTAGCGCCATCAGC',
>>>>>>>>>                                           'alphabet' =>  'dna'
>>>>>>>>>                                         }, 'Bio::PrimarySeq' )
>>>>>>>>>               }, 'Bio::Seq' );
>>>>>>>> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I  
>>>>>>>> really only need the Bio::PrimarySeq. Looking at the  
>>>>>>>> documentation for Bio::SeqIO I found that I could in theory  
>>>>>>>> adjust the sequence factory and sequence builder to my  
>>>>>>>> liking... I tried this:
>>>>>>>>> use warnings;
>>>>>>>>> use strict;
>>>>>>>>> use Data::Dumper;
>>>>>>>>> use Bio::SeqIO;
>>>>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>>>>> my $seqfactory = $in->sequence_factory; #  
>>>>>>>>> Bio::Factory::ObjectBuilderI
>>>>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>>>>> my $seq = $in->next_seq;
>>>>>>>>> print Dumper($seq);
>>>>>>>>> __END__
>>>>>>>>>> seq1 a small test sequence
>>>>>>>>> ACGTACGACTACGACTAGCGCCATCAGC
>>>>>>>> This returns:
>>>>>>>>> The factory is a Bio::Seq::SeqFastaSpeedFactory
>>>>>>>>> Can't locate object method "type" via package  
>>>>>>>>> "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl  
>>>>>>>>> line 12,<DATA>  line 1.
>>>>>>>> According to Bio::Seq::FastaSpeedFactory's documentation:
>>>>>>>>> If you want the factory to create Bio::Seq objects instead
>>>>>>>>> of the default Bio::PrimarySeq objects, use the -type  
>>>>>>>>> parameter
>>>>>>>> So, PrimarySeq should be the default type, even though in my  
>>>>>>>> case it seems not to be. Second, I can't seem to use the - 
>>>>>>>> type method to change what the return type is... It errors.
>>>>>>>>
>>>>>>>> Any ideas??? Thanks,
>>>>>>>>
>>>>>>>> Florent
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From florent.angly at gmail.com  Thu Feb 18 00:23:47 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Thu, 18 Feb 2010 15:23:47 +1000
Subject: [Bioperl-l] Parsing FASTA files into PrimarySeq objects
In-Reply-To: <4ADC962A-3118-40EE-B117-7D02E095579E@drycafe.net>
References: <4B79C716.90405@gmail.com> <4B79E0D8.3060806@bioperl.org>
	<4B7A38A8.80702@gmail.com> <4B7ACE6A.3000402@bioperl.org>
	<AF001D8E-3B3C-4405-9D31-E0BE358C9559@illinois.edu>
	<4B7AFD97.5050003@bioperl.org> <4B7C2CC0.1060108@cornell.edu>
	<4B7C7A50.3000505@bioperl.org>
	<4ADC962A-3118-40EE-B117-7D02E095579E@drycafe.net>
Message-ID: <4B7CCEE3.90206@gmail.com>

Sorry guys, I was out of internet range until now.
My intentions were not to break backward compatibility in my own 
interest. I did run the tests that were directly relevant to my change. 
My bad for not running _all_ BioPerl tests. I obviously underestimated 
the scope of my changes and I should have run all tests...

Florent

PS/ Thank god there is SVN  -_-'


On 18/02/10 13:48, Hilmar Lapp wrote:
> Thanks Jason - your help is hugely appreciated.
>
> -hilmar
>
> Sent from away
>
> On Feb 17, 2010, at 6:22 PM, Jason Stajich <jason at bioperl.org> wrote:
>
>> I rolled back.
>> The fix seems to just be to make the default Bio::Seq not 
>> Bio::PrimarySeq in terms of what the factory return and undo some of 
>> the explicit expectations in the code.  I think this speedup is a 
>> special case and Bio::Seq still needs to be the default but you 
>> override it when you want Bio::PrimarySeq objects only.
>>
>> Florent for your purposes you need to just set the type in your scripts.
>>
>> And in the future - you must run tests before committing something, 
>> especially one that touches so many files!
>>
>> I think I've unrolled most of the defaults while keeping the new type 
>> method intact.
>>
>> There are still warnings and few failed tests to followup.
>>
>> Okay - I am really now in favor of breaking the modules into packages 
>> test running taking forever and this is way unwieldy. I am looking 
>> forward to seeing things in smaller pieces somehow.
>>
>> -jason
>> Robert Buels wrote:
>>> OK, well are you guys going to roll them back and do a branch?  
>>> Broken trunk is not good.
>>>
>>> R
>>>
>>> Jason Stajich wrote:
>>>> hmm yes. Let's roll back those Florent.
>>>>
>>>> I guess we need to also discuss the concept of branches again here 
>>>> for major changes like this. The speed fix is helpful for short 
>>>> read but probably not for all systems so just having the ability to 
>>>> provide the right type when you use your scripts focused on 
>>>> short-reads might be the best way to go forward and preserve 
>>>> backwards compatibility.
>>>>
>>>> -jason
>>>>
>>>> Chris Fields wrote:
>>>>> Yes, except that tests are now failing on live.  Bio::PrimarySeq 
>>>>> isn't a Bio::SeqI, so it's a bit of an API change in a lot of 
>>>>> places expecting a Bio::SeqI.  We should make this optional for 
>>>>> the time being, until we discuss it more on list.
>>>>>
>>>>> chris
>>>>>
>>>>> On Feb 16, 2010, at 10:57 AM, Jason Stajich wrote:
>>>>>
>>>>>> Great!  thanks for committing it.
>>>>>>
>>>>>> Florent Angly wrote:
>>>>>>> Thanks for your reply Jason. It's very valuable since you coded 
>>>>>>> the modules in question!
>>>>>>>
>>>>>>> Now that I understand the purpose of these modules, I did a 
>>>>>>> little bit of documentation clarification. I also figured out 
>>>>>>> that I should implement the 'type' method in 
>>>>>>> Bio::Seq::SeqFastaSpeedFactory and made it support creating 
>>>>>>> Bio::PrimarySeq. This is all committed to SVN.
>>>>>>>
>>>>>>> When sequences are large, you are right that it does not make 
>>>>>>> much difference in time or memory resource to use one sequence 
>>>>>>> type over the other. However, that's different for short 
>>>>>>> sequences. I took a FASTA file weighting 39.3 MB and containing 
>>>>>>> 360,000 sequences of 106 bp on average.
>>>>>>>
>>>>>>> CASE 1:
>>>>>>>  Requested factory Bio::Seq::SeqFactory
>>>>>>>  Requested sequence type is Bio::Seq
>>>>>>>  Memory used: 329 MB
>>>>>>>  Time spent: 1m8.522s
>>>>>>>
>>>>>>> CASE 2:
>>>>>>>  Requested factory Bio::Seq::SeqFactory
>>>>>>>  Requested sequence type is Bio::PrimarySeq
>>>>>>>  Memory used: 246 MB
>>>>>>>  Time spent: 0m52.663s
>>>>>>>
>>>>>>> CASE 3:
>>>>>>>  Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>>>>>  Requested sequence type is Bio::Seq
>>>>>>>  Memory used: 298 MB
>>>>>>>  Time spent: 0m31.292s
>>>>>>>
>>>>>>> CASE 4:
>>>>>>>  Requested factory Bio::Seq::SeqFastaSpeedFactory
>>>>>>>  Requested sequence type is Bio::PrimarySeq
>>>>>>>  Memory used: 231 MB
>>>>>>>  Time spent: 0m28.500s
>>>>>>>
>>>>>>> Clearly, when only simple sequence attributes are needed or 
>>>>>>> FASTA files are used, it's fast and memory efficient to use the 
>>>>>>> SeqFastaSpeedFactory with PrimarySeq.
>>>>>>>
>>>>>>> Florent
>>>>>>>
>>>>>>>
>>>>>>> On 16/02/10 10:03, Jason Stajich wrote:
>>>>>>>> I don't think that aspect of the documentation vs interface was 
>>>>>>>> ever implemented - the interface object doesn't specify a type 
>>>>>>>> method or init argument even though the documentation says so. 
>>>>>>>> Not really sure why not, this was ages ago unfortunately.
>>>>>>>>
>>>>>>>> This particular factory definitely assumes you are building 
>>>>>>>> Bio::Seq objects - you can try and subclass and build your own 
>>>>>>>> to see if it makes much of a difference in speed/memory - I 
>>>>>>>> would posit it won't make a significant difference but be 
>>>>>>>> interested to see what you find.
>>>>>>>>
>>>>>>>> Just make your own Bio::Seq::PrimarySeqFactory object based on 
>>>>>>>> Bio::Seq::FastaSpeedFactory and simplify that code so it 
>>>>>>>> doesn't build Bio::Seq object wrapper around the 
>>>>>>>> Bio::PrimarySeq and do some perf tests so we'll know if it 
>>>>>>>> makes any difference here.
>>>>>>>>
>>>>>>>> -jason
>>>>>>>> Florent Angly wrote:
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> I am trying to reduce memory usage and speedup reading FASTA 
>>>>>>>>> files using the facilities provided by BioPerl.
>>>>>>>>>
>>>>>>>>> The first thing I noticed is that when using 
>>>>>>>>> Bio::SeqIO::fasta, the objects returned are Bio::Seq, not 
>>>>>>>>> Bio::PrimarySeq objects. Bio::PrimarySeq sequences are lighter 
>>>>>>>>> than Bio::Seq sequences, so it's what I need. See code below:
>>>>>>>>>> use warnings;
>>>>>>>>>> use strict;
>>>>>>>>>> use Data::Dumper;
>>>>>>>>>> use Bio::SeqIO;
>>>>>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>>>>>> my $seqfactory = $in->sequence_factory; # 
>>>>>>>>>> Bio::Factory::ObjectBuilderI
>>>>>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>>>>>> my $seq = $in->next_seq;
>>>>>>>>>> print Dumper($seq);
>>>>>>>>>> __END__
>>>>>>>>>>> seq1 a small test sequence q
>>>>>>>>>> ACGTACGACTACGACTAGCGCCATCAGC
>>>>>>>>> It returns:
>>>>>>>>>> $VAR1 = bless( {
>>>>>>>>>>                 'primary_id' =>  'seq1',
>>>>>>>>>>                 'primary_seq' =>  bless( {
>>>>>>>>>>                                           'display_id' =>  
>>>>>>>>>> 'seq1',
>>>>>>>>>>                                           'primary_id' =>  
>>>>>>>>>> 'seq1',
>>>>>>>>>>                                           'desc' =>  'a small 
>>>>>>>>>> test sequence',
>>>>>>>>>>                                           'seq' =>  
>>>>>>>>>> 'ACGTACGACTACGACTAGCGCCATCAGC',
>>>>>>>>>>                                           'alphabet' =>  'dna'
>>>>>>>>>>                                         }, 'Bio::PrimarySeq' )
>>>>>>>>>>               }, 'Bio::Seq' );
>>>>>>>>> Actually, we have a Bio::Seq containing a Bio::PrimarySeq. I 
>>>>>>>>> really only need the Bio::PrimarySeq. Looking at the 
>>>>>>>>> documentation for Bio::SeqIO I found that I could in theory 
>>>>>>>>> adjust the sequence factory and sequence builder to my 
>>>>>>>>> liking... I tried this:
>>>>>>>>>> use warnings;
>>>>>>>>>> use strict;
>>>>>>>>>> use Data::Dumper;
>>>>>>>>>> use Bio::SeqIO;
>>>>>>>>>> my $in = Bio::SeqIO->new(-fh=>\*DATA);
>>>>>>>>>> my $seqfactory = $in->sequence_factory; # 
>>>>>>>>>> Bio::Factory::ObjectBuilderI
>>>>>>>>>> print "The factory is a ".ref($seqfactory)."\n";
>>>>>>>>>> $seqfactory->type('Bio::PrimarySeq'); # gives an error
>>>>>>>>>> my $seq = $in->next_seq;
>>>>>>>>>> print Dumper($seq);
>>>>>>>>>> __END__
>>>>>>>>>>> seq1 a small test sequence
>>>>>>>>>> ACGTACGACTACGACTAGCGCCATCAGC
>>>>>>>>> This returns:
>>>>>>>>>> The factory is a Bio::Seq::SeqFastaSpeedFactory
>>>>>>>>>> Can't locate object method "type" via package 
>>>>>>>>>> "Bio::Seq::SeqFastaSpeedFactory" at ./seqbuilder_test_3.pl 
>>>>>>>>>> line 12,<DATA>  line 1.
>>>>>>>>> According to Bio::Seq::FastaSpeedFactory's documentation:
>>>>>>>>>> If you want the factory to create Bio::Seq objects instead
>>>>>>>>>> of the default Bio::PrimarySeq objects, use the -type parameter
>>>>>>>>> So, PrimarySeq should be the default type, even though in my 
>>>>>>>>> case it seems not to be. Second, I can't seem to use the -type 
>>>>>>>>> method to change what the return type is... It errors.
>>>>>>>>>
>>>>>>>>> Any ideas??? Thanks,
>>>>>>>>>
>>>>>>>>> Florent
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioperl-l mailing list
>>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From j.scholtalbers at gmail.com  Thu Feb 18 01:55:43 2010
From: j.scholtalbers at gmail.com (Jelle Scholtalbers)
Date: Thu, 18 Feb 2010 07:55:43 +0100
Subject: [Bioperl-l] primer candidates validation by comparing the wgs
	blast results between fwd and rev.
In-Reply-To: <27633496.post@talk.nabble.com>
References: <27633496.post@talk.nabble.com>
Message-ID: <b66932c31002172255j3663299bn16426b46eb90096c@mail.gmail.com>

Think you are best of by starting with:
http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast
and
http://www.bioperl.org/wiki/FAQ#I_want_to_parse_BLAST.2C_how_do_I_do_this.3F

Cheers,
Jelle

2010/2/18 teetee <sclantw at hotmail.com>

>
> I am totally new to bioperl.
>
> I would like to see if anyone could give me a hint or clue for tackling
> this
> problem I am trying to solve:
> Use bioperl/perl script and CGI to create a primer quality control web
> interface
>
> the steps I would like to be automated:
> I design many primer pairs (~500+) flanking intron regions of silkworm wgs
> sequences close to cDNA/mRNA/EST/molecular anchor loci selected. After the
> primers are generated (I wish this step could be automated but it really
> can't), I have to blast each and every of them against the wgs database of
> the same organism to make sure there is no common hits in terms of the same
> contig number result between the forward and the reverse primers blastn
> hits
> to avoid the non-target amplification except for the target intron region.
> The steps I take to validate the primers are as follows:
> 1. At NCBI blastn webpage, put in the forward primer sequence in the search
> field, label it ("job title"), choose the wgs database and the organism,
> and
> click "submit" to start search.
> 2. Open another browser tab and go to NCBI blastn webpage, put in the
> reverse primer sequence in the search field, label it ("job title"), choose
> the wgs database and the organism, and click "submit" to start search.
> 3. On the forward primer blastn result page, write down the top 20 wgs
> sequence that was from build 2 genomic sequencing project (the title of
> each
> hit has a text string with certain format like
> "Bm_scaf<number>_contig<number>").
> 4. On the reverse primer blastn result page, write down the top 20 wgs
> sequence that was from build 2 genomic sequencing project (the title of
> each
> hit has a text string with certain format like
> "Bm_scaf<number>_contig<number>").
> 5. compare the recorded blast hits from step 3 and step 4 and list the
> common hit(s) between the two primer sequences (with the same scaffold and
> contig number)
> 6. show a warning if there is more than one common hit since there should
> be
> only one target hit.
>
> Example:
> I have these two primer sequences:
> GCATCGGTGAACGAGCTA
> CGCCTGCAAACGAGAATA
>
> First I blast each of the above primer sequences against wgs database
> bombyx
> mori (organismid:7091) on blast website
>
> http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome
> After I get the results in two different browser tabs, I record down the
> results. For example, from the forward primer result page(only the first
> several hits are listed):
> =================== first few hits from forward primer blast result
> ==================
> BABH01015134.1
> Bombyx mori DNA, contig: Bm_scaf21_contig15134,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
>
> BABH01038273.1
> Bombyx mori DNA, contig: Bm_scaf121_contig38273,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
>
> AADK01021213.1
> Bombyx mori strain Dazao Ctg021213, whole genome
> shotgun sequence
> 34.2 34.2 94% 0.12 100%
>
> BAAB01106839.1
> Bombyx mori DNA, contig477862, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
>
> BAAB01154920.1
> Bombyx mori DNA, contig585939, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
>
> BABH01007204.1
> Bombyx mori DNA, contig: Bm_scaf8_contig7204,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 32.2 32.2 88% 0.48 100%
>
> BABH01020379.1
> Bombyx mori DNA, contig: Bm_scaf33_contig20379,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 32.2 32.2 88% 0.48 100%
> ================================ end of the forward blast result
> ================================ first few hits from reverse primer blast
> result ==================
> BABH01015134.1
> Bombyx mori DNA, contig:
> Bm_scaf21_contig15134, strain: p50T/Dazao,
> build 2, whole genome shotgun sequence
> 36.2 36.2 100% 0.031 100%
>
> AADK01021213.1
> Bombyx mori strain Dazao Ctg021213, whole
> genome shotgun sequence
> 36.2 36.2 100% 0.031 100%
>
> AADK01032592.1
> Bombyx mori strain Dazao Ctg032592, whole
> genome shotgun sequence
> 36.2 36.2 100% 0.031 100%
>
> BAAB01106839.1
> Bombyx mori DNA, contig477862, whole genome
> shotgun sequence
> 36.2 36.2 100% 0.031 100%
>
> BABH01028024.1
> Bombyx mori DNA, contig:
> Bm_scaf56_contig28024, strain: p50T/Dazao,
> build 2, whole genome shotgun sequence
> 30.2 30.2 83% 1.9 100%
>
> AADK01039561.1
> Bombyx mori strain Dazao Ctg039561, whole
> genome shotgun sequence
> 30.2 30.2 83% 1.9 100%
>
> AADK01056852.1
> Bombyx mori strain Dazao Ctg063892, whole
> genome shotgun sequence
> 30.2 30.2 83% 1.9 100%
>
> BABH01001710.1
> Bombyx mori DNA, contig: Bm_scaf2_contig1710,
> strain: p50T/Dazao, build 2, whole genome
> shotgun sequence
> ===============================end of the reverse result
>
> >From the list, I would record down the ones with "Bm_scaf#_contig#"(ex.
> Bm_scaf21_contig15134) since that's the string pattern I would like to
> compare with the hits from reverse primer blast results.
> After I record down the first 20 qualified blast hits(hopefully with blast
> paser program I can use more than 20), I compare them with the ones from
> the
> reverse primer search result and see if there is any common result other
> than the target.
>
> I am OK to go through this validation process manually if there are only
> tens of primers I have to design. However with 500 and maybe more primers
> to
> come I believe there is an easier way.
>
>
> I imagine the code will have the following functions:
> input: user's primer pairs, multiple entry capatability
> output: compare the blastn results between both fwd and reverse primer and
> generate a list of common blastn hits (w/ same scaf# and contig# from build
> 2 wgs sequences - naming convention: Bm_scaf#_contig#) on the wgs (accept
> the blast search parameters through the web and pass to the blast command)
> background record-keeping mechanism: create records of the blast report for
> each primer vs wgs blastn results and properly name the files.
>
> I guess my question is:
> What would be the most stright-forward approach? (I know you probably think
> I already know the method since I post the question here, but more
> suggestions the better) and where should I start?
>
> My background:
> 1. I've written codes for retrieving PDB file upon user's PDB 4-letter
> protein ID entry and atom-atom distance measurement with the same
> setup(perl
> script+web CGI interface)
> 2. I've used command-line megablast to batch blast multiple sequences
> however my impression is that it's not intend to do short sequence
> blast(primers are usually around 20-24bp long).
> ref.:
>
> http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
> 3. I can modify simple perl codes and do some text string menupilation in
> perl
> 4. I have my own linux box and have apache/perl/bioperl/cgi ready.
>
> --
> View this message in context:
> http://old.nabble.com/primer-candidates-validation-by-comparing-the-wgs-blast-results-between-fwd-and-rev.-tp27633496p27633496.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From sdavis2 at mail.nih.gov  Thu Feb 18 06:49:14 2010
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Thu, 18 Feb 2010 06:49:14 -0500
Subject: [Bioperl-l] primer candidates validation by comparing the wgs
	blast results between fwd and rev.
In-Reply-To: <27633496.post@talk.nabble.com>
References: <AcqwRwrbiahQGzlNRwKlo3g9A6+ceQ==> <27633496.post@talk.nabble.com>
Message-ID: <264855a01002180349w127d5d53mf1eb236d4be02240@mail.gmail.com>

For the problem that you describe below, you might consider primer3
(or eprimer3) for the design of the primer sets, if that part is still
in question.  As for the aligning back to the genome, you might
consider using a flavor of in silico pcr (isPcr).  There are bioperl
tools for working with isPcr, but you could also run it as a
standalone.

Sean

On Wed, Feb 17, 2010 at 9:10 PM, teetee <sclantw at hotmail.com> wrote:
>
> I am totally new to bioperl.
>
> I would like to see if anyone could give me a hint or clue for tackling this
> problem I am trying to solve:
> Use bioperl/perl script and CGI to create a primer quality control web
> interface
>
> the steps I would like to be automated:
> I design many primer pairs (~500+) flanking intron regions of silkworm wgs
> sequences close to cDNA/mRNA/EST/molecular anchor loci selected. After the
> primers are generated (I wish this step could be automated but it really
> can't), I have to blast each and every of them against the wgs database of
> the same organism to make sure there is no common hits in terms of the same
> contig number result between the forward and the reverse primers blastn hits
> to avoid the non-target amplification except for the target intron region.
> The steps I take to validate the primers are as follows:
> 1. At NCBI blastn webpage, put in the forward primer sequence in the search
> field, label it ("job title"), choose the wgs database and the organism, and
> click "submit" to start search.
> 2. Open another browser tab and go to NCBI blastn webpage, put in the
> reverse primer sequence in the search field, label it ("job title"), choose
> the wgs database and the organism, and click "submit" to start search.
> 3. On the forward primer blastn result page, write down the top 20 wgs
> sequence that was from build 2 genomic sequencing project (the title of each
> hit has a text string with certain format like
> "Bm_scaf<number>_contig<number>").
> 4. On the reverse primer blastn result page, write down the top 20 wgs
> sequence that was from build 2 genomic sequencing project (the title of each
> hit has a text string with certain format like
> "Bm_scaf<number>_contig<number>").
> 5. compare the recorded blast hits from step 3 and step 4 and list the
> common hit(s) between the two primer sequences (with the same scaffold and
> contig number)
> 6. show a warning if there is more than one common hit since there should be
> only one target hit.
>
> Example:
> I have these two primer sequences:
> GCATCGGTGAACGAGCTA
> CGCCTGCAAACGAGAATA
>
> First I blast each of the above primer sequences against wgs database bombyx
> mori (organismid:7091) on blast website
> http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome
> After I get the results in two different browser tabs, I record down the
> results. For example, from the forward primer result page(only the first
> several hits are listed):
> =================== first few hits from forward primer blast result
> ==================
> BABH01015134.1
> Bombyx mori DNA, contig: Bm_scaf21_contig15134,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
>
> BABH01038273.1
> Bombyx mori DNA, contig: Bm_scaf121_contig38273,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
>
> AADK01021213.1
> Bombyx mori strain Dazao Ctg021213, whole genome
> shotgun sequence
> 34.2 34.2 94% 0.12 100%
>
> BAAB01106839.1
> Bombyx mori DNA, contig477862, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
>
> BAAB01154920.1
> Bombyx mori DNA, contig585939, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
>
> BABH01007204.1
> Bombyx mori DNA, contig: Bm_scaf8_contig7204,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 32.2 32.2 88% 0.48 100%
>
> BABH01020379.1
> Bombyx mori DNA, contig: Bm_scaf33_contig20379,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 32.2 32.2 88% 0.48 100%
> ================================ end of the forward blast result
> ================================ first few hits from reverse primer blast
> result ==================
> BABH01015134.1
> Bombyx mori DNA, contig:
> Bm_scaf21_contig15134, strain: p50T/Dazao,
> build 2, whole genome shotgun sequence
> 36.2 36.2 100% 0.031 100%
>
> AADK01021213.1
> Bombyx mori strain Dazao Ctg021213, whole
> genome shotgun sequence
> 36.2 36.2 100% 0.031 100%
>
> AADK01032592.1
> Bombyx mori strain Dazao Ctg032592, whole
> genome shotgun sequence
> 36.2 36.2 100% 0.031 100%
>
> BAAB01106839.1
> Bombyx mori DNA, contig477862, whole genome
> shotgun sequence
> 36.2 36.2 100% 0.031 100%
>
> BABH01028024.1
> Bombyx mori DNA, contig:
> Bm_scaf56_contig28024, strain: p50T/Dazao,
> build 2, whole genome shotgun sequence
> 30.2 30.2 83% 1.9 100%
>
> AADK01039561.1
> Bombyx mori strain Dazao Ctg039561, whole
> genome shotgun sequence
> 30.2 30.2 83% 1.9 100%
>
> AADK01056852.1
> Bombyx mori strain Dazao Ctg063892, whole
> genome shotgun sequence
> 30.2 30.2 83% 1.9 100%
>
> BABH01001710.1
> Bombyx mori DNA, contig: Bm_scaf2_contig1710,
> strain: p50T/Dazao, build 2, whole genome
> shotgun sequence
> ===============================end of the reverse result
>
> >From the list, I would record down the ones with "Bm_scaf#_contig#"(ex.
> Bm_scaf21_contig15134) since that's the string pattern I would like to
> compare with the hits from reverse primer blast results.
> After I record down the first 20 qualified blast hits(hopefully with blast
> paser program I can use more than 20), I compare them with the ones from the
> reverse primer search result and see if there is any common result other
> than the target.
>
> I am OK to go through this validation process manually if there are only
> tens of primers I have to design. However with 500 and maybe more primers to
> come I believe there is an easier way.
>
>
> I imagine the code will have the following functions:
> input: user's primer pairs, multiple entry capatability
> output: compare the blastn results between both fwd and reverse primer and
> generate a list of common blastn hits (w/ same scaf# and contig# from build
> 2 wgs sequences - naming convention: Bm_scaf#_contig#) on the wgs (accept
> the blast search parameters through the web and pass to the blast command)
> background record-keeping mechanism: create records of the blast report for
> each primer vs wgs blastn results and properly name the files.
>
> I guess my question is:
> What would be the most stright-forward approach? (I know you probably think
> I already know the method since I post the question here, but more
> suggestions the better) and where should I start?
>
> My background:
> 1. I've written codes for retrieving PDB file upon user's PDB 4-letter
> protein ID entry and atom-atom distance measurement with the same setup(perl
> script+web CGI interface)
> 2. I've used command-line megablast to batch blast multiple sequences
> however my impression is that it's not intend to do short sequence
> blast(primers are usually around 20-24bp long).
> ref.:
> http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
> 3. I can modify simple perl codes and do some text string menupilation in
> perl
> 4. I have my own linux box and have apache/perl/bioperl/cgi ready.
>
> --
> View this message in context: http://old.nabble.com/primer-candidates-validation-by-comparing-the-wgs-blast-results-between-fwd-and-rev.-tp27633496p27633496.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From dan.halligan at gmail.com  Wed Feb 17 17:04:05 2010
From: dan.halligan at gmail.com (Dan)
Date: Wed, 17 Feb 2010 14:04:05 -0800 (PST)
Subject: [Bioperl-l] Merging overlapping Seq Features
Message-ID: <3091e51a-615f-4893-8dfd-8a3d661df5f2@q16g2000yqq.googlegroups.com>

Hi, I'm just trying to get to grips with Bioperl as was wondering if
anyone could help me accomplish this task: I want to merge together
any overlapping sequence features, or features within xbp of each
other, that are stored in a BED file.

I have got as far as reading the features in and iterating through
them, e.g.:

my $in = Bio::FeatureIO->new(-format => 'bed', -file => "$file");
while (my $feat = $in->next_feature) {
	print "start: ".$feat->start." end: ".$feat->end."\n";
}

Does Bioperl provide anything that could accomplish this merging, or
would it be something I would have to write myself?

Any help much appreciated

From cjfields at illinois.edu  Thu Feb 18 11:31:23 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 18 Feb 2010 10:31:23 -0600
Subject: [Bioperl-l] Merging overlapping Seq Features
In-Reply-To: <3091e51a-615f-4893-8dfd-8a3d661df5f2@q16g2000yqq.googlegroups.com>
References: <3091e51a-615f-4893-8dfd-8a3d661df5f2@q16g2000yqq.googlegroups.com>
Message-ID: <2956B7B2-5D3E-4EDA-A3D9-01E634157584@illinois.edu>

Dan,

There aren't direct means of doing this beyond asking whether one feature contains or overlaps another (not very efficient), or querying the a database to find specific overlapping features (much better but requires loading the db).  This is something I'm interested in, though, both in context with FeatureIO refactors and as a means to clean up UCSC's 'every transcript is a gene' issues in GTF

chris

On Feb 17, 2010, at 4:04 PM, Dan wrote:

> Hi, I'm just trying to get to grips with Bioperl as was wondering if
> anyone could help me accomplish this task: I want to merge together
> any overlapping sequence features, or features within xbp of each
> other, that are stored in a BED file.
> 
> I have got as far as reading the features in and iterating through
> them, e.g.:
> 
> my $in = Bio::FeatureIO->new(-format => 'bed', -file => "$file");
> while (my $feat = $in->next_feature) {
> 	print "start: ".$feat->start." end: ".$feat->end."\n";
> }
> 
> Does Bioperl provide anything that could accomplish this merging, or
> would it be something I would have to write myself?
> 
> Any help much appreciated
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From MEC at stowers.org  Thu Feb 18 11:45:06 2010
From: MEC at stowers.org (Cook, Malcolm)
Date: Thu, 18 Feb 2010 10:45:06 -0600
Subject: [Bioperl-l] Merging overlapping Seq Features
In-Reply-To: <2956B7B2-5D3E-4EDA-A3D9-01E634157584@illinois.edu>
References: <3091e51a-615f-4893-8dfd-8a3d661df5f2@q16g2000yqq.googlegroups.com>
	<2956B7B2-5D3E-4EDA-A3D9-01E634157584@illinois.edu>
Message-ID: <BD62CBAC4395B94096109020651BE2EC12E5E0C328@EXCHMB-02.stowers-institute.org>

some pointers

http://code.google.com/p/bedtools/
http://genomewiki.ucsc.edu/index.php/Kent_source_utilities such as overlapSelect


Malcolm Cook
Stowers Institute for Medical Research -  Bioinformatics
Kansas City, Missouri  USA
 
 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Chris Fields
> Sent: Thursday, February 18, 2010 10:31 AM
> To: Dan
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Merging overlapping Seq Features
> 
> Dan,
> 
> There aren't direct means of doing this beyond asking whether 
> one feature contains or overlaps another (not very 
> efficient), or querying the a database to find specific 
> overlapping features (much better but requires loading the 
> db).  This is something I'm interested in, though, both in 
> context with FeatureIO refactors and as a means to clean up 
> UCSC's 'every transcript is a gene' issues in GTF
> 
> chris
> 
> On Feb 17, 2010, at 4:04 PM, Dan wrote:
> 
> > Hi, I'm just trying to get to grips with Bioperl as was 
> wondering if 
> > anyone could help me accomplish this task: I want to merge together 
> > any overlapping sequence features, or features within xbp of each 
> > other, that are stored in a BED file.
> > 
> > I have got as far as reading the features in and iterating through 
> > them, e.g.:
> > 
> > my $in = Bio::FeatureIO->new(-format => 'bed', -file => "$file"); 
> > while (my $feat = $in->next_feature) {
> > 	print "start: ".$feat->start." end: ".$feat->end."\n"; }
> > 
> > Does Bioperl provide anything that could accomplish this 
> merging, or 
> > would it be something I would have to write myself?
> > 
> > Any help much appreciated
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

From acn at stowers.org  Thu Feb 18 12:04:57 2010
From: acn at stowers.org (Noll, Aaron)
Date: Thu, 18 Feb 2010 11:04:57 -0600
Subject: [Bioperl-l] Merging overlapping Seq Features
In-Reply-To: <BD62CBAC4395B94096109020651BE2EC12E5E0C328@EXCHMB-02.stowers-institute.org>
Message-ID: <C7A2CF59.CE0E%acn@stowers-institute.org>

Also galaxy has some tools if you download their open source python code.

http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy


On 2/18/10 10:45 AM, "Cook, Malcolm" <MEC at stowers.org> wrote:

some pointers

http://code.google.com/p/bedtools/
http://genomewiki.ucsc.edu/index.php/Kent_source_utilities such as overlapSelect


Malcolm Cook
Stowers Institute for Medical Research -  Bioinformatics
Kansas City, Missouri  USA



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> Chris Fields
> Sent: Thursday, February 18, 2010 10:31 AM
> To: Dan
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Merging overlapping Seq Features
>
> Dan,
>
> There aren't direct means of doing this beyond asking whether
> one feature contains or overlaps another (not very
> efficient), or querying the a database to find specific
> overlapping features (much better but requires loading the
> db).  This is something I'm interested in, though, both in
> context with FeatureIO refactors and as a means to clean up
> UCSC's 'every transcript is a gene' issues in GTF
>
> chris
>
> On Feb 17, 2010, at 4:04 PM, Dan wrote:
>
> > Hi, I'm just trying to get to grips with Bioperl as was
> wondering if
> > anyone could help me accomplish this task: I want to merge together
> > any overlapping sequence features, or features within xbp of each
> > other, that are stored in a BED file.
> >
> > I have got as far as reading the features in and iterating through
> > them, e.g.:
> >
> > my $in = Bio::FeatureIO->new(-format => 'bed', -file => "$file");
> > while (my $feat = $in->next_feature) {
> >     print "start: ".$feat->start." end: ".$feat->end."\n"; }
> >
> > Does Bioperl provide anything that could accomplish this
> merging, or
> > would it be something I would have to write myself?
> >
> > Any help much appreciated
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From dan.halligan at gmail.com  Thu Feb 18 11:53:17 2010
From: dan.halligan at gmail.com (Dan)
Date: Thu, 18 Feb 2010 08:53:17 -0800 (PST)
Subject: [Bioperl-l] Merging overlapping Seq Features
In-Reply-To: <BD62CBAC4395B94096109020651BE2EC12E5E0C328@EXCHMB-02.stowers-institute.org>
References: <3091e51a-615f-4893-8dfd-8a3d661df5f2@q16g2000yqq.googlegroups.com>
	<2956B7B2-5D3E-4EDA-A3D9-01E634157584@illinois.edu>
	<BD62CBAC4395B94096109020651BE2EC12E5E0C328@EXCHMB-02.stowers-institute.org>
Message-ID: <30fedccd-4432-4241-8456-fd0d26b1adc5@k19g2000yqc.googlegroups.com>

Great, thanks for the hints.  I've used some of Jim Kent's utilities
before which are very useful.

On Feb 18, 4:45?pm, "Cook, Malcolm" <M... at stowers.org> wrote:
> some pointers
>
> http://code.google.com/p/bedtools/http://genomewiki.ucsc.edu/index.php/Kent_source_utilitiessuch as overlapSelect
>
> Malcolm Cook
> Stowers Institute for Medical Research - ?Bioinformatics
> Kansas City, Missouri ?USA
>
>
>
>
>
> > -----Original Message-----
> > From: bioperl-l-boun... at lists.open-bio.org
> > [mailto:bioperl-l-boun... at lists.open-bio.org] On Behalf Of
> > Chris Fields
> > Sent: Thursday, February 18, 2010 10:31 AM
> > To: Dan
> > Cc: bioper... at bioperl.org
> > Subject: Re: [Bioperl-l] Merging overlapping Seq Features
>
> > Dan,
>
> > There aren't direct means of doing this beyond asking whether
> > one feature contains or overlaps another (not very
> > efficient), or querying the a database to find specific
> > overlapping features (much better but requires loading the
> > db). ?This is something I'm interested in, though, both in
> > context with FeatureIO refactors and as a means to clean up
> > UCSC's 'every transcript is a gene' issues in GTF
>
> > chris
>
> > On Feb 17, 2010, at 4:04 PM, Dan wrote:
>
> > > Hi, I'm just trying to get to grips with Bioperl as was
> > wondering if
> > > anyone could help me accomplish this task: I want to merge together
> > > any overlapping sequence features, or features within xbp of each
> > > other, that are stored in a BED file.
>
> > > I have got as far as reading the features in and iterating through
> > > them, e.g.:
>
> > > my $in = Bio::FeatureIO->new(-format => 'bed', -file => "$file");
> > > while (my $feat = $in->next_feature) {
> > > ? ? ? print "start: ".$feat->start." end: ".$feat->end."\n"; }
>
> > > Does Bioperl provide anything that could accomplish this
> > merging, or
> > > would it be something I would have to write myself?
>
> > > Any help much appreciated
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioper... at lists.open-bio.org
> > >http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioper... at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l


From Russell.Smithies at agresearch.co.nz  Thu Feb 18 15:05:21 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Fri, 19 Feb 2010 09:05:21 +1300
Subject: [Bioperl-l] primer candidates validation by comparing the wgs
 blast results between fwd and rev.
In-Reply-To: <27633496.post@talk.nabble.com>
References: <27633496.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61D14ACA@exchsth.agresearch.co.nz>

Here's a few thoughts:

* Design your primers with primer3 - automate the process with Bio:Tools:Run:Primer3. 
* Install the required databases locally and use Bio::Tools::Run::StandAloneBlast or Bio::Tools::Run::StandAloneBlastPlus as it will be much faster than remote blast and gives you greater control.
* You will need to be very careful with your blast parameters as trying to map primers reliably to a genome can be a bit tricky!! Perhaps reverse ePCR would be a better choice http://www.ncbi.nlm.nih.gov/projects/e-pcr/ 
* Have you had a look at primer-blast? http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi? You may be able to send requests by POST but I don't think BioPerl has methods for calling it (yet)

Hope this helps,


Russell Smithies 

Bioinformatics Applications Developer 
T +64 3 489 9085 
E? russell.smithies at agresearch.co.nz 

Invermay? Research Centre 
Puddle Alley, 
Mosgiel, 
New Zealand 
T? +64 3 489 3809?? 
F? +64 3 489 9174? 
www.agresearch.co.nz 




> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of teetee
> Sent: Thursday, 18 February 2010 3:11 p.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] primer candidates validation by comparing the wgs
> blast results between fwd and rev.
> 
> 
> I am totally new to bioperl.
> 
> I would like to see if anyone could give me a hint or clue for tackling
> this
> problem I am trying to solve:
> Use bioperl/perl script and CGI to create a primer quality control web
> interface
> 
> the steps I would like to be automated:
> I design many primer pairs (~500+) flanking intron regions of silkworm wgs
> sequences close to cDNA/mRNA/EST/molecular anchor loci selected. After the
> primers are generated (I wish this step could be automated but it really
> can't), I have to blast each and every of them against the wgs database of
> the same organism to make sure there is no common hits in terms of the
> same
> contig number result between the forward and the reverse primers blastn
> hits
> to avoid the non-target amplification except for the target intron region.
> The steps I take to validate the primers are as follows:
> 1. At NCBI blastn webpage, put in the forward primer sequence in the
> search
> field, label it ("job title"), choose the wgs database and the organism,
> and
> click "submit" to start search.
> 2. Open another browser tab and go to NCBI blastn webpage, put in the
> reverse primer sequence in the search field, label it ("job title"),
> choose
> the wgs database and the organism, and click "submit" to start search.
> 3. On the forward primer blastn result page, write down the top 20 wgs
> sequence that was from build 2 genomic sequencing project (the title of
> each
> hit has a text string with certain format like
> "Bm_scaf<number>_contig<number>").
> 4. On the reverse primer blastn result page, write down the top 20 wgs
> sequence that was from build 2 genomic sequencing project (the title of
> each
> hit has a text string with certain format like
> "Bm_scaf<number>_contig<number>").
> 5. compare the recorded blast hits from step 3 and step 4 and list the
> common hit(s) between the two primer sequences (with the same scaffold and
> contig number)
> 6. show a warning if there is more than one common hit since there should
> be
> only one target hit.
> 
> Example:
> I have these two primer sequences:
> GCATCGGTGAACGAGCTA
> CGCCTGCAAACGAGAATA
> 
> First I blast each of the above primer sequences against wgs database
> bombyx
> mori (organismid:7091) on blast website
> http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=mega
> Blast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome
> After I get the results in two different browser tabs, I record down the
> results. For example, from the forward primer result page(only the first
> several hits are listed):
> =================== first few hits from forward primer blast result
> ==================
> BABH01015134.1
> Bombyx mori DNA, contig: Bm_scaf21_contig15134,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
> 
> BABH01038273.1
> Bombyx mori DNA, contig: Bm_scaf121_contig38273,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
> 
> AADK01021213.1
> Bombyx mori strain Dazao Ctg021213, whole genome
> shotgun sequence
> 34.2 34.2 94% 0.12 100%
> 
> BAAB01106839.1
> Bombyx mori DNA, contig477862, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
> 
> BAAB01154920.1
> Bombyx mori DNA, contig585939, whole genome shotgun
> sequence
> 34.2 34.2 94% 0.12 100%
> 
> BABH01007204.1
> Bombyx mori DNA, contig: Bm_scaf8_contig7204,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 32.2 32.2 88% 0.48 100%
> 
> BABH01020379.1
> Bombyx mori DNA, contig: Bm_scaf33_contig20379,
> strain: p50T/Dazao, build 2, whole genome shotgun
> sequence
> 32.2 32.2 88% 0.48 100%
> ================================ end of the forward blast result
> ================================ first few hits from reverse primer blast
> result ==================
> BABH01015134.1
> Bombyx mori DNA, contig:
> Bm_scaf21_contig15134, strain: p50T/Dazao,
> build 2, whole genome shotgun sequence
> 36.2 36.2 100% 0.031 100%
> 
> AADK01021213.1
> Bombyx mori strain Dazao Ctg021213, whole
> genome shotgun sequence
> 36.2 36.2 100% 0.031 100%
> 
> AADK01032592.1
> Bombyx mori strain Dazao Ctg032592, whole
> genome shotgun sequence
> 36.2 36.2 100% 0.031 100%
> 
> BAAB01106839.1
> Bombyx mori DNA, contig477862, whole genome
> shotgun sequence
> 36.2 36.2 100% 0.031 100%
> 
> BABH01028024.1
> Bombyx mori DNA, contig:
> Bm_scaf56_contig28024, strain: p50T/Dazao,
> build 2, whole genome shotgun sequence
> 30.2 30.2 83% 1.9 100%
> 
> AADK01039561.1
> Bombyx mori strain Dazao Ctg039561, whole
> genome shotgun sequence
> 30.2 30.2 83% 1.9 100%
> 
> AADK01056852.1
> Bombyx mori strain Dazao Ctg063892, whole
> genome shotgun sequence
> 30.2 30.2 83% 1.9 100%
> 
> BABH01001710.1
> Bombyx mori DNA, contig: Bm_scaf2_contig1710,
> strain: p50T/Dazao, build 2, whole genome
> shotgun sequence
> ===============================end of the reverse result
> 
> >From the list, I would record down the ones with "Bm_scaf#_contig#"(ex.
> Bm_scaf21_contig15134) since that's the string pattern I would like to
> compare with the hits from reverse primer blast results.
> After I record down the first 20 qualified blast hits(hopefully with blast
> paser program I can use more than 20), I compare them with the ones from
> the
> reverse primer search result and see if there is any common result other
> than the target.
> 
> I am OK to go through this validation process manually if there are only
> tens of primers I have to design. However with 500 and maybe more primers
> to
> come I believe there is an easier way.
> 
> 
> I imagine the code will have the following functions:
> input: user's primer pairs, multiple entry capatability
> output: compare the blastn results between both fwd and reverse primer and
> generate a list of common blastn hits (w/ same scaf# and contig# from
> build
> 2 wgs sequences - naming convention: Bm_scaf#_contig#) on the wgs (accept
> the blast search parameters through the web and pass to the blast command)
> background record-keeping mechanism: create records of the blast report
> for
> each primer vs wgs blastn results and properly name the files.
> 
> I guess my question is:
> What would be the most stright-forward approach? (I know you probably
> think
> I already know the method since I post the question here, but more
> suggestions the better) and where should I start?
> 
> My background:
> 1. I've written codes for retrieving PDB file upon user's PDB 4-letter
> protein ID entry and atom-atom distance measurement with the same
> setup(perl
> script+web CGI interface)
> 2. I've used command-line megablast to batch blast multiple sequences
> however my impression is that it's not intend to do short sequence
> blast(primers are usually around 20-24bp long).
> ref.:
> http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TY
> PE=Download
> 3. I can modify simple perl codes and do some text string menupilation in
> perl
> 4. I have my own linux box and have apache/perl/bioperl/cgi ready.
> 
> --
> View this message in context: http://old.nabble.com/primer-candidates-
> validation-by-comparing-the-wgs-blast-results-between-fwd-and-rev.-
> tp27633496p27633496.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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From dan.kortschak at adelaide.edu.au  Thu Feb 18 16:20:46 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Fri, 19 Feb 2010 07:50:46 +1030
Subject: [Bioperl-l] Bioperl-l Digest, Vol 82, Issue 28
In-Reply-To: <mailman.13.1266512404.29924.bioperl-l@lists.open-bio.org>
References: <mailman.13.1266512404.29924.bioperl-l@lists.open-bio.org>
Message-ID: <1266528046.4459.5.camel@epistle>

Hi Dan,

Please try out the BEDTools module included in bioperl-run. It is
currently in BETA, but passes all tests. It interfaces to all the
BEDTools suite.

The returned results from these methods can either be raw bed
descriptions or a variety of BioPerl objects, including sequence
objects.

cheers
Dan

On Thu, 2010-02-18 at 12:00 -0500, bioperl-l-request at lists.open-bio.org
wrote:
> Dan,
> 
> There aren't direct means of doing this beyond asking whether one
> feature contains or overlaps another (not very efficient), or querying
> the a database to find specific overlapping features (much better but
> requires loading the db).  This is something I'm interested in,
> though, both in context with FeatureIO refactors and as a means to
> clean up UCSC's 'every transcript is a gene' issues in GTF
> 
> chris
> 
> On Feb 17, 2010, at 4:04 PM, Dan wrote:
> 
> > Hi, I'm just trying to get to grips with Bioperl as was wondering if
> > anyone could help me accomplish this task: I want to merge together
> > any overlapping sequence features, or features within xbp of each
> > other, that are stored in a BED file.
> > 
> > I have got as far as reading the features in and iterating through
> > them, e.g.:
> > 
> > my $in = Bio::FeatureIO->new(-format => 'bed', -file => "$file");
> > while (my $feat = $in->next_feature) {
> >       print "start: ".$feat->start." end: ".$feat->end."\n";
> > }
> > 
> > Does Bioperl provide anything that could accomplish this merging, or
> > would it be something I would have to write myself?
> > 
> > Any help much appreciated


From dan.kortschak at adelaide.edu.au  Thu Feb 18 16:43:21 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Fri, 19 Feb 2010 08:13:21 +1030
Subject: [Bioperl-l] Bioperl-l Digest, Vol 82, Issue 28
In-Reply-To: <mailman.13.1266512404.29924.bioperl-l@lists.open-bio.org>
References: <mailman.13.1266512404.29924.bioperl-l@lists.open-bio.org>
Message-ID: <1266529401.4459.10.camel@epistle>

Hi Malcolm,

It is not entirely obvious where the Kent utilities are available from
the genome wiki page (I can find a closed svn repo with the source, but
no other sites). Would you point me to a download site?

thanks
Dan Kortschak

On Thu, 2010-02-18 at 12:00 -0500, bioperl-l-request at lists.open-bio.org
wrote:
> some pointers
> 
> http://code.google.com/p/bedtools/
> http://genomewiki.ucsc.edu/index.php/Kent_source_utilities such as
> overlapSelect
> 
> 
> Malcolm Cook
> Stowers Institute for Medical Research -  Bioinformatics
> Kansas City, Missouri  USA


From cjfields at illinois.edu  Thu Feb 18 16:58:51 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 18 Feb 2010 15:58:51 -0600
Subject: [Bioperl-l] Bioperl-l Digest, Vol 82, Issue 28
In-Reply-To: <1266528046.4459.5.camel@epistle>
References: <mailman.13.1266512404.29924.bioperl-l@lists.open-bio.org>
	<1266528046.4459.5.camel@epistle>
Message-ID: <A292739C-D041-4B0C-B769-1F46DBDBC44F@illinois.edu>

Nice, forgot about those.  Thanks Dan!

chris

On Feb 18, 2010, at 3:20 PM, Dan Kortschak wrote:

> Hi Dan,
> 
> Please try out the BEDTools module included in bioperl-run. It is
> currently in BETA, but passes all tests. It interfaces to all the
> BEDTools suite.
> 
> The returned results from these methods can either be raw bed
> descriptions or a variety of BioPerl objects, including sequence
> objects.
> 
> cheers
> Dan
> 
> On Thu, 2010-02-18 at 12:00 -0500, bioperl-l-request at lists.open-bio.org
> wrote:
>> Dan,
>> 
>> There aren't direct means of doing this beyond asking whether one
>> feature contains or overlaps another (not very efficient), or querying
>> the a database to find specific overlapping features (much better but
>> requires loading the db).  This is something I'm interested in,
>> though, both in context with FeatureIO refactors and as a means to
>> clean up UCSC's 'every transcript is a gene' issues in GTF
>> 
>> chris
>> 
>> On Feb 17, 2010, at 4:04 PM, Dan wrote:
>> 
>>> Hi, I'm just trying to get to grips with Bioperl as was wondering if
>>> anyone could help me accomplish this task: I want to merge together
>>> any overlapping sequence features, or features within xbp of each
>>> other, that are stored in a BED file.
>>> 
>>> I have got as far as reading the features in and iterating through
>>> them, e.g.:
>>> 
>>> my $in = Bio::FeatureIO->new(-format => 'bed', -file => "$file");
>>> while (my $feat = $in->next_feature) {
>>>      print "start: ".$feat->start." end: ".$feat->end."\n";
>>> }
>>> 
>>> Does Bioperl provide anything that could accomplish this merging, or
>>> would it be something I would have to write myself?
>>> 
>>> Any help much appreciated
> 


From Russell.Smithies at agresearch.co.nz  Thu Feb 18 17:12:12 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Fri, 19 Feb 2010 11:12:12 +1300
Subject: [Bioperl-l] Bioperl-l Digest, Vol 82, Issue 28
In-Reply-To: <1266529401.4459.10.camel@epistle>
References: <mailman.13.1266512404.29924.bioperl-l@lists.open-bio.org>
	<1266529401.4459.10.camel@epistle>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF32C61D14BA0@exchsth.agresearch.co.nz>

http://hgdownload.cse.ucsc.edu/admin/jksrc.zip


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Dan Kortschak
> Sent: Friday, 19 February 2010 10:43 a.m.
> To: MEC at stowers.org
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bioperl-l Digest, Vol 82, Issue 28
> 
> Hi Malcolm,
> 
> It is not entirely obvious where the Kent utilities are available from
> the genome wiki page (I can find a closed svn repo with the source, but
> no other sites). Would you point me to a download site?
> 
> thanks
> Dan Kortschak
> 
> On Thu, 2010-02-18 at 12:00 -0500, bioperl-l-request at lists.open-bio.org
> wrote:
> > some pointers
> >
> > http://code.google.com/p/bedtools/
> > http://genomewiki.ucsc.edu/index.php/Kent_source_utilities such as
> > overlapSelect
> >
> >
> > Malcolm Cook
> > Stowers Institute for Medical Research -  Bioinformatics
> > Kansas City, Missouri  USA
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From MEC at stowers.org  Thu Feb 18 17:10:00 2010
From: MEC at stowers.org (Cook, Malcolm)
Date: Thu, 18 Feb 2010 16:10:00 -0600
Subject: [Bioperl-l] Bioperl-l Digest, Vol 82, Issue 28
In-Reply-To: <1266529401.4459.10.camel@epistle>
References: <mailman.13.1266512404.29924.bioperl-l@lists.open-bio.org>
	<1266529401.4459.10.camel@epistle>
Message-ID: <BD62CBAC4395B94096109020651BE2EC12E5E0C3B3@EXCHMB-02.stowers-institute.org>

Sure, Dan:

get yer exes here: http://hgdownload.cse.ucsc.edu/admin/exe/

or,

buildit yerself: http://hgdownload.cse.ucsc.edu/downloads.html



Malcolm Cook
Stowers Institute for Medical Research -  Bioinformatics
Kansas City, Missouri  USA
 
 

> -----Original Message-----
> From: Dan Kortschak [mailto:dan.kortschak at adelaide.edu.au] 
> Sent: Thursday, February 18, 2010 3:43 PM
> To: Cook, Malcolm
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: Bioperl-l Digest, Vol 82, Issue 28
> 
> Hi Malcolm,
> 
> It is not entirely obvious where the Kent utilities are 
> available from the genome wiki page (I can find a closed svn 
> repo with the source, but no other sites). Would you point me 
> to a download site?
> 
> thanks
> Dan Kortschak
> 
> On Thu, 2010-02-18 at 12:00 -0500, 
> bioperl-l-request at lists.open-bio.org
> wrote:
> > some pointers
> > 
> > http://code.google.com/p/bedtools/
> > http://genomewiki.ucsc.edu/index.php/Kent_source_utilities such as 
> > overlapSelect
> > 
> > 
> > Malcolm Cook
> > Stowers Institute for Medical Research -  Bioinformatics 
> Kansas City, 
> > Missouri  USA
> 
> 

From jay at jays.net  Thu Feb 18 17:19:55 2010
From: jay at jays.net (Jay Hannah)
Date: Thu, 18 Feb 2010 16:19:55 -0600
Subject: [Bioperl-l] can't ping code.open-bio.org
Message-ID: <4B7DBD0B.5010400@jays.net>

... from 3 Internet locations.

(cc'ing the list, FYI)

Thanks,

j

From jay at jays.net  Thu Feb 18 18:14:25 2010
From: jay at jays.net (Jay Hannah)
Date: Thu, 18 Feb 2010 17:14:25 -0600
Subject: [Bioperl-l] [O|B|F Helpdesk #896] can't ping code.open-bio.org
In-Reply-To: <rt-3.8.1-6839-1266534675-1904.896-6-0@Open Bioinformatics
	Foundation>
References: <RT-Ticket-896@Open Bioinformatics Foundation> <RT-Ticket-896@Open
	Bioinformatics Foundation> <4B7DBD0B.5010400@jays.net>
	<rt-3.8.1-5674-1266534239-519.896-15-0@Open Bioinformatics
	Foundation> <4B7DC909.5080801@bioteam.net>
	<rt-3.8.1-6839-1266534675-1904.896-6-0@Open Bioinformatics
	Foundation>
Message-ID: <4B7DC9D1.4010601@jays.net>

On 2/18/2010 5:11 PM, Chris Dagdigian via RT wrote:
> Thanks Jay, the server is back up. The usual httpd invoked kernel panic
> lockup.

Looks good now! Thanks!

j

From roy.chaudhuri at gmail.com  Fri Feb 19 07:38:56 2010
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Fri, 19 Feb 2010 12:38:56 +0000
Subject: [Bioperl-l] load_seqdatabase.pl
In-Reply-To: <003301cab14d$b972ff40$2f0c9c95@rubin>
References: <007501caaf29$f4565920$2f0c9c95@rubin> <4B7C1954.1050507@gmail.com>
	<003301cab14d$b972ff40$2f0c9c95@rubin>
Message-ID: <4B7E8660.4000901@gmail.com>

Hi Krzysztof,

Please cc all replies to the mailing list, that way others can 
contribute answers. I don't have experience of dealing with contig 
records so I'm not sure how best to deal with them in BioPerl/BioSQL. 
 From a quick search it looks like representation of this type of data 
is still on the BioSQL to do list:

http://biosql.org/wiki/Enhancement_Requests#Ability_to_fully_represent_contig_assembly

Roy.

On 19/02/2010 10:24, Krzysztof Sarapata wrote:
> Hi Roy
>
>
>
> I'm grateful for your answers.
>
>
>
> Suppose that the weak paradigm of bioSQL allows storing any feature tags in
> appropriate table. Even their which we don't expect.
>
>
>
> I consider expand existing structure on represent contig assembly. The most
> difficult for me is represent relation between sequence from contig and
> entry record. Exactly where put the contig name (e.g. NT_028395.3), may be
> in "Dbxref" table, because we know the remote location this contig? Add new
> column in "location" for gaps?
>
>
> LOCUS NC_000022 51304566 bp DNA linear CON 10-JUN-2009...CONTIG
> join(gap(10000),gap(12990000),gap(3000000),gap(50000),NT_028395.3:1..647850,gap(150000),NT_011519.10:1..3661581,gap(100000),NT_011520.12:1..29755346,gap(50000),NT_011526.7:1..829789,gap(50000),gap(10000))With
> regardsKris----- Original Message -----
> From: "Roy Chaudhuri"<roy.chaudhuri at gmail.com>
> To: "Krzysztof Sarapata"<mysarapa at cyf-kr.edu.pl>
> Cc:<bioperl-l at bioperl.org>
> Sent: Wednesday, February 17, 2010 5:29 PM
> Subject: Re: [Bioperl-l] load_seqdatabase.pl
>
>
>> Hi Krzysztof,
>>
>> The reasons for this are discussed in this post on the BioSQL list:
>> http://lists.open-bio.org/pipermail/biosql-l/2005-March/000751.html
>>
>> In short - BioPerl does not perform any magic to insert the db_xref
>> feature tags where you might expect (ie. the seqfeature_dbxref table). It
>> should be possible to write a SeqProcessor to do so, although it's pretty
>> easy to access them where they are with a query like:
>> SELECT * FROM seqfeature_qualifier_value s JOIN term t USING(term_id)
>> WHERE t.name='db_xref'
>>
>> Roy.
>>
>> On 16/02/2010 17:03, Krzysztof Sarapata wrote:
>>> Hi
>>>
>>>
>>>
>>> I've loaded GenBank file into bioSQL structure with
>>> "load_seqdatabase.pl" script.
>>>
>>> Is it correct that each entity (qualifier) from FEATURES even
>>> "db_xref"  e.g.
>>>
>>>
>>>
>>> FEATURES             Location/Qualifiers
>>>
>>> source          1..257719
>>>
>>> /organism="Homo sapiens"
>>>
>>> /mol_type="genomic DNA"
>>>
>>> /db_xref="taxon:9606"
>>>
>>> /chromosome="1"
>>>
>>> .....
>>>
>>> /db_xref="GeneID:100287102"
>>>
>>>
>>>
>>> is put into  "Seqfeature Qualifier Value" table, if we have exactly
>>> table "Dbxref"?
>>>
>>> Why value of this qualifier (db_xref) isn't put into "Dbxref" table?
>>>
>>>
>>>
>>> With regards
>>>
>>> Krzysztof Sarapata
>


From rmb32 at cornell.edu  Fri Feb 19 12:28:21 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Fri, 19 Feb 2010 09:28:21 -0800
Subject: [Bioperl-l] YAPC::NA 2010 perl conference
Message-ID: <4B7ECA35.6080609@cornell.edu>

Raise your virtual hand if you're going to YAPC::NA 2010.

It's Columbus, OH, June 21-23
http://conferences.mongueurs.net/yn2010/

I raise my virtual hand.

There should be a talk about bioperl (maybe with emphasis on the 
tradeoffs regarding monolithic versus factored out distributions)? 
There should probably also be a talk about Chado.

Rob


From clements at nescent.org  Fri Feb 19 13:57:09 2010
From: clements at nescent.org (Dave Clements)
Date: Fri, 19 Feb 2010 10:57:09 -0800
Subject: [Bioperl-l] BioPerl, CPAN Modules, and Linux Packages
Message-ID: <f135c01c1002191057t2a70ddf2vc85921d26b7fe9c3@mail.gmail.com>

Hello all,

One question that came up at last month's GMOD meeting was "What are the
best practices for mixing and matching CPAN modules and Linux packages?"

Users can sometimes find a Perl module at both CPAN and as a Linux package.
Sometimes, a module is only available from CPAN.  Installing a Linux package
is generally much easier for novice users, but then users run the risk of
their packages and CPAN modules interacting badly (don't they?).

I've scanned the BioPerl site for guidance on when to go with CPAN and when
to use a Linux package, but I can't find anything.  Would someone who
understands this be willing to create a BioPerl.org page about when to chose
what, and what problems might arise from mixed installations (and maybe even
how to address them)?  The page could just be pointers to external pages
that address this.

Thanks,

Dave C.

-- 
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
http://gmod.org/wiki/GMOD_Logo_Program
http://gmod.org/wiki/GMOD_News

From jay at jays.net  Fri Feb 19 14:37:49 2010
From: jay at jays.net (Jay Hannah)
Date: Fri, 19 Feb 2010 13:37:49 -0600
Subject: [Bioperl-l] YAPC::NA 2010 perl conference
In-Reply-To: <4B7ECA35.6080609@cornell.edu>
References: <4B7ECA35.6080609@cornell.edu>
Message-ID: <4B7EE88D.1020406@jays.net>

On 2/19/2010 11:28 AM, Robert Buels wrote:
> Raise your virtual hand if you're going to YAPC::NA 2010.
>
> It's Columbus, OH, June 21-23
> http://conferences.mongueurs.net/yn2010/
>
> I raise my virtual hand.

Me too! I created a wiki page for RSVPs/discussion:

    http://www.bioperl.org/wiki/YAPC

I'm looking forward to another hackathon.  :)

j

From rmb32 at cornell.edu  Fri Feb 19 16:33:10 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Fri, 19 Feb 2010 13:33:10 -0800
Subject: [Bioperl-l] BioPerl, CPAN Modules, and Linux Packages
In-Reply-To: <f135c01c1002191057t2a70ddf2vc85921d26b7fe9c3@mail.gmail.com>
References: <f135c01c1002191057t2a70ddf2vc85921d26b7fe9c3@mail.gmail.com>
Message-ID: <4B7F0396.9080809@cornell.edu>

I certainly understand this, but running short on time.

In my opinion, the short answer is:  do one or the other, Debian 
packages or CPAN, not both.  Also, I always recommend that people use 
local::lib to install the dependencies needed for whatever it is they 
are deploying or experimenting with, doing everything as a regular user 
account.  Within SGN, the policy is 'never run cpan as root for anything 
ever'.

If somebody else starts the page I can come along and edit.

R


Dave Clements wrote:
> Hello all,
> 
> One question that came up at last month's GMOD meeting was "What are the
> best practices for mixing and matching CPAN modules and Linux packages?"
> 
> Users can sometimes find a Perl module at both CPAN and as a Linux package.
> Sometimes, a module is only available from CPAN.  Installing a Linux package
> is generally much easier for novice users, but then users run the risk of
> their packages and CPAN modules interacting badly (don't they?).
> 
> I've scanned the BioPerl site for guidance on when to go with CPAN and when
> to use a Linux package, but I can't find anything.  Would someone who
> understands this be willing to create a BioPerl.org page about when to chose
> what, and what problems might arise from mixed installations (and maybe even
> how to address them)?  The page could just be pointers to external pages
> that address this.
> 
> Thanks,
> 
> Dave C.
> 


-- 
Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu
http://www.sgn.cornell.edu

From cjfields at illinois.edu  Fri Feb 19 20:56:54 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 19 Feb 2010 19:56:54 -0600
Subject: [Bioperl-l] ID Mapper now in Bio::DB::SwissProt
Message-ID: <488788F9-41F7-49F7-BBF0-B635ED7D6A8C@illinois.edu>

Just added an id_mapper function to Bio::DB::SwissProt.  This uses the remote UniProt ID Mapper:

http://www.uniprot.org/help/mapping

Following is the documentation:

 Title   : id_tracker
 Usage   : my $map = $self->id_mapper( -from => '',
                                       -to   => '',
                                       -ids  => \@ids);
 Function: Retrieve new ID using old ID. 
 Returns : hash reference of successfully mapped IDs
 Args    : -from : database mapping from
           -to   : database mapped to
           -ids  : a single ID or array ref of IDs to map
 Note    : For a list of valid database IDs, see:
           http://www.uniprot.org/faq/28#id_mapping_examples

Some simple tests are in t/RemoteDB/SwissProt.t.

enjoy!

chris

From adam at ali.as  Sat Feb 20 01:00:54 2010
From: adam at ali.as (Adam Kennedy)
Date: Sat, 20 Feb 2010 17:00:54 +1100
Subject: [Bioperl-l] Strawberry Perl Professional Alpha 1
Message-ID: <255d58531002192200s3096a1e8h9ac3ac814e2417f6@mail.gmail.com>

Greetings all

I'm happy to report the first alpha release of the new Strawberry Perl
Professional.

Where the current Strawberry Perl product concept was to support
experienced Perl people that are new to Windows, Strawberry Perl
Professional is intended as the matching opposite of this, to support
Windows people that are new to Perl.

The goal is to provide an easy entry to Perl, with entirely GUI tools,
no expectation that users should have to use the command line, and
with a high number of the most popular and important CPAN modules
pre-installed, so that newbies can get up and running on basic
learning tasks quickly, without having to immediately deal with the
CPAN.

Most notably for this list, it contains both the Padre Perl IDE, and a
default-options version of BioPerl in the default install, providing
both trivially easy access to BioPerl functionality, and something in
which to write the actual code that uses it.

Please note this is most definitely an alpha. The GUI CPAN client
currently crashes at startup, the new Perl Shell will crash if you
enter a command that is not a legal Perl statement, and we don't yet
have anything beyond a bare bones BioPerl install. The main elements
of the distribution, however, are fairly well battle tested and the
Perl install itself is completely sound.

I've included the full set of features below, and you should expect
further alpha releases will following over the next few months.

Best Regards

Adam Kennedy

"Strawberry Perl Professional" 5.10.1.1 Alpha 1

    * This is an ALPHA - There are known bugs, and one of the purposes
of releasing this is outside consultation.
      It's built on top of Strawberry Perl January 2010 (5.10.1.1)
    * Included are:
         1. All common graphical toolkits that I know about and can
get to build easily (Tk, Wx, and Win32::GUI at the moment. OpenGL will
be in the next version.)
         2. Graphical CPAN client (CPANPLUS::Shell::Wx) and POD viewer (Tk::Pod)
         3. The Padre perl IDE, and Perl::Tidy, Perl::Critic, and
Catalyst plugins for it.
         4. Moose and a number of MooseX modules.
         5. Catalyst::Runtime, Catalyst::Devel, and a number of
Catalyst/CatalystX modules, including the Catalyst::Manual.
         6. A console Perl-language shells (Perl::Shell) - Devel::REPL
may be in the next version. **
         7. Dist::Zilla, Devel::NYTProf, Perl::Critic, Perl::Tidy, BioPerl...
         8. ... and everything that's already in Strawberry Perl.
    * There is no release notes page for this build

From bimber at wisc.edu  Sun Feb 21 21:36:20 2010
From: bimber at wisc.edu (Ben Bimber)
Date: Sun, 21 Feb 2010 20:36:20 -0600
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and
	Bio::Assembly::IO::bowtie now available BETA
In-Reply-To: <6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle>
References: <1263869267.12881.33.camel@zoidberg.mbs.adelaide.edu.au>
	<5ACBA19439E77B43A06F4CAB897EC977019B31FE@EXCH1-COLO.accelrys.net>
	<6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle>
Message-ID: <9f985cdc1002211836k2943f33h56f4974a231db7b1@mail.gmail.com>

Hello,

I am very happy to see the bowtie wrapper.  However, I am having
trouble with the current logic to find the bowtie executable path.  In
Bio::Tools::Run::Bowtie, line 240, it uses the command 'which', which
is not windows compatible as far as I know (i'm running a PC).

I made a crude hack to get it to work on my machine, but is this
something you would consider changing in bowtie.pm?  I'm not sure what
the most versatile approach to setting program path in a wrapper would
be, but I'd love to hear it.  I have still not entirely wrapped my
head around all the methods to handle program path in wrappers, so
perhaps there's some way to override this I'm not aware of.

Thanks,
Ben




On Tue, Jan 19, 2010 at 3:18 PM, Dan Kortschak
<dan.kortschak at adelaide.edu.au> wrote:
> Great.
>
> Thanks, Scott.
>
> Dan
>
> On Tue, 2010-01-19 at 10:00 -0800, Scott Markel wrote:
>> Dan,
>>
>> Life Tech has sample data for E. coli at
>>
>> http://solidsoftwaretools.com/gf/project/ecoli2x50/
>>
>> and
>>
>> http://solidsoftwaretools.com/gf/project/dh10bfrag/.
>>
>> Reference sequences are included.
>>
>> Scott
>>
>> Scott Markel, Ph.D.
>> Principal Bioinformatics Architect ?email: ?smarkel at accelrys.com
>> Accelrys (Pipeline Pilot R&D) ? ? ? mobile: +1 858 205 3653
>> 10188 Telesis Court, Suite 100 ? ? ?voice: ?+1 858 799 5603
>> San Diego, CA 92121 ? ? ? ? ? ? ? ? fax: ? ?+1 858 799 5222
>> USA ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? web: ? ?http://www.accelrys.com
>>
>> http://www.linkedin.com/in/smarkel
>> Vice President, Board of Directors:
>> ? ? International Society for Computational Biology
>> Chair: ISCB Publications Committee
>> Associate Editor: PLoS Computational Biology
>> Editorial Board: Briefings in Bioinformatics
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dan Kortschak
>> Sent: Monday, 18 January 2010 6:48 PM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and Bio::Assembly::IO::bowtie now available BETA
>>
>> Hi All,
>>
>> A wrapper and output parser for bowtie 'ultrafast, memory-efficient
>> short read aligner' are now available in the bioperl-live and
>> bioperl-run subversion repositories (bioperl-live/trunk at 16727 and
>> bioperl-run/trunk at 16726). Bowtie details are available here:
>>
>> http://bowtie-bio.sourceforge.net/index.shtml
>>
>> The modules can return a Bio::Assembly::Scaffold object (operating via
>> the MAJ's Bio::Assembly::IO::sam module in bioperl-live/trunk
>> which requires lstein's Bio::DB::Sam, from CPAN). Note that Bio::DB::Sam
>> uses large amounts of memory - the test suite works for me with >=2GB
>> but not with 1GB due to this. (Is there a disk file system based tool
>> for this for large projects?)
>>
>> Bowtie (>0.12.0) can align in colour space, but this is not currently
>> supported by the wrapper though it should not be difficult to add. If
>> someone can point me to a small set of colour space reads and a
>> reference sequence I will be able to use these for testing.
>>
>> Thanks to the core devs for helping me with many of my problems in
>> putting this together.
>>
>> Dan
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From bbimber at gmail.com  Sun Feb 21 21:28:44 2010
From: bbimber at gmail.com (Ben Bimber)
Date: Sun, 21 Feb 2010 20:28:44 -0600
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and
	Bio::Assembly::IO::bowtie now available BETA
In-Reply-To: <6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle>
References: <1263869267.12881.33.camel@zoidberg.mbs.adelaide.edu.au>
	<5ACBA19439E77B43A06F4CAB897EC977019B31FE@EXCH1-COLO.accelrys.net>
	<6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle>
Message-ID: <9f985cdc1002211828w63811d75n48d8cb3093e6d076@mail.gmail.com>

Hello,

I just came across the bowtie wrapper and it looks very useful.
However, I am having trouble with the current logic to find the bowtie
executable path.  In Bio::Tools::Run::Bowtie, line 240, it uses the
command 'which', which is not windows compatible as far as I know (i'm
running a PC).

I made a crude hack to get it to work on my machine, but is this
something you would consider changing in bowtie.pm?  I'm not sure what
the most versatile approach to setting program path in a wrapper would
be, but I'd love to hear it.  I have still not entirely wrapped my
head around all the methods to handle program path in wrappers, so
perhaps there's a way to override this that I'm not aware of.

Thanks,
Ben




On Tue, Jan 19, 2010 at 3:18 PM, Dan Kortschak
<dan.kortschak at adelaide.edu.au> wrote:
> Great.
>
> Thanks, Scott.
>
> Dan
>
> On Tue, 2010-01-19 at 10:00 -0800, Scott Markel wrote:
>> Dan,
>>
>> Life Tech has sample data for E. coli at
>>
>> http://solidsoftwaretools.com/gf/project/ecoli2x50/
>>
>> and
>>
>> http://solidsoftwaretools.com/gf/project/dh10bfrag/.
>>
>> Reference sequences are included.
>>
>> Scott
>>
>> Scott Markel, Ph.D.
>> Principal Bioinformatics Architect ?email: ?smarkel at accelrys.com
>> Accelrys (Pipeline Pilot R&D) ? ? ? mobile: +1 858 205 3653
>> 10188 Telesis Court, Suite 100 ? ? ?voice: ?+1 858 799 5603
>> San Diego, CA 92121 ? ? ? ? ? ? ? ? fax: ? ?+1 858 799 5222
>> USA ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? web: ? ?http://www.accelrys.com
>>
>> http://www.linkedin.com/in/smarkel
>> Vice President, Board of Directors:
>> ? ? International Society for Computational Biology
>> Chair: ISCB Publications Committee
>> Associate Editor: PLoS Computational Biology
>> Editorial Board: Briefings in Bioinformatics
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dan Kortschak
>> Sent: Monday, 18 January 2010 6:48 PM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and Bio::Assembly::IO::bowtie now available BETA
>>
>> Hi All,
>>
>> A wrapper and output parser for bowtie 'ultrafast, memory-efficient
>> short read aligner' are now available in the bioperl-live and
>> bioperl-run subversion repositories (bioperl-live/trunk at 16727 and
>> bioperl-run/trunk at 16726). Bowtie details are available here:
>>
>> http://bowtie-bio.sourceforge.net/index.shtml
>>
>> The modules can return a Bio::Assembly::Scaffold object (operating via
>> the MAJ's Bio::Assembly::IO::sam module in bioperl-live/trunk
>> which requires lstein's Bio::DB::Sam, from CPAN). Note that Bio::DB::Sam
>> uses large amounts of memory - the test suite works for me with >=2GB
>> but not with 1GB due to this. (Is there a disk file system based tool
>> for this for large projects?)
>>
>> Bowtie (>0.12.0) can align in colour space, but this is not currently
>> supported by the wrapper though it should not be difficult to add. If
>> someone can point me to a small set of colour space reads and a
>> reference sequence I will be able to use these for testing.
>>
>> Thanks to the core devs for helping me with many of my problems in
>> putting this together.
>>
>> Dan
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From florent.angly at gmail.com  Sun Feb 21 22:44:13 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Mon, 22 Feb 2010 13:44:13 +1000
Subject: [Bioperl-l] BioPerl, CPAN Modules, and Linux Packages
In-Reply-To: <f135c01c1002191057t2a70ddf2vc85921d26b7fe9c3@mail.gmail.com>
References: <f135c01c1002191057t2a70ddf2vc85921d26b7fe9c3@mail.gmail.com>
Message-ID: <4B81FD8D.8020309@gmail.com>

Dave,
I tend to install the modules that are available in the repositories for 
my Linux distribution. When a module is the repository is not available 
or too old, the best thing to do is to make a suitable package for it. 
For systems that use the Debian package system, I have started using 
dh-make-perl:
http://michael.thegrebs.com/2008/07/02/dh-make-perl-will-rock-your-socks/
The nice thing is that, when building the package, dh-make-perl will 
look for dependencies. Also, it is suitable for Perl modules that are on 
CPAN, but not exclusively.
Cheers,
Florent


On 20/02/10 04:57, Dave Clements wrote:
> Hello all,
>
> One question that came up at last month's GMOD meeting was "What are the
> best practices for mixing and matching CPAN modules and Linux packages?"
>
> Users can sometimes find a Perl module at both CPAN and as a Linux package.
> Sometimes, a module is only available from CPAN.  Installing a Linux package
> is generally much easier for novice users, but then users run the risk of
> their packages and CPAN modules interacting badly (don't they?).
>
> I've scanned the BioPerl site for guidance on when to go with CPAN and when
> to use a Linux package, but I can't find anything.  Would someone who
> understands this be willing to create a BioPerl.org page about when to chose
> what, and what problems might arise from mixed installations (and maybe even
> how to address them)?  The page could just be pointers to external pages
> that address this.
>
> Thanks,
>
> Dave C.
>
>    


From dhoworth at mrc-lmb.cam.ac.uk  Mon Feb 22 07:32:31 2010
From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth)
Date: Mon, 22 Feb 2010 12:32:31 +0000
Subject: [Bioperl-l] BioPerl, CPAN Modules, and Linux Packages
In-Reply-To: <4B81FD8D.8020309@gmail.com>
References: <f135c01c1002191057t2a70ddf2vc85921d26b7fe9c3@mail.gmail.com>
	<4B81FD8D.8020309@gmail.com>
Message-ID: <4B82795F.6040107@mrc-lmb.cam.ac.uk>

Dave Clements wrote:
>> One question that came up at last month's GMOD meeting was "What are the
>> best practices for mixing and matching CPAN modules and Linux packages?"

I think there are a number of issues that may resolve differently for
different people, or even for the same person on different machines. So
there may be different best practices in different cases. For example:

- a developer setting up a personal machine or a test machine
- an admin setting up a server for use by a group of bioperl users
- a dedicated webhost
- a shared webhost

So I think it may be useful to set out the background before diving into
specific recommendations of techniques for people to use.

There are several options when installing packages:

- many packages are available from the distro packaging repositories
- almost all packages are available from CPAN
- CPAN, or other, packages can be converted to use the distro packaging
system (deb or rpm)
- packages can be installed system-wide by root
- packages can be installed privately by any user, using cpan or local::lib

There are a few main technical issues that affect how to set up machines:

- If packages are installed by root, they affect all users (unless a
user actively overrides the packages). If they're installed by a user,
they affect just that user.
- Some system applications are written in Perl and depend on finding the
version of the packages that they were built with (i.e. from the distro
package repositories).
- Some packages change frequently and tend to depend on recent versions
of other packages. More recent versions than are found in the distro
repositories may be necessary either to obtain specific new
functionality or critical bug fixes. Specific releases, neither the
newest nor that supplied by the distro, may be required in a few awkward
cases.

There's a useful feature of Perl that is exploited by distros to provide
some flexibility in this regard - the @INC path array. I'm most familiar
with openSUSE so I'll use that as an example. I expect that other
distros have similar mechanisms. So the default environment for a normal
user looks something like:

@INC:
    /usr/lib/perl5/5.8.8/x86_64-linux-thread-multi
    /usr/lib/perl5/5.8.8
    /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
    /usr/lib/perl5/site_perl/5.8.8
    /usr/lib/perl5/site_perl
    /usr/lib/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
    /usr/lib/perl5/vendor_perl/5.8.8
    /usr/lib/perl5/vendor_perl

Packages in directories at the top are preferred to those at the bottom.
Core perl packages go in the /usr/lib/perl5/5.8.8 directories. When
extra packages are installed from the openSUSE repositories, they are
placed in the vendor_perl directories. Packages installed from CPAN are
installed into the site_perl directories.

So a normal user will see packages installed from CPAN in preference to
those installed from the system repositories.

Applications installed from the system repositories are built without
the site_perl directories so they link to the compatible system
libraries regardless of whether newer CPAN versions have been installed
for other applications. This keeps the system stable.

Cheers, Dave

PS feel free to extract any of this if it's useful.

From jajams at utu.fi  Mon Feb 22 09:57:27 2010
From: jajams at utu.fi (=?iso-8859-1?B?Ikpvb25hcyBK5G1zZW4i?=)
Date: Mon, 22 Feb 2010 16:57:27 +0200
Subject: [Bioperl-l] hmmer3/hmmscan
Message-ID: <fb76f2af73343.4b82b777@utu.fi>

Hi! Does Bioperl support parsing hmmscan/hmmer3?

Best regards,
Joonas J?msen.


From tuco at pasteur.fr  Mon Feb 22 10:39:06 2010
From: tuco at pasteur.fr (Emmanuel Quevillon)
Date: Mon, 22 Feb 2010 16:39:06 +0100
Subject: [Bioperl-l] Possible parsing bug for Bio::Restriction::IO::withrefm
	?
Message-ID: <4B82A51A.9060705@pasteur.fr>

Hi,

I am just playing with Bio::Restriction::* modules and found a
possible bug in parsing the site part of the enzyme definition in
Rebase file.

It looks like it does not take into account enzyme cutting such site :
<3>CCTCAGC(-5/-2)
<3>CCGCTC(-3/-3)
<3>CCGC(-3/-1)
<3>CACGTC(-3/-3)
<3>GAATGC(1/-1)
<3>GAATGC(1/-1)
<3>GAATGC(1/-1)

Is it a normal behaviour where as parsing is supposed to support
kind of stuff (B::R::IO::withrefm line 143):


my ($precut, $recog, $postcut) = ( $site =~
m/^(?:\((\w+\/\w+)\))?([\w^]+)(?:\((\w+\/\w+)\))?/ );

For example, this regex is incapable of determining the overhang of
BmgBI which is defined as :

<1>BmgBI
<2>BtrI,AjiI
<3>CACGTC(-3/-3)
<4>?(5)
<5>Bacillus thermoglucosidasius
<6>NEB 1353
<7>N

Shouldn't it be a blunt enzyme?

The overhang for this enzyme is returned as 'unknown' and cut and
complementary cut are undef.

I propose to change the regex to :

m/^(?:\((-?\w+\/-?\w+)\))?([\w^]+)(?:\((-?\w+\/-?\w+)\))?/ )

unless I making a terrible mistake?

Thanks in advance

Regards

-- 
-------------------------
Emmanuel Quevillon
Biological Software and Databases Group
Institut Pasteur
+33 1 44 38 95 98
tuco at_ pasteur dot fr
-------------------------

From maj at fortinbras.us  Mon Feb 22 11:05:34 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 22 Feb 2010 11:05:34 -0500
Subject: [Bioperl-l] Possible parsing bug for
	Bio::Restriction::IO::withrefm?
In-Reply-To: <4B82A51A.9060705@pasteur.fr>
References: <4B82A51A.9060705@pasteur.fr>
Message-ID: <C8A3D982C5A1494EADB13385330E3DAA@NewLife>

Hi Emanuel- I would not be surprised if there were a problem here;
I would say if your patch passes tests and also solves the issue you
raise, make the patch and add a test for this particular situation, if you
have time. 
thanks! MAJ
----- Original Message ----- 
From: "Emmanuel Quevillon" <tuco at pasteur.fr>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Monday, February 22, 2010 10:39 AM
Subject: [Bioperl-l] Possible parsing bug for Bio::Restriction::IO::withrefm?


> Hi,
> 
> I am just playing with Bio::Restriction::* modules and found a
> possible bug in parsing the site part of the enzyme definition in
> Rebase file.
> 
> It looks like it does not take into account enzyme cutting such site :
> <3>CCTCAGC(-5/-2)
> <3>CCGCTC(-3/-3)
> <3>CCGC(-3/-1)
> <3>CACGTC(-3/-3)
> <3>GAATGC(1/-1)
> <3>GAATGC(1/-1)
> <3>GAATGC(1/-1)
> 
> Is it a normal behaviour where as parsing is supposed to support
> kind of stuff (B::R::IO::withrefm line 143):
> 
> 
> my ($precut, $recog, $postcut) = ( $site =~
> m/^(?:\((\w+\/\w+)\))?([\w^]+)(?:\((\w+\/\w+)\))?/ );
> 
> For example, this regex is incapable of determining the overhang of
> BmgBI which is defined as :
> 
> <1>BmgBI
> <2>BtrI,AjiI
> <3>CACGTC(-3/-3)
> <4>?(5)
> <5>Bacillus thermoglucosidasius
> <6>NEB 1353
> <7>N
> 
> Shouldn't it be a blunt enzyme?
> 
> The overhang for this enzyme is returned as 'unknown' and cut and
> complementary cut are undef.
> 
> I propose to change the regex to :
> 
> m/^(?:\((-?\w+\/-?\w+)\))?([\w^]+)(?:\((-?\w+\/-?\w+)\))?/ )
> 
> unless I making a terrible mistake?
> 
> Thanks in advance
> 
> Regards
> 
> -- 
> -------------------------
> Emmanuel Quevillon
> Biological Software and Databases Group
> Institut Pasteur
> +33 1 44 38 95 98
> tuco at_ pasteur dot fr
> -------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
>

From maj at fortinbras.us  Mon Feb 22 11:01:40 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 22 Feb 2010 11:01:40 -0500
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie
	andBio::Assembly::IO::bowtie now available BETA
In-Reply-To: <9f985cdc1002211828w63811d75n48d8cb3093e6d076@mail.gmail.com>
References: <1263869267.12881.33.camel@zoidberg.mbs.adelaide.edu.au><5ACBA19439E77B43A06F4CAB897EC977019B31FE@EXCH1-COLO.accelrys.net><6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle>
	<9f985cdc1002211828w63811d75n48d8cb3093e6d076@mail.gmail.com>
Message-ID: <6DCA647E40D847A5BCC7815EB711B791@NewLife>

Hi Ben-- this is definitely a valid issue. The newest wrappers are
works in progress; can you submit a bug report at bugzilla.bioperl.org ?
(as a Windows users, I call it a bug, but Dan may disagree!) (FYI,
some improvements to the wrapper interfaces are coming soon that
will attempt to standardize some of these kinds of issues, so stay tuned)
MAJ
----- Original Message ----- 
From: "Ben Bimber" <bbimber at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Sunday, February 21, 2010 9:28 PM
Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie andBio::Assembly::IO::bowtie 
now available BETA


Hello,

I just came across the bowtie wrapper and it looks very useful.
However, I am having trouble with the current logic to find the bowtie
executable path.  In Bio::Tools::Run::Bowtie, line 240, it uses the
command 'which', which is not windows compatible as far as I know (i'm
running a PC).

I made a crude hack to get it to work on my machine, but is this
something you would consider changing in bowtie.pm?  I'm not sure what
the most versatile approach to setting program path in a wrapper would
be, but I'd love to hear it.  I have still not entirely wrapped my
head around all the methods to handle program path in wrappers, so
perhaps there's a way to override this that I'm not aware of.

Thanks,
Ben




On Tue, Jan 19, 2010 at 3:18 PM, Dan Kortschak
<dan.kortschak at adelaide.edu.au> wrote:
> Great.
>
> Thanks, Scott.
>
> Dan
>
> On Tue, 2010-01-19 at 10:00 -0800, Scott Markel wrote:
>> Dan,
>>
>> Life Tech has sample data for E. coli at
>>
>> http://solidsoftwaretools.com/gf/project/ecoli2x50/
>>
>> and
>>
>> http://solidsoftwaretools.com/gf/project/dh10bfrag/.
>>
>> Reference sequences are included.
>>
>> Scott
>>
>> Scott Markel, Ph.D.
>> Principal Bioinformatics Architect email: smarkel at accelrys.com
>> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
>> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
>> San Diego, CA 92121 fax: +1 858 799 5222
>> USA web: http://www.accelrys.com
>>
>> http://www.linkedin.com/in/smarkel
>> Vice President, Board of Directors:
>> International Society for Computational Biology
>> Chair: ISCB Publications Committee
>> Associate Editor: PLoS Computational Biology
>> Editorial Board: Briefings in Bioinformatics
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org 
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dan Kortschak
>> Sent: Monday, 18 January 2010 6:48 PM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and Bio::Assembly::IO::bowtie 
>> now available BETA
>>
>> Hi All,
>>
>> A wrapper and output parser for bowtie 'ultrafast, memory-efficient
>> short read aligner' are now available in the bioperl-live and
>> bioperl-run subversion repositories (bioperl-live/trunk at 16727 and
>> bioperl-run/trunk at 16726). Bowtie details are available here:
>>
>> http://bowtie-bio.sourceforge.net/index.shtml
>>
>> The modules can return a Bio::Assembly::Scaffold object (operating via
>> the MAJ's Bio::Assembly::IO::sam module in bioperl-live/trunk
>> which requires lstein's Bio::DB::Sam, from CPAN). Note that Bio::DB::Sam
>> uses large amounts of memory - the test suite works for me with >=2GB
>> but not with 1GB due to this. (Is there a disk file system based tool
>> for this for large projects?)
>>
>> Bowtie (>0.12.0) can align in colour space, but this is not currently
>> supported by the wrapper though it should not be difficult to add. If
>> someone can point me to a small set of colour space reads and a
>> reference sequence I will be able to use these for testing.
>>
>> Thanks to the core devs for helping me with many of my problems in
>> putting this together.
>>
>> Dan
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From bimber at wisc.edu  Mon Feb 22 11:40:26 2010
From: bimber at wisc.edu (Ben Bimber)
Date: Mon, 22 Feb 2010 10:40:26 -0600
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie
	andBio::Assembly::IO::bowtie now available BETA
In-Reply-To: <21464_1266856150_ZZg0S4_DKRPYk.00_6DCA647E40D847A5BCC7815EB711B791@NewLife>
References: <1263869267.12881.33.camel@zoidberg.mbs.adelaide.edu.au>
	<5ACBA19439E77B43A06F4CAB897EC977019B31FE@EXCH1-COLO.accelrys.net>
	<6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle>
	<9f985cdc1002211828w63811d75n48d8cb3093e6d076@mail.gmail.com>
	<21464_1266856150_ZZg0S4_DKRPYk.00_6DCA647E40D847A5BCC7815EB711B791@NewLife>
Message-ID: <9f985cdc1002220840w295712b0k91d9938240094de0@mail.gmail.com>

Mark,

Thanks for the reply.  I'll put in that bug.

I'm actually writing a couple wrappers for other utilities based on
bioperl.  Is there a preferred method to handle setting file path at
the moment?  Could you point me to a wrapper that uses this?

Ideally, I'd prefer to support both letting the user either set the
path via an environmental variable or when they create the factory:

	my $factory = Bio::Tools::Run::XXXXX->new(
            -command => 'blat',
            -prog_dir => '/myPath',
            );

-Ben


On Mon, Feb 22, 2010 at 10:01 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
> Hi Ben-- this is definitely a valid issue. The newest wrappers are
> works in progress; can you submit a bug report at bugzilla.bioperl.org ?
> (as a Windows users, I call it a bug, but Dan may disagree!) (FYI,
> some improvements to the wrapper interfaces are coming soon that
> will attempt to standardize some of these kinds of issues, so stay tuned)
> MAJ
> ----- Original Message ----- From: "Ben Bimber" <bbimber at gmail.com>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Sunday, February 21, 2010 9:28 PM
> Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie
> andBio::Assembly::IO::bowtie now available BETA
>
>
> Hello,
>
> I just came across the bowtie wrapper and it looks very useful.
> However, I am having trouble with the current logic to find the bowtie
> executable path. ?In Bio::Tools::Run::Bowtie, line 240, it uses the
> command 'which', which is not windows compatible as far as I know (i'm
> running a PC).
>
> I made a crude hack to get it to work on my machine, but is this
> something you would consider changing in bowtie.pm? ?I'm not sure what
> the most versatile approach to setting program path in a wrapper would
> be, but I'd love to hear it. ?I have still not entirely wrapped my
> head around all the methods to handle program path in wrappers, so
> perhaps there's a way to override this that I'm not aware of.
>
> Thanks,
> Ben
>
>
>
>
> On Tue, Jan 19, 2010 at 3:18 PM, Dan Kortschak
> <dan.kortschak at adelaide.edu.au> wrote:
>>
>> Great.
>>
>> Thanks, Scott.
>>
>> Dan
>>
>> On Tue, 2010-01-19 at 10:00 -0800, Scott Markel wrote:
>>>
>>> Dan,
>>>
>>> Life Tech has sample data for E. coli at
>>>
>>> http://solidsoftwaretools.com/gf/project/ecoli2x50/
>>>
>>> and
>>>
>>> http://solidsoftwaretools.com/gf/project/dh10bfrag/.
>>>
>>> Reference sequences are included.
>>>
>>> Scott
>>>
>>> Scott Markel, Ph.D.
>>> Principal Bioinformatics Architect email: smarkel at accelrys.com
>>> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
>>> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
>>> San Diego, CA 92121 fax: +1 858 799 5222
>>> USA web: http://www.accelrys.com
>>>
>>> http://www.linkedin.com/in/smarkel
>>> Vice President, Board of Directors:
>>> International Society for Computational Biology
>>> Chair: ISCB Publications Committee
>>> Associate Editor: PLoS Computational Biology
>>> Editorial Board: Briefings in Bioinformatics
>>>
>>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dan Kortschak
>>> Sent: Monday, 18 January 2010 6:48 PM
>>> To: bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and
>>> Bio::Assembly::IO::bowtie now available BETA
>>>
>>> Hi All,
>>>
>>> A wrapper and output parser for bowtie 'ultrafast, memory-efficient
>>> short read aligner' are now available in the bioperl-live and
>>> bioperl-run subversion repositories (bioperl-live/trunk at 16727 and
>>> bioperl-run/trunk at 16726). Bowtie details are available here:
>>>
>>> http://bowtie-bio.sourceforge.net/index.shtml
>>>
>>> The modules can return a Bio::Assembly::Scaffold object (operating via
>>> the MAJ's Bio::Assembly::IO::sam module in bioperl-live/trunk
>>> which requires lstein's Bio::DB::Sam, from CPAN). Note that Bio::DB::Sam
>>> uses large amounts of memory - the test suite works for me with >=2GB
>>> but not with 1GB due to this. (Is there a disk file system based tool
>>> for this for large projects?)
>>>
>>> Bowtie (>0.12.0) can align in colour space, but this is not currently
>>> supported by the wrapper though it should not be difficult to add. If
>>> someone can point me to a small set of colour space reads and a
>>> reference sequence I will be able to use these for testing.
>>>
>>> Thanks to the core devs for helping me with many of my problems in
>>> putting this together.
>>>
>>> Dan
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From jason.stajich at gmail.com  Mon Feb 22 11:41:06 2010
From: jason.stajich at gmail.com (Jason Stajich)
Date: Mon, 22 Feb 2010 11:41:06 -0500
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie
	andBio::Assembly::IO::bowtie now available BETA
In-Reply-To: <6DCA647E40D847A5BCC7815EB711B791@NewLife>
References: <1263869267.12881.33.camel@zoidberg.mbs.adelaide.edu.au><5ACBA19439E77B43A06F4CAB897EC977019B31FE@EXCH1-COLO.accelrys.net><6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle>
	<9f985cdc1002211828w63811d75n48d8cb3093e6d076@mail.gmail.com>
	<6DCA647E40D847A5BCC7815EB711B791@NewLife>
Message-ID: <C436D5D8-85E4-4D96-9A7E-1DD5E625C747@gmail.com>

We had a perl only executable funding routine in bio::root:: or the  
runwrapper module - dan did you not want to use it?

Sent from my iPod

On Feb 22, 2010, at 11:01, "Mark A. Jensen" <maj at fortinbras.us> wrote:

> Hi Ben-- this is definitely a valid issue. The newest wrappers are
> works in progress; can you submit a bug report at  
> bugzilla.bioperl.org ?
> (as a Windows users, I call it a bug, but Dan may disagree!) (FYI,
> some improvements to the wrapper interfaces are coming soon that
> will attempt to standardize some of these kinds of issues, so stay  
> tuned)
> MAJ
> ----- Original Message ----- From: "Ben Bimber" <bbimber at gmail.com>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Sunday, February 21, 2010 9:28 PM
> Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie  
> andBio::Assembly::IO::bowtie now available BETA
>
>
> Hello,
>
> I just came across the bowtie wrapper and it looks very useful.
> However, I am having trouble with the current logic to find the bowtie
> executable path.  In Bio::Tools::Run::Bowtie, line 240, it uses the
> command 'which', which is not windows compatible as far as I know (i'm
> running a PC).
>
> I made a crude hack to get it to work on my machine, but is this
> something you would consider changing in bowtie.pm?  I'm not sure what
> the most versatile approach to setting program path in a wrapper would
> be, but I'd love to hear it.  I have still not entirely wrapped my
> head around all the methods to handle program path in wrappers, so
> perhaps there's a way to override this that I'm not aware of.
>
> Thanks,
> Ben
>
>
>
>
> On Tue, Jan 19, 2010 at 3:18 PM, Dan Kortschak
> <dan.kortschak at adelaide.edu.au> wrote:
>> Great.
>>
>> Thanks, Scott.
>>
>> Dan
>>
>> On Tue, 2010-01-19 at 10:00 -0800, Scott Markel wrote:
>>> Dan,
>>>
>>> Life Tech has sample data for E. coli at
>>>
>>> http://solidsoftwaretools.com/gf/project/ecoli2x50/
>>>
>>> and
>>>
>>> http://solidsoftwaretools.com/gf/project/dh10bfrag/.
>>>
>>> Reference sequences are included.
>>>
>>> Scott
>>>
>>> Scott Markel, Ph.D.
>>> Principal Bioinformatics Architect email: smarkel at accelrys.com
>>> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
>>> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
>>> San Diego, CA 92121 fax: +1 858 799 5222
>>> USA web: http://www.accelrys.com
>>>
>>> http://www.linkedin.com/in/smarkel
>>> Vice President, Board of Directors:
>>> International Society for Computational Biology
>>> Chair: ISCB Publications Committee
>>> Associate Editor: PLoS Computational Biology
>>> Editorial Board: Briefings in Bioinformatics
>>>
>>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
>>> bounces at lists.open-bio.org] On Behalf Of Dan Kortschak
>>> Sent: Monday, 18 January 2010 6:48 PM
>>> To: bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and  
>>> Bio::Assembly::IO::bowtie now available BETA
>>>
>>> Hi All,
>>>
>>> A wrapper and output parser for bowtie 'ultrafast, memory-efficient
>>> short read aligner' are now available in the bioperl-live and
>>> bioperl-run subversion repositories (bioperl-live/trunk at 16727 and
>>> bioperl-run/trunk at 16726). Bowtie details are available here:
>>>
>>> http://bowtie-bio.sourceforge.net/index.shtml
>>>
>>> The modules can return a Bio::Assembly::Scaffold object (operating  
>>> via
>>> the MAJ's Bio::Assembly::IO::sam module in bioperl-live/trunk
>>> which requires lstein's Bio::DB::Sam, from CPAN). Note that  
>>> Bio::DB::Sam
>>> uses large amounts of memory - the test suite works for me with  
>>> >=2GB
>>> but not with 1GB due to this. (Is there a disk file system based  
>>> tool
>>> for this for large projects?)
>>>
>>> Bowtie (>0.12.0) can align in colour space, but this is not  
>>> currently
>>> supported by the wrapper though it should not be difficult to add.  
>>> If
>>> someone can point me to a small set of colour space reads and a
>>> reference sequence I will be able to use these for testing.
>>>
>>> Thanks to the core devs for helping me with many of my problems in
>>> putting this together.
>>>
>>> Dan
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From sharpton at berkeley.edu  Mon Feb 22 11:34:12 2010
From: sharpton at berkeley.edu (Thomas Sharpton)
Date: Mon, 22 Feb 2010 08:34:12 -0800
Subject: [Bioperl-l] hmmer3/hmmscan
In-Reply-To: <fb76f2af73343.4b82b777@utu.fi>
References: <fb76f2af73343.4b82b777@utu.fi>
Message-ID: <97A65763-35D1-441F-B724-A9F4DDF4F651@berkeley.edu>

Hi Joonas,

I've developed a SearchIO module for HMMER3 hmmsearch and am in the  
middle of expanding this to cover hmmscan as well (been meaning to  
contact the list about the hmmsearch module as it is). I can contact  
you when the expansion is finished (will also ping the list), which  
will hopefully be within the next week.

-Tom

On Feb 22, 2010, at 6:57 AM, Joonas J?msen wrote:

> Hi! Does Bioperl support parsing hmmscan/hmmer3?
>
> Best regards,
> Joonas J?msen.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From maj at fortinbras.us  Mon Feb 22 12:41:56 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 22 Feb 2010 12:41:56 -0500
Subject: [Bioperl-l] Bio::Tools::Run::BowtieandBio::Assembly::IO::bowtie
	now available BETA
In-Reply-To: <C436D5D8-85E4-4D96-9A7E-1DD5E625C747@gmail.com>
References: <1263869267.12881.33.camel@zoidberg.mbs.adelaide.edu.au><5ACBA19439E77B43A06F4CAB897EC977019B31FE@EXCH1-COLO.accelrys.net><6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle><9f985cdc1002211828w63811d75n48d8cb3093e6d076@mail.gmail.com><6DCA647E40D847A5BCC7815EB711B791@NewLife>
	<C436D5D8-85E4-4D96-9A7E-1DD5E625C747@gmail.com>
Message-ID: <F8D5488DC22646B6AE4F6F48F1C25DD5@NewLife>

I believe we are using it, I think that the 'which' solution is somewhat crufty
at this stage ...
----- Original Message ----- 
From: "Jason Stajich" <jason.stajich at gmail.com>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <bioperl-l at lists.open-bio.org>; "Ben Bimber" <bbimber at gmail.com>
Sent: Monday, February 22, 2010 11:41 AM
Subject: Re: [Bioperl-l] Bio::Tools::Run::BowtieandBio::Assembly::IO::bowtie now 
available BETA


> We had a perl only executable funding routine in bio::root:: or the 
> runwrapper module - dan did you not want to use it?
>
> Sent from my iPod
>
> On Feb 22, 2010, at 11:01, "Mark A. Jensen" <maj at fortinbras.us> wrote:
>
>> Hi Ben-- this is definitely a valid issue. The newest wrappers are
>> works in progress; can you submit a bug report at  bugzilla.bioperl.org ?
>> (as a Windows users, I call it a bug, but Dan may disagree!) (FYI,
>> some improvements to the wrapper interfaces are coming soon that
>> will attempt to standardize some of these kinds of issues, so stay  tuned)
>> MAJ
>> ----- Original Message ----- From: "Ben Bimber" <bbimber at gmail.com>
>> To: <bioperl-l at lists.open-bio.org>
>> Sent: Sunday, February 21, 2010 9:28 PM
>> Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie 
>> andBio::Assembly::IO::bowtie now available BETA
>>
>>
>> Hello,
>>
>> I just came across the bowtie wrapper and it looks very useful.
>> However, I am having trouble with the current logic to find the bowtie
>> executable path.  In Bio::Tools::Run::Bowtie, line 240, it uses the
>> command 'which', which is not windows compatible as far as I know (i'm
>> running a PC).
>>
>> I made a crude hack to get it to work on my machine, but is this
>> something you would consider changing in bowtie.pm?  I'm not sure what
>> the most versatile approach to setting program path in a wrapper would
>> be, but I'd love to hear it.  I have still not entirely wrapped my
>> head around all the methods to handle program path in wrappers, so
>> perhaps there's a way to override this that I'm not aware of.
>>
>> Thanks,
>> Ben
>>
>>
>>
>>
>> On Tue, Jan 19, 2010 at 3:18 PM, Dan Kortschak
>> <dan.kortschak at adelaide.edu.au> wrote:
>>> Great.
>>>
>>> Thanks, Scott.
>>>
>>> Dan
>>>
>>> On Tue, 2010-01-19 at 10:00 -0800, Scott Markel wrote:
>>>> Dan,
>>>>
>>>> Life Tech has sample data for E. coli at
>>>>
>>>> http://solidsoftwaretools.com/gf/project/ecoli2x50/
>>>>
>>>> and
>>>>
>>>> http://solidsoftwaretools.com/gf/project/dh10bfrag/.
>>>>
>>>> Reference sequences are included.
>>>>
>>>> Scott
>>>>
>>>> Scott Markel, Ph.D.
>>>> Principal Bioinformatics Architect email: smarkel at accelrys.com
>>>> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
>>>> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
>>>> San Diego, CA 92121 fax: +1 858 799 5222
>>>> USA web: http://www.accelrys.com
>>>>
>>>> http://www.linkedin.com/in/smarkel
>>>> Vice President, Board of Directors:
>>>> International Society for Computational Biology
>>>> Chair: ISCB Publications Committee
>>>> Associate Editor: PLoS Computational Biology
>>>> Editorial Board: Briefings in Bioinformatics
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
>>>> bounces at lists.open-bio.org] On Behalf Of Dan Kortschak
>>>> Sent: Monday, 18 January 2010 6:48 PM
>>>> To: bioperl-l at lists.open-bio.org
>>>> Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and  Bio::Assembly::IO::bowtie 
>>>> now available BETA
>>>>
>>>> Hi All,
>>>>
>>>> A wrapper and output parser for bowtie 'ultrafast, memory-efficient
>>>> short read aligner' are now available in the bioperl-live and
>>>> bioperl-run subversion repositories (bioperl-live/trunk at 16727 and
>>>> bioperl-run/trunk at 16726). Bowtie details are available here:
>>>>
>>>> http://bowtie-bio.sourceforge.net/index.shtml
>>>>
>>>> The modules can return a Bio::Assembly::Scaffold object (operating  via
>>>> the MAJ's Bio::Assembly::IO::sam module in bioperl-live/trunk
>>>> which requires lstein's Bio::DB::Sam, from CPAN). Note that  Bio::DB::Sam
>>>> uses large amounts of memory - the test suite works for me with
>>>> >=2GB
>>>> but not with 1GB due to this. (Is there a disk file system based  tool
>>>> for this for large projects?)
>>>>
>>>> Bowtie (>0.12.0) can align in colour space, but this is not  currently
>>>> supported by the wrapper though it should not be difficult to add.  If
>>>> someone can point me to a small set of colour space reads and a
>>>> reference sequence I will be able to use these for testing.
>>>>
>>>> Thanks to the core devs for helping me with many of my problems in
>>>> putting this together.
>>>>
>>>> Dan
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From rmb32 at cornell.edu  Mon Feb 22 13:10:02 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Mon, 22 Feb 2010 10:10:02 -0800
Subject: [Bioperl-l] BioPerl, CPAN Modules, and Linux Packages
In-Reply-To: <4B81FD8D.8020309@gmail.com>
References: <f135c01c1002191057t2a70ddf2vc85921d26b7fe9c3@mail.gmail.com>
	<4B81FD8D.8020309@gmail.com>
Message-ID: <4B82C87A.30203@cornell.edu>

Florent Angly wrote:
 > or too old, the best thing to do is to make a suitable package for it.

We used to do this at SGN, and it's OK if you're not really using CPAN 
much, but it does not scale well if you use a lot of modules from CPAN. 
  You end up having to maintain in-house large numbers of interrelated 
Debian packages, and every time somebody wants to start using a new 
module, or there's a critical upstream bugfix, you need to make new 
releases of at least one, possibly many, of your in-house Debian packages.

Rob



From maj at fortinbras.us  Mon Feb 22 12:53:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 22 Feb 2010 12:53:25 -0500
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie
	andBio::Assembly::IO::bowtie now available BETA
In-Reply-To: <9f985cdc1002220840w295712b0k91d9938240094de0@mail.gmail.com>
References: <1263869267.12881.33.camel@zoidberg.mbs.adelaide.edu.au>
	<5ACBA19439E77B43A06F4CAB897EC977019B31FE@EXCH1-COLO.accelrys.net>
	<6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle>
	<9f985cdc1002211828w63811d75n48d8cb3093e6d076@mail.gmail.com>
	<21464_1266856150_ZZg0S4_DKRPYk.00_6DCA647E40D847A5BCC7815EB711B791@NewLife>
	<9f985cdc1002220840w295712b0k91d9938240094de0@mail.gmail.com>
Message-ID: <95EC0F7536CA4515A249F18A25224C2A@NewLife>

Hi Ben--
I'd direct you to Bio::Tools::Run::WrapperBase and 
B:T:R:WrapperBase::CommandExts
(in bioperl-live). You'll want your wrapper to inherit from B:T:R:WrapperBase; 
then
(as Jason pointed out) the executable() and program_dir() methods will be 
available
to it. You can rely on executable() to find the path using the PATH variable, or 
you can
use executable/program_dir to set these paths explicitly. ComandExts adds 
methods
to WrapperBase that allow more complex programs or groups of programs to be
defined in a set of global config variables: Bowtie, BWA, Maq, and Samtools use 
this
module.
(What I'm secretly working on is a package called WrapperMaker, that uses XML
based on an XML Schema to define program names, commands, inputs and other 
details
(rather than an ugly Config module exporting hard to remember global variables),
passing them to CommandExts and providing a nice WrapperBase object
transparently. This is getting there, but isn't ready for primetime.)
cheers MAJ
----- Original Message ----- 
From: "Ben Bimber" <bimber at wisc.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Monday, February 22, 2010 11:40 AM
Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie andBio::Assembly::IO::bowtie 
now available BETA


Mark,

Thanks for the reply.  I'll put in that bug.

I'm actually writing a couple wrappers for other utilities based on
bioperl.  Is there a preferred method to handle setting file path at
the moment?  Could you point me to a wrapper that uses this?

Ideally, I'd prefer to support both letting the user either set the
path via an environmental variable or when they create the factory:

my $factory = Bio::Tools::Run::XXXXX->new(
            -command => 'blat',
            -prog_dir => '/myPath',
            );

-Ben


On Mon, Feb 22, 2010 at 10:01 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
> Hi Ben-- this is definitely a valid issue. The newest wrappers are
> works in progress; can you submit a bug report at bugzilla.bioperl.org ?
> (as a Windows users, I call it a bug, but Dan may disagree!) (FYI,
> some improvements to the wrapper interfaces are coming soon that
> will attempt to standardize some of these kinds of issues, so stay tuned)
> MAJ
> ----- Original Message ----- From: "Ben Bimber" <bbimber at gmail.com>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Sunday, February 21, 2010 9:28 PM
> Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie
> andBio::Assembly::IO::bowtie now available BETA
>
>
> Hello,
>
> I just came across the bowtie wrapper and it looks very useful.
> However, I am having trouble with the current logic to find the bowtie
> executable path. In Bio::Tools::Run::Bowtie, line 240, it uses the
> command 'which', which is not windows compatible as far as I know (i'm
> running a PC).
>
> I made a crude hack to get it to work on my machine, but is this
> something you would consider changing in bowtie.pm? I'm not sure what
> the most versatile approach to setting program path in a wrapper would
> be, but I'd love to hear it. I have still not entirely wrapped my
> head around all the methods to handle program path in wrappers, so
> perhaps there's a way to override this that I'm not aware of.
>
> Thanks,
> Ben
>
>
>
>
> On Tue, Jan 19, 2010 at 3:18 PM, Dan Kortschak
> <dan.kortschak at adelaide.edu.au> wrote:
>>
>> Great.
>>
>> Thanks, Scott.
>>
>> Dan
>>
>> On Tue, 2010-01-19 at 10:00 -0800, Scott Markel wrote:
>>>
>>> Dan,
>>>
>>> Life Tech has sample data for E. coli at
>>>
>>> http://solidsoftwaretools.com/gf/project/ecoli2x50/
>>>
>>> and
>>>
>>> http://solidsoftwaretools.com/gf/project/dh10bfrag/.
>>>
>>> Reference sequences are included.
>>>
>>> Scott
>>>
>>> Scott Markel, Ph.D.
>>> Principal Bioinformatics Architect email: smarkel at accelrys.com
>>> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
>>> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
>>> San Diego, CA 92121 fax: +1 858 799 5222
>>> USA web: http://www.accelrys.com
>>>
>>> http://www.linkedin.com/in/smarkel
>>> Vice President, Board of Directors:
>>> International Society for Computational Biology
>>> Chair: ISCB Publications Committee
>>> Associate Editor: PLoS Computational Biology
>>> Editorial Board: Briefings in Bioinformatics
>>>
>>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dan Kortschak
>>> Sent: Monday, 18 January 2010 6:48 PM
>>> To: bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and
>>> Bio::Assembly::IO::bowtie now available BETA
>>>
>>> Hi All,
>>>
>>> A wrapper and output parser for bowtie 'ultrafast, memory-efficient
>>> short read aligner' are now available in the bioperl-live and
>>> bioperl-run subversion repositories (bioperl-live/trunk at 16727 and
>>> bioperl-run/trunk at 16726). Bowtie details are available here:
>>>
>>> http://bowtie-bio.sourceforge.net/index.shtml
>>>
>>> The modules can return a Bio::Assembly::Scaffold object (operating via
>>> the MAJ's Bio::Assembly::IO::sam module in bioperl-live/trunk
>>> which requires lstein's Bio::DB::Sam, from CPAN). Note that Bio::DB::Sam
>>> uses large amounts of memory - the test suite works for me with >=2GB
>>> but not with 1GB due to this. (Is there a disk file system based tool
>>> for this for large projects?)
>>>
>>> Bowtie (>0.12.0) can align in colour space, but this is not currently
>>> supported by the wrapper though it should not be difficult to add. If
>>> someone can point me to a small set of colour space reads and a
>>> reference sequence I will be able to use these for testing.
>>>
>>> Thanks to the core devs for helping me with many of my problems in
>>> putting this together.
>>>
>>> Dan
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From cjfields at illinois.edu  Mon Feb 22 13:46:39 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 22 Feb 2010 12:46:39 -0600
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie
 andBio::Assembly::IO::bowtie now available BETA
In-Reply-To: <95EC0F7536CA4515A249F18A25224C2A@NewLife>
References: <1263869267.12881.33.camel@zoidberg.mbs.adelaide.edu.au>
	<5ACBA19439E77B43A06F4CAB897EC977019B31FE@EXCH1-COLO.accelrys.net>
	<6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle>
	<9f985cdc1002211828w63811d75n48d8cb3093e6d076@mail.gmail.com>
	<21464_1266856150_ZZg0S4_DKRPYk.00_6DCA647E40D847A5BCC7815EB711B791@NewLife>
	<9f985cdc1002220840w295712b0k91d9938240094de0@mail.gmail.com>
	<95EC0F7536CA4515A249F18A25224C2A@NewLife>
Message-ID: <1266864399.564.19.camel@pyrimidine.igb.uiuc.edu>

On Mon, 2010-02-22 at 12:53 -0500, Mark A. Jensen wrote:
> ... I'm secretly working on is a package called WrapperMaker, that uses XML
> based on an XML Schema to define program names, commands, inputs and other 
> details
> (rather than an ugly Config module exporting hard to remember global variables),
> passing them to CommandExts and providing a nice WrapperBase object
> transparently. This is getting there, but isn't ready for primetime.)
> cheers MAJ

Sounds promising; I could foresee having a config-file based approach
usable across other Bio* languages; they would just need to come up with
similar wrappers and parsers.  Might be something to bring up with the
biopython/bioruby crowd.

Also, have you thought about possibly abstracting out parts so that one
could describe the relevant bits in alternative formats (JSON, YAML,
etc) other than XML?  Something like this might be handy:

http://search.cpan.org/~bricas/Config-Any-0.19/

chris


From maj at fortinbras.us  Mon Feb 22 14:07:29 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 22 Feb 2010 14:07:29 -0500
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie
	andBio::Assembly::IO::bowtie now available BETA
In-Reply-To: <1266864399.564.19.camel@pyrimidine.igb.uiuc.edu>
References: <1263869267.12881.33.camel@zoidberg.mbs.adelaide.edu.au><5ACBA19439E77B43A06F4CAB897EC977019B31FE@EXCH1-COLO.accelrys.net><6815_1263936129_ZZg0P4mbwkuHv.00_1263935900.4813.0.camel@epistle><9f985cdc1002211828w63811d75n48d8cb3093e6d076@mail.gmail.com><21464_1266856150_ZZg0S4_DKRPYk.00_6DCA647E40D847A5BCC7815EB711B791@NewLife><9f985cdc1002220840w295712b0k91d9938240094de0@mail.gmail.com><95EC0F7536CA4515A249F18A25224C2A@NewLife>
	<1266864399.564.19.camel@pyrimidine.igb.uiuc.edu>
Message-ID: <0953716217FA4BB1A3214B6078E20496@NewLife>

It's actually seems to work pretty well so far--validation on xsd + integration 
with
wrapperbase/commandexts. One does:

use Bio::Tools::WrapperMaker;

$fac = Bio::Tools::WrapperMaker->compile( -defs => 'samtools.xml' );

$fac->set_parameters( -command => 'view', -bam_out => 1, -sam_in => 1);
$fac->run( -bam => 'my.sam', -out => 'my.bam');

or put it in a namespace

Bio::Tools::WrapperMaker->compile( -defs => 'samtools.xml', -namespace => 
"My::Samtools");

$fac = My::Samtools->new();
...

I've been working on a WrapperMaker defs editor
at Fortinbras so people don't have to write XML.
Tuits are in short supply lately, but I'm thinking this might be a
good Summer O Code project...
MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "bioperl-l" <bioperl-l at lists.open-bio.org>; "Ben Bimber" <bimber at wisc.edu>
Sent: Monday, February 22, 2010 1:46 PM
Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie andBio::Assembly::IO::bowtie 
now available BETA


> On Mon, 2010-02-22 at 12:53 -0500, Mark A. Jensen wrote:
>> ... I'm secretly working on is a package called WrapperMaker, that uses XML
>> based on an XML Schema to define program names, commands, inputs and other
>> details
>> (rather than an ugly Config module exporting hard to remember global 
>> variables),
>> passing them to CommandExts and providing a nice WrapperBase object
>> transparently. This is getting there, but isn't ready for primetime.)
>> cheers MAJ
>
> Sounds promising; I could foresee having a config-file based approach
> usable across other Bio* languages; they would just need to come up with
> similar wrappers and parsers.  Might be something to bring up with the
> biopython/bioruby crowd.
>
> Also, have you thought about possibly abstracting out parts so that one
> could describe the relevant bits in alternative formats (JSON, YAML,
> etc) other than XML?  Something like this might be handy:
>
> http://search.cpan.org/~bricas/Config-Any-0.19/
>
> chris
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From cjfields at illinois.edu  Mon Feb 22 16:09:23 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 22 Feb 2010 15:09:23 -0600
Subject: [Bioperl-l] Bioperl on GitHub
Message-ID: <1266872963.4519.103.camel@pyrimidine.igb.uiuc.edu>

All,

As a backup for the anonymous svn access on code.open-bio.org, I have
set up a few READ-ONLY mirrors on GitHub for the main trunk code of
several BioPerl distributions, generated using git-svn:  

http://github.com/bioperl

These are sync'ed every 15 minutes.

Note the emphasis on 'read-only'; we don't anticipate migrating code
over to github completely, at least at the moment.  Based on that and
several issues with git/svn two-way syncing (outlined in the git-svn man
pages and elsewhere), we will not support pull requests directly in
github.

enjoy!

chris


From s.denaxas at gmail.com  Mon Feb 22 16:20:53 2010
From: s.denaxas at gmail.com (Spiros Denaxas)
Date: Mon, 22 Feb 2010 21:20:53 +0000
Subject: [Bioperl-l] Bioperl on GitHub
In-Reply-To: <1266872963.4519.103.camel@pyrimidine.igb.uiuc.edu>
References: <1266872963.4519.103.camel@pyrimidine.igb.uiuc.edu>
Message-ID: <bba689ec1002221320o4f1a6bc9qbabe7c1794d5c426@mail.gmail.com>

Nice one Chris, thank you.

Spiros

On Mon, Feb 22, 2010 at 9:09 PM, Chris Fields <cjfields at illinois.edu> wrote:
> All,
>
> As a backup for the anonymous svn access on code.open-bio.org, I have
> set up a few READ-ONLY mirrors on GitHub for the main trunk code of
> several BioPerl distributions, generated using git-svn:
>
> http://github.com/bioperl
>
> These are sync'ed every 15 minutes.
>
> Note the emphasis on 'read-only'; we don't anticipate migrating code
> over to github completely, at least at the moment. ?Based on that and
> several issues with git/svn two-way syncing (outlined in the git-svn man
> pages and elsewhere), we will not support pull requests directly in
> github.
>
> enjoy!
>
> chris
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From maj at fortinbras.us  Mon Feb 22 16:28:01 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 22 Feb 2010 16:28:01 -0500
Subject: [Bioperl-l] Bioperl on GitHub
In-Reply-To: <1266872963.4519.103.camel@pyrimidine.igb.uiuc.edu>
References: <1266872963.4519.103.camel@pyrimidine.igb.uiuc.edu>
Message-ID: <0C5EB0508A5248ABBED3DEEFC7D6CDFA@NewLife>

+1
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Monday, February 22, 2010 4:09 PM
Subject: [Bioperl-l] Bioperl on GitHub


> All,
> 
> As a backup for the anonymous svn access on code.open-bio.org, I have
> set up a few READ-ONLY mirrors on GitHub for the main trunk code of
> several BioPerl distributions, generated using git-svn:  
> 
> http://github.com/bioperl
> 
> These are sync'ed every 15 minutes.
> 
> Note the emphasis on 'read-only'; we don't anticipate migrating code
> over to github completely, at least at the moment.  Based on that and
> several issues with git/svn two-way syncing (outlined in the git-svn man
> pages and elsewhere), we will not support pull requests directly in
> github.
> 
> enjoy!
> 
> chris
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
>

From dan.kortschak at adelaide.edu.au  Mon Feb 22 17:18:05 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Tue, 23 Feb 2010 08:48:05 +1030
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie
 andBio::Assembly::IO::bowtie now available BETA
In-Reply-To: <mailman.13.1266858004.18870.bioperl-l@lists.open-bio.org>
References: <mailman.13.1266858004.18870.bioperl-l@lists.open-bio.org>
Message-ID: <1266877085.4521.32.camel@epistle>

Hi Jason,

No I didn't use that, but I'm happy to change those part of the new
method so that it works with our cousins (MAJ, it's not that I don't
consider it a bug, I just very rarely even consider Windows at all - yes
that's bad, but I find my life works better that way ;) - though I'm
glad to have people find things that I am unable to test, and fix them
when found).

It should be a simple case of using the executable[s] methods which go
through B:R:IO->exists_exe.

Ben would you log a bug? Also note that as the module stands the
executable location[s] with WrapperBase[::CommandExts] derived modules
can be changed through the executable[s] methods, so your desire to have
a user specified executable path is available. The function of that
method was not completely resolved when I wrote the new method, so the
unix command was used - it will be fixed. As far as using an $ENV{} var,
I'd be happy to do that deeply if there is already an established
variable defining the executable locations, though I don't think this is
the case (there is a var for index locations - which I don't query, and
completely ignore, this may be a bug request).

cheers
Dan

On Mon, 2010-02-22 at 12:00 -0500, Jason Stajich wrote:
> We had a perl only executable funding routine in bio::root:: or the  
> runwrapper module - dan did you not want to use it?
> 
> Sent from my iPod
> 
> On Feb 22, 2010, at 11:01, "Mark A. Jensen" <maj at fortinbras.us> wrote:
> 
> > Hi Ben-- this is definitely a valid issue. The newest wrappers are
> > works in progress; can you submit a bug report at  
> > bugzilla.bioperl.org ?
> > (as a Windows users, I call it a bug, but Dan may disagree!) (FYI,
> > some improvements to the wrapper interfaces are coming soon that
> > will attempt to standardize some of these kinds of issues, so stay  
> > tuned)
> > MAJ
> > ----- Original Message ----- From: "Ben Bimber" <bbimber at gmail.com>
> > To: <bioperl-l at lists.open-bio.org>
> > Sent: Sunday, February 21, 2010 9:28 PM
> > Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie  
> > andBio::Assembly::IO::bowtie now available BETA
> >
> >
> > Hello,
> >
> > I just came across the bowtie wrapper and it looks very useful.
> > However, I am having trouble with the current logic to find the
> bowtie
> > executable path.  In Bio::Tools::Run::Bowtie, line 240, it uses the
> > command 'which', which is not windows compatible as far as I know
> (i'm
> > running a PC).
> >
> > I made a crude hack to get it to work on my machine, but is this
> > something you would consider changing in bowtie.pm?  I'm not sure
> what
> > the most versatile approach to setting program path in a wrapper
> would
> > be, but I'd love to hear it.  I have still not entirely wrapped my
> > head around all the methods to handle program path in wrappers, so
> > perhaps there's a way to override this that I'm not aware of.
> >
> > Thanks,
> > Ben


From bbimber at gmail.com  Mon Feb 22 17:23:01 2010
From: bbimber at gmail.com (Ben Bimber)
Date: Mon, 22 Feb 2010 16:23:01 -0600
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie
	andBio::Assembly::IO::bowtie now available BETA
In-Reply-To: <1266877085.4521.32.camel@epistle>
References: <mailman.13.1266858004.18870.bioperl-l@lists.open-bio.org>
	<1266877085.4521.32.camel@epistle>
Message-ID: <9f985cdc1002221423l1081351fh69e9570a51fccf70@mail.gmail.com>

Dan,

I believe I did enter a bug this morning.  An env variable is not
necessary.  As long as we have some reasonable mechanism to specify
exe location when we run this on different servers that's all we need.
 thanks for making the change.

-ben



On Mon, Feb 22, 2010 at 4:18 PM, Dan Kortschak
<dan.kortschak at adelaide.edu.au> wrote:
> Hi Jason,
>
> No I didn't use that, but I'm happy to change those part of the new
> method so that it works with our cousins (MAJ, it's not that I don't
> consider it a bug, I just very rarely even consider Windows at all - yes
> that's bad, but I find my life works better that way ;) - though I'm
> glad to have people find things that I am unable to test, and fix them
> when found).
>
> It should be a simple case of using the executable[s] methods which go
> through B:R:IO->exists_exe.
>
> Ben would you log a bug? Also note that as the module stands the
> executable location[s] with WrapperBase[::CommandExts] derived modules
> can be changed through the executable[s] methods, so your desire to have
> a user specified executable path is available. The function of that
> method was not completely resolved when I wrote the new method, so the
> unix command was used - it will be fixed. As far as using an $ENV{} var,
> I'd be happy to do that deeply if there is already an established
> variable defining the executable locations, though I don't think this is
> the case (there is a var for index locations - which I don't query, and
> completely ignore, this may be a bug request).
>
> cheers
> Dan
>
> On Mon, 2010-02-22 at 12:00 -0500, Jason Stajich wrote:
>> We had a perl only executable funding routine in bio::root:: or the
>> runwrapper module - dan did you not want to use it?
>>
>> Sent from my iPod
>>
>> On Feb 22, 2010, at 11:01, "Mark A. Jensen" <maj at fortinbras.us> wrote:
>>
>> > Hi Ben-- this is definitely a valid issue. The newest wrappers are
>> > works in progress; can you submit a bug report at
>> > bugzilla.bioperl.org ?
>> > (as a Windows users, I call it a bug, but Dan may disagree!) (FYI,
>> > some improvements to the wrapper interfaces are coming soon that
>> > will attempt to standardize some of these kinds of issues, so stay
>> > tuned)
>> > MAJ
>> > ----- Original Message ----- From: "Ben Bimber" <bbimber at gmail.com>
>> > To: <bioperl-l at lists.open-bio.org>
>> > Sent: Sunday, February 21, 2010 9:28 PM
>> > Subject: Re: [Bioperl-l] Bio::Tools::Run::Bowtie
>> > andBio::Assembly::IO::bowtie now available BETA
>> >
>> >
>> > Hello,
>> >
>> > I just came across the bowtie wrapper and it looks very useful.
>> > However, I am having trouble with the current logic to find the
>> bowtie
>> > executable path. ?In Bio::Tools::Run::Bowtie, line 240, it uses the
>> > command 'which', which is not windows compatible as far as I know
>> (i'm
>> > running a PC).
>> >
>> > I made a crude hack to get it to work on my machine, but is this
>> > something you would consider changing in bowtie.pm? ?I'm not sure
>> what
>> > the most versatile approach to setting program path in a wrapper
>> would
>> > be, but I'd love to hear it. ?I have still not entirely wrapped my
>> > head around all the methods to handle program path in wrappers, so
>> > perhaps there's a way to override this that I'm not aware of.
>> >
>> > Thanks,
>> > Ben
>
>


From dan.kortschak at adelaide.edu.au  Mon Feb 22 18:27:45 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Tue, 23 Feb 2010 09:57:45 +1030
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and
 Bio::Assembly::IO::bowtie now available BETA
In-Reply-To: <mailman.13.1266858004.18870.bioperl-l@lists.open-bio.org>
References: <mailman.13.1266858004.18870.bioperl-l@lists.open-bio.org>
Message-ID: <1266881265.4521.37.camel@epistle>

Hi Ben,

That has been fixed in bioperl-run/trunk at 16869. Please check to see if
the fix works for you under Windows.

If you want to use an environment variable, you will need to use the
executables method after constructing the factory unless you are keeping
all the executables in one directory in which case you can pass that
directory to the object during construction using the -prog_dir param.

Dan

On Mon, 2010-02-22 at 12:00 -0500, Ben Bimber wrote:

> Hello,
> 
> I just came across the bowtie wrapper and it looks very useful.
> However, I am having trouble with the current logic to find the bowtie
> executable path.  In Bio::Tools::Run::Bowtie, line 240, it uses the
> command 'which', which is not windows compatible as far as I know (i'm
> running a PC).


From dan.kortschak at adelaide.edu.au  Mon Feb 22 19:41:44 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Tue, 23 Feb 2010 11:11:44 +1030
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and
 Bio::Assembly::IO::bowtie now available BETA
In-Reply-To: <9f985cdc1002221612x324893b2x54b7d9b79306e244@mail.gmail.com>
References: <mailman.13.1266858004.18870.bioperl-l@lists.open-bio.org>
	<24604_1266881801_ZZg0S1a~jx2Cm.00_1266881265.4521.37.camel@epistle>
	<9f985cdc1002221612x324893b2x54b7d9b79306e244@mail.gmail.com>
Message-ID: <1266885705.4521.54.camel@epistle>

Hi Ben,

Have you done a ./Build test? It would be nice to know if it passes that
(do you have bowtie's location in your $PATH?).

I've had a look through CommandExts, and I think you should pass
-program_dir, rather than -prog_dir (I know I've previously been saying
the latter, but I don't use that method, so you'll forgive me). You can
see this from line 454-474.

cheers
Dan

On Mon, 2010-02-22 at 18:12 -0600, Ben Bimber wrote:
> Hi Dan,
> 
> Maybe I'm missing something obvious, but this should work, right?
> 
> 	my $bowtiefac = Bio::Tools::Run::Bowtie->new(
>         -command             => 'single',
>         -prog_dir 			 => '/utils/bowtie/',
>         -max_seed_mismatches => 1,
>         -seed_length         => 28,
>         -max_qual_mismatch   => 70,
>         -quiet				 => 1,
>         -want 				 => 'raw',
> 	-unaligned_file		 => $output_dir . 'unaligned.fq',
> 	);
> 		
> 
> It throws this error for me:
> 
> MSG: Could not find the executable 'bowtie'. You can use
> $self->program_dir() and $self->program_name() to specify the location
> of the program.
> STACK Bio::Tools::Run::AssemblerBase::_check_executable
> C:/Perl/site/lib/Bio/Tools/Run/AssemblerBase.pm:178
> STACK Bio::Tools::Run::Bowtie::run C:/Perl/site/lib/Bio/Tools/Run/Bowtie.pm:295
> STACK Bimber::run_bowtie
> C:/Projects/PerlScripts/SequenceTools/Utilities/Bimber.pm:122
> STACK toplevel C:/Projects/PerlScripts/SequenceTools/test.pl:32
> 
> 
> Any chance this has something to do w/ inheriting from assemblerbase?
> other wrappers like StandAloneBlastPlus (program_dir() works on PC) do
> not.
> 
> The error is throw during creation, so I cannot set the program_dir
> after creation unless there is something I'm missing.
> 
> -Ben
> 
> 
> 
> 
> 
> 
> On Mon, Feb 22, 2010 at 5:27 PM, Dan Kortschak
> <dan.kortschak at adelaide.edu.au> wrote:
> > Hi Ben,
> >
> > That has been fixed in bioperl-run/trunk at 16869. Please check to see if
> > the fix works for you under Windows.
> >
> > If you want to use an environment variable, you will need to use the
> > executables method after constructing the factory unless you are keeping
> > all the executables in one directory in which case you can pass that
> > directory to the object during construction using the -prog_dir param.
> >
> > Dan
> >
> > On Mon, 2010-02-22 at 12:00 -0500, Ben Bimber wrote:
> >
> >> Hello,
> >>
> >> I just came across the bowtie wrapper and it looks very useful.
> >> However, I am having trouble with the current logic to find the bowtie
> >> executable path.  In Bio::Tools::Run::Bowtie, line 240, it uses the
> >> command 'which', which is not windows compatible as far as I know (i'm
> >> running a PC).
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >


From nml5566 at gmail.com  Mon Feb 22 20:33:43 2010
From: nml5566 at gmail.com (Nathan Liles)
Date: Mon, 22 Feb 2010 19:33:43 -0600
Subject: [Bioperl-l] latest bioperl commit
Message-ID: <4B833077.5050702@gmail.com>

I just made a major commit to the bioperl svn. These changes all affect 
the genbank2gff3.pl converter. The following is a brief synopsis of the 
changes:

New command line options added:

/--noinfer /: don't infer exon/mRNA subfeatures

         For prokaryotes, sometimes having the converter infer these 
subfeatures from genes is less than desirable. This will turn that off.
/
     --sofile=so.obo /: obo file used to create up-to-date type mappings

         If you pass a so.obo file to the converter, it will try to 
match every primary tag with a valid SO ID. So, for nebulous tags like 
misc_feature, it will try give it a more descriptive name based on the 
note field. It will also validate parent/child SO relationships and ID 
uniqueness. If you don't have a local file, you can use --sofile=live to 
grab the latest file from sequenceontology.org.

/--manual /: manual curation

         Since the converter will likely do a terrible job guessing 
tags, passing this flag will allow you manually choose the proper term 
for a GenBank entry. It will give you a list of best matches, search SO 
from the command line, and allow user input when all else fails. This 
flag only works in conjunction with --sofile

/--conf/ : path to config file

         Because no one wants to manually annotate a GenBank file every 
time they convert it, and because even the best matches can't beat a 
human curator, the converter also has the option to save manual curation 
preferences to a conf file. Any preferences saved to a conf file will be 
automatically applied to the GFF3 everytime you convert it. The conf 
file consists of "rules" for when to match a primary tag to a GenBank 
entry. The generated conf file will be in YAML format. So, if you are 
comfortable with the format, it should be easy to manually create/edit 
the file. If you use the --manual flag and input a term, it will ask you 
if you want to save your preference to the conf file. At the moment, 
there is no conf file documentation.

I'm always open to hearing any feedback/suggestions/bug reports.

    -Nathan Liles

From bimber at wisc.edu  Mon Feb 22 21:15:28 2010
From: bimber at wisc.edu (Ben Bimber)
Date: Mon, 22 Feb 2010 20:15:28 -0600
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and
	Bio::Assembly::IO::bowtie now available BETA
In-Reply-To: <2093_1266886082_ZZg0S3adznHtU.00_1266885705.4521.54.camel@epistle>
References: <mailman.13.1266858004.18870.bioperl-l@lists.open-bio.org>
	<24604_1266881801_ZZg0S1a~jx2Cm.00_1266881265.4521.37.camel@epistle>
	<9f985cdc1002221612x324893b2x54b7d9b79306e244@mail.gmail.com>
	<2093_1266886082_ZZg0S3adznHtU.00_1266885705.4521.54.camel@epistle>
Message-ID: <9f985cdc1002221815t641e6144h582a142a01bb6f5d@mail.gmail.com>

you're right, dumb mistake.  I just read through the bowtie wrapper
and commandexts and at least I think I have a better understanding of
how it works though.  bowtie's working great now.  thanks for the
help.

-ben





On Mon, Feb 22, 2010 at 6:41 PM, Dan Kortschak
<dan.kortschak at adelaide.edu.au> wrote:
> Hi Ben,
>
> Have you done a ./Build test? It would be nice to know if it passes that
> (do you have bowtie's location in your $PATH?).
>
> I've had a look through CommandExts, and I think you should pass
> -program_dir, rather than -prog_dir (I know I've previously been saying
> the latter, but I don't use that method, so you'll forgive me). You can
> see this from line 454-474.
>
> cheers
> Dan
>
> On Mon, 2010-02-22 at 18:12 -0600, Ben Bimber wrote:
>> Hi Dan,
>>
>> Maybe I'm missing something obvious, but this should work, right?
>>
>> ? ? ? my $bowtiefac = Bio::Tools::Run::Bowtie->new(
>> ? ? ? ? -command ? ? ? ? ? ? => 'single',
>> ? ? ? ? -prog_dir ? ? ? ? ? ? ? ? ? ? ?=> '/utils/bowtie/',
>> ? ? ? ? -max_seed_mismatches => 1,
>> ? ? ? ? -seed_length ? ? ? ? => 28,
>> ? ? ? ? -max_qual_mismatch ? => 70,
>> ? ? ? ? -quiet ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? => 1,
>> ? ? ? ? -want ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?=> 'raw',
>> ? ? ? -unaligned_file ? ? ? ? ?=> $output_dir . 'unaligned.fq',
>> ? ? ? );
>>
>>
>> It throws this error for me:
>>
>> MSG: Could not find the executable 'bowtie'. You can use
>> $self->program_dir() and $self->program_name() to specify the location
>> of the program.
>> STACK Bio::Tools::Run::AssemblerBase::_check_executable
>> C:/Perl/site/lib/Bio/Tools/Run/AssemblerBase.pm:178
>> STACK Bio::Tools::Run::Bowtie::run C:/Perl/site/lib/Bio/Tools/Run/Bowtie.pm:295
>> STACK Bimber::run_bowtie
>> C:/Projects/PerlScripts/SequenceTools/Utilities/Bimber.pm:122
>> STACK toplevel C:/Projects/PerlScripts/SequenceTools/test.pl:32
>>
>>
>> Any chance this has something to do w/ inheriting from assemblerbase?
>> other wrappers like StandAloneBlastPlus (program_dir() works on PC) do
>> not.
>>
>> The error is throw during creation, so I cannot set the program_dir
>> after creation unless there is something I'm missing.
>>
>> -Ben
>>
>>
>>
>>
>>
>>
>> On Mon, Feb 22, 2010 at 5:27 PM, Dan Kortschak
>> <dan.kortschak at adelaide.edu.au> wrote:
>> > Hi Ben,
>> >
>> > That has been fixed in bioperl-run/trunk at 16869. Please check to see if
>> > the fix works for you under Windows.
>> >
>> > If you want to use an environment variable, you will need to use the
>> > executables method after constructing the factory unless you are keeping
>> > all the executables in one directory in which case you can pass that
>> > directory to the object during construction using the -prog_dir param.
>> >
>> > Dan
>> >
>> > On Mon, 2010-02-22 at 12:00 -0500, Ben Bimber wrote:
>> >
>> >> Hello,
>> >>
>> >> I just came across the bowtie wrapper and it looks very useful.
>> >> However, I am having trouble with the current logic to find the bowtie
>> >> executable path. ?In Bio::Tools::Run::Bowtie, line 240, it uses the
>> >> command 'which', which is not windows compatible as far as I know (i'm
>> >> running a PC).
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From biopython at maubp.freeserve.co.uk  Tue Feb 23 05:00:26 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 23 Feb 2010 10:00:26 +0000
Subject: [Bioperl-l] Bioperl on GitHub
In-Reply-To: <1266872963.4519.103.camel@pyrimidine.igb.uiuc.edu>
References: <1266872963.4519.103.camel@pyrimidine.igb.uiuc.edu>
Message-ID: <320fb6e01002230200n1cca6fbcy753fb8e6d63c4dec@mail.gmail.com>

On Mon, Feb 22, 2010 at 9:09 PM, Chris Fields <cjfields at illinois.edu> wrote:
> All,
>
> As a backup for the anonymous svn access on code.open-bio.org, I have
> set up a few READ-ONLY mirrors on GitHub for the main trunk code of
> several BioPerl distributions, generated using git-svn:
>
> http://github.com/bioperl
>
> These are sync'ed every 15 minutes.
>
> Note the emphasis on 'read-only'; we don't anticipate migrating code
> over to github completely, at least at the moment. ?Based on that and
> several issues with git/svn two-way syncing (outlined in the git-svn man
> pages and elsewhere), we will not support pull requests directly in
> github.
>
> enjoy!
>
> chris

Cool :)

It looks like one day many of the OpenBio projects will be on git
(currently BioRuby and more recently Biopython) ...

Peter


From tuco at pasteur.fr  Tue Feb 23 06:05:20 2010
From: tuco at pasteur.fr (Emmanuel Quevillon)
Date: Tue, 23 Feb 2010 12:05:20 +0100
Subject: [Bioperl-l] Possible parsing bug
	for	Bio::Restriction::IO::withrefm?
In-Reply-To: <C8A3D982C5A1494EADB13385330E3DAA@NewLife>
References: <4B82A51A.9060705@pasteur.fr>
	<C8A3D982C5A1494EADB13385330E3DAA@NewLife>
Message-ID: <4B83B670.9000309@pasteur.fr>

Mark A. Jensen wrote:
> Hi Emanuel- I would not be surprised if there were a problem here;
> I would say if your patch passes tests and also solves the issue you
> raise, make the patch and add a test for this particular situation, if you
> have time. thanks! MAJ

Hi Mark,

I am writing a small test for this changes made into
Bio::Restriction::IO::withrefm

I'll upload all (test + patch + seq_data) on bugzilla once it is done

Cheers

Emmanuel


-- 
-------------------------
Emmanuel Quevillon
Biological Software and Databases Group
Institut Pasteur
+33 1 44 38 95 98
tuco at_ pasteur dot fr
-------------------------

From cjfields at illinois.edu  Tue Feb 23 08:25:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 23 Feb 2010 07:25:17 -0600
Subject: [Bioperl-l] Bioperl on GitHub
In-Reply-To: <320fb6e01002230200n1cca6fbcy753fb8e6d63c4dec@mail.gmail.com>
References: <1266872963.4519.103.camel@pyrimidine.igb.uiuc.edu>
	<320fb6e01002230200n1cca6fbcy753fb8e6d63c4dec@mail.gmail.com>
Message-ID: <BBD329B8-12B1-4D9F-BF4F-0F87766B30A4@illinois.edu>

On Feb 23, 2010, at 4:00 AM, Peter wrote:

> On Mon, Feb 22, 2010 at 9:09 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> All,
>> 
>> As a backup for the anonymous svn access on code.open-bio.org, I have
>> set up a few READ-ONLY mirrors on GitHub for the main trunk code of
>> several BioPerl distributions, generated using git-svn:
>> 
>> http://github.com/bioperl
>> 
>> These are sync'ed every 15 minutes.
>> 
>> Note the emphasis on 'read-only'; we don't anticipate migrating code
>> over to github completely, at least at the moment.  Based on that and
>> several issues with git/svn two-way syncing (outlined in the git-svn man
>> pages and elsewhere), we will not support pull requests directly in
>> github.
>> 
>> enjoy!
>> 
>> chris
> 
> Cool :)
> 
> It looks like one day many of the OpenBio projects will be on git
> (currently BioRuby and more recently Biopython) ...
> 
> Peter

I think it's possible we may move to git (and mirror to github) completely at some point, and have the svn become read-only; wouldn't be surprised if it happens sooner than later.  We'll see how mirroring works out for the time being.

chris

From biopython at maubp.freeserve.co.uk  Tue Feb 23 08:52:23 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 23 Feb 2010 13:52:23 +0000
Subject: [Bioperl-l] Bioperl on GitHub
In-Reply-To: <BBD329B8-12B1-4D9F-BF4F-0F87766B30A4@illinois.edu>
References: <1266872963.4519.103.camel@pyrimidine.igb.uiuc.edu>
	<320fb6e01002230200n1cca6fbcy753fb8e6d63c4dec@mail.gmail.com>
	<BBD329B8-12B1-4D9F-BF4F-0F87766B30A4@illinois.edu>
Message-ID: <320fb6e01002230552n5ca644e8x2d5704bb8a461cfa@mail.gmail.com>

On Tue, Feb 23, 2010 at 1:25 PM, Chris Fields <cjfields at illinois.edu> wrote:
> On Feb 23, 2010, at 4:00 AM, Peter wrote:
>>
>> Cool :)
>>
>> It looks like one day many of the OpenBio projects will be on git
>> (currently BioRuby and more recently Biopython) ...
>>
>> Peter
>
> I think it's possible we may move to git (and mirror to github)
> completely at some point, and have the svn become read-only;
> wouldn't be surprised if it happens sooner than later. ?We'll see
> how mirroring works out for the time being.

I'd be pleased if we could have the Biopython (and BioRuby?)
git repositories mirrored on both github and the OBF servers.
Perhaps we should continue this discussion on the common
OpenBio mailing list once the BioPerl team have had some
time to play with git on github.

Peter


From tuco at pasteur.fr  Tue Feb 23 09:09:02 2010
From: tuco at pasteur.fr (Emmanuel Quevillon)
Date: Tue, 23 Feb 2010 15:09:02 +0100
Subject: [Bioperl-l] Possible parsing bug
	for	Bio::Restriction::IO::withrefm?
In-Reply-To: <C8A3D982C5A1494EADB13385330E3DAA@NewLife>
References: <4B82A51A.9060705@pasteur.fr>
	<C8A3D982C5A1494EADB13385330E3DAA@NewLife>
Message-ID: <4B83E17E.2020006@pasteur.fr>

Mark A. Jensen wrote:
> Hi Emanuel- I would not be surprised if there were a problem here;
> I would say if your patch passes tests and also solves the issue you
> raise, make the patch and add a test for this particular situation, if you
> have time. thanks! MAJ


Patch and test file submitted to Bugzilla

Cheers

Emmanuel
-- 
-------------------------
Emmanuel Quevillon
Biological Software and Databases Group
Institut Pasteur
+33 1 44 38 95 98
tuco at_ pasteur dot fr
-------------------------

From hlapp at drycafe.net  Tue Feb 23 10:21:02 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Tue, 23 Feb 2010 10:21:02 -0500
Subject: [Bioperl-l] latest bioperl commit
In-Reply-To: <4B833077.5050702@gmail.com>
References: <4B833077.5050702@gmail.com>
Message-ID: <9FF879AF-CEC2-484F-A83F-854A95EECF34@drycafe.net>

Thanks for your help Nathan - these sound like very useful additions!

	-hilmar

On Feb 22, 2010, at 8:33 PM, Nathan Liles wrote:

> I just made a major commit to the bioperl svn. These changes all  
> affect the genbank2gff3.pl converter. The following is a brief  
> synopsis of the changes:
>
> New command line options added:
>
> /--noinfer /: don't infer exon/mRNA subfeatures
>
>        For prokaryotes, sometimes having the converter infer these  
> subfeatures from genes is less than desirable. This will turn that  
> off.
> /
>    --sofile=so.obo /: obo file used to create up-to-date type mappings
>
>        If you pass a so.obo file to the converter, it will try to  
> match every primary tag with a valid SO ID. So, for nebulous tags  
> like misc_feature, it will try give it a more descriptive name based  
> on the note field. It will also validate parent/child SO  
> relationships and ID uniqueness. If you don't have a local file, you  
> can use --sofile=live to grab the latest file from  
> sequenceontology.org.
>
> /--manual /: manual curation
>
>        Since the converter will likely do a terrible job guessing  
> tags, passing this flag will allow you manually choose the proper  
> term for a GenBank entry. It will give you a list of best matches,  
> search SO from the command line, and allow user input when all else  
> fails. This flag only works in conjunction with --sofile
>
> /--conf/ : path to config file
>
>        Because no one wants to manually annotate a GenBank file  
> every time they convert it, and because even the best matches can't  
> beat a human curator, the converter also has the option to save  
> manual curation preferences to a conf file. Any preferences saved to  
> a conf file will be automatically applied to the GFF3 everytime you  
> convert it. The conf file consists of "rules" for when to match a  
> primary tag to a GenBank entry. The generated conf file will be in  
> YAML format. So, if you are comfortable with the format, it should  
> be easy to manually create/edit the file. If you use the --manual  
> flag and input a term, it will ask you if you want to save your  
> preference to the conf file. At the moment, there is no conf file  
> documentation.
>
> I'm always open to hearing any feedback/suggestions/bug reports.
>
>   -Nathan Liles
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From avilella at gmail.com  Tue Feb 23 11:51:21 2010
From: avilella at gmail.com (Albert Vilella)
Date: Tue, 23 Feb 2010 16:51:21 +0000
Subject: [Bioperl-l] Bio::Index::Fastq support for gzipped files
Message-ID: <358f4d651002230851m56cc4f86k16422e7c53477112@mail.gmail.com>

Hi,

Maybe already answered somewhere but, do we have support for gzipped
fasta/fastq files?

Google tells me biopython does, but I couldn't guess for bioperl...

Cheers,

Albert.

On Mon, Jan 4, 2010 at 9:59 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Bio::Index::Fastq, maybe? ?To tell the truth, I haven't tried it since we refactored FASTQ parsing, so let us know if it doesn't work.
>
> chris
>
> On Jan 4, 2010, at 2:00 PM, Albert Vilella wrote:
>
>> Hi all,
>>
>> What is the best way to index fastq files, so that once clustered, I
>> can provide a list of seq_ids and get
>> them back in fastq format from the indexed db?
>>
>> Cheers,
>>
>> Albert.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From biopython at maubp.freeserve.co.uk  Tue Feb 23 12:01:16 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 23 Feb 2010 17:01:16 +0000
Subject: [Bioperl-l] Bio::Index::Fastq support for gzipped files
In-Reply-To: <358f4d651002230851m56cc4f86k16422e7c53477112@mail.gmail.com>
References: <358f4d651002230851m56cc4f86k16422e7c53477112@mail.gmail.com>
Message-ID: <320fb6e01002230901m3494451cifd44d507599a14c9@mail.gmail.com>

On Tue, Feb 23, 2010 at 4:51 PM, Albert Vilella <avilella at gmail.com> wrote:
> Hi,
>
> Maybe already answered somewhere but, do we have support for
> gzipped fasta/fastq files?
>
> Google tells me biopython does, but I couldn't guess for bioperl...
>

To clarify, we've discussed this on the Biopython mailing list, and
Renato Alves and I have been exploring possible implementation
on git branches, but we don't yet have indexing of gzipped files on
the trunk. But it would be nice :)

Peter

From maj at fortinbras.us  Tue Feb 23 12:31:12 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Tue, 23 Feb 2010 12:31:12 -0500
Subject: [Bioperl-l] Possible parsing bug
	for	Bio::Restriction::IO::withrefm?
In-Reply-To: <4B83E17E.2020006@pasteur.fr>
References: <4B82A51A.9060705@pasteur.fr>
	<C8A3D982C5A1494EADB13385330E3DAA@NewLife>
	<4B83E17E.2020006@pasteur.fr>
Message-ID: <35AC947EDFA84FF8B59B383EC8F63850@NewLife>

thanks Emmanuel-- I'll have a look- MAJ
----- Original Message ----- 
From: "Emmanuel Quevillon" <tuco at pasteur.fr>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Tuesday, February 23, 2010 9:09 AM
Subject: Re: [Bioperl-l] Possible parsing bug for 
Bio::Restriction::IO::withrefm?


> Mark A. Jensen wrote:
>> Hi Emanuel- I would not be surprised if there were a problem here;
>> I would say if your patch passes tests and also solves the issue you
>> raise, make the patch and add a test for this particular situation, if you
>> have time. thanks! MAJ
>
>
> Patch and test file submitted to Bugzilla
>
> Cheers
>
> Emmanuel
> -- 
> -------------------------
> Emmanuel Quevillon
> Biological Software and Databases Group
> Institut Pasteur
> +33 1 44 38 95 98
> tuco at_ pasteur dot fr
> -------------------------
>
> 


From cjfields at illinois.edu  Tue Feb 23 12:47:44 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 23 Feb 2010 11:47:44 -0600
Subject: [Bioperl-l] Bio::Index::Fastq support for gzipped files
In-Reply-To: <320fb6e01002230901m3494451cifd44d507599a14c9@mail.gmail.com>
References: <358f4d651002230851m56cc4f86k16422e7c53477112@mail.gmail.com>
	<320fb6e01002230901m3494451cifd44d507599a14c9@mail.gmail.com>
Message-ID: <2D003DD7-6D5C-41CC-94DB-358DD118976D@illinois.edu>

On Feb 23, 2010, at 11:01 AM, Peter wrote:

> On Tue, Feb 23, 2010 at 4:51 PM, Albert Vilella <avilella at gmail.com> wrote:
>> Hi,
>> 
>> Maybe already answered somewhere but, do we have support for
>> gzipped fasta/fastq files?
>> 
>> Google tells me biopython does, but I couldn't guess for bioperl...
>> 
> 
> To clarify, we've discussed this on the Biopython mailing list, and
> Renato Alves and I have been exploring possible implementation
> on git branches, but we don't yet have indexing of gzipped files on
> the trunk. But it would be nice :)
> 
> Peter

I don't think the various PerlIO gzip modules implement tell() to index the positions.  Mark Jensen released the PerlIO::via::gzip module on CPAN, so he would be the one who could say more about it and the possible problems one would face.

chris



From cjm at berkeleybop.org  Tue Feb 23 13:17:11 2010
From: cjm at berkeleybop.org (Chris Mungall)
Date: Tue, 23 Feb 2010 10:17:11 -0800
Subject: [Bioperl-l] experimental IO module for exporting OWL from GFF
In-Reply-To: <12F203C3-689B-423E-9691-86EB1D500A7D@illinois.edu>
References: <CE668EC6-1ED5-4BD8-868C-729031724A09@berkeleybop.org>
	<7DFBF7E8A6DB45F3AB836EBAFBE597AC@NewLife>
	<12F203C3-689B-423E-9691-86EB1D500A7D@illinois.edu>
Message-ID: <3BE91EC1-F2C0-4705-BC9A-C48A2473D55A@berkeleybop.org>


I thought it made sense to put this in its own distribution

	http://github.com/cmungall/bioperl-owl

I may push it to CPAN if there's interest

On Jun 25, 2009, at 6:35 PM, Chris Fields wrote:

> I agree.  Just to note, FeatureIO (even though it's in core) will be  
> operated on at some future point to be simplified (and likely will  
> move away from Bio::SF::Annotated).
>
> chris
>
> On Jun 25, 2009, at 8:08 PM, Mark A. Jensen wrote:
>
>> This sounds very Dev to me. Also cool.
>> MAJ
>> ----- Original Message ----- From: "Chris Mungall" <cjm at berkeleybop.org 
>> >
>> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
>> Sent: Thursday, June 25, 2009 8:32 PM
>> Subject: [Bioperl-l] experimental IO module for exporting OWL from  
>> GFF
>>
>>
>>>
>>> I've written a module Bio::FeatureIO::seqont_owl, which generates   
>>> Sequence Ontology compliant RDF/OWL. This will allow for example   
>>> loading of GFF into triplestores and inference using OWL reasoners.
>>>
>>> - It's experimental, fairly incomplete, and subject to change
>>> - Relies on an experimental extension of SO
>>> - Probably of interest to a minority of bp users
>>> - It's not yet fully documented (but there will be a paper)
>>> - It doesn't introduce any additional dependencies (all done via   
>>> XML::Writer, which is already a dependency)
>>> - Doesn't otherwise impinge on existing code
>>>
>>> I'd like to get this under source control. Is the appropriate  
>>> place  for this:
>>>
>>> - HEAD
>>> - a branch
>>> - bioperl-dev
>>> - a separate repository

>>>
>>> ?
>>>
>>> Cheers
>>> Chris
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



From nml5566 at gmail.com  Tue Feb 23 16:11:59 2010
From: nml5566 at gmail.com (Nathan Liles)
Date: Tue, 23 Feb 2010 15:11:59 -0600
Subject: [Bioperl-l] svn repository down?
Message-ID: <4B84449F.5090305@gmail.com>

I can't do a checkout of code.open-bio.org/bioperl/bioperl-live/trunk 
<svn://code.open-bio.org/bioperl/bioperl-live/trunk>. I get the "Can't 
connect to host 'xxx': Address already in use". Is anyone else having 
this problem? Is there a fix for this?

-Nathan Liles

From cjfields at illinois.edu  Tue Feb 23 16:26:54 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 23 Feb 2010 15:26:54 -0600
Subject: [Bioperl-l] svn repository down?
In-Reply-To: <4B84449F.5090305@gmail.com>
References: <4B84449F.5090305@gmail.com>
Message-ID: <1266960414.24836.2.camel@pyrimidine.igb.uiuc.edu>

That's the anon svn repository; there have been some problems with it
over the last few weeks.  I set up a backup repo on GitHub:

http://github.com/bioperl/bioperl-live

chris

On Tue, 2010-02-23 at 15:11 -0600, Nathan Liles wrote:
> I can't do a checkout of code.open-bio.org/bioperl/bioperl-live/trunk 
> <svn://code.open-bio.org/bioperl/bioperl-live/trunk>. I get the "Can't 
> connect to host 'xxx': Address already in use". Is anyone else having 
> this problem? Is there a fix for this?
> 
> -Nathan Liles
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From charles-listes+bioperl at plessy.org  Tue Feb 23 23:15:09 2010
From: charles-listes+bioperl at plessy.org (Charles Plessy)
Date: Wed, 24 Feb 2010 13:15:09 +0900
Subject: [Bioperl-l] Tons of test failing in bioperl-live
In-Reply-To: <812CC488-05C8-4B53-9988-D39DDED7CD9F@illinois.edu>
References: <812CC488-05C8-4B53-9988-D39DDED7CD9F@illinois.edu>
Message-ID: <20100224041509.GA12675@kunpuu.plessy.org>

Dear Chris,

talking about tests, there are a couple of them that fail in the absence of
network connection. I have submitted a patch in the BioPerl bugzilla, that
adds ?-requires_networking => 1? to them in order to get skipped when
network test are disabled. Could you review this patch? I would like to
apply it on the BioPerl Debian package soon (since we aim at freezing our
packages in March).

http://bugzilla.open-bio.org/show_bug.cgi?id=2975

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

From robert.bradbury at gmail.com  Wed Feb 24 02:08:33 2010
From: robert.bradbury at gmail.com (Robert Bradbury)
Date: Wed, 24 Feb 2010 02:08:33 -0500
Subject: [Bioperl-l] Tons of test failing in bioperl-live
In-Reply-To: <20100224041509.GA12675@kunpuu.plessy.org>
References: <812CC488-05C8-4B53-9988-D39DDED7CD9F@illinois.edu>
	<20100224041509.GA12675@kunpuu.plessy.org>
Message-ID: <deaa866a1002232308m6b5bf7baq4b533f2dc98b222d@mail.gmail.com>

One of the things I observe in dealing with the ongoing rapid upgrades to
the chrome browser is the extent to which Google seems to be running
continuous tests (due to the massive amount of hardware they have
available).  Is it reasonable to use spare cloud computing resources to rund
the tests in the cloud at Google, Amazon, IBM, etc?  (Or NCBI/JGI/Sanger
when their blast servers have idle moments?)

Is there some estimate of how long the test suite takes?  I'm about to
upgrade hardware and might have substantially more space & CPU available to
run tests on a semi-frequent basis.

Just a suggestion.
R.

From avilella at gmail.com  Wed Feb 24 03:48:59 2010
From: avilella at gmail.com (Albert Vilella)
Date: Wed, 24 Feb 2010 08:48:59 +0000
Subject: [Bioperl-l] Bio::Index::Fastq support for gzipped files
In-Reply-To: <320fb6e01002230901m3494451cifd44d507599a14c9@mail.gmail.com>
References: <358f4d651002230851m56cc4f86k16422e7c53477112@mail.gmail.com>
	<320fb6e01002230901m3494451cifd44d507599a14c9@mail.gmail.com>
Message-ID: <358f4d651002240048q4b65c67fk1920bf7933d8c40e@mail.gmail.com>

aaah, so we can still be first in bioperl ;-)

On Tue, Feb 23, 2010 at 5:01 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Feb 23, 2010 at 4:51 PM, Albert Vilella <avilella at gmail.com> wrote:
>> Hi,
>>
>> Maybe already answered somewhere but, do we have support for
>> gzipped fasta/fastq files?
>>
>> Google tells me biopython does, but I couldn't guess for bioperl...
>>
>
> To clarify, we've discussed this on the Biopython mailing list, and
> Renato Alves and I have been exploring possible implementation
> on git branches, but we don't yet have indexing of gzipped files on
> the trunk. But it would be nice :)
>
> Peter
>

From avilella at gmail.com  Wed Feb 24 06:32:41 2010
From: avilella at gmail.com (Albert Vilella)
Date: Wed, 24 Feb 2010 11:32:41 +0000
Subject: [Bioperl-l] indexed fastq files
In-Reply-To: <07EBA105-6A34-490C-B0B9-4772DF386CBA@illinois.edu>
References: <358f4d651001041200m1f715b83k743f4d2ee6b6312b@mail.gmail.com>
	<07EBA105-6A34-490C-B0B9-4772DF386CBA@illinois.edu>
Message-ID: <358f4d651002240332u4b7dc2c8j6626e732211a8da4@mail.gmail.com>

Hi Chris,

I am finding that Bio::Index::Fastq seek is chopping off the first
character of the fastq entry. I'm on Linux using bioperl-1.6.1 and
debugged the problem to this point in AbstractSeq.pm:143, where there
is this funny commented line:

		# $begin-- if( $^O =~ /mswin/i); # workaround for Win DB_File bug
		seek($fh, $begin, 0);

If I apply this $begin--, everything works fine, but I am not using
windows, I am on a Linux cluster.

Any ideas why this was tagged as a "Win DB_File bug"?

Cheers,

Albert.

On Mon, Jan 4, 2010 at 9:59 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Bio::Index::Fastq, maybe? ?To tell the truth, I haven't tried it since we refactored FASTQ parsing, so let us know if it doesn't work.
>
> chris
>
> On Jan 4, 2010, at 2:00 PM, Albert Vilella wrote:
>
>> Hi all,
>>
>> What is the best way to index fastq files, so that once clustered, I
>> can provide a list of seq_ids and get
>> them back in fastq format from the indexed db?
>>
>> Cheers,
>>
>> Albert.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From avilella at gmail.com  Wed Feb 24 06:45:23 2010
From: avilella at gmail.com (Albert Vilella)
Date: Wed, 24 Feb 2010 11:45:23 +0000
Subject: [Bioperl-l] indexed fastq files
In-Reply-To: <358f4d651002240332u4b7dc2c8j6626e732211a8da4@mail.gmail.com>
References: <358f4d651001041200m1f715b83k743f4d2ee6b6312b@mail.gmail.com>
	<07EBA105-6A34-490C-B0B9-4772DF386CBA@illinois.edu>
	<358f4d651002240332u4b7dc2c8j6626e732211a8da4@mail.gmail.com>
Message-ID: <358f4d651002240345k3ac9a5b3ia66f6bfabcd0d9b0@mail.gmail.com>

BTW, I should mention that my index file was created with this options
on the same linux system:

my $db  = Bio::Index::Fastq->new(-filename => $fastafile,
-dbm_package=>'DB_File');

So it looks more like DB_File dependent than "Win DB_File"...

On Wed, Feb 24, 2010 at 11:32 AM, Albert Vilella <avilella at gmail.com> wrote:
> Hi Chris,
>
> I am finding that Bio::Index::Fastq seek is chopping off the first
> character of the fastq entry. I'm on Linux using bioperl-1.6.1 and
> debugged the problem to this point in AbstractSeq.pm:143, where there
> is this funny commented line:
>
> ? ? ? ? ? ? ? ?# $begin-- if( $^O =~ /mswin/i); # workaround for Win DB_File bug
> ? ? ? ? ? ? ? ?seek($fh, $begin, 0);
>
> If I apply this $begin--, everything works fine, but I am not using
> windows, I am on a Linux cluster.
>
> Any ideas why this was tagged as a "Win DB_File bug"?
>
> Cheers,
>
> Albert.
>
> On Mon, Jan 4, 2010 at 9:59 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> Bio::Index::Fastq, maybe? ?To tell the truth, I haven't tried it since we refactored FASTQ parsing, so let us know if it doesn't work.
>>
>> chris
>>
>> On Jan 4, 2010, at 2:00 PM, Albert Vilella wrote:
>>
>>> Hi all,
>>>
>>> What is the best way to index fastq files, so that once clustered, I
>>> can provide a list of seq_ids and get
>>> them back in fastq format from the indexed db?
>>>
>>> Cheers,
>>>
>>> Albert.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>


From bbimber at gmail.com  Mon Feb 22 19:12:14 2010
From: bbimber at gmail.com (Ben Bimber)
Date: Mon, 22 Feb 2010 18:12:14 -0600
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and
	Bio::Assembly::IO::bowtie now available BETA
In-Reply-To: <24604_1266881801_ZZg0S1a~jx2Cm.00_1266881265.4521.37.camel@epistle>
References: <mailman.13.1266858004.18870.bioperl-l@lists.open-bio.org>
	<24604_1266881801_ZZg0S1a~jx2Cm.00_1266881265.4521.37.camel@epistle>
Message-ID: <9f985cdc1002221612x324893b2x54b7d9b79306e244@mail.gmail.com>

Hi Dan,

Maybe I'm missing something obvious, but this should work, right?

	my $bowtiefac = Bio::Tools::Run::Bowtie->new(
        -command             => 'single',
        -prog_dir 			 => '/utils/bowtie/',
        -max_seed_mismatches => 1,
        -seed_length         => 28,
        -max_qual_mismatch   => 70,
        -quiet				 => 1,
        -want 				 => 'raw',
	-unaligned_file		 => $output_dir . 'unaligned.fq',
	);
		

It throws this error for me:

MSG: Could not find the executable 'bowtie'. You can use
$self->program_dir() and $self->program_name() to specify the location
of the program.
STACK Bio::Tools::Run::AssemblerBase::_check_executable
C:/Perl/site/lib/Bio/Tools/Run/AssemblerBase.pm:178
STACK Bio::Tools::Run::Bowtie::run C:/Perl/site/lib/Bio/Tools/Run/Bowtie.pm:295
STACK Bimber::run_bowtie
C:/Projects/PerlScripts/SequenceTools/Utilities/Bimber.pm:122
STACK toplevel C:/Projects/PerlScripts/SequenceTools/test.pl:32


Any chance this has something to do w/ inheriting from assemblerbase?
other wrappers like StandAloneBlastPlus (program_dir() works on PC) do
not.

The error is throw during creation, so I cannot set the program_dir
after creation unless there is something I'm missing.

-Ben






On Mon, Feb 22, 2010 at 5:27 PM, Dan Kortschak
<dan.kortschak at adelaide.edu.au> wrote:
> Hi Ben,
>
> That has been fixed in bioperl-run/trunk at 16869. Please check to see if
> the fix works for you under Windows.
>
> If you want to use an environment variable, you will need to use the
> executables method after constructing the factory unless you are keeping
> all the executables in one directory in which case you can pass that
> directory to the object during construction using the -prog_dir param.
>
> Dan
>
> On Mon, 2010-02-22 at 12:00 -0500, Ben Bimber wrote:
>
>> Hello,
>>
>> I just came across the bowtie wrapper and it looks very useful.
>> However, I am having trouble with the current logic to find the bowtie
>> executable path. ?In Bio::Tools::Run::Bowtie, line 240, it uses the
>> command 'which', which is not windows compatible as far as I know (i'm
>> running a PC).
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From jskittrell at unmc.edu  Tue Feb 23 18:43:48 2010
From: jskittrell at unmc.edu (Jeff S Kittrell)
Date: Tue, 23 Feb 2010 17:43:48 -0600
Subject: [Bioperl-l] sim4cc vs sim4
Message-ID: <OF22B2884A.7FE0FC0D-ON862576D3.0081EF74-862576D3.00825A26@unmc.edu>

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From jskittrell at unmc.edu  Wed Feb 24 11:45:35 2010
From: jskittrell at unmc.edu (Jeff S Kittrell)
Date: Wed, 24 Feb 2010 10:45:35 -0600
Subject: [Bioperl-l] Bioperl newbie Bio::Tools::Sim4::Results question
Message-ID: <OFF32D1334.C5F27C0E-ON862576D4.005BCCD2-862576D4.005C10D9@unmc.edu>

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From shameer at ncbs.res.in  Wed Feb 24 11:59:16 2010
From: shameer at ncbs.res.in (K. Shameer)
Date: Wed, 24 Feb 2010 22:29:16 +0530 (IST)
Subject: [Bioperl-l] Any module for chromosome region analysis ?
Message-ID: <48201.207.229.236.211.1267030756.squirrel@mail.ncbs.res.in>

Hello all,

I am looking for a standard way / bioperl module that can take up
different chromosome regions (in basepairs) and give the unique and common
regions.
For example these are the regions and I need to get the common regions
(start - end) among all 5 regions:
24328000 - 29166946
25388351 - 27114603
22310186 - 25239677
28511024 - 29638159
23729632 - 26385029

Thanks,
Shameer



From roy.chaudhuri at gmail.com  Wed Feb 24 13:14:04 2010
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 24 Feb 2010 18:14:04 +0000
Subject: [Bioperl-l] Any module for chromosome region analysis ?
In-Reply-To: <48201.207.229.236.211.1267030756.squirrel@mail.ncbs.res.in>
References: <48201.207.229.236.211.1267030756.squirrel@mail.ncbs.res.in>
Message-ID: <4B856C6C.90703@gmail.com>

Hi Shameer,

You could do this using Bio::Range, but that only allows you to 
determine the intersection between two ranges at once, so you'd need to 
do the calculation in several stages. It also doesn't have a method to 
determine positions that are unique to one of the ranges (although it 
possibly should).

As this isn't a problem that is specific to biology, it's also worth 
hunting around on CPAN for modules that may be useful. 
Set::IntSpan::Fast looks suitable, particularly the intersection and 
diff methods. I haven't tried it, though.

Roy.

On 24/02/2010 16:59, K. Shameer wrote:
> Hello all,
>
> I am looking for a standard way / bioperl module that can take up
> different chromosome regions (in basepairs) and give the unique and common
> regions.
> For example these are the regions and I need to get the common regions
> (start - end) among all 5 regions:
> 24328000 - 29166946
> 25388351 - 27114603
> 22310186 - 25239677
> 28511024 - 29638159
> 23729632 - 26385029
>
> Thanks,
> Shameer
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From shameer at ncbs.res.in  Wed Feb 24 14:31:06 2010
From: shameer at ncbs.res.in (K. Shameer)
Date: Thu, 25 Feb 2010 01:01:06 +0530 (IST)
Subject: [Bioperl-l] Any module for chromosome region analysis ?
In-Reply-To: <4B856C6C.90703@gmail.com>
References: <48201.207.229.236.211.1267030756.squirrel@mail.ncbs.res.in>
	<4B856C6C.90703@gmail.com>
Message-ID: <45502.207.229.236.211.1267039866.squirrel@mail.ncbs.res.in>

Hello Roy,

Thanks for the pointers.

--
Shameer

> Hi Shameer,
>
> You could do this using Bio::Range, but that only allows you to
> determine the intersection between two ranges at once, so you'd need to
> do the calculation in several stages. It also doesn't have a method to
> determine positions that are unique to one of the ranges (although it
> possibly should).
>
> As this isn't a problem that is specific to biology, it's also worth
> hunting around on CPAN for modules that may be useful.
> Set::IntSpan::Fast looks suitable, particularly the intersection and
> diff methods. I haven't tried it, though.
>
> Roy.
>
> On 24/02/2010 16:59, K. Shameer wrote:
>> Hello all,
>>
>> I am looking for a standard way / bioperl module that can take up
>> different chromosome regions (in basepairs) and give the unique and
>> common
>> regions.
>> For example these are the regions and I need to get the common regions
>> (start - end) among all 5 regions:
>> 24328000 - 29166946
>> 25388351 - 27114603
>> 22310186 - 25239677
>> 28511024 - 29638159
>> 23729632 - 26385029
>>
>> Thanks,
>> Shameer
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From jason at bioperl.org  Wed Feb 24 14:50:32 2010
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Feb 2010 11:50:32 -0800
Subject: [Bioperl-l] sim4cc vs sim4
In-Reply-To: <OF22B2884A.7FE0FC0D-ON862576D3.0081EF74-862576D3.00825A26@unmc.edu>
References: <OF22B2884A.7FE0FC0D-ON862576D3.0081EF74-862576D3.00825A26@unmc.edu>
Message-ID: <4B858308.7000207@bioperl.org>

sending an example can help -- I guess the formats are different enough 
that the parser doesn't work.  Why people don't just generate a GFF or 
simple tab format when they write a new tool, I don't know....

-jason

Jeff S Kittrell wrote:
>
> Has anyone used the sim4 file parser on a sim4cc? When I parse the 
> file with SearchIO(-format => 'sim4') or Bio::Tools::Sim4::Results the 
> query string returns a null. I assume there is some slight difference 
> between the two file formats? Any help is appreciated.
>
> Jeff
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From jason at bioperl.org  Wed Feb 24 14:52:08 2010
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Feb 2010 11:52:08 -0800
Subject: [Bioperl-l] Bioperl newbie Bio::Tools::Sim4::Results question
In-Reply-To: <OFF32D1334.C5F27C0E-ON862576D4.005BCCD2-862576D4.005C10D9@unmc.edu>
References: <OFF32D1334.C5F27C0E-ON862576D4.005BCCD2-862576D4.005C10D9@unmc.edu>
Message-ID: <4B858368.6090107@bioperl.org>

Do you want the sequence name or the sequence itsself?
I don't think the sequence is in the report, it is just locations of the 
exons in the report.

You can use Bio::DB::Fasta to index your genome and EST db and then pull 
out the sequence locations with code like:
  $db->seq(NAME, START => END)

-jason
Jeff S Kittrell wrote:
>
> Hello,
> I new at bioperl so sorry if this question is mundane. I am parsing a 
> sim4 file with
> Bio::Tools::Sim4::Results and can not for the life of me figure out 
> how to extract the query or
> hit sequence.
>
> thanks for your help,
> jeff kittrell
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From jason at bioperl.org  Wed Feb 24 14:55:41 2010
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Feb 2010 11:55:41 -0800
Subject: [Bioperl-l] Any module for chromosome region analysis ?
In-Reply-To: <45502.207.229.236.211.1267039866.squirrel@mail.ncbs.res.in>
References: <48201.207.229.236.211.1267030756.squirrel@mail.ncbs.res.in>	<4B856C6C.90703@gmail.com>
	<45502.207.229.236.211.1267039866.squirrel@mail.ncbs.res.in>
Message-ID: <4B85843D.9070602@bioperl.org>

You can use the collapse_nums method in Bio::Search::BlastUtils which is 
just an implementation of the connectivity algorithm but the Range 
description that Roy points out may be more useful since you'd have to 
unroll the ranges into the full set of numbers.

collapse_nums

  Usage     : @cnums = collapse_nums( @numbers );
  Purpose   : Collapses a list of numbers into a set of ranges of 
consecutive terms:
            : Useful for condensing long lists of consecutive numbers.
            :  EXPANDED:
            :     1 2 3 4 5 6 10 12 13 14 15 17 18 20 21 22 24 26 30 31 32
            :  COLLAPSED:
            :     1-6 10 12-15 17 18 20-22 24 26 30-32
  Argument  : List of numbers sorted numerically.
  Returns   : List of numbers mixed with ranges of numbers (see above).
  Throws    : n/a

-jason
K. Shameer wrote:
> Hello Roy,
>
> Thanks for the pointers.
>
> --
> Shameer
>
>    
>> Hi Shameer,
>>
>> You could do this using Bio::Range, but that only allows you to
>> determine the intersection between two ranges at once, so you'd need to
>> do the calculation in several stages. It also doesn't have a method to
>> determine positions that are unique to one of the ranges (although it
>> possibly should).
>>
>> As this isn't a problem that is specific to biology, it's also worth
>> hunting around on CPAN for modules that may be useful.
>> Set::IntSpan::Fast looks suitable, particularly the intersection and
>> diff methods. I haven't tried it, though.
>>
>> Roy.
>>
>> On 24/02/2010 16:59, K. Shameer wrote:
>>      
>>> Hello all,
>>>
>>> I am looking for a standard way / bioperl module that can take up
>>> different chromosome regions (in basepairs) and give the unique and
>>> common
>>> regions.
>>> For example these are the regions and I need to get the common regions
>>> (start - end) among all 5 regions:
>>> 24328000 - 29166946
>>> 25388351 - 27114603
>>> 22310186 - 25239677
>>> 28511024 - 29638159
>>> 23729632 - 26385029
>>>
>>> Thanks,
>>> Shameer
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>        
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>      
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>    

From michael.watson at bbsrc.ac.uk  Wed Feb 24 15:28:56 2010
From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C))
Date: Wed, 24 Feb 2010 20:28:56 +0000
Subject: [Bioperl-l] sim4cc vs sim4
In-Reply-To: <4B858308.7000207@bioperl.org>
References: <OF22B2884A.7FE0FC0D-ON862576D3.0081EF74-862576D3.00825A26@unmc.edu>,
	<4B858308.7000207@bioperl.org>
Message-ID: <8D08960C647E64438CE5740657CBBDC501F91061BB@iahcexch1.iah.bbsrc.ac.uk>

Law's first law:

http://bioinformatics.roslin.ac.uk/lawslaws.html
________________________________________
From: bioperl-l-bounces at lists.open-bio.org [bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jason Stajich [jason at bioperl.org]
Sent: 24 February 2010 19:50
To: Jeff S Kittrell
Cc: bioperl-l
Subject: Re: [Bioperl-l] sim4cc vs sim4

sending an example can help -- I guess the formats are different enough
that the parser doesn't work.  Why people don't just generate a GFF or
simple tab format when they write a new tool, I don't know....

-jason

Jeff S Kittrell wrote:
>
> Has anyone used the sim4 file parser on a sim4cc? When I parse the
> file with SearchIO(-format => 'sim4') or Bio::Tools::Sim4::Results the
> query string returns a null. I assume there is some slight difference
> between the two file formats? Any help is appreciated.
>
> Jeff
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l


From shameer at ncbs.res.in  Wed Feb 24 17:05:25 2010
From: shameer at ncbs.res.in (K. Shameer)
Date: Thu, 25 Feb 2010 03:35:25 +0530 (IST)
Subject: [Bioperl-l] Any module for chromosome region analysis ?
Message-ID: <54935.129.176.197.23.1267049125.squirrel@mail.ncbs.res.in>

Hi Jason,

Thanks for this information. I will go through this.

In case if somebody land this page from google using similar queries :
Please note that as I wanted this analysis to be completed asap, I
extracted genes in the chromosome regions using BioMart and used
List::Compare based methods to get the desired results.

Thanks,
Shameer

> You can use the collapse_nums method in Bio::Search::BlastUtils which is
> just an implementation of the connectivity algorithm but the Range
> description that Roy points out may be more useful since you'd have to
> unroll the ranges into the full set of numbers.
>
> collapse_nums
>
>   Usage     : @cnums = collapse_nums( @numbers );
>   Purpose   : Collapses a list of numbers into a set of ranges of
> consecutive terms:
>             : Useful for condensing long lists of consecutive numbers.
>             :  EXPANDED:
>             :     1 2 3 4 5 6 10 12 13 14 15 17 18 20 21 22 24 26 30 31 32
>             :  COLLAPSED:
>             :     1-6 10 12-15 17 18 20-22 24 26 30-32
>   Argument  : List of numbers sorted numerically.
>   Returns   : List of numbers mixed with ranges of numbers (see above).
>   Throws    : n/a
>
> -jason
> K. Shameer wrote:
>> Hello Roy,
>>
>> Thanks for the pointers.
>>
>> --
>> Shameer
>>
>>
>>> Hi Shameer,
>>>
>>> You could do this using Bio::Range, but that only allows you to
>>> determine the intersection between two ranges at once, so you'd need to
>>> do the calculation in several stages. It also doesn't have a method to
>>> determine positions that are unique to one of the ranges (although it
>>> possibly should).
>>>
>>> As this isn't a problem that is specific to biology, it's also worth
>>> hunting around on CPAN for modules that may be useful.
>>> Set::IntSpan::Fast looks suitable, particularly the intersection and
>>> diff methods. I haven't tried it, though.
>>>
>>> Roy.
>>>
>>> On 24/02/2010 16:59, K. Shameer wrote:
>>>
>>>> Hello all,
>>>>
>>>> I am looking for a standard way / bioperl module that can take up
>>>> different chromosome regions (in basepairs) and give the unique and
>>>> common
>>>> regions.
>>>> For example these are the regions and I need to get the common regions
>>>> (start - end) among all 5 regions:
>>>> 24328000 - 29166946
>>>> 25388351 - 27114603
>>>> 22310186 - 25239677
>>>> 28511024 - 29638159
>>>> 23729632 - 26385029
>>>>
>>>> Thanks,
>>>> Shameer
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>




From jskittrell at unmc.edu  Wed Feb 24 16:38:36 2010
From: jskittrell at unmc.edu (Jeff S Kittrell)
Date: Wed, 24 Feb 2010 15:38:36 -0600
Subject: [Bioperl-l] sim4cc vs sim4
In-Reply-To: <4B858308.7000207@bioperl.org>
References: <OF22B2884A.7FE0FC0D-ON862576D3.0081EF74-862576D3.00825A26@unmc.edu>
	<4B858308.7000207@bioperl.org>
Message-ID: <OFA3907EE7.F1A796F0-ON862576D4.007588F6-862576D4.0076E472@unmc.edu>

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From bimber at wisc.edu  Thu Feb 25 07:35:01 2010
From: bimber at wisc.edu (Ben Bimber)
Date: Thu, 25 Feb 2010 06:35:01 -0600
Subject: [Bioperl-l] is the Bio::Align::AlignI doc right?
Message-ID: <9f985cdc1002250435n278ef964o8ba474a149ba6f09@mail.gmail.com>

below is a Bio::Align::AlignI example found here:

http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Align/AlignI.pm#column_from_residue_number


 Title   : column_from_residue_number
 Usage   : $col = $ali->column_from_residue_number( $seqname, $resnumber)
 Function:

           This function gives the position in the alignment
           (i.e. column number) of the given residue number in the
           sequence with the given name. For example, for the
           alignment

             Seq1/91-97 AC..DEF.GH
             Seq2/24-30 ACGG.RTY..
             Seq3/43-51 AC.DDEFGHI

           column_from_residue_number( "Seq1", 94 ) returns 5.
           column_from_residue_number( "Seq2", 25 ) returns 2.
           column_from_residue_number( "Seq3", 50 ) returns 9.


Perhaps I am simply misunderstanding the method, but shouldnt the first
example return 6, not 5?

E is the 94th residue.  It is in the 6th column.  Am I missing something?

From bimber at wisc.edu  Thu Feb 25 07:39:50 2010
From: bimber at wisc.edu (Ben Bimber)
Date: Thu, 25 Feb 2010 06:39:50 -0600
Subject: [Bioperl-l] suggestions on module/method to translate SNPs?
Message-ID: <9f985cdc1002250439g241ac3a8r71277562ca5c49e2@mail.gmail.com>

I am parsing an alignment to identify positions of difference from a
reference.  Bio::Variation has objects that describe NT mutations.  Are
there methods that exist to translate these SNPs based on an annotated
reference sequence?  perhaps i'm simply looking in the wrong place, but for
the most part these object just seem to be containers to store attributes,
not manipulate them.

thanks for any help.

From maj at fortinbras.us  Thu Feb 25 07:46:55 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Thu, 25 Feb 2010 07:46:55 -0500
Subject: [Bioperl-l] is the Bio::Align::AlignI doc right?
In-Reply-To: <9f985cdc1002250435n278ef964o8ba474a149ba6f09@mail.gmail.com>
References: <9f985cdc1002250435n278ef964o8ba474a149ba6f09@mail.gmail.com>
Message-ID: <6A62D864E309498FAFE40D3E50B18815@NewLife>

Hi Ben-- you are correct, someone brought this up a while back
and it was corrected in revision 15841. MAJ
----- Original Message ----- 
From: "Ben Bimber" <bimber at wisc.edu>
To: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Thursday, February 25, 2010 7:35 AM
Subject: [Bioperl-l] is the Bio::Align::AlignI doc right?


> below is a Bio::Align::AlignI example found here:
>
> http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Align/AlignI.pm#column_from_residue_number
>
>
> Title   : column_from_residue_number
> Usage   : $col = $ali->column_from_residue_number( $seqname, $resnumber)
> Function:
>
>           This function gives the position in the alignment
>           (i.e. column number) of the given residue number in the
>           sequence with the given name. For example, for the
>           alignment
>
>             Seq1/91-97 AC..DEF.GH
>             Seq2/24-30 ACGG.RTY..
>             Seq3/43-51 AC.DDEFGHI
>
>           column_from_residue_number( "Seq1", 94 ) returns 5.
>           column_from_residue_number( "Seq2", 25 ) returns 2.
>           column_from_residue_number( "Seq3", 50 ) returns 9.
>
>
> Perhaps I am simply misunderstanding the method, but shouldnt the first
> example return 6, not 5?
>
> E is the 94th residue.  It is in the 6th column.  Am I missing something?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 


From cjfields at illinois.edu  Thu Feb 25 08:24:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 25 Feb 2010 07:24:17 -0600
Subject: [Bioperl-l] is the Bio::Align::AlignI doc right?
In-Reply-To: <9f985cdc1002250435n278ef964o8ba474a149ba6f09@mail.gmail.com>
References: <9f985cdc1002250435n278ef964o8ba474a149ba6f09@mail.gmail.com>
Message-ID: <EC571FC1-A690-4A7A-B1BE-F8961833CAC3@illinois.edu>

Yes, but this has been long corrected on main trunk and the latest CPAN code (1.6.1).  v.1.2.3 is very old, very very very old.  Dinosaurs and perl 5.6.1-old.  You should update, even if you are using ensembl's perl API ;>

chris

On Feb 25, 2010, at 6:35 AM, Ben Bimber wrote:

> below is a Bio::Align::AlignI example found here:
> 
> http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Align/AlignI.pm#column_from_residue_number
> 
> 
> Title   : column_from_residue_number
> Usage   : $col = $ali->column_from_residue_number( $seqname, $resnumber)
> Function:
> 
>           This function gives the position in the alignment
>           (i.e. column number) of the given residue number in the
>           sequence with the given name. For example, for the
>           alignment
> 
>             Seq1/91-97 AC..DEF.GH
>             Seq2/24-30 ACGG.RTY..
>             Seq3/43-51 AC.DDEFGHI
> 
>           column_from_residue_number( "Seq1", 94 ) returns 5.
>           column_from_residue_number( "Seq2", 25 ) returns 2.
>           column_from_residue_number( "Seq3", 50 ) returns 9.
> 
> 
> Perhaps I am simply misunderstanding the method, but shouldnt the first
> example return 6, not 5?
> 
> E is the 94th residue.  It is in the 6th column.  Am I missing something?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From mauricio at open-bio.org  Thu Feb 25 12:15:55 2010
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Thu, 25 Feb 2010 11:15:55 -0600
Subject: [Bioperl-l] is the Bio::Align::AlignI doc right?
In-Reply-To: <EC571FC1-A690-4A7A-B1BE-F8961833CAC3@illinois.edu>
References: <9f985cdc1002250435n278ef964o8ba474a149ba6f09@mail.gmail.com>
	<EC571FC1-A690-4A7A-B1BE-F8961833CAC3@illinois.edu>
Message-ID: <4B86B04B.9030301@open-bio.org>

You should use our online documentation once you upgrade:

http://doc.bioperl.org/

Here is the updated POD in the 1.6.1 release:

http://doc.bioperl.org/releases/bioperl-1.6.1/Bio/Align/AlignI.html#POD32

Mauricio.

On 2/25/10 7:24 AM, Chris Fields wrote:
> Yes, but this has been long corrected on main trunk and the latest CPAN code (1.6.1).  v.1.2.3 is very old, very very very old.  Dinosaurs and perl 5.6.1-old.  You should update, even if you are using ensembl's perl API ;>
>
> chris
>
> On Feb 25, 2010, at 6:35 AM, Ben Bimber wrote:
>
>> below is a Bio::Align::AlignI example found here:
>>
>> http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Align/AlignI.pm#column_from_residue_number
>>
>>
>> Title   : column_from_residue_number
>> Usage   : $col = $ali->column_from_residue_number( $seqname, $resnumber)
>> Function:
>>
>>            This function gives the position in the alignment
>>            (i.e. column number) of the given residue number in the
>>            sequence with the given name. For example, for the
>>            alignment
>>
>>              Seq1/91-97 AC..DEF.GH
>>              Seq2/24-30 ACGG.RTY..
>>              Seq3/43-51 AC.DDEFGHI
>>
>>            column_from_residue_number( "Seq1", 94 ) returns 5.
>>            column_from_residue_number( "Seq2", 25 ) returns 2.
>>            column_from_residue_number( "Seq3", 50 ) returns 9.
>>
>>
>> Perhaps I am simply misunderstanding the method, but shouldnt the first
>> example return 6, not 5?
>>
>> E is the 94th residue.  It is in the 6th column.  Am I missing something?
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From dan.kortschak at adelaide.edu.au  Thu Feb 25 15:59:50 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Fri, 26 Feb 2010 07:29:50 +1030
Subject: [Bioperl-l] Any module for chromosome region analysis ?
In-Reply-To: <mailman.1868.1267101307.3372.bioperl-l@lists.open-bio.org>
References: <mailman.1868.1267101307.3372.bioperl-l@lists.open-bio.org>
Message-ID: <1267131590.4355.2.camel@epistle>

Hi Shameer,

The RUNTools bioperl module will do this for you using the 'merge'
command.

Dan

On Thu, 2010-02-25 at 07:35 -0500, bioperl-l-request at lists.open-bio.org
wrote:
> Hello all,
> 
> I am looking for a standard way / bioperl module that can take up
> different chromosome regions (in basepairs) and give the unique and
> common
> regions.
> For example these are the regions and I need to get the common regions
> (start - end) among all 5 regions:
> 24328000 - 29166946
> 25388351 - 27114603
> 22310186 - 25239677
> 28511024 - 29638159
> 23729632 - 26385029
> 
> Thanks,
> Shameer


From dan.kortschak at adelaide.edu.au  Thu Feb 25 16:01:37 2010
From: dan.kortschak at adelaide.edu.au (Dan Kortschak)
Date: Fri, 26 Feb 2010 07:31:37 +1030
Subject: [Bioperl-l] Any module for chromosome region analysis ?
In-Reply-To: <1267131590.4355.2.camel@epistle>
References: <mailman.1868.1267101307.3372.bioperl-l@lists.open-bio.org>
	<1267131590.4355.2.camel@epistle>
Message-ID: <1267131697.4355.3.camel@epistle>

Correction - 'intersect' command.

On Fri, 2010-02-26 at 07:29 +1030, Dan Kortschak wrote:
> Hi Shameer,
> 
> The RUNTools bioperl module will do this for you using the 'merge'
> command.
> 
> Dan
> 
> On Thu, 2010-02-25 at 07:35 -0500, bioperl-l-request at lists.open-bio.org
> wrote:
> > Hello all,
> > 
> > I am looking for a standard way / bioperl module that can take up
> > different chromosome regions (in basepairs) and give the unique and
> > common
> > regions.
> > For example these are the regions and I need to get the common regions
> > (start - end) among all 5 regions:
> > 24328000 - 29166946
> > 25388351 - 27114603
> > 22310186 - 25239677
> > 28511024 - 29638159
> > 23729632 - 26385029
> > 
> > Thanks,
> > Shameer


From avilella at gmail.com  Fri Feb 26 02:20:27 2010
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Feb 2010 07:20:27 +0000
Subject: [Bioperl-l] indexed fastq files
In-Reply-To: <358f4d651002240345k3ac9a5b3ia66f6bfabcd0d9b0@mail.gmail.com>
References: <358f4d651001041200m1f715b83k743f4d2ee6b6312b@mail.gmail.com>
	<07EBA105-6A34-490C-B0B9-4772DF386CBA@illinois.edu>
	<358f4d651002240332u4b7dc2c8j6626e732211a8da4@mail.gmail.com>
	<358f4d651002240345k3ac9a5b3ia66f6bfabcd0d9b0@mail.gmail.com>
Message-ID: <358f4d651002252320t54cd7fe1r571ebef6d52a9b19@mail.gmail.com>

Hi all, would it be fine if I add an offset option to get this seek() to work?
Bio/Index/AbstractSeq.pm:131

sub fetch {
	my( $self, $id, $db_file_offset ) = @_;
	my $db = $self->db();
	my $seq;

	if (my $rec = $db->{ $id }) {
		my ($file, $begin) = $self->unpack_record( $rec );

		# Get the (possibly cached) SeqIO object
		my $seqio = $self->_get_SeqIO_object( $file );
		my $fh = $seqio->_fh();

		# move to start of record
		# $begin-- if( $^O =~ /mswin/i); # workaround for Win DB_File bug
		$begin-- if(defined($db_file_offset)); # avilella 20100224
		seek($fh, $begin, 0);

		$seq = $seqio->next_seq();	
	}

	# we essentially assumme that the primary_id for the database
	# is the display_id
	if (ref($seq) && $seq->isa('Bio::PrimarySeqI') &&
		 $seq->primary_id =~ /^\D+$/) {
		$seq->primary_id( $seq->display_id() );
	}
	return $seq;
}


On Wed, Feb 24, 2010 at 11:45 AM, Albert Vilella <avilella at gmail.com> wrote:
> BTW, I should mention that my index file was created with this options
> on the same linux system:
>
> my $db ?= Bio::Index::Fastq->new(-filename => $fastafile,
> -dbm_package=>'DB_File');
>
> So it looks more like DB_File dependent than "Win DB_File"...
>
> On Wed, Feb 24, 2010 at 11:32 AM, Albert Vilella <avilella at gmail.com> wrote:
>> Hi Chris,
>>
>> I am finding that Bio::Index::Fastq seek is chopping off the first
>> character of the fastq entry. I'm on Linux using bioperl-1.6.1 and
>> debugged the problem to this point in AbstractSeq.pm:143, where there
>> is this funny commented line:
>>
>> ? ? ? ? ? ? ? ?# $begin-- if( $^O =~ /mswin/i); # workaround for Win DB_File bug
>> ? ? ? ? ? ? ? ?seek($fh, $begin, 0);
>>
>> If I apply this $begin--, everything works fine, but I am not using
>> windows, I am on a Linux cluster.
>>
>> Any ideas why this was tagged as a "Win DB_File bug"?
>>
>> Cheers,
>>
>> Albert.
>>
>> On Mon, Jan 4, 2010 at 9:59 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>> Bio::Index::Fastq, maybe? ?To tell the truth, I haven't tried it since we refactored FASTQ parsing, so let us know if it doesn't work.
>>>
>>> chris
>>>
>>> On Jan 4, 2010, at 2:00 PM, Albert Vilella wrote:
>>>
>>>> Hi all,
>>>>
>>>> What is the best way to index fastq files, so that once clustered, I
>>>> can provide a list of seq_ids and get
>>>> them back in fastq format from the indexed db?
>>>>
>>>> Cheers,
>>>>
>>>> Albert.
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>


From paolo.pavan at gmail.com  Fri Feb 26 08:05:11 2010
From: paolo.pavan at gmail.com (Paolo Pavan)
Date: Fri, 26 Feb 2010 14:05:11 +0100
Subject: [Bioperl-l] Alignment from blast report
Message-ID: <56be91b61002260505j6a512587tc2d6623be21ba1b3@mail.gmail.com>

Hi all,
I have just a brief question: I've got some megablast reports such the
one I've pasted below.
I'm aware of the existence of the Bio::Search::IO::megablast and the
Bio::Search::HSP::BlastHSP::get_aln but, is there a way to get the
entire alignment represented as a Bio::SimpleAlign object or
Bio::Align::AlignI implementing one?

Thank you all,
Paolo


MEGABLAST 2.2.16 [Mar-25-2007]


Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000),
"A greedy algorithm for aligning DNA sequences",
J Comput Biol 2000; 7(1-2):203-14.

Database: 00038-00053.fasta
?????????? 2 sequences; 2001 total letters

Searching..................................................done

Query= 00038-00053
???????? (802 letters)



???????????????????????????????????????????????????????????????? Score??? E
Sequences producing significant alignments:????????????????????? (bits) Value

______00038
226?? 1e-62
______00053
115?? 3e-29

1_0???????? 472
ccgacaataattcttgttggaatcttcggcagttttttgtacaggagccagtagttcaaa 531
______00038 883
ccgacaataattcttgttggaatcttcggcagttttttgtacaggagccagtagttcaaa 942
______00053????? ------------------------------------------------------------

1_0???????? 532
aagaaagcgatcaataaaa-taaaaatcacaaaaaaattaccaaaaacatatttataaat 590
______00038 943
aagaaagcgatcaataaaaataaaaatcacaaaaaaattaccaaaaacatatttataaa- 1001
______00053????? ------------------------------------------------------------

1_0???????? 591
attggcaaaaaaattgccaacaattcccaaacggaaaattcccaaaacaaagagagcgtc 650
______00038 1000
------------------------------------------------------------ 1001
______00053????? ------------------------------------------------------------

1_0???????? 651
gataaccaatatcaaaatagtttttgaatttattttttgtgtttttttagtttttcttct 710
______00038 1000
------------------------------------------------------------ 1001
______00053????? ------------------------------------------------------------

1_0???????? 711
acgtcgtgttgccatttatccagcattaagtctataaaaaaaaacggtcagataaaaatg 770
______00038 1000
------------------------------------------------------------ 1001
______00053 1??? -------------------------ttaagtctataaaaaaaa-cggtcagataaaaatg 34

1_0???????? 771? ccttaagtatttactttaacttgtcttgatca 802
______00038 1000 -------------------------------- 1001
______00053 35?? ccttaagtatt-actttaacttgtcttgatca 65
? Database: 00038-00053.fasta
??? Posted date:? Feb 25, 2010? 4:47 PM
? Number of letters in database: 2001
? Number of sequences in database:? 2

Lambda???? K????? H
??? 1.37??? 0.711???? 1.31

Gapped
Lambda???? K????? H
??? 1.37??? 0.711???? 1.31


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 0, Extension: 0
Number of Sequences: 2
Number of Hits to DB: 17
Number of extensions: 3
Number of successful extensions: 3
Number of sequences better than 10.0: 2
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 802
Length of database: 2001
Length adjustment: 10
Effective length of query: 792
Effective length of database: 1981
Effective search space:? 1568952
Effective search space used:? 1568952
X1: 9 (17.8 bits)
X2: 20 (39.6 bits)
X3: 51 (101.1 bits)
S1: 9 (18.3 bits)
S2: 9 (18.3 bits)


From cjfields at illinois.edu  Fri Feb 26 08:28:02 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 26 Feb 2010 07:28:02 -0600
Subject: [Bioperl-l] indexed fastq files
In-Reply-To: <358f4d651002252320t54cd7fe1r571ebef6d52a9b19@mail.gmail.com>
References: <358f4d651001041200m1f715b83k743f4d2ee6b6312b@mail.gmail.com>
	<07EBA105-6A34-490C-B0B9-4772DF386CBA@illinois.edu>
	<358f4d651002240332u4b7dc2c8j6626e732211a8da4@mail.gmail.com>
	<358f4d651002240345k3ac9a5b3ia66f6bfabcd0d9b0@mail.gmail.com>
	<358f4d651002252320t54cd7fe1r571ebef6d52a9b19@mail.gmail.com>
Message-ID: <75B1980F-24D0-436F-9327-AA0603BF5186@illinois.edu>

Sure, go ahead.  I can look at adding tests for this module as well.

chris

On Feb 26, 2010, at 1:20 AM, Albert Vilella wrote:

> Hi all, would it be fine if I add an offset option to get this seek() to work?
> Bio/Index/AbstractSeq.pm:131
> 
> sub fetch {
> 	my( $self, $id, $db_file_offset ) = @_;
> 	my $db = $self->db();
> 	my $seq;
> 
> 	if (my $rec = $db->{ $id }) {
> 		my ($file, $begin) = $self->unpack_record( $rec );
> 
> 		# Get the (possibly cached) SeqIO object
> 		my $seqio = $self->_get_SeqIO_object( $file );
> 		my $fh = $seqio->_fh();
> 
> 		# move to start of record
> 		# $begin-- if( $^O =~ /mswin/i); # workaround for Win DB_File bug
> 		$begin-- if(defined($db_file_offset)); # avilella 20100224
> 		seek($fh, $begin, 0);
> 
> 		$seq = $seqio->next_seq();	
> 	}
> 
> 	# we essentially assumme that the primary_id for the database
> 	# is the display_id
> 	if (ref($seq) && $seq->isa('Bio::PrimarySeqI') &&
> 		 $seq->primary_id =~ /^\D+$/) {
> 		$seq->primary_id( $seq->display_id() );
> 	}
> 	return $seq;
> }
> 
> 
> On Wed, Feb 24, 2010 at 11:45 AM, Albert Vilella <avilella at gmail.com> wrote:
>> BTW, I should mention that my index file was created with this options
>> on the same linux system:
>> 
>> my $db  = Bio::Index::Fastq->new(-filename => $fastafile,
>> -dbm_package=>'DB_File');
>> 
>> So it looks more like DB_File dependent than "Win DB_File"...
>> 
>> On Wed, Feb 24, 2010 at 11:32 AM, Albert Vilella <avilella at gmail.com> wrote:
>>> Hi Chris,
>>> 
>>> I am finding that Bio::Index::Fastq seek is chopping off the first
>>> character of the fastq entry. I'm on Linux using bioperl-1.6.1 and
>>> debugged the problem to this point in AbstractSeq.pm:143, where there
>>> is this funny commented line:
>>> 
>>>               # $begin-- if( $^O =~ /mswin/i); # workaround for Win DB_File bug
>>>               seek($fh, $begin, 0);
>>> 
>>> If I apply this $begin--, everything works fine, but I am not using
>>> windows, I am on a Linux cluster.
>>> 
>>> Any ideas why this was tagged as a "Win DB_File bug"?
>>> 
>>> Cheers,
>>> 
>>> Albert.
>>> 
>>> On Mon, Jan 4, 2010 at 9:59 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> Bio::Index::Fastq, maybe?  To tell the truth, I haven't tried it since we refactored FASTQ parsing, so let us know if it doesn't work.
>>>> 
>>>> chris
>>>> 
>>>> On Jan 4, 2010, at 2:00 PM, Albert Vilella wrote:
>>>> 
>>>>> Hi all,
>>>>> 
>>>>> What is the best way to index fastq files, so that once clustered, I
>>>>> can provide a list of seq_ids and get
>>>>> them back in fastq format from the indexed db?
>>>>> 
>>>>> Cheers,
>>>>> 
>>>>> Albert.
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>> 
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From paolo.pavan at gmail.com  Fri Feb 26 09:17:08 2010
From: paolo.pavan at gmail.com (Paolo Pavan)
Date: Fri, 26 Feb 2010 15:17:08 +0100
Subject: [Bioperl-l] Alignment from blast report
In-Reply-To: <56be91b61002260505j6a512587tc2d6623be21ba1b3@mail.gmail.com>
References: <56be91b61002260505j6a512587tc2d6623be21ba1b3@mail.gmail.com>
Message-ID: <56be91b61002260617k744f12c3u1be774c314b3a4c8@mail.gmail.com>

Sorry,
Maybe I forgot to add this is the megablast -m 5 output.

Thank you again,
Paolo

2010/2/26 Paolo Pavan <paolo.pavan at gmail.com>:
> Hi all,
> I have just a brief question: I've got some megablast reports such the
> one I've pasted below.
> I'm aware of the existence of the Bio::Search::IO::megablast and the
> Bio::Search::HSP::BlastHSP::get_aln but, is there a way to get the
> entire alignment represented as a Bio::SimpleAlign object or
> Bio::Align::AlignI implementing one?
>
> Thank you all,
> Paolo
>
>
> MEGABLAST 2.2.16 [Mar-25-2007]
>
>
> Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000),
> "A greedy algorithm for aligning DNA sequences",
> J Comput Biol 2000; 7(1-2):203-14.
>
> Database: 00038-00053.fasta
> ?????????? 2 sequences; 2001 total letters
>
> Searching..................................................done
>
> Query= 00038-00053
> ???????? (802 letters)
>
>
>
> ???????????????????????????????????????????????????????????????? Score??? E
> Sequences producing significant alignments:????????????????????? (bits) Value
>
> ______00038
> 226?? 1e-62
> ______00053
> 115?? 3e-29
>
> 1_0???????? 472
> ccgacaataattcttgttggaatcttcggcagttttttgtacaggagccagtagttcaaa 531
> ______00038 883
> ccgacaataattcttgttggaatcttcggcagttttttgtacaggagccagtagttcaaa 942
> ______00053????? ------------------------------------------------------------
>
> 1_0???????? 532
> aagaaagcgatcaataaaa-taaaaatcacaaaaaaattaccaaaaacatatttataaat 590
> ______00038 943
> aagaaagcgatcaataaaaataaaaatcacaaaaaaattaccaaaaacatatttataaa- 1001
> ______00053????? ------------------------------------------------------------
>
> 1_0???????? 591
> attggcaaaaaaattgccaacaattcccaaacggaaaattcccaaaacaaagagagcgtc 650
> ______00038 1000
> ------------------------------------------------------------ 1001
> ______00053????? ------------------------------------------------------------
>
> 1_0???????? 651
> gataaccaatatcaaaatagtttttgaatttattttttgtgtttttttagtttttcttct 710
> ______00038 1000
> ------------------------------------------------------------ 1001
> ______00053????? ------------------------------------------------------------
>
> 1_0???????? 711
> acgtcgtgttgccatttatccagcattaagtctataaaaaaaaacggtcagataaaaatg 770
> ______00038 1000
> ------------------------------------------------------------ 1001
> ______00053 1??? -------------------------ttaagtctataaaaaaaa-cggtcagataaaaatg 34
>
> 1_0???????? 771? ccttaagtatttactttaacttgtcttgatca 802
> ______00038 1000 -------------------------------- 1001
> ______00053 35?? ccttaagtatt-actttaacttgtcttgatca 65
> ? Database: 00038-00053.fasta
> ??? Posted date:? Feb 25, 2010? 4:47 PM
> ? Number of letters in database: 2001
> ? Number of sequences in database:? 2
>
> Lambda???? K????? H
> ??? 1.37??? 0.711???? 1.31
>
> Gapped
> Lambda???? K????? H
> ??? 1.37??? 0.711???? 1.31
>
>
> Matrix: blastn matrix:1 -3
> Gap Penalties: Existence: 0, Extension: 0
> Number of Sequences: 2
> Number of Hits to DB: 17
> Number of extensions: 3
> Number of successful extensions: 3
> Number of sequences better than 10.0: 2
> Number of HSP's gapped: 2
> Number of HSP's successfully gapped: 2
> Length of query: 802
> Length of database: 2001
> Length adjustment: 10
> Effective length of query: 792
> Effective length of database: 1981
> Effective search space:? 1568952
> Effective search space used:? 1568952
> X1: 9 (17.8 bits)
> X2: 20 (39.6 bits)
> X3: 51 (101.1 bits)
> S1: 9 (18.3 bits)
> S2: 9 (18.3 bits)
>


From robert.bradbury at gmail.com  Sat Feb 27 12:46:02 2010
From: robert.bradbury at gmail.com (Robert Bradbury)
Date: Sat, 27 Feb 2010 12:46:02 -0500
Subject: [Bioperl-l] Any module for chromosome region analysis ?
In-Reply-To: <1267131697.4355.3.camel@epistle>
References: <mailman.1868.1267101307.3372.bioperl-l@lists.open-bio.org>
	<1267131590.4355.2.camel@epistle> <1267131697.4355.3.camel@epistle>
Message-ID: <deaa866a1002270946o3a108b54q5684c9b33a943197@mail.gmail.com>

I'm not sure if the species being dealt with are "common", but it would seem
to me that a logical addition to bioperl would be an extension that took a
genome location (or locations) and interfaced one into a browser of those
regions in external databases (e.g. UCSC Genome Browser, Ensemble, etc.).
The only cases where that wouldn't work is if one is dealing with novel
species that aren't in the databases yet.

Robert

From bimber at wisc.edu  Sun Feb 28 18:10:35 2010
From: bimber at wisc.edu (Ben Bimber)
Date: Sun, 28 Feb 2010 17:10:35 -0600
Subject: [Bioperl-l] Bio::Tools::Run::StandaloneBlastPlus and outformat
Message-ID: <9f985cdc1002281510o698291cu2c9b1e579536ad6d@mail.gmail.com>

Not sure if this is a bug or if I'm missing something:

In the standaloneBlastPlus wrapper, I can specify an output format
('-outfmt' in blastn) using '-outformat'.  blastn allows an integer to
specify output format (ie. 6 for tabular).  It also allows a some number of
string to specify additonal columns.  in this case, the whole block is
quoted:

-outfmt "6 qgi qacc sseqid sallseqid sgi sacc sallacc qstart qend sstart
send qseq sseq length pident nident mismatch positive gapopen qframe sframe"

The blastplus wrapper throws an error if you try to pass anything besides an
integer as -outformat.  Is there another way to specify output format or is
this a limitation of the module?

thanks,
ben

From maj at fortinbras.us  Sun Feb 28 21:33:23 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Sun, 28 Feb 2010 21:33:23 -0500
Subject: [Bioperl-l] Bio::Tools::Run::StandaloneBlastPlus and outformat
In-Reply-To: <9f985cdc1002281510o698291cu2c9b1e579536ad6d@mail.gmail.com>
References: <9f985cdc1002281510o698291cu2c9b1e579536ad6d@mail.gmail.com>
Message-ID: <A3C7FD406AD945E28BB7F1CA0A4BFDB7@NewLife>

Ben -- Might be a bug; can you send your script and the error you get 
Thanks MAJ
----- Original Message ----- 
From: "Ben Bimber" <bimber at wisc.edu>
To: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Sunday, February 28, 2010 6:10 PM
Subject: [Bioperl-l] Bio::Tools::Run::StandaloneBlastPlus and outformat


> Not sure if this is a bug or if I'm missing something:
> 
> In the standaloneBlastPlus wrapper, I can specify an output format
> ('-outfmt' in blastn) using '-outformat'.  blastn allows an integer to
> specify output format (ie. 6 for tabular).  It also allows a some number of
> string to specify additonal columns.  in this case, the whole block is
> quoted:
> 
> -outfmt "6 qgi qacc sseqid sallseqid sgi sacc sallacc qstart qend sstart
> send qseq sseq length pident nident mismatch positive gapopen qframe sframe"
> 
> The blastplus wrapper throws an error if you try to pass anything besides an
> integer as -outformat.  Is there another way to specify output format or is
> this a limitation of the module?
> 
> thanks,
> ben
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
>

From dishatandon.vit at gmail.com  Fri Feb 26 08:43:02 2010
From: dishatandon.vit at gmail.com (disha)
Date: Fri, 26 Feb 2010 05:43:02 -0800 (PST)
Subject: [Bioperl-l] Installing bioperl on windows
Message-ID: <30b0ffab-3ad6-4b59-8c19-2f203ff6c4f9@f17g2000prh.googlegroups.com>

Please tell me the procedure (detailed ) for installing bioperl on
windows vista.I tried the steps mentioned on the site but failed at
the initial steps