From bill at genenformics.com  Sun Jun  1 00:28:04 2008
From: bill at genenformics.com (bill at genenformics.com)
Date: Sat, 31 May 2008 21:28:04 -0700 (PDT)
Subject: [Bioperl-l] How to extract list of SNPs for a given gene?
In-Reply-To: <b48e0cf80805312119j6875ce2bhc754d895590f3c4d@mail.gmail.com>
References: <6F230E9769AA8D4EB4BC401DF133EDB7180C4A@NIHCESMLBX15.nih.gov>
	<b48e0cf80805312119j6875ce2bhc754d895590f3c4d@mail.gmail.com>
Message-ID: <61887.98.218.182.229.1212294484.squirrel@webmail.dreamhost.com>

Hi, Abhijit,

Gene2Snp, a standalone application which find SNPs for given Entrez Genes,
can be freely downloaded from
http://www.genenformics.com/download.html

A sample output is available at
http://www.genenformics.com/Gene2Snp_example_result.txt

This application may consume lots of CPU/memory due to complexity of locus
region.

Bill at genenformics.com

> From: artendulkar at gmail.com [mailto:artendulkar at gmail.com]
> Sent: Tuesday, May 20, 2008 4:21 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] How to extract list of SNPs for a given gene?
>
> Hi,
> Can anyone please tell me how to get list of SNPs in any particular gene
> using BioPerl, given NCBI Gene ID?
> Is there any method, which takes NCBI gene ID as argument and returns
> list
> of SNPs by connecting to dbSNP?
> Thank you.
> Abhijit
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From cjfields at uiuc.edu  Sun Jun  1 12:51:38 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Sun, 1 Jun 2008 11:51:38 -0500
Subject: [Bioperl-l] Fwd: BPlite
In-Reply-To: <B3A3F62F-682A-42E0-A28D-A08F909A588F@bioperl.org>
References: <48412383.5080201@ucsf.edu>
	<B3A3F62F-682A-42E0-A28D-A08F909A588F@bioperl.org>
Message-ID: <5DB8D706-5312-4D70-B71A-60915A84C825@uiuc.edu>

The problem is BPLite has been officially deprecated in favor of  
Bio::SearchIO BLAST parsing (including Sendu's BLAST-based pull  
parser).  If there is interest in resurrecting BPLite we would need  
someone to actively maintain it.

chris

On May 31, 2008, at 4:53 PM, Jason Stajich wrote:

>
>
> Begin forwarded message:
>
>> From: Anatoly Urisman <urisman at gmail.com>
>> Date: May 31, 2008 5:08:03 AM CDT
>> To: jason...
>> Subject: BPlite
>>
>> Hi Jason,
>> I was wondering if you are aware of a fix to the BPlite.pm module  
>> that supports the new NCBI blastall output (i.e. reports are not  
>> delimited by something like BLASTN 2.2.8 [Jan-05-2004]).
>> Thanks.
>> Anatoly Urisman, MD-PhD
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Tue Jun  3 11:25:26 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 3 Jun 2008 10:25:26 -0500
Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl and the Google Summer of Code
Message-ID: <BB355615-26D9-4A31-8DDD-414AD9E2AC62@uiuc.edu>

On behalf of the BioPerl core developers, Google, and the National  
Evolutionary Synthesis Center (NESCent), I would like to congratulate  
Mira Han on being accepted as a student for the Google Summer of Code  
(GSoC) and welcome her to the BioPerl community.  Mira's accepted  
project proposal involves developing phyloXML support for BioPerl.   
Following is the proposal abstract:

"PhyloXML is an XML document model for phylogenetic data that  
incorporates various annotation types, including user customized data.  
The format is currently not supported by BioPerl. I propose a SAX  
based data structure and interface for PhyloXML support in BioPerl. I  
will use most of the existing IO structures such as TreeIO and  
TreeEventBuilder and subclass them to extend the functions specific to  
PhyloXML. The objects will be connected to various existing BioPerl  
modules, such as SeqI, TaxonI, AnnotationI by reference in order to  
accommodate different phyloXML elements."

NESCent, under the Phyloinformatics Summer of Code, is participating  
as a mentoring organization in the GSoC for the second year.  This  
year, five projects (including Mira's) are being funded by Google,  
with a sixth project being funded by external sources.  Mira's co- 
mentors for this project are myself, Jason Stajich, Rutger Vos, and  
Christian Zmasek (the primary developer of phyloXML).  However, I  
encourage Mira to ask questions on the BioPerl mail list for feedback  
from the greater BioPerl community.

Further information on phyloXML:

http://www.phyloxml.org/

Further information on NESCent's Phyloinformatics Summer of Code,  
including all funded projects:

https://www.nescent.org/wg/phyloinformatics/index.php?title=Phyloinformatics_Summer_of_Code_2008

Sincerely,

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
The Institute for Genomic Biology
University of Illinois Urbana-Champaign





From miraceti at gmail.com  Tue Jun  3 11:58:00 2008
From: miraceti at gmail.com (miraceti)
Date: Tue, 3 Jun 2008 11:58:00 -0400
Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl and the Google Summer of Code
In-Reply-To: <BB355615-26D9-4A31-8DDD-414AD9E2AC62@uiuc.edu>
References: <BB355615-26D9-4A31-8DDD-414AD9E2AC62@uiuc.edu>
Message-ID: <dadd130806030858s13cbc2dahb6e5e93238e6889a@mail.gmail.com>

Thanks for the welcome,
I'm very excited to be part of the great community,
Here is the wiki page for the project,
*http://www.bioperl.org/wiki/PhyloXML_support_in_BioPerl
*I'll look forward to interacting with you and getting lots of help!

Mira Han

On Tue, Jun 3, 2008 at 11:25 AM, Chris Fields <cjfields at uiuc.edu> wrote:

> On behalf of the BioPerl core developers, Google, and the National
> Evolutionary Synthesis Center (NESCent), I would like to congratulate Mira
> Han on being accepted as a student for the Google Summer of Code (GSoC) and
> welcome her to the BioPerl community.  Mira's accepted project proposal
> involves developing phyloXML support for BioPerl.  Following is the proposal
> abstract:
>
> "PhyloXML is an XML document model for phylogenetic data that incorporates
> various annotation types, including user customized data. The format is
> currently not supported by BioPerl. I propose a SAX based data structure and
> interface for PhyloXML support in BioPerl. I will use most of the existing
> IO structures such as TreeIO and TreeEventBuilder and subclass them to
> extend the functions specific to PhyloXML. The objects will be connected to
> various existing BioPerl modules, such as SeqI, TaxonI, AnnotationI by
> reference in order to accommodate different phyloXML elements."
>
> NESCent, under the Phyloinformatics Summer of Code, is participating as a
> mentoring organization in the GSoC for the second year.  This year, five
> projects (including Mira's) are being funded by Google, with a sixth project
> being funded by external sources.  Mira's co-mentors for this project are
> myself, Jason Stajich, Rutger Vos, and Christian Zmasek (the primary
> developer of phyloXML).  However, I encourage Mira to ask questions on the
> BioPerl mail list for feedback from the greater BioPerl community.
>
> Further information on phyloXML:
>
> http://www.phyloxml.org/
>
> Further information on NESCent's Phyloinformatics Summer of Code, including
> all funded projects:
>
>
> https://www.nescent.org/wg/phyloinformatics/index.php?title=Phyloinformatics_Summer_of_Code_2008
>
> Sincerely,
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> The Institute for Genomic Biology
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From bamboowarrior at gmail.com  Tue Jun  3 16:50:37 2008
From: bamboowarrior at gmail.com (Arkady)
Date: Tue, 3 Jun 2008 15:50:37 -0500
Subject: [Bioperl-l] liftOver API
Message-ID: <91656c3f0806031350i442c6359v9c3461247e4340c6@mail.gmail.com>

Hi folks,

I've seen references occasionally to ensembl API or a BioPerl module
for converting between (human) genome assemblies (e.g. hg17 to hg18).
I'm also, of course, aware of liftOver, and of the chain file format.
But I'm more interested in the API. Does this still exist? Where can I
find it?

If not, does anyone have something that does this?

Cheers,
John Woods

From ousmane.diallo at crchum.qc.ca  Tue Jun  3 17:21:42 2008
From: ousmane.diallo at crchum.qc.ca (Ousmane Diallo)
Date: Tue, 03 Jun 2008 17:21:42 -0400
Subject: [Bioperl-l] How to get protein ID and get protein accession from GI
Message-ID: <4845B5E6.4050703@crchum.qc.ca>

hello,
Could somebody help me on how to get the protein ID and ACCESSION using the mRNA gi or accession.


my $db_obj = Bio::DB::GenBank->new();    
my $seq_obj = $db_obj->get_Seq_by_acc('123456') ;   # I pass here the mrna acc to get the seq_obj
my $gi = $seq_obj->primary_id ;                     # I get here the gi


I need to get the protein ID and protein ACCESSION"

THANKS!!


From pallavi.sarmah at igib.res.in  Wed Jun  4 08:33:08 2008
From: pallavi.sarmah at igib.res.in (Pallavi Sarmah)
Date: Wed, 4 Jun 2008 18:03:08 +0530
Subject: [Bioperl-l] Bioperl-ext installation error
Message-ID: <4C33FA201D55F743B5DE794497FCA8971F0C88@n1ex>



Hi,
I am trying to install Bioperl-ext and when rum the Makefile.PL it gives me the following error. 

ERROR from evaluation of /home/pallavi/Pallavi/downloads/bioperl-ext-1.5.1/Bio/SeqIO/staden/Makefile.PL: Invalid version '

' for Bio::SeqIO::staden::read.

Can anyone let me know the remedy for this. I stuck with this for last 2-3 days.

Pallavi


From sidd.basu at gmail.com  Wed Jun  4 10:54:13 2008
From: sidd.basu at gmail.com (Siddhartha Basu)
Date: Wed, 4 Jun 2008 09:54:13 -0500
Subject: [Bioperl-l] Re: How to get protein ID and get protein
	accession	from GI
In-Reply-To: <4845B5E6.4050703@crchum.qc.ca>
References: <4845B5E6.4050703@crchum.qc.ca>
Message-ID: <4846ac97.c505be0a.0446.1dc2@mx.google.com>

Hi,
You have to get the 'Feature' object for that.

On Tue, 03 Jun 2008, Ousmane Diallo wrote:

> hello,
> Could somebody help me on how to get the protein ID and ACCESSION using the mRNA gi or accession.
>
>
> my $db_obj = Bio::DB::GenBank->new();    my $seq_obj = 
> $db_obj->get_Seq_by_acc('123456') ;   # I pass here the mrna acc to get the 
> seq_obj
> my $gi = $seq_obj->primary_id ;                     # I get here the gi

my ($feat) = grep { $_->primary_tag() eq 'Protein' } $seq_obj->get_SeqFeatures();
print $feat->seq_id(),"\n";

For details and explanations read the Howto here .....

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

-siddhartha

>
>
> I need to get the protein ID and protein ACCESSION"
>
> THANKS!!
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From jay at jays.net  Wed Jun  4 10:19:03 2008
From: jay at jays.net (Jay Hannah)
Date: Wed, 4 Jun 2008 09:19:03 -0500
Subject: [Bioperl-l] How to get protein ID and get protein accession
	from GI
In-Reply-To: <4845B5E6.4050703@crchum.qc.ca>
References: <4845B5E6.4050703@crchum.qc.ca>
Message-ID: <200F7B8D-3066-48A8-9965-9E4E215749D9@jays.net>

On Jun 3, 2008, at 4:21 PM, Ousmane Diallo wrote:
> Could somebody help me on how to get the protein ID and ACCESSION  
> using the mRNA gi or accession.
>
> my $db_obj = Bio::DB::GenBank->new();
> my $seq_obj = $db_obj->get_Seq_by_acc('123456') ;   # I pass here  
> the mrna acc to get the seq_obj
> my $gi = $seq_obj->primary_id ;                     # I get here  
> the gi
>
> I need to get the protein ID and protein ACCESSION"

Please provide a real MRNA accession # you're interested in. I prefer  
sending example code that I know actually works on your data of  
interest.  :)

Thanks,

j
http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah

From bill at genenformics.com  Thu Jun  5 01:16:07 2008
From: bill at genenformics.com (bill at genenformics.com)
Date: Wed, 4 Jun 2008 22:16:07 -0700 (PDT)
Subject: [Bioperl-l] How to get protein ID and get protein accession
 from GI
Message-ID: <62133.98.218.171.90.1212642967.squirrel@webmail.dreamhost.com>

Hi, Ousmane,

IdConvert, a standalone application which convert protein/nucleotide
gi/acc, can be freely downloaded from
http://www.genenformics.com/download.html

A sample output is available at
http://www.genenformics.com/IdConvert_example_result.txt

The following is a test run:
>IdConvert.exe 300,NM_005252,399,NP_001225
#Input	Nuc_GI	Nuc_Acc	Pro_GI	Pro_Acc	Desc
300	299	X59693.1	300	CAA42214.1	ubiquinol--cytochrome c reductase [Bos
taurus]
NM_005252	6552332	NM_005252.2	4885241	NP_005243.1	v-fos FBJ murine
osteosarcoma viral oncogene homolog [Homo sapiens]
399	399	V00111.1	400	CAA23445.1	unnamed protein product [Bos taurus]
NP_001225	15451858	NM_001234.3	4502589	NP_001225.1	caveolin 3 [Homo sapiens]

Bill at genenformics.com



> hello,
> Could somebody help me on how to get the protein ID and ACCESSION using
> the mRNA gi or accession.
>
>
> my $db_obj = Bio::DB::GenBank->new();
> my $seq_obj = $db_obj->get_Seq_by_acc('123456') ;   # I pass here the mrna
> acc to get the seq_obj
> my $gi = $seq_obj->primary_id ;                     # I get here the gi
>
>
> I need to get the protein ID and protein ACCESSION"
>
> THANKS!!
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From bug-bioperl at rt.cpan.org  Thu Jun  5 12:01:13 2008
From: bug-bioperl at rt.cpan.org (=?UTF-8?B?Q8OpZHJpYyBDYWJhdQ==?= via RT)
Date: Thu, 05 Jun 2008 12:01:13 -0400
Subject: [Bioperl-l] [rt.cpan.org #36480] Bug in Bio::Search::SearchUtils.pm
In-Reply-To: <00ba01c8c725$49c454a0$dd4cfde0$@Cabau@tours.inra.fr>
References: <RT-Ticket-36480@rt.cpan.org>
	<00ba01c8c725$49c454a0$dd4cfde0$@Cabau@tours.inra.fr>
Message-ID: <rt-3.6.HEAD-32321-1212681672-446.36480-4-0@rt.cpan.org>


Thu Jun 05 12:01:11 2008: Request 36480 was acted upon.
Transaction: Ticket created by Cedric.Cabau at tours.inra.fr
       Queue: bioperl
     Subject: Bug in Bio::Search::SearchUtils.pm
   Broken in: (no value)
    Severity: (no value)
       Owner: Nobody
  Requestors: Cedric.Cabau at tours.inra.fr
      Status: new
 Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=36480 >


BioPerl version: bioperl-1.5.2_102
Module: Bio::Search::SearchUtils.pm
OS: CentOS Linux version 2.6.18-53.1.14.el5 (gcc version 4.1.2 20070626 (Red
Hat 4.1.2-14))
Perl: v5.8.8 built for x86_64-linux-thread-multi

Bug description:

Methods tile_hsps looks (among other things) if alignment is ambiguous.
Inside loop foreach $hsp ( $sbjct->hsps() ) { at line 177, methods $qoverlap
= &_adjust_contigs() (line 200) and $soverlap = &_adjust_contigs() (line
206) are used to know if current HSP overlap previous ones on query and on
subject. The problem is that in this loop, only the result of the last
comparison which means the last HSP with previous ones is kept in variables
$qoverlap and $soverlap.

After the loop, we found (line 299):

if($qoverlap) {
  if($soverlap) { $sbjct->ambiguous_aln('qs'); }
  else { $sbjct->ambiguous_aln('q');  }
}
elsif($soverlap) { 
  $sbjct->ambiguous_aln('s'); 
}

Only the result of the last comparison is stored in $sbjct and method
ambiguous_aln from module Bio::Search::Hit::GenericHit will return wrong
value if the alignment presents overlapping HSPs but last HSP not overlap
with previous ones.

To solve this bug, I just modify in line 200:

$qoverlap = &_adjust_contigs('query', $hsp, $qstart, $qstop, \@qcontigs,
$max_overlap, $frame, $qstrand);

by

$qoverlap += &_adjust_contigs('query', $hsp, $qstart, $qstop, \@qcontigs,
$max_overlap, $frame, $qstrand);

and in line 206:

$soverlap = &_adjust_contigs('sbjct', $hsp, $sstart, $sstop, \@scontigs,
$max_overlap, $frame, $sstrand);

by

$soverlap += &_adjust_contigs('sbjct', $hsp, $sstart, $sstop, \@scontigs,
$max_overlap, $frame, $sstrand);

to keep trace of overlaps in the whole HSPs screening process.

Regards,

Cedric

--

+---------------------------------------------------------------+
| C?dric Cabau                  INRA - SIGENAE - URA            |
| Tel : 02.47.42.75.42          Fax : 02.47.42.77.78            |
| http://www.sigenae.org        INRA - UR 83 - 37380 Nouzilly   |
+---------------------------------------------------------------+



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From jvaughn7 at utk.edu  Thu Jun  5 11:53:54 2008
From: jvaughn7 at utk.edu (JustinV)
Date: Thu, 5 Jun 2008 08:53:54 -0700 (PDT)
Subject: [Bioperl-l]  updating a reciprocal blast file
Message-ID: <17673277.post@talk.nabble.com>


I have a large reciprocal blast file that contains 3 proteomes.  I'd like to
integrate another proteome for downstream clustering.    I imagine a
command-line script that takes as input the new proteome in fasta format,
the directory of the the old proteomes in fasta format, and the pre-existing
reciprocal blast file, and then performs the proper blasts and updates the
pre-existing reciprocal blast file accordingly.  I am using blast locally
and the downstream processing is done by OrthoMCL.  I assume this has been
handled before, but I can't track down the code.  If anyone is familiar with
a pre-exisiting script or has pertinent advice, I'd be much obliged.

Justin
-- 
View this message in context: http://www.nabble.com/updating-a-reciprocal-blast-file-tp17673277p17673277.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From jason at bioperl.org  Thu Jun  5 16:18:40 2008
From: jason at bioperl.org (Jason Stajich)
Date: Thu, 5 Jun 2008 13:18:40 -0700
Subject: [Bioperl-l] updating a reciprocal blast file
In-Reply-To: <17673277.post@talk.nabble.com>
References: <17673277.post@talk.nabble.com>
Message-ID: <167EE308-F6F6-4EE9-A773-255A68906ABB@bioperl.org>

Are you keeping each pairwise in a separate file and then combining  
it all?
  http://fungalgenomes.org/~stajich/scripts/pairwise_blast_jobs_big.pl

Are you fixing E-values so they are scaled across different sized  
databases? You will probably want to add a Z= parameter to insure  
values are useable.

I also had to hack ORTHOMCL locally to cache things in DB_Files as it  
was too memory intensive the way it runs on my big datasets.

-jason
On Jun 5, 2008, at 8:53 AM, JustinV wrote:

>
> I have a large reciprocal blast file that contains 3 proteomes.   
> I'd like to
> integrate another proteome for downstream clustering.    I imagine a
> command-line script that takes as input the new proteome in fasta  
> format,
> the directory of the the old proteomes in fasta format, and the pre- 
> existing
> reciprocal blast file, and then performs the proper blasts and  
> updates the
> pre-existing reciprocal blast file accordingly.  I am using blast  
> locally
> and the downstream processing is done by OrthoMCL.  I assume this  
> has been
> handled before, but I can't track down the code.  If anyone is  
> familiar with
> a pre-exisiting script or has pertinent advice, I'd be much obliged.
>
> Justin
> -- 
> View this message in context: http://www.nabble.com/updating-a- 
> reciprocal-blast-file-tp17673277p17673277.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 jvaughn7 at utk.edu  Fri Jun  6 10:18:16 2008
From: jvaughn7 at utk.edu (JustinV)
Date: Fri, 6 Jun 2008 07:18:16 -0700 (PDT)
Subject: [Bioperl-l] updating a reciprocal blast file
In-Reply-To: <167EE308-F6F6-4EE9-A773-255A68906ABB@bioperl.org>
References: <17673277.post@talk.nabble.com>
	<167EE308-F6F6-4EE9-A773-255A68906ABB@bioperl.org>
Message-ID: <17693254.post@talk.nabble.com>


Jason,

Thanks for the suggestions.

The blast report is a single file containing each query in the 3 proteomes
against a database of the 3 proteomes.  As you probably remember, OrthoMCL
offers many modes of running that head-off various levels of processing.  In
any case, the reciprocal blast is the bottle-neck.  Mode -3 forgoes this
step, but it requires a single, exhaustive blast report.  Perhaps, I could
run the reciprocal blasts separately as you suggested and then integrate
them with your pairwise_blast_jobs_big.pl.  I have to say, this code looks a
little spooky.  Wouldn't it be possible to just resort (by normalized
e-value, discussed below) and reprint each set of query hits based on a hash
or index of the results of that query against the new proteome?  And then
tack on the results of new proteome against the updated database to the end
of the total blast report.

In terms of normalizing the e-value, since I am using a consistent scoring
matrix, can't I just recalculate the scores based on new database size:

(new e-value) = (new database size) * (old e-value) / (old database size)

as in http://www.springerlink.com/content/55m318wwqdgtw85h/ (methods) and
elsewhere.

As of yet, I've been satisfied with the run time downstream of the
reciprocal blast, but, as I've said, I'm currently only using three plant
(dicot) proteomes.  By "hack ORTHOMCL locally to cache things in DB_Files"
do you mean serializing the blastSeq objects from early blasts in the
blast_parse subroutine using bioperl-db or something?  Maybe this is dumb
assumption.  In any case, I'd be curious to see your modified version of the
OrthoMCL script.

Justin


Jason Stajich-3 wrote:
> 
> Are you keeping each pairwise in a separate file and then combining  
> it all?
>   http://fungalgenomes.org/~stajich/scripts/pairwise_blast_jobs_big.pl
> 
> Are you fixing E-values so they are scaled across different sized  
> databases? You will probably want to add a Z= parameter to insure  
> values are useable.
> 
> I also had to hack ORTHOMCL locally to cache things in DB_Files as it  
> was too memory intensive the way it runs on my big datasets.
> 
> -jason
> On Jun 5, 2008, at 8:53 AM, JustinV wrote:
> 
>>
>> I have a large reciprocal blast file that contains 3 proteomes.   
>> I'd like to
>> integrate another proteome for downstream clustering.    I imagine a
>> command-line script that takes as input the new proteome in fasta  
>> format,
>> the directory of the the old proteomes in fasta format, and the pre- 
>> existing
>> reciprocal blast file, and then performs the proper blasts and  
>> updates the
>> pre-existing reciprocal blast file accordingly.  I am using blast  
>> locally
>> and the downstream processing is done by OrthoMCL.  I assume this  
>> has been
>> handled before, but I can't track down the code.  If anyone is  
>> familiar with
>> a pre-exisiting script or has pertinent advice, I'd be much obliged.
>>
>> Justin
>> -- 
>> View this message in context: http://www.nabble.com/updating-a- 
>> reciprocal-blast-file-tp17673277p17673277.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
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://www.nabble.com/updating-a-reciprocal-blast-file-tp17673277p17693254.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From whuang.ustc at gmail.com  Sun Jun  8 23:27:42 2008
From: whuang.ustc at gmail.com (Wen Huang)
Date: Sun, 8 Jun 2008 22:27:42 -0500
Subject: [Bioperl-l] EMBL format field
Message-ID: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>

Hi all,

I have a EMBL file that I want to extract one of the line

###file###
ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
XX
PA   AB000170.1
XX
DE   Sus scrofa (pig) endopeptidase 24.16 type M1
XX
OS   Sus scrofa (pig)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;  
Mammalia;
OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.
OX   NCBI_TaxID=9823;
.........

I want the accession number in the line that starts with PA, AB000170  
in this example.

Can anybody kindly help, tell me which module and method I should use?  
I tried various things like $seq_obj -> primary_id, display_id,  
get_secondary_id, etc.. they did not work...

Thanks a lot!

Wen

From Marc.Logghe at ablynx.com  Mon Jun  9 04:47:11 2008
From: Marc.Logghe at ablynx.com (Marc Logghe)
Date: Mon, 9 Jun 2008 10:47:11 +0200
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
Message-ID: <03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>

Hi Wen,
A dump of that sequence object (Data::Dumper is your friend !) reveals
that the PA EMBL field is not saved into the object. However, you will
find the string 'AB000170.1' in the embedded CDS feature, more precisely
the seqid of the location object. I don't know whether that is always
the case, but it is in your particular example.
So, to get your hands on that value you have to do:

my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
my $parent_id = $cds->location->seq_id;

HTH,
Marc

Marc Logghe
Senior Bioinformatician
Ablynx nv
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Wen Huang
> Sent: Monday, June 09, 2008 5:28 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] EMBL format field
> 
> Hi all,
> 
> I have a EMBL file that I want to extract one of the line
> 
> ###file###
> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
> XX
> PA   AB000170.1
> XX
> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
> XX
> OS   Sus scrofa (pig)
> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
> Mammalia;
> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.
> OX   NCBI_TaxID=9823;
> .........
> 
> I want the accession number in the line that starts with PA, AB000170
> in this example.
> 
> Can anybody kindly help, tell me which module and method I should use?
> I tried various things like $seq_obj -> primary_id, display_id,
> get_secondary_id, etc.. they did not work...
> 
> Thanks a lot!
> 
> Wen
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From hlapp at gmx.net  Mon Jun  9 08:30:07 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Mon, 9 Jun 2008 08:30:07 -0400
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
Message-ID: <C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>

If this is the case with the latest version of BioPerl it should be  
filed as a bug report for the embl parser. The ID ought to be  
reported in $seq->get_secondary_accessions() (which returns an  
array). If it doesn't, it sounds like a bug to me.

	-hilmar

On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
> Hi Wen,
> A dump of that sequence object (Data::Dumper is your friend !) reveals
> that the PA EMBL field is not saved into the object. However, you will
> find the string 'AB000170.1' in the embedded CDS feature, more  
> precisely
> the seqid of the location object. I don't know whether that is always
> the case, but it is in your particular example.
> So, to get your hands on that value you have to do:
>
> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
> my $parent_id = $cds->location->seq_id;
>
> HTH,
> Marc
>
> Marc Logghe
> Senior Bioinformatician
> Ablynx nv
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>> Sent: Monday, June 09, 2008 5:28 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] EMBL format field
>>
>> Hi all,
>>
>> I have a EMBL file that I want to extract one of the line
>>
>> ###file###
>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>> XX
>> PA   AB000170.1
>> XX
>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>> XX
>> OS   Sus scrofa (pig)
>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;  
>> Euteleostomi;
>> Mammalia;
>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.
>> OX   NCBI_TaxID=9823;
>> .........
>>
>> I want the accession number in the line that starts with PA, AB000170
>> in this example.
>>
>> Can anybody kindly help, tell me which module and method I should  
>> use?
>> I tried various things like $seq_obj -> primary_id, display_id,
>> get_secondary_id, etc.. they did not work...
>>
>> Thanks a lot!
>>
>> Wen
>> _______________________________________________
>> 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

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================




From whuang.ustc at gmail.com  Mon Jun  9 10:05:35 2008
From: whuang.ustc at gmail.com (Wen Huang)
Date: Mon, 9 Jun 2008 09:05:35 -0500
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
Message-ID: <D56E2C78-55AB-4278-809E-363255142899@gmail.com>

Hi Marc,

Thanks a lot! It does work!!

Wen
On Jun 9, 2008, at 3:47 AM, Marc Logghe wrote:

> Hi Wen,
> A dump of that sequence object (Data::Dumper is your friend !) reveals
> that the PA EMBL field is not saved into the object. However, you will
> find the string 'AB000170.1' in the embedded CDS feature, more  
> precisely
> the seqid of the location object. I don't know whether that is always
> the case, but it is in your particular example.
> So, to get your hands on that value you have to do:
>
> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
> my $parent_id = $cds->location->seq_id;
>
> HTH,
> Marc
>
> Marc Logghe
> Senior Bioinformatician
> Ablynx nv
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>> Sent: Monday, June 09, 2008 5:28 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] EMBL format field
>>
>> Hi all,
>>
>> I have a EMBL file that I want to extract one of the line
>>
>> ###file###
>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>> XX
>> PA   AB000170.1
>> XX
>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>> XX
>> OS   Sus scrofa (pig)
>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;  
>> Euteleostomi;
>> Mammalia;
>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.
>> OX   NCBI_TaxID=9823;
>> .........
>>
>> I want the accession number in the line that starts with PA, AB000170
>> in this example.
>>
>> Can anybody kindly help, tell me which module and method I should  
>> use?
>> I tried various things like $seq_obj -> primary_id, display_id,
>> get_secondary_id, etc.. they did not work...
>>
>> Thanks a lot!
>>
>> Wen
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From whuang.ustc at gmail.com  Mon Jun  9 10:07:28 2008
From: whuang.ustc at gmail.com (Wen Huang)
Date: Mon, 9 Jun 2008 09:07:28 -0500
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
Message-ID: <45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>

Hilmar,

I tried that, it did not work. Marc's way can work.

Thanks,
Wen

On Jun 9, 2008, at 7:30 AM, Hilmar Lapp wrote:

> If this is the case with the latest version of BioPerl it should be  
> filed as a bug report for the embl parser. The ID ought to be  
> reported in $seq->get_secondary_accessions() (which returns an  
> array). If it doesn't, it sounds like a bug to me.
>
> 	-hilmar
>
> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>> Hi Wen,
>> A dump of that sequence object (Data::Dumper is your friend !)  
>> reveals
>> that the PA EMBL field is not saved into the object. However, you  
>> will
>> find the string 'AB000170.1' in the embedded CDS feature, more  
>> precisely
>> the seqid of the location object. I don't know whether that is always
>> the case, but it is in your particular example.
>> So, to get your hands on that value you have to do:
>>
>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
>> my $parent_id = $cds->location->seq_id;
>>
>> HTH,
>> Marc
>>
>> Marc Logghe
>> Senior Bioinformatician
>> Ablynx nv
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>> Sent: Monday, June 09, 2008 5:28 AM
>>> To: bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] EMBL format field
>>>
>>> Hi all,
>>>
>>> I have a EMBL file that I want to extract one of the line
>>>
>>> ###file###
>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>> XX
>>> PA   AB000170.1
>>> XX
>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>> XX
>>> OS   Sus scrofa (pig)
>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;  
>>> Euteleostomi;
>>> Mammalia;
>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.
>>> OX   NCBI_TaxID=9823;
>>> .........
>>>
>>> I want the accession number in the line that starts with PA,  
>>> AB000170
>>> in this example.
>>>
>>> Can anybody kindly help, tell me which module and method I should  
>>> use?
>>> I tried various things like $seq_obj -> primary_id, display_id,
>>> get_secondary_id, etc.. they did not work...
>>>
>>> Thanks a lot!
>>>
>>> Wen
>>> _______________________________________________
>>> 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
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>


From cjfields at uiuc.edu  Mon Jun  9 14:12:29 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 9 Jun 2008 13:12:29 -0500
Subject: [Bioperl-l] [Wg-phyloinformatics] Re: phyloXML weekly report
In-Reply-To: <C4722AB7.4012%mirhan@indiana.edu>
References: <C4722AB7.4012%mirhan@indiana.edu>
Message-ID: <87FB1AA1-943D-4BCC-8F00-2CC5F05FFEAB@uiuc.edu>

[cross-posting to bioperl-l for archiving]

On Jun 8, 2008, at 11:32 PM, Han, Mira wrote:

> ...
> issues:
> There are a lot of <if/elsif>s when processing the elements,
> I tried to make a hash of function references that point to the  
> member functions,
> But when I tried calling it through the hash, it was giving me an  
> error that I'm trying to call a method on an unblessed object.

I ran into something similar when setting up a few SeqIO modules  
(Bio::SeqIO::gbdriver being on of them) which passed on data chunks to  
method handlers.  It has something to do with how the method is set up  
in the class (package) namespace and how you refer to it.  It's a  
little tricky b/c you run into semantic issues with perl's 'hammered- 
on' OO, but it can be done.

If you call using '$self->{lookup}->{$tag}->(@args)' directly, what  
happens is you can successfully call the method since you are still in  
the proper module namespace.  However, since you aren't calling from  
the invocant ($self) directly but rather from a reference in the  
invocant, it treats the call like a subroutine instead of a method.   
Therefore no invocant is passed as the first argument (you will  
instead get either the first element in @args or 'undef' assigned to  
$self within the method).  Not sure if this is supposed to be a  
feature or a bug.  Regardless, any attempt within the method to do  
something with $self will result in a 'using an unblessed reference'  
or 'not a hash reference'.

There are two solutions, both of which work.  If you have method  
references stored in a hash table in the invocant:

$self->{lookup}->{tag1} = \&foo;
$self->{lookup}->{tag2} = \&bar;
....

you can grab the actual code reference (checking using 'exists') and  
use it directly on the invocant, but NOT as a code reference.  This  
acts as a symbolic reference, which is allowed for subroutine and  
method calls (I think it's supposed to be DWIM-my):

if (exists $self->{lookup}->{$tag}) {
     my $method = $self->{lookup}->{$tag};
     $self->$method(@args);
} else {...}

The above also works if you use strings in the lookup table which  
contain the name of the methods (again, symbolic reference):

$self->{lookup}->{tag1} = 'foo';
$self->{lookup}->{tag2} = 'bar';

Alternately, you can pass the invocant in explicitly (which looks  
weird to me, hence my above solution):

if (exists $self->{lookup}->{$tag}) {
     $self->{lookup}->{$tag}->($self, @args);
} else {...}

perl6 fixes a lot of these issues, but of course it won't be out for a  
while longer.

> I'd like to figure out how to do it,
> But before that, is hashing really better than lots of if-elses?

Using a stack of if-elsifs isn't as efficient as a lookup since you  
would test each case in succession (so something that is further down  
the if-elseif test stack would have passed through and failed each  
previous test case before success).  A lookup table would test simply  
based on the existence of a value stored under a key (tag).

An alternative is to use 5.10 features (smart matching and given-when,  
which is like a switch statement), but that will limit usage for those  
still using 5.8.8, which is probably a majority of users, since 5.10  
came out just last December.

chris

>
>
> Mira
>
>
>
> On 6/2/08 10:29 AM, "Han, Mira" <mirhan at indiana.edu> wrote:
>
>
>
> Last week (May 26-30):
> 1. made skeleton files for TreeIO:: PhyloEventBuilder,  
> TreeIO::phyloXML, Tree::NodePhyloXML
> 2. managed to connect and load them up but there is a bus error  
> problem.
> I think it's probably due to some of the function calls that I'm  
> making
> That I haven't looked into properly. I'm suspecting it will go away  
> once I properly
> build in the end_element for <clade>
>
> This week (Jun 2-6):
> 1. implement start_element, and end_element for <phylogeny> and  
> <clade>
> -    start_element: <phylogeny>: add treelevel, <clade>: push data  
> to current_items.
> -    end_element: <phylogeny>: minus treelevel, <clade>: pop data  
> from current_elements, use new() to build node from popped data.
> 2. get rid of that bus error
> 3. TreeIO::phyloXML::Next_tree() : look for element </phylogeny>
> _______________________________________________
> Wg-phyloinformatics mailing list
> Wg-phyloinformatics at nescent.org
> https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Mon Jun  9 15:08:23 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 9 Jun 2008 14:08:23 -0500
Subject: [Bioperl-l] [Wg-phyloinformatics] Re: phyloXML weekly report
In-Reply-To: <OFF55660E8.1AA687E1-ON85257463.0065663D-85257463.0065A8D7@gsk.com>
References: <OFF55660E8.1AA687E1-ON85257463.0065663D-85257463.0065A8D7@gsk.com>
Message-ID: <763316E4-F480-45FC-BC81-A450D61CAB2D@uiuc.edu>

Yes, that works as well.

chris

On Jun 9, 2008, at 1:30 PM, aaron.j.mackey at gsk.com wrote:

> How about just:
>
>  $self->${ $self->{lookup}->{tag} }(@args)
>
> i.e., shorthand for:
>
>  $method = $self->{lookup}->{tag}
>  $self->$method(@args);
>
> -Aaron
>
> wg-phyloinformatics-bounces at nescent.org wrote on 06/09/2008 02:12:29  
> PM:
>
>> [cross-posting to bioperl-l for archiving]
>>
>> On Jun 8, 2008, at 11:32 PM, Han, Mira wrote:
>>
>>> ...
>>> issues:
>>> There are a lot of <if/elsif>s when processing the elements,
>>> I tried to make a hash of function references that point to the
>>> member functions,
>>> But when I tried calling it through the hash, it was giving me an
>>> error that I'm trying to call a method on an unblessed object.
>>
>> I ran into something similar when setting up a few SeqIO modules
>> (Bio::SeqIO::gbdriver being on of them) which passed on data chunks  
>> to
>> method handlers.  It has something to do with how the method is set  
>> up
>> in the class (package) namespace and how you refer to it.  It's a
>> little tricky b/c you run into semantic issues with perl's 'hammered-
>> on' OO, but it can be done.
>>
>> If you call using '$self->{lookup}->{$tag}->(@args)' directly, what
>> happens is you can successfully call the method since you are still  
>> in
>> the proper module namespace.  However, since you aren't calling from
>> the invocant ($self) directly but rather from a reference in the
>> invocant, it treats the call like a subroutine instead of a method.
>> Therefore no invocant is passed as the first argument (you will
>> instead get either the first element in @args or 'undef' assigned to
>> $self within the method).  Not sure if this is supposed to be a
>> feature or a bug.  Regardless, any attempt within the method to do
>> something with $self will result in a 'using an unblessed reference'
>> or 'not a hash reference'.
>>
>> There are two solutions, both of which work.  If you have method
>> references stored in a hash table in the invocant:
>>
>> $self->{lookup}->{tag1} = \&foo;
>> $self->{lookup}->{tag2} = \&bar;
>> ....
>>
>> you can grab the actual code reference (checking using 'exists') and
>> use it directly on the invocant, but NOT as a code reference.  This
>> acts as a symbolic reference, which is allowed for subroutine and
>> method calls (I think it's supposed to be DWIM-my):
>>
>> if (exists $self->{lookup}->{$tag}) {
>>     my $method = $self->{lookup}->{$tag};
>>     $self->$method(@args);
>> } else {...}
>>
>> The above also works if you use strings in the lookup table which
>> contain the name of the methods (again, symbolic reference):
>>
>> $self->{lookup}->{tag1} = 'foo';
>> $self->{lookup}->{tag2} = 'bar';
>>
>> Alternately, you can pass the invocant in explicitly (which looks
>> weird to me, hence my above solution):
>>
>> if (exists $self->{lookup}->{$tag}) {
>>     $self->{lookup}->{$tag}->($self, @args);
>> } else {...}
>>
>> perl6 fixes a lot of these issues, but of course it won't be out  
>> for a
>> while longer.
>>
>>> I'd like to figure out how to do it,
>>> But before that, is hashing really better than lots of if-elses?
>>
>> Using a stack of if-elsifs isn't as efficient as a lookup since you
>> would test each case in succession (so something that is further down
>> the if-elseif test stack would have passed through and failed each
>> previous test case before success).  A lookup table would test simply
>> based on the existence of a value stored under a key (tag).
>>
>> An alternative is to use 5.10 features (smart matching and given- 
>> when,
>> which is like a switch statement), but that will limit usage for  
>> those
>> still using 5.8.8, which is probably a majority of users, since 5.10
>> came out just last December.
>>
>> chris
>>
>>>
>>>
>>> Mira
>>>
>>>
>>>
>>> On 6/2/08 10:29 AM, "Han, Mira" <mirhan at indiana.edu> wrote:
>>>
>>>
>>>
>>> Last week (May 26-30):
>>> 1. made skeleton files for TreeIO:: PhyloEventBuilder,
>>> TreeIO::phyloXML, Tree::NodePhyloXML
>>> 2. managed to connect and load them up but there is a bus error
>>> problem.
>>> I think it's probably due to some of the function calls that I'm
>>> making
>>> That I haven't looked into properly. I'm suspecting it will go away
>>> once I properly
>>> build in the end_element for <clade>
>>>
>>> This week (Jun 2-6):
>>> 1. implement start_element, and end_element for <phylogeny> and
>>> <clade>
>>> -    start_element: <phylogeny>: add treelevel, <clade>: push data
>>> to current_items.
>>> -    end_element: <phylogeny>: minus treelevel, <clade>: pop data
>>> from current_elements, use new() to build node from popped data.
>>> 2. get rid of that bus error
>>> 3. TreeIO::phyloXML::Next_tree() : look for element </phylogeny>
>>> _______________________________________________
>>> Wg-phyloinformatics mailing list
>>> Wg-phyloinformatics at nescent.org
>>> https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Marie-Claude Hofmann
>> College of Veterinary Medicine
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>> _______________________________________________
>> Wg-phyloinformatics mailing list
>> Wg-phyloinformatics at nescent.org
>> https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
>>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From aaron.j.mackey at gsk.com  Mon Jun  9 14:30:22 2008
From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com)
Date: Mon, 9 Jun 2008 14:30:22 -0400
Subject: [Bioperl-l] [Wg-phyloinformatics] Re: phyloXML weekly report
In-Reply-To: <87FB1AA1-943D-4BCC-8F00-2CC5F05FFEAB@uiuc.edu>
Message-ID: <OFF55660E8.1AA687E1-ON85257463.0065663D-85257463.0065A8D7@gsk.com>

How about just:

  $self->${ $self->{lookup}->{tag} }(@args)

i.e., shorthand for:

  $method = $self->{lookup}->{tag}
  $self->$method(@args);

-Aaron

wg-phyloinformatics-bounces at nescent.org wrote on 06/09/2008 02:12:29 PM:

> [cross-posting to bioperl-l for archiving]
> 
> On Jun 8, 2008, at 11:32 PM, Han, Mira wrote:
> 
> > ...
> > issues:
> > There are a lot of <if/elsif>s when processing the elements,
> > I tried to make a hash of function references that point to the 
> > member functions,
> > But when I tried calling it through the hash, it was giving me an 
> > error that I'm trying to call a method on an unblessed object.
> 
> I ran into something similar when setting up a few SeqIO modules 
> (Bio::SeqIO::gbdriver being on of them) which passed on data chunks to 
> method handlers.  It has something to do with how the method is set up 
> in the class (package) namespace and how you refer to it.  It's a 
> little tricky b/c you run into semantic issues with perl's 'hammered- 
> on' OO, but it can be done.
> 
> If you call using '$self->{lookup}->{$tag}->(@args)' directly, what 
> happens is you can successfully call the method since you are still in 
> the proper module namespace.  However, since you aren't calling from 
> the invocant ($self) directly but rather from a reference in the 
> invocant, it treats the call like a subroutine instead of a method. 
> Therefore no invocant is passed as the first argument (you will 
> instead get either the first element in @args or 'undef' assigned to 
> $self within the method).  Not sure if this is supposed to be a 
> feature or a bug.  Regardless, any attempt within the method to do 
> something with $self will result in a 'using an unblessed reference' 
> or 'not a hash reference'.
> 
> There are two solutions, both of which work.  If you have method 
> references stored in a hash table in the invocant:
> 
> $self->{lookup}->{tag1} = \&foo;
> $self->{lookup}->{tag2} = \&bar;
> ....
> 
> you can grab the actual code reference (checking using 'exists') and 
> use it directly on the invocant, but NOT as a code reference.  This 
> acts as a symbolic reference, which is allowed for subroutine and 
> method calls (I think it's supposed to be DWIM-my):
> 
> if (exists $self->{lookup}->{$tag}) {
>      my $method = $self->{lookup}->{$tag};
>      $self->$method(@args);
> } else {...}
> 
> The above also works if you use strings in the lookup table which 
> contain the name of the methods (again, symbolic reference):
> 
> $self->{lookup}->{tag1} = 'foo';
> $self->{lookup}->{tag2} = 'bar';
> 
> Alternately, you can pass the invocant in explicitly (which looks 
> weird to me, hence my above solution):
> 
> if (exists $self->{lookup}->{$tag}) {
>      $self->{lookup}->{$tag}->($self, @args);
> } else {...}
> 
> perl6 fixes a lot of these issues, but of course it won't be out for a 
> while longer.
> 
> > I'd like to figure out how to do it,
> > But before that, is hashing really better than lots of if-elses?
> 
> Using a stack of if-elsifs isn't as efficient as a lookup since you 
> would test each case in succession (so something that is further down 
> the if-elseif test stack would have passed through and failed each 
> previous test case before success).  A lookup table would test simply 
> based on the existence of a value stored under a key (tag).
> 
> An alternative is to use 5.10 features (smart matching and given-when, 
> which is like a switch statement), but that will limit usage for those 
> still using 5.8.8, which is probably a majority of users, since 5.10 
> came out just last December.
> 
> chris
> 
> >
> >
> > Mira
> >
> >
> >
> > On 6/2/08 10:29 AM, "Han, Mira" <mirhan at indiana.edu> wrote:
> >
> >
> >
> > Last week (May 26-30):
> > 1. made skeleton files for TreeIO:: PhyloEventBuilder, 
> > TreeIO::phyloXML, Tree::NodePhyloXML
> > 2. managed to connect and load them up but there is a bus error 
> > problem.
> > I think it's probably due to some of the function calls that I'm 
> > making
> > That I haven't looked into properly. I'm suspecting it will go away 
> > once I properly
> > build in the end_element for <clade>
> >
> > This week (Jun 2-6):
> > 1. implement start_element, and end_element for <phylogeny> and 
> > <clade>
> > -    start_element: <phylogeny>: add treelevel, <clade>: push data 
> > to current_items.
> > -    end_element: <phylogeny>: minus treelevel, <clade>: pop data 
> > from current_elements, use new() to build node from popped data.
> > 2. get rid of that bus error
> > 3. TreeIO::phyloXML::Next_tree() : look for element </phylogeny>
> > _______________________________________________
> > Wg-phyloinformatics mailing list
> > Wg-phyloinformatics at nescent.org
> > https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
> 
> 
> 
> 
> _______________________________________________
> Wg-phyloinformatics mailing list
> Wg-phyloinformatics at nescent.org
> https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
> 



From miraceti at gmail.com  Tue Jun 10 00:37:03 2008
From: miraceti at gmail.com (miraceti)
Date: Tue, 10 Jun 2008 00:37:03 -0400
Subject: [Bioperl-l] [Wg-phyloinformatics] Re: phyloXML weekly report
In-Reply-To: <763316E4-F480-45FC-BC81-A450D61CAB2D@uiuc.edu>
References: <OFF55660E8.1AA687E1-ON85257463.0065663D-85257463.0065A8D7@gsk.com>
	<763316E4-F480-45FC-BC81-A450D61CAB2D@uiuc.edu>
Message-ID: <dadd130806092137g3d90c624ya767320ac347a11d@mail.gmail.com>

Thanks for that,
It now works.

FYI,
    my $method = $self->{'_start_element'}->{$reader->name};
    $self->$method();
Worked.
    $self->{'_start_element'}->{$reader->name}($self);
Worked.
    $self->${$self->{'_start_element'}->{$reader->name}};
Gave error: Not a SCALAR reference at
/usr/local/src/bioperl-live/Bio/TreeIO/phyloxml.pm line 197
    $self->${\scalar($self->{'_start_element'}->{$reader->name})};
Worked.

I'm using the first way.

Mira

On Mon, Jun 9, 2008 at 3:08 PM, Chris Fields <cjfields at uiuc.edu> wrote:

> Yes, that works as well.
>
> chris
>
>
> On Jun 9, 2008, at 1:30 PM, aaron.j.mackey at gsk.com wrote:
>
>  How about just:
>>
>>  $self->${ $self->{lookup}->{tag} }(@args)
>>
>> i.e., shorthand for:
>>
>>  $method = $self->{lookup}->{tag}
>>  $self->$method(@args);
>>
>> -Aaron
>>
>> wg-phyloinformatics-bounces at nescent.org wrote on 06/09/2008 02:12:29 PM:
>>
>>  [cross-posting to bioperl-l for archiving]
>>>
>>> On Jun 8, 2008, at 11:32 PM, Han, Mira wrote:
>>>
>>>  ...
>>>> issues:
>>>> There are a lot of <if/elsif>s when processing the elements,
>>>> I tried to make a hash of function references that point to the
>>>> member functions,
>>>> But when I tried calling it through the hash, it was giving me an
>>>> error that I'm trying to call a method on an unblessed object.
>>>>
>>>
>>> I ran into something similar when setting up a few SeqIO modules
>>> (Bio::SeqIO::gbdriver being on of them) which passed on data chunks to
>>> method handlers.  It has something to do with how the method is set up
>>> in the class (package) namespace and how you refer to it.  It's a
>>> little tricky b/c you run into semantic issues with perl's 'hammered-
>>> on' OO, but it can be done.
>>>
>>> If you call using '$self->{lookup}->{$tag}->(@args)' directly, what
>>> happens is you can successfully call the method since you are still in
>>> the proper module namespace.  However, since you aren't calling from
>>> the invocant ($self) directly but rather from a reference in the
>>> invocant, it treats the call like a subroutine instead of a method.
>>> Therefore no invocant is passed as the first argument (you will
>>> instead get either the first element in @args or 'undef' assigned to
>>> $self within the method).  Not sure if this is supposed to be a
>>> feature or a bug.  Regardless, any attempt within the method to do
>>> something with $self will result in a 'using an unblessed reference'
>>> or 'not a hash reference'.
>>>
>>> There are two solutions, both of which work.  If you have method
>>> references stored in a hash table in the invocant:
>>>
>>> $self->{lookup}->{tag1} = \&foo;
>>> $self->{lookup}->{tag2} = \&bar;
>>> ....
>>>
>>> you can grab the actual code reference (checking using 'exists') and
>>> use it directly on the invocant, but NOT as a code reference.  This
>>> acts as a symbolic reference, which is allowed for subroutine and
>>> method calls (I think it's supposed to be DWIM-my):
>>>
>>> if (exists $self->{lookup}->{$tag}) {
>>>    my $method = $self->{lookup}->{$tag};
>>>    $self->$method(@args);
>>> } else {...}
>>>
>>> The above also works if you use strings in the lookup table which
>>> contain the name of the methods (again, symbolic reference):
>>>
>>> $self->{lookup}->{tag1} = 'foo';
>>> $self->{lookup}->{tag2} = 'bar';
>>>
>>> Alternately, you can pass the invocant in explicitly (which looks
>>> weird to me, hence my above solution):
>>>
>>> if (exists $self->{lookup}->{$tag}) {
>>>    $self->{lookup}->{$tag}->($self, @args);
>>> } else {...}
>>>
>>> perl6 fixes a lot of these issues, but of course it won't be out for a
>>> while longer.
>>>
>>>  I'd like to figure out how to do it,
>>>> But before that, is hashing really better than lots of if-elses?
>>>>
>>>
>>> Using a stack of if-elsifs isn't as efficient as a lookup since you
>>> would test each case in succession (so something that is further down
>>> the if-elseif test stack would have passed through and failed each
>>> previous test case before success).  A lookup table would test simply
>>> based on the existence of a value stored under a key (tag).
>>>
>>> An alternative is to use 5.10 features (smart matching and given-when,
>>> which is like a switch statement), but that will limit usage for those
>>> still using 5.8.8, which is probably a majority of users, since 5.10
>>> came out just last December.
>>>
>>> chris
>>>
>>>
>>>>
>>>> Mira
>>>>
>>>>
>>>>
>>>> On 6/2/08 10:29 AM, "Han, Mira" <mirhan at indiana.edu> wrote:
>>>>
>>>>
>>>>
>>>> Last week (May 26-30):
>>>> 1. made skeleton files for TreeIO:: PhyloEventBuilder,
>>>> TreeIO::phyloXML, Tree::NodePhyloXML
>>>> 2. managed to connect and load them up but there is a bus error
>>>> problem.
>>>> I think it's probably due to some of the function calls that I'm
>>>> making
>>>> That I haven't looked into properly. I'm suspecting it will go away
>>>> once I properly
>>>> build in the end_element for <clade>
>>>>
>>>> This week (Jun 2-6):
>>>> 1. implement start_element, and end_element for <phylogeny> and
>>>> <clade>
>>>> -    start_element: <phylogeny>: add treelevel, <clade>: push data
>>>> to current_items.
>>>> -    end_element: <phylogeny>: minus treelevel, <clade>: pop data
>>>> from current_elements, use new() to build node from popped data.
>>>> 2. get rid of that bus error
>>>> 3. TreeIO::phyloXML::Next_tree() : look for element </phylogeny>
>>>> _______________________________________________
>>>> Wg-phyloinformatics mailing list
>>>> Wg-phyloinformatics at nescent.org
>>>> https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
>>>>
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Marie-Claude Hofmann
>>> College of Veterinary Medicine
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Wg-phyloinformatics mailing list
>>> Wg-phyloinformatics at nescent.org
>>> https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
>>>
>>>
>>
>>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From yezhiqiang at gmail.com  Tue Jun 10 07:43:50 2008
From: yezhiqiang at gmail.com (Zhi-Qiang Ye)
Date: Tue, 10 Jun 2008 19:43:50 +0800
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
Message-ID: <34198fe40806100443g6c18f47dj881d68c0bf14ba8f@mail.gmail.com>

That's weird. I also met this problem. I tried a embl-format file like this:

ID   CB271253; SV 1; linear; mRNA; EST; INV; 591 BP.
XX
AC   CB271253;
XX
DT   24-FEB-2003 (Rel. 74, Created)
DT   24-FEB-2003 (Rel. 74, Last updated, Version 1)
XX
DE   taa17c02.x2 Hydra EST -II Hydra magnipapillata cDNA 3' similar to
DE   SW:OPSD_RABIT P49912 RHODOPSIN. ;, mRNA sequence.

from: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&id=CB271253&style=raw

the $seq object's   ->id, ->display_id  are "unkown id" ...



ZQ Ye

2008/6/9 Hilmar Lapp <hlapp at gmx.net>:
> If this is the case with the latest version of BioPerl it should be filed as
> a bug report for the embl parser. The ID ought to be reported in
> $seq->get_secondary_accessions() (which returns an array). If it doesn't, it
> sounds like a bug to me.
>
>        -hilmar
>
> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>
>> Hi Wen,
>> A dump of that sequence object (Data::Dumper is your friend !) reveals
>> that the PA EMBL field is not saved into the object. However, you will
>> find the string 'AB000170.1' in the embedded CDS feature, more precisely
>> the seqid of the location object. I don't know whether that is always
>> the case, but it is in your particular example.
>> So, to get your hands on that value you have to do:
>>
>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
>> my $parent_id = $cds->location->seq_id;
>>
>> HTH,
>> Marc
>>
>> Marc Logghe
>> Senior Bioinformatician
>> Ablynx nv
>>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>> Sent: Monday, June 09, 2008 5:28 AM
>>> To: bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] EMBL format field
>>>
>>> Hi all,
>>>
>>> I have a EMBL file that I want to extract one of the line
>>>
>>> ###file###
>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>> XX
>>> PA   AB000170.1
>>> XX
>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>> XX
>>> OS   Sus scrofa (pig)
>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
>>> Mammalia;
>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.
>>> OX   NCBI_TaxID=9823;
>>> .........
>>>
>>> I want the accession number in the line that starts with PA, AB000170
>>> in this example.
>>>
>>> Can anybody kindly help, tell me which module and method I should use?
>>> I tried various things like $seq_obj -> primary_id, display_id,
>>> get_secondary_id, etc.. they did not work...
>>>
>>> Thanks a lot!
>>>
>>> Wen
>>> _______________________________________________
>>> 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
>
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From jeremydt at gmail.com  Tue Jun 10 14:50:19 2008
From: jeremydt at gmail.com (Jeremy Davis-Turak)
Date: Tue, 10 Jun 2008 11:50:19 -0700
Subject: [Bioperl-l] Error installing bioperl
Message-ID: <378b225b0806101150i5fe6ff2as831d6ee8b5254b4c@mail.gmail.com>

Hi, I'm getting the following error, either using CPAN or make with
bioperl-1.4 (also with bioperl-1.2)

Writing Makefile for Bio
make: *** No rule to make target
`/usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi/CORE/config.h', needed by
`Makefile'.  Stop.


Can you please help?

Thanks,

Jeremy

From Kevin.M.Brown at asu.edu  Tue Jun 10 15:10:40 2008
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Tue, 10 Jun 2008 12:10:40 -0700
Subject: [Bioperl-l] Error installing bioperl
In-Reply-To: <378b225b0806101150i5fe6ff2as831d6ee8b5254b4c@mail.gmail.com>
References: <378b225b0806101150i5fe6ff2as831d6ee8b5254b4c@mail.gmail.com>
Message-ID: <1A4207F8295607498283FE9E93B775B404F2AFCD@EX02.asurite.ad.asu.edu>

Bioperl 1.4 is a very old version.  Try following the install directions
at http://www.bioperl.org/wiki/Installing_BioPerl 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Jeremy Davis-Turak
> Sent: Tuesday, June 10, 2008 11:50 AM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Error installing bioperl
> 
> Hi, I'm getting the following error, either using CPAN or make with
> bioperl-1.4 (also with bioperl-1.2)
> 
> Writing Makefile for Bio
> make: *** No rule to make target
> `/usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi/CORE/config
> .h', needed by
> `Makefile'.  Stop.
> 
> 
> Can you please help?
> 
> Thanks,
> 
> Jeremy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From heikki at sanbi.ac.za  Tue Jun 10 19:22:10 2008
From: heikki at sanbi.ac.za (Heikki Lehvaslaiho)
Date: Wed, 11 Jun 2008 01:22:10 +0200
Subject: [Bioperl-l] A lot of POD fixes in bioperl-live and bioperl run
Message-ID: <200806110122.10982.heikki@sanbi.ac.za>

I have recently done a lot fixes in the inline Plain Old Documenation
(POD) texts in bioperl-live and bioperl-run. Last ones (hopefully) were 
committed a few minutes ago. This has resulted quite large updates from SVN.

I wanted to apologize the inconvenience and to explain reasons for these small 
and pedantic fixes.

In contrast to perl, POD is sensitive to white space. This makes it relatively 
difficult to find and fix all minor errors in POD. I've now gone through the 
trouble of fixing all POD mistakes causing even the smallest warning in the 
podchecker.

The main reason for doing this was to reduce the the number of warnings
reported by the pod.pl bioperl maintenence tool. Too many minor warnings make 
it difficult to recognise more serious errors affecting the integrity and 
readability of POD documentation.

One example case is when a paragraph that was supposed to be 'in
verbatim', is in fact touching the previous paragraph and the pod
engine formats it and destroys the intended ascii graph or table.
The only way POD engine is able to report this is to warn about unescaped 
special characters.

    -Heikki
-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________

From jason at bioperl.org  Tue Jun 10 19:55:56 2008
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 10 Jun 2008 16:55:56 -0700
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <34198fe40806100443g6c18f47dj881d68c0bf14ba8f@mail.gmail.com>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<34198fe40806100443g6c18f47dj881d68c0bf14ba8f@mail.gmail.com>
Message-ID: <46E681F5-CB56-4ADA-BEB9-00083CFA78F9@bioperl.org>

What version of bioperl? It works for me using  this code I get  
'CB271253' printed out.

#!/usr/bin/perl -w
use strict;
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-format => 'embl', -file => shift);
while( my $seq = $in->next_seq ) {
  print $seq->id,"\n";
}

On Jun 10, 2008, at 4:43 AM, Zhi-Qiang Ye wrote:

> That's weird. I also met this problem. I tried a embl-format file  
> like this:
>
> ID   CB271253; SV 1; linear; mRNA; EST; INV; 591 BP.
> XX
> AC   CB271253;
> XX
> DT   24-FEB-2003 (Rel. 74, Created)
> DT   24-FEB-2003 (Rel. 74, Last updated, Version 1)
> XX
> DE   taa17c02.x2 Hydra EST -II Hydra magnipapillata cDNA 3' similar to
> DE   SW:OPSD_RABIT P49912 RHODOPSIN. ;, mRNA sequence.
>
> from: http://www.ebi.ac.uk/cgi-bin/dbfetch? 
> db=embl&id=CB271253&style=raw
>
> the $seq object's   ->id, ->display_id  are "unkown id" ...
>
>
>
> ZQ Ye
>
> 2008/6/9 Hilmar Lapp <hlapp at gmx.net>:
>> If this is the case with the latest version of BioPerl it should  
>> be filed as
>> a bug report for the embl parser. The ID ought to be reported in
>> $seq->get_secondary_accessions() (which returns an array). If it  
>> doesn't, it
>> sounds like a bug to me.
>>
>>        -hilmar
>>
>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>
>>> Hi Wen,
>>> A dump of that sequence object (Data::Dumper is your friend !)  
>>> reveals
>>> that the PA EMBL field is not saved into the object. However, you  
>>> will
>>> find the string 'AB000170.1' in the embedded CDS feature, more  
>>> precisely
>>> the seqid of the location object. I don't know whether that is  
>>> always
>>> the case, but it is in your particular example.
>>> So, to get your hands on that value you have to do:
>>>
>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
>>> my $parent_id = $cds->location->seq_id;
>>>
>>> HTH,
>>> Marc
>>>
>>> Marc Logghe
>>> Senior Bioinformatician
>>> Ablynx nv
>>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>> To: bioperl-l at lists.open-bio.org
>>>> Subject: [Bioperl-l] EMBL format field
>>>>
>>>> Hi all,
>>>>
>>>> I have a EMBL file that I want to extract one of the line
>>>>
>>>> ###file###
>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>> XX
>>>> PA   AB000170.1
>>>> XX
>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>> XX
>>>> OS   Sus scrofa (pig)
>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;  
>>>> Euteleostomi;
>>>> Mammalia;
>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.
>>>> OX   NCBI_TaxID=9823;
>>>> .........
>>>>
>>>> I want the accession number in the line that starts with PA,  
>>>> AB000170
>>>> in this example.
>>>>
>>>> Can anybody kindly help, tell me which module and method I  
>>>> should use?
>>>> I tried various things like $seq_obj -> primary_id, display_id,
>>>> get_secondary_id, etc.. they did not work...
>>>>
>>>> Thanks a lot!
>>>>
>>>> Wen
>>>> _______________________________________________
>>>> 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
>>
>> --
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>> _______________________________________________
>> 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  Tue Jun 10 19:57:42 2008
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 10 Jun 2008 16:57:42 -0700
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>
Message-ID: <468D955B-533C-439A-96EA-B7CC6392BFE3@bioperl.org>

PA is a field that we don't currently parse, something that should be  
filed as a bug on bugzilla.
Would you be able to do this?

-jason
On Jun 9, 2008, at 7:07 AM, Wen Huang wrote:

> Hilmar,
>
> I tried that, it did not work. Marc's way can work.
>
> Thanks,
> Wen
>
> On Jun 9, 2008, at 7:30 AM, Hilmar Lapp wrote:
>
>> If this is the case with the latest version of BioPerl it should  
>> be filed as a bug report for the embl parser. The ID ought to be  
>> reported in $seq->get_secondary_accessions() (which returns an  
>> array). If it doesn't, it sounds like a bug to me.
>>
>> 	-hilmar
>>
>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>> Hi Wen,
>>> A dump of that sequence object (Data::Dumper is your friend !)  
>>> reveals
>>> that the PA EMBL field is not saved into the object. However, you  
>>> will
>>> find the string 'AB000170.1' in the embedded CDS feature, more  
>>> precisely
>>> the seqid of the location object. I don't know whether that is  
>>> always
>>> the case, but it is in your particular example.
>>> So, to get your hands on that value you have to do:
>>>
>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
>>> my $parent_id = $cds->location->seq_id;
>>>
>>> HTH,
>>> Marc
>>>
>>> Marc Logghe
>>> Senior Bioinformatician
>>> Ablynx nv
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>> To: bioperl-l at lists.open-bio.org
>>>> Subject: [Bioperl-l] EMBL format field
>>>>
>>>> Hi all,
>>>>
>>>> I have a EMBL file that I want to extract one of the line
>>>>
>>>> ###file###
>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>> XX
>>>> PA   AB000170.1
>>>> XX
>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>> XX
>>>> OS   Sus scrofa (pig)
>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;  
>>>> Euteleostomi;
>>>> Mammalia;
>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.
>>>> OX   NCBI_TaxID=9823;
>>>> .........
>>>>
>>>> I want the accession number in the line that starts with PA,  
>>>> AB000170
>>>> in this example.
>>>>
>>>> Can anybody kindly help, tell me which module and method I  
>>>> should use?
>>>> I tried various things like $seq_obj -> primary_id, display_id,
>>>> get_secondary_id, etc.. they did not work...
>>>>
>>>> Thanks a lot!
>>>>
>>>> Wen
>>>> _______________________________________________
>>>> 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
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From cjfields at uiuc.edu  Tue Jun 10 20:19:55 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 10 Jun 2008 19:19:55 -0500
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <468D955B-533C-439A-96EA-B7CC6392BFE3@bioperl.org>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>
	<468D955B-533C-439A-96EA-B7CC6392BFE3@bioperl.org>
Message-ID: <2542BB6E-AC43-4D5A-8788-2330E59A6E6F@uiuc.edu>

PA is an odd field; it isn't described in the EMBL user manual:

http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html

but appears in mRNA files, so I'm guessing it stands for the (p)rotein  
(a)ccession.  I don't think this should be stored as primary/secondary  
accession, but maybe as a DBLink annootation?

chris

On Jun 10, 2008, at 6:57 PM, Jason Stajich wrote:

> PA is a field that we don't currently parse, something that should  
> be filed as a bug on bugzilla.
> Would you be able to do this?
>
> -jason
> On Jun 9, 2008, at 7:07 AM, Wen Huang wrote:
>
>> Hilmar,
>>
>> I tried that, it did not work. Marc's way can work.
>>
>> Thanks,
>> Wen
>>
>> On Jun 9, 2008, at 7:30 AM, Hilmar Lapp wrote:
>>
>>> If this is the case with the latest version of BioPerl it should  
>>> be filed as a bug report for the embl parser. The ID ought to be  
>>> reported in $seq->get_secondary_accessions() (which returns an  
>>> array). If it doesn't, it sounds like a bug to me.
>>>
>>> 	-hilmar
>>>
>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>> Hi Wen,
>>>> A dump of that sequence object (Data::Dumper is your friend !)  
>>>> reveals
>>>> that the PA EMBL field is not saved into the object. However, you  
>>>> will
>>>> find the string 'AB000170.1' in the embedded CDS feature, more  
>>>> precisely
>>>> the seqid of the location object. I don't know whether that is  
>>>> always
>>>> the case, but it is in your particular example.
>>>> So, to get your hands on that value you have to do:
>>>>
>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
>>>> my $parent_id = $cds->location->seq_id;
>>>>
>>>> HTH,
>>>> Marc
>>>>
>>>> Marc Logghe
>>>> Senior Bioinformatician
>>>> Ablynx nv
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>> To: bioperl-l at lists.open-bio.org
>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>
>>>>> Hi all,
>>>>>
>>>>> I have a EMBL file that I want to extract one of the line
>>>>>
>>>>> ###file###
>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>> XX
>>>>> PA   AB000170.1
>>>>> XX
>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>> XX
>>>>> OS   Sus scrofa (pig)
>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;  
>>>>> Euteleostomi;
>>>>> Mammalia;
>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae;  
>>>>> Sus.
>>>>> OX   NCBI_TaxID=9823;
>>>>> .........
>>>>>
>>>>> I want the accession number in the line that starts with PA,  
>>>>> AB000170
>>>>> in this example.
>>>>>
>>>>> Can anybody kindly help, tell me which module and method I  
>>>>> should use?
>>>>> I tried various things like $seq_obj -> primary_id, display_id,
>>>>> get_secondary_id, etc.. they did not work...
>>>>>
>>>>> Thanks a lot!
>>>>>
>>>>> Wen
>>>>> _______________________________________________
>>>>> 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
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>
>> _______________________________________________
>> 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

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From jason at bioperl.org  Tue Jun 10 20:36:20 2008
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 10 Jun 2008 17:36:20 -0700
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <2542BB6E-AC43-4D5A-8788-2330E59A6E6F@uiuc.edu>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>
	<468D955B-533C-439A-96EA-B7CC6392BFE3@bioperl.org>
	<2542BB6E-AC43-4D5A-8788-2330E59A6E6F@uiuc.edu>
Message-ID: <9A1F4E7F-A231-410C-8890-14ECDC7D0258@bioperl.org>

I agree if it isn't the accession # it shouldn't be stored there.  I  
guess it is a DBlink, but it is going to be hacky to round-trip this  
as you'll have to have a special case for records that are mRNAs...

-jason
On Jun 10, 2008, at 5:19 PM, Chris Fields wrote:

> PA is an odd field; it isn't described in the EMBL user manual:
>
> http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
>
> but appears in mRNA files, so I'm guessing it stands for the (p) 
> rotein (a)ccession.  I don't think this should be stored as primary/ 
> secondary accession, but maybe as a DBLink annootation?
>
> chris
>
> On Jun 10, 2008, at 6:57 PM, Jason Stajich wrote:
>
>> PA is a field that we don't currently parse, something that should  
>> be filed as a bug on bugzilla.
>> Would you be able to do this?
>>
>> -jason
>> On Jun 9, 2008, at 7:07 AM, Wen Huang wrote:
>>
>>> Hilmar,
>>>
>>> I tried that, it did not work. Marc's way can work.
>>>
>>> Thanks,
>>> Wen
>>>
>>> On Jun 9, 2008, at 7:30 AM, Hilmar Lapp wrote:
>>>
>>>> If this is the case with the latest version of BioPerl it should  
>>>> be filed as a bug report for the embl parser. The ID ought to be  
>>>> reported in $seq->get_secondary_accessions() (which returns an  
>>>> array). If it doesn't, it sounds like a bug to me.
>>>>
>>>> 	-hilmar
>>>>
>>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>> Hi Wen,
>>>>> A dump of that sequence object (Data::Dumper is your friend !)  
>>>>> reveals
>>>>> that the PA EMBL field is not saved into the object. However,  
>>>>> you will
>>>>> find the string 'AB000170.1' in the embedded CDS feature, more  
>>>>> precisely
>>>>> the seqid of the location object. I don't know whether that is  
>>>>> always
>>>>> the case, but it is in your particular example.
>>>>> So, to get your hands on that value you have to do:
>>>>>
>>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
>>>>> my $parent_id = $cds->location->seq_id;
>>>>>
>>>>> HTH,
>>>>> Marc
>>>>>
>>>>> Marc Logghe
>>>>> Senior Bioinformatician
>>>>> Ablynx nv
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I have a EMBL file that I want to extract one of the line
>>>>>>
>>>>>> ###file###
>>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>>> XX
>>>>>> PA   AB000170.1
>>>>>> XX
>>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>>> XX
>>>>>> OS   Sus scrofa (pig)
>>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;  
>>>>>> Euteleostomi;
>>>>>> Mammalia;
>>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae;  
>>>>>> Sus.
>>>>>> OX   NCBI_TaxID=9823;
>>>>>> .........
>>>>>>
>>>>>> I want the accession number in the line that starts with PA,  
>>>>>> AB000170
>>>>>> in this example.
>>>>>>
>>>>>> Can anybody kindly help, tell me which module and method I  
>>>>>> should use?
>>>>>> I tried various things like $seq_obj -> primary_id, display_id,
>>>>>> get_secondary_id, etc.. they did not work...
>>>>>>
>>>>>> Thanks a lot!
>>>>>>
>>>>>> Wen
>>>>>> _______________________________________________
>>>>>> 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
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> 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
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>


From whuang.ustc at gmail.com  Tue Jun 10 20:51:51 2008
From: whuang.ustc at gmail.com (Wen Huang)
Date: Tue, 10 Jun 2008 19:51:51 -0500
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <9A1F4E7F-A231-410C-8890-14ECDC7D0258@bioperl.org>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>
	<468D955B-533C-439A-96EA-B7CC6392BFE3@bioperl.org>
	<2542BB6E-AC43-4D5A-8788-2330E59A6E6F@uiuc.edu>
	<9A1F4E7F-A231-410C-8890-14ECDC7D0258@bioperl.org>
Message-ID: <D49F8A91-65D8-4A7B-8D5F-301EEE40E8D9@gmail.com>

Hi Everybody,

Thank you for your thoughtful discussion and help. I have found  
another way to get around it (by grep and awk), but not so perl-ish.

I don't think I know how to submit a bug report to bugzilla, but I do  
think that it is not a good idea to include the parent id in a PA  
line, or even in the file...

The file I got is from EMBL-CDS databank, I wanted to get the mRNA  
from which they are derived. I guess it is better to include it as a  
DBlink as Jason pointed out.

Thanks,
Wen

On Jun 10, 2008, at 7:36 PM, Jason Stajich wrote:

> I agree if it isn't the accession # it shouldn't be stored there.  I  
> guess it is a DBlink, but it is going to be hacky to round-trip this  
> as you'll have to have a special case for records that are mRNAs...
>
> -jason
> On Jun 10, 2008, at 5:19 PM, Chris Fields wrote:
>
>> PA is an odd field; it isn't described in the EMBL user manual:
>>
>> http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
>>
>> but appears in mRNA files, so I'm guessing it stands for the  
>> (p)rotein (a)ccession.  I don't think this should be stored as  
>> primary/secondary accession, but maybe as a DBLink annootation?
>>
>> chris
>>
>> On Jun 10, 2008, at 6:57 PM, Jason Stajich wrote:
>>
>>> PA is a field that we don't currently parse, something that should  
>>> be filed as a bug on bugzilla.
>>> Would you be able to do this?
>>>
>>> -jason
>>> On Jun 9, 2008, at 7:07 AM, Wen Huang wrote:
>>>
>>>> Hilmar,
>>>>
>>>> I tried that, it did not work. Marc's way can work.
>>>>
>>>> Thanks,
>>>> Wen
>>>>
>>>> On Jun 9, 2008, at 7:30 AM, Hilmar Lapp wrote:
>>>>
>>>>> If this is the case with the latest version of BioPerl it should  
>>>>> be filed as a bug report for the embl parser. The ID ought to be  
>>>>> reported in $seq->get_secondary_accessions() (which returns an  
>>>>> array). If it doesn't, it sounds like a bug to me.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>>> Hi Wen,
>>>>>> A dump of that sequence object (Data::Dumper is your friend !)  
>>>>>> reveals
>>>>>> that the PA EMBL field is not saved into the object. However,  
>>>>>> you will
>>>>>> find the string 'AB000170.1' in the embedded CDS feature, more  
>>>>>> precisely
>>>>>> the seqid of the location object. I don't know whether that is  
>>>>>> always
>>>>>> the case, but it is in your particular example.
>>>>>> So, to get your hands on that value you have to do:
>>>>>>
>>>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq- 
>>>>>> >get_SeqFeatures;
>>>>>> my $parent_id = $cds->location->seq_id;
>>>>>>
>>>>>> HTH,
>>>>>> Marc
>>>>>>
>>>>>> Marc Logghe
>>>>>> Senior Bioinformatician
>>>>>> Ablynx nv
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I have a EMBL file that I want to extract one of the line
>>>>>>>
>>>>>>> ###file###
>>>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>>>> XX
>>>>>>> PA   AB000170.1
>>>>>>> XX
>>>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>>>> XX
>>>>>>> OS   Sus scrofa (pig)
>>>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;  
>>>>>>> Euteleostomi;
>>>>>>> Mammalia;
>>>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae;  
>>>>>>> Sus.
>>>>>>> OX   NCBI_TaxID=9823;
>>>>>>> .........
>>>>>>>
>>>>>>> I want the accession number in the line that starts with PA,  
>>>>>>> AB000170
>>>>>>> in this example.
>>>>>>>
>>>>>>> Can anybody kindly help, tell me which module and method I  
>>>>>>> should use?
>>>>>>> I tried various things like $seq_obj -> primary_id, display_id,
>>>>>>> get_secondary_id, etc.. they did not work...
>>>>>>>
>>>>>>> Thanks a lot!
>>>>>>>
>>>>>>> Wen
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Marie-Claude Hofmann
>> College of Veterinary Medicine
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>


From hlapp at gmx.net  Tue Jun 10 21:35:50 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Tue, 10 Jun 2008 21:35:50 -0400
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <9A1F4E7F-A231-410C-8890-14ECDC7D0258@bioperl.org>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>
	<468D955B-533C-439A-96EA-B7CC6392BFE3@bioperl.org>
	<2542BB6E-AC43-4D5A-8788-2330E59A6E6F@uiuc.edu>
	<9A1F4E7F-A231-410C-8890-14ECDC7D0258@bioperl.org>
Message-ID: <283146E5-0041-42CF-B881-90624D5DE393@gmx.net>


On Jun 10, 2008, at 8:36 PM, Jason Stajich wrote:
> I agree if it isn't the accession # it shouldn't be stored there.   
> I guess it is a DBlink, but it is going to be hacky to round-trip  
> this as you'll have to have a special case for records that are  
> mRNAs...

I think I agree with that - didn't realize it is the accession of the  
(translated) protein. It would be ideal to convert this into a DBLink  
annotation indeed, but that's an opinion and an interpretation of the  
file (even if a very useful one). As such I believe it should be the  
matter of a SeqProcessor.

Hmm - except that at that point the information has been lost already  
so there's actually nothing that the SeqProcessor could massage.

So what if the line would simply be a B::Annotation::SimpleValue with  
'PA' as key and the accession# as value? That wouldn't be an  
interpretation, and yet would make the value available to a  
SeqProcessor for converting into a DBLink.

	-hilmar

>
> -jason
> On Jun 10, 2008, at 5:19 PM, Chris Fields wrote:
>
>> PA is an odd field; it isn't described in the EMBL user manual:
>>
>> http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
>>
>> but appears in mRNA files, so I'm guessing it stands for the (p) 
>> rotein (a)ccession.  I don't think this should be stored as  
>> primary/secondary accession, but maybe as a DBLink annootation?
>>
>> chris
>>
>> On Jun 10, 2008, at 6:57 PM, Jason Stajich wrote:
>>
>>> PA is a field that we don't currently parse, something that  
>>> should be filed as a bug on bugzilla.
>>> Would you be able to do this?
>>>
>>> -jason
>>> On Jun 9, 2008, at 7:07 AM, Wen Huang wrote:
>>>
>>>> Hilmar,
>>>>
>>>> I tried that, it did not work. Marc's way can work.
>>>>
>>>> Thanks,
>>>> Wen
>>>>
>>>> On Jun 9, 2008, at 7:30 AM, Hilmar Lapp wrote:
>>>>
>>>>> If this is the case with the latest version of BioPerl it  
>>>>> should be filed as a bug report for the embl parser. The ID  
>>>>> ought to be reported in $seq->get_secondary_accessions() (which  
>>>>> returns an array). If it doesn't, it sounds like a bug to me.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>>> Hi Wen,
>>>>>> A dump of that sequence object (Data::Dumper is your friend !)  
>>>>>> reveals
>>>>>> that the PA EMBL field is not saved into the object. However,  
>>>>>> you will
>>>>>> find the string 'AB000170.1' in the embedded CDS feature, more  
>>>>>> precisely
>>>>>> the seqid of the location object. I don't know whether that is  
>>>>>> always
>>>>>> the case, but it is in your particular example.
>>>>>> So, to get your hands on that value you have to do:
>>>>>>
>>>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq- 
>>>>>> >get_SeqFeatures;
>>>>>> my $parent_id = $cds->location->seq_id;
>>>>>>
>>>>>> HTH,
>>>>>> Marc
>>>>>>
>>>>>> Marc Logghe
>>>>>> Senior Bioinformatician
>>>>>> Ablynx nv
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I have a EMBL file that I want to extract one of the line
>>>>>>>
>>>>>>> ###file###
>>>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>>>> XX
>>>>>>> PA   AB000170.1
>>>>>>> XX
>>>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>>>> XX
>>>>>>> OS   Sus scrofa (pig)
>>>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;  
>>>>>>> Euteleostomi;
>>>>>>> Mammalia;
>>>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina;  
>>>>>>> Suidae; Sus.
>>>>>>> OX   NCBI_TaxID=9823;
>>>>>>> .........
>>>>>>>
>>>>>>> I want the accession number in the line that starts with PA,  
>>>>>>> AB000170
>>>>>>> in this example.
>>>>>>>
>>>>>>> Can anybody kindly help, tell me which module and method I  
>>>>>>> should use?
>>>>>>> I tried various things like $seq_obj -> primary_id, display_id,
>>>>>>> get_secondary_id, etc.. they did not work...
>>>>>>>
>>>>>>> Thanks a lot!
>>>>>>>
>>>>>>> Wen
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Marie-Claude Hofmann
>> College of Veterinary Medicine
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>
> _______________________________________________
> 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 gmx dot net :
===========================================================




From bill at genenformics.com  Tue Jun 10 21:43:55 2008
From: bill at genenformics.com (bill at genenformics.com)
Date: Tue, 10 Jun 2008 18:43:55 -0700 (PDT)
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <283146E5-0041-42CF-B881-90624D5DE393@gmx.net>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>
	<468D955B-533C-439A-96EA-B7CC6392BFE3@bioperl.org>
	<2542BB6E-AC43-4D5A-8788-2330E59A6E6F@uiuc.edu>
	<9A1F4E7F-A231-410C-8890-14ECDC7D0258@bioperl.org>
	<283146E5-0041-42CF-B881-90624D5DE393@gmx.net>
Message-ID: <61099.98.218.171.90.1213148635.squirrel@webmail.dreamhost.com>

This can be accomplished using IdConvert if protein accession/gi is known:

$> ./IdConvert.exe BAA19060
#Input  Nuc_GI  Nuc_Acc Pro_GI  Pro_Acc Desc
BAA19060        1783121 AB000170.1      1783123 BAA19061.1     
endopeptidase 24.16 type M3 [Sus scrofa]

Download IdConvert from http://www.genenformics.com/download.html for free.

Bill at genenformics.com


>
> On Jun 10, 2008, at 8:36 PM, Jason Stajich wrote:
>> I agree if it isn't the accession # it shouldn't be stored there.
>> I guess it is a DBlink, but it is going to be hacky to round-trip
>> this as you'll have to have a special case for records that are
>> mRNAs...
>
> I think I agree with that - didn't realize it is the accession of the
> (translated) protein. It would be ideal to convert this into a DBLink
> annotation indeed, but that's an opinion and an interpretation of the
> file (even if a very useful one). As such I believe it should be the
> matter of a SeqProcessor.
>
> Hmm - except that at that point the information has been lost already
> so there's actually nothing that the SeqProcessor could massage.
>
> So what if the line would simply be a B::Annotation::SimpleValue with
> 'PA' as key and the accession# as value? That wouldn't be an
> interpretation, and yet would make the value available to a
> SeqProcessor for converting into a DBLink.
>
> 	-hilmar
>
>>
>> -jason
>> On Jun 10, 2008, at 5:19 PM, Chris Fields wrote:
>>
>>> PA is an odd field; it isn't described in the EMBL user manual:
>>>
>>> http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
>>>
>>> but appears in mRNA files, so I'm guessing it stands for the (p)
>>> rotein (a)ccession.  I don't think this should be stored as
>>> primary/secondary accession, but maybe as a DBLink annootation?
>>>
>>> chris
>>>
>>> On Jun 10, 2008, at 6:57 PM, Jason Stajich wrote:
>>>
>>>> PA is a field that we don't currently parse, something that
>>>> should be filed as a bug on bugzilla.
>>>> Would you be able to do this?
>>>>
>>>> -jason
>>>> On Jun 9, 2008, at 7:07 AM, Wen Huang wrote:
>>>>
>>>>> Hilmar,
>>>>>
>>>>> I tried that, it did not work. Marc's way can work.
>>>>>
>>>>> Thanks,
>>>>> Wen
>>>>>
>>>>> On Jun 9, 2008, at 7:30 AM, Hilmar Lapp wrote:
>>>>>
>>>>>> If this is the case with the latest version of BioPerl it
>>>>>> should be filed as a bug report for the embl parser. The ID
>>>>>> ought to be reported in $seq->get_secondary_accessions() (which
>>>>>> returns an array). If it doesn't, it sounds like a bug to me.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>>>> Hi Wen,
>>>>>>> A dump of that sequence object (Data::Dumper is your friend !)
>>>>>>> reveals
>>>>>>> that the PA EMBL field is not saved into the object. However,
>>>>>>> you will
>>>>>>> find the string 'AB000170.1' in the embedded CDS feature, more
>>>>>>> precisely
>>>>>>> the seqid of the location object. I don't know whether that is
>>>>>>> always
>>>>>>> the case, but it is in your particular example.
>>>>>>> So, to get your hands on that value you have to do:
>>>>>>>
>>>>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq-
>>>>>>> >get_SeqFeatures;
>>>>>>> my $parent_id = $cds->location->seq_id;
>>>>>>>
>>>>>>> HTH,
>>>>>>> Marc
>>>>>>>
>>>>>>> Marc Logghe
>>>>>>> Senior Bioinformatician
>>>>>>> Ablynx nv
>>>>>>>> -----Original Message-----
>>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I have a EMBL file that I want to extract one of the line
>>>>>>>>
>>>>>>>> ###file###
>>>>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>>>>> XX
>>>>>>>> PA   AB000170.1
>>>>>>>> XX
>>>>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>>>>> XX
>>>>>>>> OS   Sus scrofa (pig)
>>>>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
>>>>>>>> Euteleostomi;
>>>>>>>> Mammalia;
>>>>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina;
>>>>>>>> Suidae; Sus.
>>>>>>>> OX   NCBI_TaxID=9823;
>>>>>>>> .........
>>>>>>>>
>>>>>>>> I want the accession number in the line that starts with PA,
>>>>>>>> AB000170
>>>>>>>> in this example.
>>>>>>>>
>>>>>>>> Can anybody kindly help, tell me which module and method I
>>>>>>>> should use?
>>>>>>>> I tried various things like $seq_obj -> primary_id, display_id,
>>>>>>>> get_secondary_id, etc.. they did not work...
>>>>>>>>
>>>>>>>> Thanks a lot!
>>>>>>>>
>>>>>>>> Wen
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>
>>>>>> --
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Marie-Claude Hofmann
>>> College of Veterinary Medicine
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> 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 gmx dot net :
> ===========================================================
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From hlapp at gmx.net  Tue Jun 10 22:09:13 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Tue, 10 Jun 2008 22:09:13 -0400
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <61099.98.218.171.90.1213148635.squirrel@webmail.dreamhost.com>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>
	<468D955B-533C-439A-96EA-B7CC6392BFE3@bioperl.org>
	<2542BB6E-AC43-4D5A-8788-2330E59A6E6F@uiuc.edu>
	<9A1F4E7F-A231-410C-8890-14ECDC7D0258@bioperl.org>
	<283146E5-0041-42CF-B881-90624D5DE393@gmx.net>
	<61099.98.218.171.90.1213148635.squirrel@webmail.dreamhost.com>
Message-ID: <EEDE7A33-5FF7-4CA9-BC7B-33DA611CB931@gmx.net>

Bill,

this mailing list is about BioPerl. There are many programs and web- 
sites out there that convert between IDs, that wasn't the question.

We welcome your participation in helping to solve Bioperl-related  
problems, and sometimes the easiest solution is to use other, cross- 
platform open-source tools.

For peddling commercial products, no matter how useful they are and  
how little the cost, please use other forums.

	-hilmar

On Jun 10, 2008, at 9:43 PM, bill at genenformics.com wrote:
> This can be accomplished using IdConvert if protein accession/gi is  
> known:
>
> $> ./IdConvert.exe BAA19060
> #Input  Nuc_GI  Nuc_Acc Pro_GI  Pro_Acc Desc
> BAA19060        1783121 AB000170.1      1783123 BAA19061.1
> endopeptidase 24.16 type M3 [Sus scrofa]
>
> Download IdConvert from http://www.genenformics.com/download.html  
> for free.
>
> Bill at genenformics.com
>
>
>>
>> On Jun 10, 2008, at 8:36 PM, Jason Stajich wrote:
>>> I agree if it isn't the accession # it shouldn't be stored there.
>>> I guess it is a DBlink, but it is going to be hacky to round-trip
>>> this as you'll have to have a special case for records that are
>>> mRNAs...
>>
>> I think I agree with that - didn't realize it is the accession of the
>> (translated) protein. It would be ideal to convert this into a DBLink
>> annotation indeed, but that's an opinion and an interpretation of the
>> file (even if a very useful one). As such I believe it should be the
>> matter of a SeqProcessor.
>>
>> Hmm - except that at that point the information has been lost already
>> so there's actually nothing that the SeqProcessor could massage.
>>
>> So what if the line would simply be a B::Annotation::SimpleValue with
>> 'PA' as key and the accession# as value? That wouldn't be an
>> interpretation, and yet would make the value available to a
>> SeqProcessor for converting into a DBLink.
>>
>> 	-hilmar
>>
>>>
>>> -jason
>>> On Jun 10, 2008, at 5:19 PM, Chris Fields wrote:
>>>
>>>> PA is an odd field; it isn't described in the EMBL user manual:
>>>>
>>>> http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
>>>>
>>>> but appears in mRNA files, so I'm guessing it stands for the (p)
>>>> rotein (a)ccession.  I don't think this should be stored as
>>>> primary/secondary accession, but maybe as a DBLink annootation?
>>>>
>>>> chris
>>>>
>>>> On Jun 10, 2008, at 6:57 PM, Jason Stajich wrote:
>>>>
>>>>> PA is a field that we don't currently parse, something that
>>>>> should be filed as a bug on bugzilla.
>>>>> Would you be able to do this?
>>>>>
>>>>> -jason
>>>>> On Jun 9, 2008, at 7:07 AM, Wen Huang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>>
>>>>>> I tried that, it did not work. Marc's way can work.
>>>>>>
>>>>>> Thanks,
>>>>>> Wen
>>>>>>
>>>>>> On Jun 9, 2008, at 7:30 AM, Hilmar Lapp wrote:
>>>>>>
>>>>>>> If this is the case with the latest version of BioPerl it
>>>>>>> should be filed as a bug report for the embl parser. The ID
>>>>>>> ought to be reported in $seq->get_secondary_accessions() (which
>>>>>>> returns an array). If it doesn't, it sounds like a bug to me.
>>>>>>>
>>>>>>> 	-hilmar
>>>>>>>
>>>>>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>>>>> Hi Wen,
>>>>>>>> A dump of that sequence object (Data::Dumper is your friend !)
>>>>>>>> reveals
>>>>>>>> that the PA EMBL field is not saved into the object. However,
>>>>>>>> you will
>>>>>>>> find the string 'AB000170.1' in the embedded CDS feature, more
>>>>>>>> precisely
>>>>>>>> the seqid of the location object. I don't know whether that is
>>>>>>>> always
>>>>>>>> the case, but it is in your particular example.
>>>>>>>> So, to get your hands on that value you have to do:
>>>>>>>>
>>>>>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq-
>>>>>>>>> get_SeqFeatures;
>>>>>>>> my $parent_id = $cds->location->seq_id;
>>>>>>>>
>>>>>>>> HTH,
>>>>>>>> Marc
>>>>>>>>
>>>>>>>> Marc Logghe
>>>>>>>> Senior Bioinformatician
>>>>>>>> Ablynx nv
>>>>>>>>> -----Original Message-----
>>>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> I have a EMBL file that I want to extract one of the line
>>>>>>>>>
>>>>>>>>> ###file###
>>>>>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>>>>>> XX
>>>>>>>>> PA   AB000170.1
>>>>>>>>> XX
>>>>>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>>>>>> XX
>>>>>>>>> OS   Sus scrofa (pig)
>>>>>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
>>>>>>>>> Euteleostomi;
>>>>>>>>> Mammalia;
>>>>>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina;
>>>>>>>>> Suidae; Sus.
>>>>>>>>> OX   NCBI_TaxID=9823;
>>>>>>>>> .........
>>>>>>>>>
>>>>>>>>> I want the accession number in the line that starts with PA,
>>>>>>>>> AB000170
>>>>>>>>> in this example.
>>>>>>>>>
>>>>>>>>> Can anybody kindly help, tell me which module and method I
>>>>>>>>> should use?
>>>>>>>>> I tried various things like $seq_obj -> primary_id,  
>>>>>>>>> display_id,
>>>>>>>>> get_secondary_id, etc.. they did not work...
>>>>>>>>>
>>>>>>>>> Thanks a lot!
>>>>>>>>>
>>>>>>>>> Wen
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>
>>>>>>> --
>>>>>>> ===========================================================
>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>> ===========================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Marie-Claude Hofmann
>>>> College of Veterinary Medicine
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> 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 gmx dot net :
>> ===========================================================
>>
>>
>>
>> _______________________________________________
>> 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 gmx dot net :
===========================================================




From bill at genenformics.com  Tue Jun 10 22:33:45 2008
From: bill at genenformics.com (bill at genenformics.com)
Date: Tue, 10 Jun 2008 19:33:45 -0700 (PDT)
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <EEDE7A33-5FF7-4CA9-BC7B-33DA611CB931@gmx.net>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>
	<468D955B-533C-439A-96EA-B7CC6392BFE3@bioperl.org>
	<2542BB6E-AC43-4D5A-8788-2330E59A6E6F@uiuc.edu>
	<9A1F4E7F-A231-410C-8890-14ECDC7D0258@bioperl.org>
	<283146E5-0041-42CF-B881-90624D5DE393@gmx.net>
	<61099.98.218.171.90.1213148635.squirrel@webmail.dreamhost.com>
	<EEDE7A33-5FF7-4CA9-BC7B-33DA611CB931@gmx.net>
Message-ID: <61609.98.218.171.90.1213151625.squirrel@webmail.dreamhost.com>

Hi, Hilmar,

Thank you for your advice.

I am a BioPerl user and I step in only when there is no
efficient/effective BioPerl method to solve specific problems.

Please forgive us for providing free solutions.

Bill at genenformics.com

> Bill,
>
> this mailing list is about BioPerl. There are many programs and web-
> sites out there that convert between IDs, that wasn't the question.
>
> We welcome your participation in helping to solve Bioperl-related
> problems, and sometimes the easiest solution is to use other, cross-
> platform open-source tools.
>
> For peddling commercial products, no matter how useful they are and
> how little the cost, please use other forums.
>
> 	-hilmar
>
> On Jun 10, 2008, at 9:43 PM, bill at genenformics.com wrote:
>> This can be accomplished using IdConvert if protein accession/gi is
>> known:
>>
>> $> ./IdConvert.exe BAA19060
>> #Input  Nuc_GI  Nuc_Acc Pro_GI  Pro_Acc Desc
>> BAA19060        1783121 AB000170.1      1783123 BAA19061.1
>> endopeptidase 24.16 type M3 [Sus scrofa]
>>
>> Download IdConvert from http://www.genenformics.com/download.html
>> for free.
>>
>> Bill at genenformics.com
>>
>>
>>>
>>> On Jun 10, 2008, at 8:36 PM, Jason Stajich wrote:
>>>> I agree if it isn't the accession # it shouldn't be stored there.
>>>> I guess it is a DBlink, but it is going to be hacky to round-trip
>>>> this as you'll have to have a special case for records that are
>>>> mRNAs...
>>>
>>> I think I agree with that - didn't realize it is the accession of the
>>> (translated) protein. It would be ideal to convert this into a DBLink
>>> annotation indeed, but that's an opinion and an interpretation of the
>>> file (even if a very useful one). As such I believe it should be the
>>> matter of a SeqProcessor.
>>>
>>> Hmm - except that at that point the information has been lost already
>>> so there's actually nothing that the SeqProcessor could massage.
>>>
>>> So what if the line would simply be a B::Annotation::SimpleValue with
>>> 'PA' as key and the accession# as value? That wouldn't be an
>>> interpretation, and yet would make the value available to a
>>> SeqProcessor for converting into a DBLink.
>>>
>>> 	-hilmar
>>>
>>>>
>>>> -jason
>>>> On Jun 10, 2008, at 5:19 PM, Chris Fields wrote:
>>>>
>>>>> PA is an odd field; it isn't described in the EMBL user manual:
>>>>>
>>>>> http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
>>>>>
>>>>> but appears in mRNA files, so I'm guessing it stands for the (p)
>>>>> rotein (a)ccession.  I don't think this should be stored as
>>>>> primary/secondary accession, but maybe as a DBLink annootation?
>>>>>
>>>>> chris
>>>>>
>>>>> On Jun 10, 2008, at 6:57 PM, Jason Stajich wrote:
>>>>>
>>>>>> PA is a field that we don't currently parse, something that
>>>>>> should be filed as a bug on bugzilla.
>>>>>> Would you be able to do this?
>>>>>>
>>>>>> -jason
>>>>>> On Jun 9, 2008, at 7:07 AM, Wen Huang wrote:
>>>>>>
>>>>>>> Hilmar,
>>>>>>>
>>>>>>> I tried that, it did not work. Marc's way can work.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Wen
>>>>>>>
>>>>>>> On Jun 9, 2008, at 7:30 AM, Hilmar Lapp wrote:
>>>>>>>
>>>>>>>> If this is the case with the latest version of BioPerl it
>>>>>>>> should be filed as a bug report for the embl parser. The ID
>>>>>>>> ought to be reported in $seq->get_secondary_accessions() (which
>>>>>>>> returns an array). If it doesn't, it sounds like a bug to me.
>>>>>>>>
>>>>>>>> 	-hilmar
>>>>>>>>
>>>>>>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>>>>>> Hi Wen,
>>>>>>>>> A dump of that sequence object (Data::Dumper is your friend !)
>>>>>>>>> reveals
>>>>>>>>> that the PA EMBL field is not saved into the object. However,
>>>>>>>>> you will
>>>>>>>>> find the string 'AB000170.1' in the embedded CDS feature, more
>>>>>>>>> precisely
>>>>>>>>> the seqid of the location object. I don't know whether that is
>>>>>>>>> always
>>>>>>>>> the case, but it is in your particular example.
>>>>>>>>> So, to get your hands on that value you have to do:
>>>>>>>>>
>>>>>>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq-
>>>>>>>>>> get_SeqFeatures;
>>>>>>>>> my $parent_id = $cds->location->seq_id;
>>>>>>>>>
>>>>>>>>> HTH,
>>>>>>>>> Marc
>>>>>>>>>
>>>>>>>>> Marc Logghe
>>>>>>>>> Senior Bioinformatician
>>>>>>>>> Ablynx nv
>>>>>>>>>> -----Original Message-----
>>>>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>>>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>>>>>>
>>>>>>>>>> Hi all,
>>>>>>>>>>
>>>>>>>>>> I have a EMBL file that I want to extract one of the line
>>>>>>>>>>
>>>>>>>>>> ###file###
>>>>>>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>>>>>>> XX
>>>>>>>>>> PA   AB000170.1
>>>>>>>>>> XX
>>>>>>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>>>>>>> XX
>>>>>>>>>> OS   Sus scrofa (pig)
>>>>>>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
>>>>>>>>>> Euteleostomi;
>>>>>>>>>> Mammalia;
>>>>>>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina;
>>>>>>>>>> Suidae; Sus.
>>>>>>>>>> OX   NCBI_TaxID=9823;
>>>>>>>>>> .........
>>>>>>>>>>
>>>>>>>>>> I want the accession number in the line that starts with PA,
>>>>>>>>>> AB000170
>>>>>>>>>> in this example.
>>>>>>>>>>
>>>>>>>>>> Can anybody kindly help, tell me which module and method I
>>>>>>>>>> should use?
>>>>>>>>>> I tried various things like $seq_obj -> primary_id,
>>>>>>>>>> display_id,
>>>>>>>>>> get_secondary_id, etc.. they did not work...
>>>>>>>>>>
>>>>>>>>>> Thanks a lot!
>>>>>>>>>>
>>>>>>>>>> Wen
>>>>>>>>>> _______________________________________________
>>>>>>>>>> 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
>>>>>>>>
>>>>>>>> --
>>>>>>>> ===========================================================
>>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>>> ===========================================================
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Marie-Claude Hofmann
>>>>> College of Veterinary Medicine
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> 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 gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>> _______________________________________________
>>> 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 gmx dot net :
> ===========================================================
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From cjfields at uiuc.edu  Tue Jun 10 22:59:43 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 10 Jun 2008 21:59:43 -0500
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <61609.98.218.171.90.1213151625.squirrel@webmail.dreamhost.com>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<45F42C94-02FD-429B-816F-883C7855A97D@gmail.com>
	<468D955B-533C-439A-96EA-B7CC6392BFE3@bioperl.org>
	<2542BB6E-AC43-4D5A-8788-2330E59A6E6F@uiuc.edu>
	<9A1F4E7F-A231-410C-8890-14ECDC7D0258@bioperl.org>
	<283146E5-0041-42CF-B881-90624D5DE393@gmx.net>
	<61099.98.218.171.90.1213148635.squirrel@webmail.dreamhost.com>
	<EEDE7A33-5FF7-4CA9-BC7B-33DA611CB931@gmx.net>
	<61609.98.218.171.90.1213151625.squirrel@webmail.dreamhost.com>
Message-ID: <3804E643-9BBC-4B28-B1DE-D75AA2C9FE74@uiuc.edu>

Bill,

It's okay to offer suggestions to problems, particularly if no one  
answers, but I have to agree with Hilmar in this case.

The specific problem: your 'solution' is tied to commercial software  
(albeit free), which appear to be closed-source and with questionable  
licensing.  I couldn't find documentation on your website addressing  
either issue.  Therefore, I couldn't recommend using it unless the  
latter two issues were clarified, preferably by becoming open-source.

chris

On Jun 10, 2008, at 9:33 PM, bill at genenformics.com wrote:

> Hi, Hilmar,
>
> Thank you for your advice.
>
> I am a BioPerl user and I step in only when there is no
> efficient/effective BioPerl method to solve specific problems.
>
> Please forgive us for providing free solutions.
>
> Bill at genenformics.com
>
>> Bill,
>>
>> this mailing list is about BioPerl. There are many programs and web-
>> sites out there that convert between IDs, that wasn't the question.
>>
>> We welcome your participation in helping to solve Bioperl-related
>> problems, and sometimes the easiest solution is to use other, cross-
>> platform open-source tools.
>>
>> For peddling commercial products, no matter how useful they are and
>> how little the cost, please use other forums.
>>
>> 	-hilmar
>>
>> On Jun 10, 2008, at 9:43 PM, bill at genenformics.com wrote:
>>> This can be accomplished using IdConvert if protein accession/gi is
>>> known:
>>>
>>> $> ./IdConvert.exe BAA19060
>>> #Input  Nuc_GI  Nuc_Acc Pro_GI  Pro_Acc Desc
>>> BAA19060        1783121 AB000170.1      1783123 BAA19061.1
>>> endopeptidase 24.16 type M3 [Sus scrofa]
>>>
>>> Download IdConvert from http://www.genenformics.com/download.html
>>> for free.
>>>
>>> Bill at genenformics.com
>>>
>>>
>>>>
>>>> On Jun 10, 2008, at 8:36 PM, Jason Stajich wrote:
>>>>> I agree if it isn't the accession # it shouldn't be stored there.
>>>>> I guess it is a DBlink, but it is going to be hacky to round-trip
>>>>> this as you'll have to have a special case for records that are
>>>>> mRNAs...
>>>>
>>>> I think I agree with that - didn't realize it is the accession of  
>>>> the
>>>> (translated) protein. It would be ideal to convert this into a  
>>>> DBLink
>>>> annotation indeed, but that's an opinion and an interpretation of  
>>>> the
>>>> file (even if a very useful one). As such I believe it should be  
>>>> the
>>>> matter of a SeqProcessor.
>>>>
>>>> Hmm - except that at that point the information has been lost  
>>>> already
>>>> so there's actually nothing that the SeqProcessor could massage.
>>>>
>>>> So what if the line would simply be a B::Annotation::SimpleValue  
>>>> with
>>>> 'PA' as key and the accession# as value? That wouldn't be an
>>>> interpretation, and yet would make the value available to a
>>>> SeqProcessor for converting into a DBLink.
>>>>
>>>> 	-hilmar
>>>>
>>>>>
>>>>> -jason
>>>>> On Jun 10, 2008, at 5:19 PM, Chris Fields wrote:
>>>>>
>>>>>> PA is an odd field; it isn't described in the EMBL user manual:
>>>>>>
>>>>>> http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
>>>>>>
>>>>>> but appears in mRNA files, so I'm guessing it stands for the (p)
>>>>>> rotein (a)ccession.  I don't think this should be stored as
>>>>>> primary/secondary accession, but maybe as a DBLink annootation?
>>>>>>
>>>>>> chris
>>>>>>
>>>>>> On Jun 10, 2008, at 6:57 PM, Jason Stajich wrote:
>>>>>>
>>>>>>> PA is a field that we don't currently parse, something that
>>>>>>> should be filed as a bug on bugzilla.
>>>>>>> Would you be able to do this?
>>>>>>>
>>>>>>> -jason
>>>>>>> On Jun 9, 2008, at 7:07 AM, Wen Huang wrote:
>>>>>>>
>>>>>>>> Hilmar,
>>>>>>>>
>>>>>>>> I tried that, it did not work. Marc's way can work.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Wen
>>>>>>>>
>>>>>>>> On Jun 9, 2008, at 7:30 AM, Hilmar Lapp wrote:
>>>>>>>>
>>>>>>>>> If this is the case with the latest version of BioPerl it
>>>>>>>>> should be filed as a bug report for the embl parser. The ID
>>>>>>>>> ought to be reported in $seq->get_secondary_accessions()  
>>>>>>>>> (which
>>>>>>>>> returns an array). If it doesn't, it sounds like a bug to me.
>>>>>>>>>
>>>>>>>>> 	-hilmar
>>>>>>>>>
>>>>>>>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>>>>>>> Hi Wen,
>>>>>>>>>> A dump of that sequence object (Data::Dumper is your  
>>>>>>>>>> friend !)
>>>>>>>>>> reveals
>>>>>>>>>> that the PA EMBL field is not saved into the object. However,
>>>>>>>>>> you will
>>>>>>>>>> find the string 'AB000170.1' in the embedded CDS feature,  
>>>>>>>>>> more
>>>>>>>>>> precisely
>>>>>>>>>> the seqid of the location object. I don't know whether that  
>>>>>>>>>> is
>>>>>>>>>> always
>>>>>>>>>> the case, but it is in your particular example.
>>>>>>>>>> So, to get your hands on that value you have to do:
>>>>>>>>>>
>>>>>>>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq-
>>>>>>>>>>> get_SeqFeatures;
>>>>>>>>>> my $parent_id = $cds->location->seq_id;
>>>>>>>>>>
>>>>>>>>>> HTH,
>>>>>>>>>> Marc
>>>>>>>>>>
>>>>>>>>>> Marc Logghe
>>>>>>>>>> Senior Bioinformatician
>>>>>>>>>> Ablynx nv
>>>>>>>>>>> -----Original Message-----
>>>>>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl- 
>>>>>>>>>>> l-
>>>>>>>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>>>>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>>>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>>>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>>>>>>>
>>>>>>>>>>> Hi all,
>>>>>>>>>>>
>>>>>>>>>>> I have a EMBL file that I want to extract one of the line
>>>>>>>>>>>
>>>>>>>>>>> ###file###
>>>>>>>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>>>>>>>> XX
>>>>>>>>>>> PA   AB000170.1
>>>>>>>>>>> XX
>>>>>>>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>>>>>>>> XX
>>>>>>>>>>> OS   Sus scrofa (pig)
>>>>>>>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
>>>>>>>>>>> Euteleostomi;
>>>>>>>>>>> Mammalia;
>>>>>>>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina;
>>>>>>>>>>> Suidae; Sus.
>>>>>>>>>>> OX   NCBI_TaxID=9823;
>>>>>>>>>>> .........
>>>>>>>>>>>
>>>>>>>>>>> I want the accession number in the line that starts with PA,
>>>>>>>>>>> AB000170
>>>>>>>>>>> in this example.
>>>>>>>>>>>
>>>>>>>>>>> Can anybody kindly help, tell me which module and method I
>>>>>>>>>>> should use?
>>>>>>>>>>> I tried various things like $seq_obj -> primary_id,
>>>>>>>>>>> display_id,
>>>>>>>>>>> get_secondary_id, etc.. they did not work...
>>>>>>>>>>>
>>>>>>>>>>> Thanks a lot!
>>>>>>>>>>>
>>>>>>>>>>> Wen
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> ===========================================================
>>>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>>>> ===========================================================
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>
>>>>>> Christopher Fields
>>>>>> Postdoctoral Researcher
>>>>>> Lab of Dr. Marie-Claude Hofmann
>>>>>> College of Veterinary Medicine
>>>>>> University of Illinois Urbana-Champaign
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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 gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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 gmx dot net :
>> ===========================================================
>>
>>
>>
>> _______________________________________________
>> 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

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Tue Jun 10 23:00:04 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 10 Jun 2008 22:00:04 -0500
Subject: [Bioperl-l] A lot of POD fixes in bioperl-live and bioperl run
In-Reply-To: <200806110122.10982.heikki@sanbi.ac.za>
References: <200806110122.10982.heikki@sanbi.ac.za>
Message-ID: <2BCA7C8B-CDAC-49A8-9809-F9127DB05BEC@uiuc.edu>

Thanks for the work on this Heikki!

chris

On Jun 10, 2008, at 6:22 PM, Heikki Lehvaslaiho wrote:

> I have recently done a lot fixes in the inline Plain Old Documenation
> (POD) texts in bioperl-live and bioperl-run. Last ones (hopefully)  
> were
> committed a few minutes ago. This has resulted quite large updates  
> from SVN.
>
> I wanted to apologize the inconvenience and to explain reasons for  
> these small
> and pedantic fixes.
>
> In contrast to perl, POD is sensitive to white space. This makes it  
> relatively
> difficult to find and fix all minor errors in POD. I've now gone  
> through the
> trouble of fixing all POD mistakes causing even the smallest warning  
> in the
> podchecker.
>
> The main reason for doing this was to reduce the the number of  
> warnings
> reported by the pod.pl bioperl maintenence tool. Too many minor  
> warnings make
> it difficult to recognise more serious errors affecting the  
> integrity and
> readability of POD documentation.
>
> One example case is when a paragraph that was supposed to be 'in
> verbatim', is in fact touching the previous paragraph and the pod
> engine formats it and destroys the intended ascii graph or table.
> The only way POD engine is able to report this is to warn about  
> unescaped
> special characters.
>
>    -Heikki
> -- 
> ______ _/      _/_____________________________________________________
>      _/      _/
>     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
>   _/  _/  _/  SANBI, South African National Bioinformatics Institute
>  _/  _/  _/  University of Western Cape, South Africa
>     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
> ___ _/_/_/_/_/________________________________________________________
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From hiekeen at gmail.com  Wed Jun 11 04:49:30 2008
From: hiekeen at gmail.com (Jinyan Huang)
Date: Wed, 11 Jun 2008 16:49:30 +0800
Subject: [Bioperl-l] How to get all TF which target to sox-oct cis-element?
Message-ID: <fb5dae380806110149n7063360cg61c739424f21ae84@mail.gmail.com>

How to get all TF which target to sox-oct cis-element ATGCA(T)A(T)A(G/C)A(T)?

Thank you very much.

-- 
Best regards,
Jinyan Huang (ekeen)
School of Life Sciences and Technology, 1302 Room
Tongji University
Siping Road 1239, Shanghai 200092
P.R. China
Tel :0086-21-65981041
Msn: hiekeen at hotmail.com
eMail: hiekeen at gmail.com

From dalloliogm at gmail.com  Wed Jun 11 05:46:37 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Wed, 11 Jun 2008 11:46:37 +0200
Subject: [Bioperl-l] preparing nexus files for Mr. Bayes
Message-ID: <5aa3b3570806110246naa24dcaj462d8025048aad41@mail.gmail.com>

Hi,
I was wondering whether there is any bioperl module I can use to
handle nexus files for Mr.Bayes.

mr. Bayes is a program for bayesian estimation of phylogeny, which
uses an alignment file in a customized nexus format as input.
I would need a module to prepare these files, doing tasks like:
- joining more than an alignment in a single file/line
- substitute matching chars with '.'
- customizing parameters displayed in the headers of the output nexus file
- manage mrbayes' extensions, like adding information about partitions and taxas
- adding batch instructions for the mr bayes interpreter
- and similar stuff.

I have tried Bio::AlignIO but I see it doesn't handle all of this,
what I am looing for is bit more specific.
Moreover, I found a bug in the way mrbayes recognizes the output from
Bio::AlignIO (https://sourceforge.net/tracker/index.php?func=detail&aid=1990655&group_id=129302&atid=714418).

Is there any existing module already available?
If there is not, I am going to have to write such scripts anyway.
I would like to contribute them to bioperl, even if I am not a very
good perl programmer, I prefer python.

-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it

From jason at bioperl.org  Wed Jun 11 11:13:20 2008
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 11 Jun 2008 08:13:20 -0700
Subject: [Bioperl-l] preparing nexus files for Mr. Bayes
In-Reply-To: <5aa3b3570806110246naa24dcaj462d8025048aad41@mail.gmail.com>
References: <5aa3b3570806110246naa24dcaj462d8025048aad41@mail.gmail.com>
Message-ID: <32D2B523-8C68-44B3-80B4-E8BB82FB4232@bioperl.org>

Giovanni -

Bits and pieces already exist, there is little to handle the text  
blocks that exist in NEXUS files because BioPerl has has been focused  
on the alignment data not the analysis.  Arlin Stolzfus has started a  
Bio::NEXUS project that is supposed to fully parse all NEXUS data in  
and out but I don't know what the status is right now.

If you look at the Bio::AlignIO::nexus documentation you need to turn  
off symbols and endblock when writing for MrBayes NEXUS.

my $out = Bio::AlignIO->new(-format => 'nexus',
			    -show_symbols => 0,
			    -show_endblock => 0);


# after you have written out the alignment
$out->write_aln;
# you can then print out whatever execution blocks you want with  
standard print statements.
print $out->_fh "begin mrbayes;\n"; ...


As for the other things, the Bio::SimpleAlign module lets you swap  
the match character (see map_char and gap_char methods).

For joining alignments and setting up partitions, you can join  
multiple alignments by making a new Bio::SimpleAlign and adding  
concatenated sequences together.

my %matrix;
  for my $aln ( @alns ) {
   for my $seq ( $aln->each_seq ) {
             my $id = $seq->id;
             $matrix{$id} .= $seq->seq;
   }
  }
  my $bigaln = Bio::SimpleAlign->new;
  while( my ($id,$seq) = each %matrix ) {
      $bigaln->add_seq(Bio::LocatableSeq->new(-id  => $id,
                                                 -seq => $seq));
  }


In general there is not a single solution to a lot of these tasks  
(although there should be one that concatenates a set of  alignments)  
so there are not ready-to-use functions.  I have my custom code I use  
to join datasets and establish partitions but much is specific to how  
I organize the data on my system so I don't know how informative it  
would be.

I'm not sure python code would be much good here... =) if you jump  
ship you should talk to Frank Kauff who has written some python code  
to manipulate alignments for biopython.

-jason

On Jun 11, 2008, at 2:46 AM, Giovanni Marco Dall'Olio wrote:

> Hi,
> I was wondering whether there is any bioperl module I can use to
> handle nexus files for Mr.Bayes.
>
> mr. Bayes is a program for bayesian estimation of phylogeny, which
> uses an alignment file in a customized nexus format as input.
> I would need a module to prepare these files, doing tasks like:
> - joining more than an alignment in a single file/line
> - substitute matching chars with '.'
> - customizing parameters displayed in the headers of the output  
> nexus file
> - manage mrbayes' extensions, like adding information about  
> partitions and taxas
> - adding batch instructions for the mr bayes interpreter
> - and similar stuff.
>
> I have tried Bio::AlignIO but I see it doesn't handle all of this,
> what I am looing for is bit more specific.
> Moreover, I found a bug in the way mrbayes recognizes the output from
> Bio::AlignIO (https://sourceforge.net/tracker/index.php? 
> func=detail&aid=1990655&group_id=129302&atid=714418).
>
> Is there any existing module already available?
> If there is not, I am going to have to write such scripts anyway.
> I would like to contribute them to bioperl, even if I am not a very
> good perl programmer, I prefer python.
>
> -- 
> -----------------------------------------------------------
>
> My Blog on Bioinformatics (italian): http://bioinfoblog.it
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From MEC at stowers-institute.org  Wed Jun 11 11:18:11 2008
From: MEC at stowers-institute.org (Cook, Malcolm)
Date: Wed, 11 Jun 2008 10:18:11 -0500
Subject: [Bioperl-l] Position Announcement - Programmer Analyst /
 Bioinformatics - Stowers Institute for Medical Research - Kansas City,
 Missouri
Message-ID: <BD62CBAC4395B94096109020651BE2EC129EC9BD4A@exchmb-02.stowers-institute.org>

Programmer Analyst

     The Stowers Institute for Medical Research has an opening for a Programmer Analyst to support the Bioinformatics Center.

     Responsibilities include development and analysis of software requirements; designing, evaluating, coding, documenting, deploying, and supporting custom and third-party software and bioinformatics applications; and assisting in maintenance of biological sequence databases.

     In addition to excellent communication skills the successful candidate will have experience with at least one scripting language (Perl, Python, Unix shell, etc); web applications development; source code management systems; Unix/Linux and Windows systems administration; relational database applications (MySQL, Postgresql, etc.); pipeline/ workflow systems; cluster computing; a variety of DNA/ protein sequence analysis applications; and either Bioperl, EnsembleAPI, GMOD/GBrowse, or NCBI C++ toolkit. Experience with biological sequence database management, customizing genome browsers display using track formats such as GFF and bed, and Vector NTI is preferred.

     The minimum requirements include an undergraduate degree in computer science, bioinformatics, physical science, mathematics, or a related field; and at least two years experience in development, utilization, or support of a group utilizing bioinformatics applications.

        Apply at <http://www.stowers-institute.org/ScientistsSought/ScientistsSought.asp#resume>

Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri




From cjfields at uiuc.edu  Wed Jun 11 17:01:10 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 11 Jun 2008 16:01:10 -0500
Subject: [Bioperl-l] treexml
In-Reply-To: <925346D6-B9B5-4573-991F-0D3F5436FE63@BERKELEY.EDU>
References: <925346D6-B9B5-4573-991F-0D3F5436FE63@BERKELEY.EDU>
Message-ID: <57DFF483-3159-4BC1-BB48-EE56B0F7498C@uiuc.edu>


On Jun 11, 2008, at 3:50 PM, Jason Stajich wrote:

> Hey Mira -
>
> Looks like things are going well. I just wanted to check and see if  
> it is totally necessary to create new classes or if you can use the  
> get/set tag/value pair interface that already exists?
>
> These are the functions that are present in Bio::Tree::TreeI and  
> Bio::Tree::NodeI :
>  add_tag_value
>  remove_tag
>  get_all_tags
>  get_tag_values
>  has_tag
>
> These are the same functions we use in SeqFeatureI interface as  
> well.  It is just possible to re-use these rather than making a new  
> function for every data type - this way we don't have to change the  
> interface for different richness of data.

I agree; it simplifies the interface, even if it sacrifices small  
conveniences.

> BTW (and this may be me who did it, but maybe Sendu remembers) - I  
> am not sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does anyone  
> know? Trees are containers around a set of Nodes which are linked  
> together to form a tree and the Tree object holds a pointer to the  
> root node.

Not sure myself; maybe this was part of Sendu's Taxonomy overhaul a  
while back?

> -jason
> --
> Jason Stajich
> Miller Research Fellow
> University of California, Berkeley
> lab: 510.642.8441
> http://pmb.berkeley.edu/~taylor/people/js.html
> http://fungalgenomes.or

-c

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From JASON_STAJICH at BERKELEY.EDU  Wed Jun 11 16:50:34 2008
From: JASON_STAJICH at BERKELEY.EDU (Jason Stajich)
Date: Wed, 11 Jun 2008 13:50:34 -0700
Subject: [Bioperl-l] treexml
Message-ID: <925346D6-B9B5-4573-991F-0D3F5436FE63@BERKELEY.EDU>

Hey Mira -

Looks like things are going well. I just wanted to check and see if  
it is totally necessary to create new classes or if you can use the  
get/set tag/value pair interface that already exists?

These are the functions that are present in Bio::Tree::TreeI and  
Bio::Tree::NodeI :
  add_tag_value
  remove_tag
  get_all_tags
  get_tag_values
  has_tag

These are the same functions we use in SeqFeatureI interface as  
well.  It is just possible to re-use these rather than making a new  
function for every data type - this way we don't have to change the  
interface for different richness of data.

BTW (and this may be me who did it, but maybe Sendu remembers) - I am  
not sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does anyone  
know? Trees are containers around a set of Nodes which are linked  
together to form a tree and the Tree object holds a pointer to the  
root node.

-jason
--
Jason Stajich
Miller Research Fellow
University of California, Berkeley
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html
http://fungalgenomes.org


From miraceti at gmail.com  Wed Jun 11 20:50:22 2008
From: miraceti at gmail.com (miraceti)
Date: Wed, 11 Jun 2008 20:50:22 -0400
Subject: [Bioperl-l] treexml
In-Reply-To: <57DFF483-3159-4BC1-BB48-EE56B0F7498C@uiuc.edu>
References: <925346D6-B9B5-4573-991F-0D3F5436FE63@BERKELEY.EDU>
	<57DFF483-3159-4BC1-BB48-EE56B0F7498C@uiuc.edu>
Message-ID: <dadd130806111750i7cfbb878u967d80e0f3eb36d5@mail.gmail.com>

I can remove the TreePhyloXML class,
And use the tag functions for Bio::Tree::TreeI.
Yeah, it seems like TreePhyloXML is overkill.
I don't know about the node though.
I think it would be cleaner to have a NodePhyloXML,
Since there are much more than scalar values that will be connected to the
node,
Such as annotations, sequences, etc.


On Wed, Jun 11, 2008 at 5:01 PM, Chris Fields <cjfields at uiuc.edu> wrote:

>
> On Jun 11, 2008, at 3:50 PM, Jason Stajich wrote:
>
>  Hey Mira -
>>
>> Looks like things are going well. I just wanted to check and see if it is
>> totally necessary to create new classes or if you can use the get/set
>> tag/value pair interface that already exists?
>>
>> These are the functions that are present in Bio::Tree::TreeI and
>> Bio::Tree::NodeI :
>>  add_tag_value
>>  remove_tag
>>  get_all_tags
>>  get_tag_values
>>  has_tag
>>
>> These are the same functions we use in SeqFeatureI interface as well.  It
>> is just possible to re-use these rather than making a new function for every
>> data type - this way we don't have to change the interface for different
>> richness of data.
>>
>
> I agree; it simplifies the interface, even if it sacrifices small
> conveniences.
>
>  BTW (and this may be me who did it, but maybe Sendu remembers) - I am not
>> sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does anyone know? Trees are
>> containers around a set of Nodes which are linked together to form a tree
>> and the Tree object holds a pointer to the root node.
>>
>
> Not sure myself; maybe this was part of Sendu's Taxonomy overhaul a while
> back?
>
>  -jason
>> --
>> Jason Stajich
>> Miller Research Fellow
>> University of California, Berkeley
>> lab: 510.642.8441
>> http://pmb.berkeley.edu/~taylor/people/js.html
>> http://fungalgenomes.or
>>
>
> -c
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>
>
> _______________________________________________
> 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 Jun 11 20:56:26 2008
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 11 Jun 2008 17:56:26 -0700
Subject: [Bioperl-l] treexml
In-Reply-To: <C475EA9B.4056%mirhan@indiana.edu>
References: <C475EA9B.4056%mirhan@indiana.edu>
Message-ID: <9EC82D14-EDFE-4734-AA72-E65911411628@bioperl.org>


On Jun 11, 2008, at 5:48 PM, Han, Mira wrote:

>
> I can remove the TreePhyloXML class,
> And use the tag functions for Bio::Tree::TreeI.
> Yeah, it seems like TreePhyloXML is overkill.
> I don't know about the node though.
> I think it would be cleaner to have a NodePhyloXML,
> Since there are much more than scalar values that will be connected  
> to the node,
> Such as annotations, sequences, etc.

Mira -
That sounds quite fine to me.  I agree that the NodePhyloXML is  
probably going to be different enough from the generic Node object to  
justify making a sub-class.  You may want to inherit from the  
interfaces like Bio::AnnotatableI in the NodePhyloXML if you are  
attaching annotations, etc.

For example I do this for the Bio::Tree::AlleleNode which are nodes  
in a tree and also Individuals from a Population for popgen analyses.

-jason
>
>
> On 6/11/08 4:50 PM, "Jason Stajich" <JASON_STAJICH at BERKELEY.EDU>  
> wrote:
>
> Hey Mira -
>
> Looks like things are going well. I just wanted to check and see if  
> it is totally necessary to create new classes or if you can use the  
> get/set tag/value pair interface that already exists?
>
> These are the functions that are present in Bio::Tree::TreeI and  
> Bio::Tree::NodeI :
>  add_tag_value
>  remove_tag
>  get_all_tags
>  get_tag_values
>  has_tag
>
> These are the same functions we use in SeqFeatureI interface as  
> well.  It is just possible to re-use these rather than making a new  
> function for every data type - this way we don't have to change the  
> interface for different richness of data.
>
> BTW (and this may be me who did it, but maybe Sendu remembers) - I  
> am not sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does anyone  
> know? Trees are containers around a set of Nodes which are linked  
> together to form a tree and the Tree object holds a pointer to the  
> root node.
>
> -jason
>
> --
> Jason Stajich
> Miller Research Fellow
> University of California, Berkeley
> lab: 510.642.8441
> http://pmb.berkeley.edu/~taylor/people/js.html
> http://fungalgenomes.org
>
>
>
>


From yezhiqiang at gmail.com  Thu Jun 12 05:06:32 2008
From: yezhiqiang at gmail.com (Zhi-Qiang Ye)
Date: Thu, 12 Jun 2008 17:06:32 +0800
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <46E681F5-CB56-4ADA-BEB9-00083CFA78F9@bioperl.org>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<34198fe40806100443g6c18f47dj881d68c0bf14ba8f@mail.gmail.com>
	<46E681F5-CB56-4ADA-BEB9-00083CFA78F9@bioperl.org>
Message-ID: <34198fe40806120206i31cee6f5xfe6f57b3b9e2a84b@mail.gmail.com>

Hi, Jason

     I used exactly your code, and the result is still 'unknown id'.
Where can I get the version of bioperl?
I used ubuntu gutsy, the version in ubuntu's package management system is 1.4-1.

     I installed BioPerl 1.4 on another computer, IA64 with redhat
linux.  It has the same problem.
In the process of installation using CPAN, make test always failed. So
I used 'force install ....'.
I am not sure it is the reason.

Thanks.
Zhi-Qiang Ye

2008/6/11 Jason Stajich <jason at bioperl.org>:
> What version of bioperl? It works for me using  this code I get 'CB271253'
> printed out.
>
> #!/usr/bin/perl -w
> use strict;
> use Bio::SeqIO;
> my $in = Bio::SeqIO->new(-format => 'embl', -file => shift);
> while( my $seq = $in->next_seq ) {
>  print $seq->id,"\n";
> }
>
> On Jun 10, 2008, at 4:43 AM, Zhi-Qiang Ye wrote:
>
>> That's weird. I also met this problem. I tried a embl-format file like
>> this:
>>
>> ID   CB271253; SV 1; linear; mRNA; EST; INV; 591 BP.
>> XX
>> AC   CB271253;
>> XX
>> DT   24-FEB-2003 (Rel. 74, Created)
>> DT   24-FEB-2003 (Rel. 74, Last updated, Version 1)
>> XX
>> DE   taa17c02.x2 Hydra EST -II Hydra magnipapillata cDNA 3' similar to
>> DE   SW:OPSD_RABIT P49912 RHODOPSIN. ;, mRNA sequence.
>>
>> from: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&id=CB271253&style=raw
>>
>> the $seq object's   ->id, ->display_id  are "unkown id" ...
>>
>>
>>
>> ZQ Ye
>>
>> 2008/6/9 Hilmar Lapp <hlapp at gmx.net>:
>>>
>>> If this is the case with the latest version of BioPerl it should be filed
>>> as
>>> a bug report for the embl parser. The ID ought to be reported in
>>> $seq->get_secondary_accessions() (which returns an array). If it doesn't,
>>> it
>>> sounds like a bug to me.
>>>
>>>       -hilmar
>>>
>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>
>>>> Hi Wen,
>>>> A dump of that sequence object (Data::Dumper is your friend !) reveals
>>>> that the PA EMBL field is not saved into the object. However, you will
>>>> find the string 'AB000170.1' in the embedded CDS feature, more precisely
>>>> the seqid of the location object. I don't know whether that is always
>>>> the case, but it is in your particular example.
>>>> So, to get your hands on that value you have to do:
>>>>
>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
>>>> my $parent_id = $cds->location->seq_id;
>>>>
>>>> HTH,
>>>> Marc
>>>>
>>>> Marc Logghe
>>>> Senior Bioinformatician
>>>> Ablynx nv
>>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>> To: bioperl-l at lists.open-bio.org
>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>
>>>>> Hi all,
>>>>>
>>>>> I have a EMBL file that I want to extract one of the line
>>>>>
>>>>> ###file###
>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>> XX
>>>>> PA   AB000170.1
>>>>> XX
>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>> XX
>>>>> OS   Sus scrofa (pig)
>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
>>>>> Mammalia;
>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.
>>>>> OX   NCBI_TaxID=9823;
>>>>> .........
>>>>>
>>>>> I want the accession number in the line that starts with PA, AB000170
>>>>> in this example.
>>>>>
>>>>> Can anybody kindly help, tell me which module and method I should use?
>>>>> I tried various things like $seq_obj -> primary_id, display_id,
>>>>> get_secondary_id, etc.. they did not work...
>>>>>
>>>>> Thanks a lot!
>>>>>
>>>>> Wen
>>>>> _______________________________________________

From bix at sendu.me.uk  Thu Jun 12 05:54:04 2008
From: bix at sendu.me.uk (Sendu Bala)
Date: Thu, 12 Jun 2008 10:54:04 +0100
Subject: [Bioperl-l] treexml
In-Reply-To: <57DFF483-3159-4BC1-BB48-EE56B0F7498C@uiuc.edu>
References: <925346D6-B9B5-4573-991F-0D3F5436FE63@BERKELEY.EDU>
	<57DFF483-3159-4BC1-BB48-EE56B0F7498C@uiuc.edu>
Message-ID: <4850F23C.4070809@sendu.me.uk>

Chris Fields wrote:
> On Jun 11, 2008, at 3:50 PM, Jason Stajich wrote:
>> BTW (and this may be me who did it, but maybe Sendu remembers) - I am 
>> not sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does anyone know? 
>> Trees are containers around a set of Nodes which are linked together 
>> to form a tree and the Tree object holds a pointer to the root node.
> 
> Not sure myself; maybe this was part of Sendu's Taxonomy overhaul a 
> while back?

I don't think it was me. It's worth noting that if you change TreeI to 
inherit from RootI instead of NodeI, it doesn't seem to cause any 
problems in the obviously related test scripts.

Maybe it's there as a convenience thing? I don't know.

From cjfields at uiuc.edu  Thu Jun 12 08:21:31 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 12 Jun 2008 07:21:31 -0500
Subject: [Bioperl-l] treexml
In-Reply-To: <4850F23C.4070809@sendu.me.uk>
References: <925346D6-B9B5-4573-991F-0D3F5436FE63@BERKELEY.EDU>
	<57DFF483-3159-4BC1-BB48-EE56B0F7498C@uiuc.edu>
	<4850F23C.4070809@sendu.me.uk>
Message-ID: <3CDC860D-05D8-4D6F-B5FC-D76309C510C3@uiuc.edu>

Looks like it has been there for a while:

http://code.open-bio.org/svnweb/index.cgi/bioperl/diff/bioperl-live/trunk/Bio/Tree/TreeI.pm?rev1=2900;rev2=2901

Jason was the committer, back in 2001.  Maybe (as Sendu indicates) it  
should be changed to RootI.

chris

On Jun 12, 2008, at 4:54 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> On Jun 11, 2008, at 3:50 PM, Jason Stajich wrote:
>>> BTW (and this may be me who did it, but maybe Sendu remembers) - I  
>>> am not sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does  
>>> anyone know? Trees are containers around a set of Nodes which are  
>>> linked together to form a tree and the Tree object holds a pointer  
>>> to the root node.
>> Not sure myself; maybe this was part of Sendu's Taxonomy overhaul a  
>> while back?
>
> I don't think it was me. It's worth noting that if you change TreeI  
> to inherit from RootI instead of NodeI, it doesn't seem to cause any  
> problems in the obviously related test scripts.
>
> Maybe it's there as a convenience thing? I don't know.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From hlapp at gmx.net  Thu Jun 12 09:58:25 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu, 12 Jun 2008 09:58:25 -0400
Subject: [Bioperl-l] treexml
In-Reply-To: <9EC82D14-EDFE-4734-AA72-E65911411628@bioperl.org>
References: <C475EA9B.4056%mirhan@indiana.edu>
	<9EC82D14-EDFE-4734-AA72-E65911411628@bioperl.org>
Message-ID: <922F0238-F390-4A33-99F6-8473CDF22980@gmx.net>

I agree with implementing Bio::AnnotatableI. I'm not sure we need to  
have a node class specifically tailored to PhyloXML but maybe we do.

But even if we do, the annotatable capability sounds generic enough  
for having a Bio::Tree::AnnotatableNode, from which  
Bio::Tree::NodePhyloXML would inherit and do all the things that are  
really specific to PhyloXML?

	-hilmar

On Jun 11, 2008, at 8:56 PM, Jason Stajich wrote:
>
> On Jun 11, 2008, at 5:48 PM, Han, Mira wrote:
>
>>
>> I can remove the TreePhyloXML class,
>> And use the tag functions for Bio::Tree::TreeI.
>> Yeah, it seems like TreePhyloXML is overkill.
>> I don't know about the node though.
>> I think it would be cleaner to have a NodePhyloXML,
>> Since there are much more than scalar values that will be  
>> connected to the node,
>> Such as annotations, sequences, etc.
>
> Mira -
> That sounds quite fine to me.  I agree that the NodePhyloXML is  
> probably going to be different enough from the generic Node object  
> to justify making a sub-class.  You may want to inherit from the  
> interfaces like Bio::AnnotatableI in the NodePhyloXML if you are  
> attaching annotations, etc.
>
> For example I do this for the Bio::Tree::AlleleNode which are nodes  
> in a tree and also Individuals from a Population for popgen analyses.
>
> -jason
>>
>>
>> On 6/11/08 4:50 PM, "Jason Stajich" <JASON_STAJICH at BERKELEY.EDU>  
>> wrote:
>>
>> Hey Mira -
>>
>> Looks like things are going well. I just wanted to check and see  
>> if it is totally necessary to create new classes or if you can use  
>> the get/set tag/value pair interface that already exists?
>>
>> These are the functions that are present in Bio::Tree::TreeI and  
>> Bio::Tree::NodeI :
>>  add_tag_value
>>  remove_tag
>>  get_all_tags
>>  get_tag_values
>>  has_tag
>>
>> These are the same functions we use in SeqFeatureI interface as  
>> well.  It is just possible to re-use these rather than making a  
>> new function for every data type - this way we don't have to  
>> change the interface for different richness of data.
>>
>> BTW (and this may be me who did it, but maybe Sendu remembers) - I  
>> am not sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does  
>> anyone know? Trees are containers around a set of Nodes which are  
>> linked together to form a tree and the Tree object holds a pointer  
>> to the root node.
>>
>> -jason
>>
>> --
>> Jason Stajich
>> Miller Research Fellow
>> University of California, Berkeley
>> lab: 510.642.8441
>> http://pmb.berkeley.edu/~taylor/people/js.html
>> http://fungalgenomes.org
>>
>>
>>
>>
>
> _______________________________________________
> 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 gmx dot net :
===========================================================




From mirhan at indiana.edu  Thu Jun 12 11:44:08 2008
From: mirhan at indiana.edu (Han, Mira)
Date: Thu, 12 Jun 2008 11:44:08 -0400
Subject: [Bioperl-l] treexml
In-Reply-To: <922F0238-F390-4A33-99F6-8473CDF22980@gmx.net>
Message-ID: <C476BC88.91E3%mirhan@indiana.edu>


I'll do that,
I was thinking of having an annotationCollectionI reference as a variable,
But inheriting from AnnotatableI sounds better.
Do you mean I should make a more generic AnnotatableNode instead of NodePhyloXML?

Mira


On 6/12/08 9:58 AM, "Hilmar Lapp" <hlapp at gmx.net> wrote:

I agree with implementing Bio::AnnotatableI. I'm not sure we need to
have a node class specifically tailored to PhyloXML but maybe we do.

But even if we do, the annotatable capability sounds generic enough
for having a Bio::Tree::AnnotatableNode, from which
Bio::Tree::NodePhyloXML would inherit and do all the things that are
really specific to PhyloXML?

        -hilmar

On Jun 11, 2008, at 8:56 PM, Jason Stajich wrote:
>
> On Jun 11, 2008, at 5:48 PM, Han, Mira wrote:
>
>>
>> I can remove the TreePhyloXML class,
>> And use the tag functions for Bio::Tree::TreeI.
>> Yeah, it seems like TreePhyloXML is overkill.
>> I don't know about the node though.
>> I think it would be cleaner to have a NodePhyloXML,
>> Since there are much more than scalar values that will be
>> connected to the node,
>> Such as annotations, sequences, etc.
>
> Mira -
> That sounds quite fine to me.  I agree that the NodePhyloXML is
> probably going to be different enough from the generic Node object
> to justify making a sub-class.  You may want to inherit from the
> interfaces like Bio::AnnotatableI in the NodePhyloXML if you are
> attaching annotations, etc.
>
> For example I do this for the Bio::Tree::AlleleNode which are nodes
> in a tree and also Individuals from a Population for popgen analyses.
>
> -jason
>>
>>
>> On 6/11/08 4:50 PM, "Jason Stajich" <JASON_STAJICH at BERKELEY.EDU>
>> wrote:
>>
>> Hey Mira -
>>
>> Looks like things are going well. I just wanted to check and see
>> if it is totally necessary to create new classes or if you can use
>> the get/set tag/value pair interface that already exists?
>>
>> These are the functions that are present in Bio::Tree::TreeI and
>> Bio::Tree::NodeI :
>>  add_tag_value
>>  remove_tag
>>  get_all_tags
>>  get_tag_values
>>  has_tag
>>
>> These are the same functions we use in SeqFeatureI interface as
>> well.  It is just possible to re-use these rather than making a
>> new function for every data type - this way we don't have to
>> change the interface for different richness of data.
>>
>> BTW (and this may be me who did it, but maybe Sendu remembers) - I
>> am not sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does
>> anyone know? Trees are containers around a set of Nodes which are
>> linked together to form a tree and the Tree object holds a pointer
>> to the root node.
>>
>> -jason
>>
>> --
>> Jason Stajich
>> Miller Research Fellow
>> University of California, Berkeley
>> lab: 510.642.8441
>> http://pmb.berkeley.edu/~taylor/people/js.html
>> http://fungalgenomes.org
>>
>>
>>
>>
>
> _______________________________________________
> 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 gmx dot net :
===========================================================







From Kevin.M.Brown at asu.edu  Thu Jun 12 11:22:11 2008
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Thu, 12 Jun 2008 08:22:11 -0700
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <34198fe40806120206i31cee6f5xfe6f57b3b9e2a84b@mail.gmail.com>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com><03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com><C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net><34198fe40806100443g6c18f47dj881d68c0bf14ba8f@mail.gmail.com><46E681F5-CB56-4ADA-BEB9-00083CFA78F9@bioperl.org>
	<34198fe40806120206i31cee6f5xfe6f57b3b9e2a84b@mail.gmail.com>
Message-ID: <1A4207F8295607498283FE9E93B775B404F2B374@EX02.asurite.ad.asu.edu>

See the following links for where to get a more current version.  1.4 is
years old and lots of parts are non-functional due to website and file
format changes.

http://www.bioperl.org/wiki/Installing_BioPerl

http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Zhi-Qiang Ye
> Sent: Thursday, June 12, 2008 2:07 AM
> To: Jason Stajich
> Cc: bioperl list
> Subject: Re: [Bioperl-l] EMBL format field
> 
> Hi, Jason
> 
>      I used exactly your code, and the result is still 'unknown id'.
> Where can I get the version of bioperl?
> I used ubuntu gutsy, the version in ubuntu's package 
> management system is 1.4-1.
> 
>      I installed BioPerl 1.4 on another computer, IA64 with redhat
> linux.  It has the same problem.
> In the process of installation using CPAN, make test always failed. So
> I used 'force install ....'.
> I am not sure it is the reason.
> 
> Thanks.
> Zhi-Qiang Ye
> 
> 2008/6/11 Jason Stajich <jason at bioperl.org>:
> > What version of bioperl? It works for me using  this code I 
> get 'CB271253'
> > printed out.
> >
> > #!/usr/bin/perl -w
> > use strict;
> > use Bio::SeqIO;
> > my $in = Bio::SeqIO->new(-format => 'embl', -file => shift);
> > while( my $seq = $in->next_seq ) {
> >  print $seq->id,"\n";
> > }
> >
> > On Jun 10, 2008, at 4:43 AM, Zhi-Qiang Ye wrote:
> >
> >> That's weird. I also met this problem. I tried a 
> embl-format file like
> >> this:
> >>
> >> ID   CB271253; SV 1; linear; mRNA; EST; INV; 591 BP.
> >> XX
> >> AC   CB271253;
> >> XX
> >> DT   24-FEB-2003 (Rel. 74, Created)
> >> DT   24-FEB-2003 (Rel. 74, Last updated, Version 1)
> >> XX
> >> DE   taa17c02.x2 Hydra EST -II Hydra magnipapillata cDNA 
> 3' similar to
> >> DE   SW:OPSD_RABIT P49912 RHODOPSIN. ;, mRNA sequence.
> >>
> >> from: 
> http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&id=CB271253&style=raw
> >>
> >> the $seq object's   ->id, ->display_id  are "unkown id" ...
> >>
> >>
> >>
> >> ZQ Ye
> >>
> >> 2008/6/9 Hilmar Lapp <hlapp at gmx.net>:
> >>>
> >>> If this is the case with the latest version of BioPerl it 
> should be filed
> >>> as
> >>> a bug report for the embl parser. The ID ought to be reported in
> >>> $seq->get_secondary_accessions() (which returns an 
> array). If it doesn't,
> >>> it
> >>> sounds like a bug to me.
> >>>
> >>>       -hilmar
> >>>
> >>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
> >>>>
> >>>> Hi Wen,
> >>>> A dump of that sequence object (Data::Dumper is your 
> friend !) reveals
> >>>> that the PA EMBL field is not saved into the object. 
> However, you will
> >>>> find the string 'AB000170.1' in the embedded CDS 
> feature, more precisely
> >>>> the seqid of the location object. I don't know whether 
> that is always
> >>>> the case, but it is in your particular example.
> >>>> So, to get your hands on that value you have to do:
> >>>>
> >>>> my ($cds) = grep {$_->primary_tag eq 'CDS'} 
> $seq->get_SeqFeatures;
> >>>> my $parent_id = $cds->location->seq_id;
> >>>>
> >>>> HTH,
> >>>> Marc
> >>>>
> >>>> Marc Logghe
> >>>> Senior Bioinformatician
> >>>> Ablynx nv
> >>>>>
> >>>>> -----Original Message-----
> >>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
> >>>>> Sent: Monday, June 09, 2008 5:28 AM
> >>>>> To: bioperl-l at lists.open-bio.org
> >>>>> Subject: [Bioperl-l] EMBL format field
> >>>>>
> >>>>> Hi all,
> >>>>>
> >>>>> I have a EMBL file that I want to extract one of the line
> >>>>>
> >>>>> ###file###
> >>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
> >>>>> XX
> >>>>> PA   AB000170.1
> >>>>> XX
> >>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
> >>>>> XX
> >>>>> OS   Sus scrofa (pig)
> >>>>> OC   Eukaryota; Metazoa; Chordata; Craniata; 
> Vertebrata; Euteleostomi;
> >>>>> Mammalia;
> >>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; 
> Suidae; Sus.
> >>>>> OX   NCBI_TaxID=9823;
> >>>>> .........
> >>>>>
> >>>>> I want the accession number in the line that starts 
> with PA, AB000170
> >>>>> in this example.
> >>>>>
> >>>>> Can anybody kindly help, tell me which module and 
> method I should use?
> >>>>> I tried various things like $seq_obj -> primary_id, display_id,
> >>>>> get_secondary_id, etc.. they did not work...
> >>>>>
> >>>>> Thanks a lot!
> >>>>>
> >>>>> Wen
> >>>>> _______________________________________________
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From cjfields at uiuc.edu  Thu Jun 12 13:03:55 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 12 Jun 2008 12:03:55 -0500
Subject: [Bioperl-l] treexml
In-Reply-To: <922F0238-F390-4A33-99F6-8473CDF22980@gmx.net>
References: <C475EA9B.4056%mirhan@indiana.edu>
	<9EC82D14-EDFE-4734-AA72-E65911411628@bioperl.org>
	<922F0238-F390-4A33-99F6-8473CDF22980@gmx.net>
Message-ID: <4EAAD507-FF89-4F9A-909A-1E1C7B0187C8@uiuc.edu>

Yes, that sounds correct to me.  I could see this being useful for  
other rich tree file formats so it probably should be genericized.

chris

On Jun 12, 2008, at 8:58 AM, Hilmar Lapp wrote:

> I agree with implementing Bio::AnnotatableI. I'm not sure we need to  
> have a node class specifically tailored to PhyloXML but maybe we do.
>
> But even if we do, the annotatable capability sounds generic enough  
> for having a Bio::Tree::AnnotatableNode, from which  
> Bio::Tree::NodePhyloXML would inherit and do all the things that are  
> really specific to PhyloXML?
>
> 	-hilmar
>
> On Jun 11, 2008, at 8:56 PM, Jason Stajich wrote:
>>
>> On Jun 11, 2008, at 5:48 PM, Han, Mira wrote:
>>
>>>
>>> I can remove the TreePhyloXML class,
>>> And use the tag functions for Bio::Tree::TreeI.
>>> Yeah, it seems like TreePhyloXML is overkill.
>>> I don't know about the node though.
>>> I think it would be cleaner to have a NodePhyloXML,
>>> Since there are much more than scalar values that will be  
>>> connected to the node,
>>> Such as annotations, sequences, etc.
>>
>> Mira -
>> That sounds quite fine to me.  I agree that the NodePhyloXML is  
>> probably going to be different enough from the generic Node object  
>> to justify making a sub-class.  You may want to inherit from the  
>> interfaces like Bio::AnnotatableI in the NodePhyloXML if you are  
>> attaching annotations, etc.
>>
>> For example I do this for the Bio::Tree::AlleleNode which are nodes  
>> in a tree and also Individuals from a Population for popgen analyses.
>>
>> -jason
>>>
>>>
>>> On 6/11/08 4:50 PM, "Jason Stajich" <JASON_STAJICH at BERKELEY.EDU>  
>>> wrote:
>>>
>>> Hey Mira -
>>>
>>> Looks like things are going well. I just wanted to check and see  
>>> if it is totally necessary to create new classes or if you can use  
>>> the get/set tag/value pair interface that already exists?
>>>
>>> These are the functions that are present in Bio::Tree::TreeI and  
>>> Bio::Tree::NodeI :
>>> add_tag_value
>>> remove_tag
>>> get_all_tags
>>> get_tag_values
>>> has_tag
>>>
>>> These are the same functions we use in SeqFeatureI interface as  
>>> well.  It is just possible to re-use these rather than making a  
>>> new function for every data type - this way we don't have to  
>>> change the interface for different richness of data.
>>>
>>> BTW (and this may be me who did it, but maybe Sendu remembers) - I  
>>> am not sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does  
>>> anyone know? Trees are containers around a set of Nodes which are  
>>> linked together to form a tree and the Tree object holds a pointer  
>>> to the root node.
>>>
>>> -jason
>>>
>>> --
>>> Jason Stajich
>>> Miller Research Fellow
>>> University of California, Berkeley
>>> lab: 510.642.8441
>>> http://pmb.berkeley.edu/~taylor/people/js.html
>>> http://fungalgenomes.org
>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> 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 gmx dot net :
> ===========================================================
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From vbhonagiri at yahoo.com  Thu Jun 12 17:18:20 2008
From: vbhonagiri at yahoo.com (veena bhonagiri)
Date: Thu, 12 Jun 2008 14:18:20 -0700 (PDT)
Subject: [Bioperl-l] Hi
Message-ID: <267026.87405.qm@web35304.mail.mud.yahoo.com>

Hi,
I was looking for a parser to convert gff3 to gff2 format. Is there one available?

thanks,
Veena


      

From barry.moore at genetics.utah.edu  Thu Jun 12 17:44:29 2008
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu, 12 Jun 2008 15:44:29 -0600
Subject: [Bioperl-l] Hi
In-Reply-To: <267026.87405.qm@web35304.mail.mud.yahoo.com>
References: <267026.87405.qm@web35304.mail.mud.yahoo.com>
Message-ID: <D4E2EBF9-27FE-40D1-8956-8B52AA841F8D@genetics.utah.edu>

Did you really want to go backwards from gff3 to gff2 or did you mean  
from gff2 to gff3?

If you want to go from GTF/GFF2 forward to GFF3 there is a script  
available through the Sequence Ontology for doing this (http:// 
song.cvs.sourceforge.net/song/software/scripts/gtf2gff3/).  It  
handles a wide variety of GTF and GFF2 files, however since there is  
a lot of variability of implementations of those formats I can't  
guarantee that it will handle every flavor.  For example, it does not  
work on GTF from the UCSC
table browser because those files use the same ID for gene and  
transcript, so it is impossible to group multiple transcripts to a  
gene. The version released will has been tested on Ensembl and  
Twinscan GTF.  I happen to be working on extending that script right  
now to handle a GFF2/GFF3 hybrid found in WS180 release from WormBase  
so if it doesn't handle your case it may soon.  If you use it and  
have feedback I'd appreciate hearing from you.

Barry

Barry Moore
Senior Research Specialist
Eccles Institute of Human Genetics
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




On Jun 12, 2008, at 3:18 PM, veena bhonagiri wrote:

> Hi,
> I was looking for a parser to convert gff3 to gff2 format. Is there  
> one available?
>
> thanks,
> Veena
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From heikki at sanbi.ac.za  Fri Jun 13 07:33:21 2008
From: heikki at sanbi.ac.za (Heikki Lehvaslaiho)
Date: Fri, 13 Jun 2008 13:33:21 +0200
Subject: [Bioperl-l] preparing nexus files for Mr. Bayes
In-Reply-To: <32D2B523-8C68-44B3-80B4-E8BB82FB4232@bioperl.org>
References: <5aa3b3570806110246naa24dcaj462d8025048aad41@mail.gmail.com>
	<32D2B523-8C68-44B3-80B4-E8BB82FB4232@bioperl.org>
Message-ID: <200806131333.21902.heikki@sanbi.ac.za>


FYI,

According  http://search.cpan.org/dist/Bio-NEXUS/, the Bio::NEXUS modules have 
been recently updated (Apr 23 2008). It would definitely be worth testing 
them and possibly create subclasses to handle PAUP and MrBayes command 
blocks.

   -Heikki


On Wednesday 11 June 2008 17:13:20 Jason Stajich wrote:
> Giovanni -
>
> Bits and pieces already exist, there is little to handle the text
> blocks that exist in NEXUS files because BioPerl has has been focused
> on the alignment data not the analysis.  Arlin Stolzfus has started a
> Bio::NEXUS project that is supposed to fully parse all NEXUS data in
> and out but I don't know what the status is right now.
>
> If you look at the Bio::AlignIO::nexus documentation you need to turn
> off symbols and endblock when writing for MrBayes NEXUS.
>
> my $out = Bio::AlignIO->new(-format => 'nexus',
> 			    -show_symbols => 0,
> 			    -show_endblock => 0);
>
>
> # after you have written out the alignment
> $out->write_aln;
> # you can then print out whatever execution blocks you want with
> standard print statements.
> print $out->_fh "begin mrbayes;\n"; ...
>
>
> As for the other things, the Bio::SimpleAlign module lets you swap
> the match character (see map_char and gap_char methods).
>
> For joining alignments and setting up partitions, you can join
> multiple alignments by making a new Bio::SimpleAlign and adding
> concatenated sequences together.
>
> my %matrix;
>   for my $aln ( @alns ) {
>    for my $seq ( $aln->each_seq ) {
>              my $id = $seq->id;
>              $matrix{$id} .= $seq->seq;
>    }
>   }
>   my $bigaln = Bio::SimpleAlign->new;
>   while( my ($id,$seq) = each %matrix ) {
>       $bigaln->add_seq(Bio::LocatableSeq->new(-id  => $id,
>                                                  -seq => $seq));
>   }
>
>
> In general there is not a single solution to a lot of these tasks
> (although there should be one that concatenates a set of  alignments)
> so there are not ready-to-use functions.  I have my custom code I use
> to join datasets and establish partitions but much is specific to how
> I organize the data on my system so I don't know how informative it
> would be.
>
> I'm not sure python code would be much good here... =) if you jump
> ship you should talk to Frank Kauff who has written some python code
> to manipulate alignments for biopython.
>
> -jason
>
> On Jun 11, 2008, at 2:46 AM, Giovanni Marco Dall'Olio wrote:
> > Hi,
> > I was wondering whether there is any bioperl module I can use to
> > handle nexus files for Mr.Bayes.
> >
> > mr. Bayes is a program for bayesian estimation of phylogeny, which
> > uses an alignment file in a customized nexus format as input.
> > I would need a module to prepare these files, doing tasks like:
> > - joining more than an alignment in a single file/line
> > - substitute matching chars with '.'
> > - customizing parameters displayed in the headers of the output
> > nexus file
> > - manage mrbayes' extensions, like adding information about
> > partitions and taxas
> > - adding batch instructions for the mr bayes interpreter
> > - and similar stuff.
> >
> > I have tried Bio::AlignIO but I see it doesn't handle all of this,
> > what I am looing for is bit more specific.
> > Moreover, I found a bug in the way mrbayes recognizes the output from
> > Bio::AlignIO (https://sourceforge.net/tracker/index.php?
> > func=detail&aid=1990655&group_id=129302&atid=714418).
> >
> > Is there any existing module already available?
> > If there is not, I am going to have to write such scripts anyway.
> > I would like to contribute them to bioperl, even if I am not a very
> > good perl programmer, I prefer python.
> >
> > --
> > -----------------------------------------------------------
> >
> > My Blog on Bioinformatics (italian): http://bioinfoblog.it
> > _______________________________________________
> > 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



-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________

From yezhiqiang at gmail.com  Sat Jun 14 09:39:45 2008
From: yezhiqiang at gmail.com (Zhi-Qiang Ye)
Date: Sat, 14 Jun 2008 21:39:45 +0800
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <1A4207F8295607498283FE9E93B775B404F2B374@EX02.asurite.ad.asu.edu>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<34198fe40806100443g6c18f47dj881d68c0bf14ba8f@mail.gmail.com>
	<46E681F5-CB56-4ADA-BEB9-00083CFA78F9@bioperl.org>
	<34198fe40806120206i31cee6f5xfe6f57b3b9e2a84b@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B404F2B374@EX02.asurite.ad.asu.edu>
Message-ID: <34198fe40806140639g1c2edc3aqe8fce6d03a102642@mail.gmail.com>

   Thank all of you.  I finally get the newest version of bioperl
installed and solved the problem.

   I noticed that ensembl API still uses bioperl-1.2.3, which
misleaded me that bioperl-1.4 is very up-to-date ...


Regards,
Zhi-Qiang


2008/6/12 Kevin Brown <Kevin.M.Brown at asu.edu>:
> See the following links for where to get a more current version.  1.4 is
> years old and lots of parts are non-functional due to website and file
> format changes.
>
> http://www.bioperl.org/wiki/Installing_BioPerl
>
> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>> Zhi-Qiang Ye
>> Sent: Thursday, June 12, 2008 2:07 AM
>> To: Jason Stajich
>> Cc: bioperl list
>> Subject: Re: [Bioperl-l] EMBL format field
>>
>> Hi, Jason
>>
>>      I used exactly your code, and the result is still 'unknown id'.
>> Where can I get the version of bioperl?
>> I used ubuntu gutsy, the version in ubuntu's package
>> management system is 1.4-1.
>>
>>      I installed BioPerl 1.4 on another computer, IA64 with redhat
>> linux.  It has the same problem.
>> In the process of installation using CPAN, make test always failed. So
>> I used 'force install ....'.
>> I am not sure it is the reason.
>>
>> Thanks.
>> Zhi-Qiang Ye
>>
>> 2008/6/11 Jason Stajich <jason at bioperl.org>:
>> > What version of bioperl? It works for me using  this code I
>> get 'CB271253'
>> > printed out.
>> >
>> > #!/usr/bin/perl -w
>> > use strict;
>> > use Bio::SeqIO;
>> > my $in = Bio::SeqIO->new(-format => 'embl', -file => shift);
>> > while( my $seq = $in->next_seq ) {
>> >  print $seq->id,"\n";
>> > }
>> >
>> > On Jun 10, 2008, at 4:43 AM, Zhi-Qiang Ye wrote:
>> >
>> >> That's weird. I also met this problem. I tried a
>> embl-format file like
>> >> this:
>> >>
>> >> ID   CB271253; SV 1; linear; mRNA; EST; INV; 591 BP.
>> >> XX
>> >> AC   CB271253;
>> >> XX
>> >> DT   24-FEB-2003 (Rel. 74, Created)
>> >> DT   24-FEB-2003 (Rel. 74, Last updated, Version 1)
>> >> XX
>> >> DE   taa17c02.x2 Hydra EST -II Hydra magnipapillata cDNA
>> 3' similar to
>> >> DE   SW:OPSD_RABIT P49912 RHODOPSIN. ;, mRNA sequence.
>> >>
>> >> from:
>> http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&id=CB271253&style=raw
>> >>
>> >> the $seq object's   ->id, ->display_id  are "unkown id" ...
>> >>
>> >>
>> >>
>> >> ZQ Ye
>> >>
>> >> 2008/6/9 Hilmar Lapp <hlapp at gmx.net>:
>> >>>
>> >>> If this is the case with the latest version of BioPerl it
>> should be filed
>> >>> as
>> >>> a bug report for the embl parser. The ID ought to be reported in
>> >>> $seq->get_secondary_accessions() (which returns an
>> array). If it doesn't,
>> >>> it
>> >>> sounds like a bug to me.
>> >>>
>> >>>       -hilmar
>> >>>
>> >>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>> >>>>
>> >>>> Hi Wen,
>> >>>> A dump of that sequence object (Data::Dumper is your
>> friend !) reveals
>> >>>> that the PA EMBL field is not saved into the object.
>> However, you will
>> >>>> find the string 'AB000170.1' in the embedded CDS
>> feature, more precisely
>> >>>> the seqid of the location object. I don't know whether
>> that is always
>> >>>> the case, but it is in your particular example.
>> >>>> So, to get your hands on that value you have to do:
>> >>>>
>> >>>> my ($cds) = grep {$_->primary_tag eq 'CDS'}
>> $seq->get_SeqFeatures;
>> >>>> my $parent_id = $cds->location->seq_id;
>> >>>>
>> >>>> HTH,
>> >>>> Marc
>> >>>>
>> >>>> Marc Logghe
>> >>>> Senior Bioinformatician
>> >>>> Ablynx nv
>> >>>>>
>> >>>>> -----Original Message-----
>> >>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> >>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>> >>>>> Sent: Monday, June 09, 2008 5:28 AM
>> >>>>> To: bioperl-l at lists.open-bio.org
>> >>>>> Subject: [Bioperl-l] EMBL format field
>> >>>>>
>> >>>>> Hi all,
>> >>>>>
>> >>>>> I have a EMBL file that I want to extract one of the line
>> >>>>>
>> >>>>> ###file###
>> >>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>> >>>>> XX
>> >>>>> PA   AB000170.1
>> >>>>> XX
>> >>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>> >>>>> XX
>> >>>>> OS   Sus scrofa (pig)
>> >>>>> OC   Eukaryota; Metazoa; Chordata; Craniata;
>> Vertebrata; Euteleostomi;
>> >>>>> Mammalia;
>> >>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina;
>> Suidae; Sus.
>> >>>>> OX   NCBI_TaxID=9823;
>> >>>>> .........
>> >>>>>
>> >>>>> I want the accession number in the line that starts
>> with PA, AB000170
>> >>>>> in this example.
>> >>>>>
>> >>>>> Can anybody kindly help, tell me which module and
>> method I should use?
>> >>>>> I tried various things like $seq_obj -> primary_id, display_id,
>> >>>>> get_secondary_id, etc.. they did not work...
>> >>>>>
>> >>>>> Thanks a lot!
>> >>>>>
>> >>>>> Wen
>> >>>>> _______________________________________________
>> _______________________________________________
>> Bioperl-l mailing list

From cjfields at uiuc.edu  Sat Jun 14 22:25:26 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Sat, 14 Jun 2008 21:25:26 -0500
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <34198fe40806140639g1c2edc3aqe8fce6d03a102642@mail.gmail.com>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<34198fe40806100443g6c18f47dj881d68c0bf14ba8f@mail.gmail.com>
	<46E681F5-CB56-4ADA-BEB9-00083CFA78F9@bioperl.org>
	<34198fe40806120206i31cee6f5xfe6f57b3b9e2a84b@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B404F2B374@EX02.asurite.ad.asu.edu>
	<34198fe40806140639g1c2edc3aqe8fce6d03a102642@mail.gmail.com>
Message-ID: <AA4401CC-5EF2-4120-886C-82E8E57D6792@uiuc.edu>

See this FAQ question, as well as the one following it.

chris

On Jun 14, 2008, at 8:39 AM, Zhi-Qiang Ye wrote:

>  Thank all of you.  I finally get the newest version of bioperl
> installed and solved the problem.
>
>  I noticed that ensembl API still uses bioperl-1.2.3, which
> misleaded me that bioperl-1.4 is very up-to-date ...
>
>
> Regards,
> Zhi-Qiang
>
>
> 2008/6/12 Kevin Brown <Kevin.M.Brown at asu.edu>:
>> See the following links for where to get a more current version.   
>> 1.4 is
>> years old and lots of parts are non-functional due to website and  
>> file
>> format changes.
>>
>> http://www.bioperl.org/wiki/Installing_BioPerl
>>
>> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>>> Zhi-Qiang Ye
>>> Sent: Thursday, June 12, 2008 2:07 AM
>>> To: Jason Stajich
>>> Cc: bioperl list
>>> Subject: Re: [Bioperl-l] EMBL format field
>>>
>>> Hi, Jason
>>>
>>>    I used exactly your code, and the result is still 'unknown id'.
>>> Where can I get the version of bioperl?
>>> I used ubuntu gutsy, the version in ubuntu's package
>>> management system is 1.4-1.
>>>
>>>    I installed BioPerl 1.4 on another computer, IA64 with redhat
>>> linux.  It has the same problem.
>>> In the process of installation using CPAN, make test always  
>>> failed. So
>>> I used 'force install ....'.
>>> I am not sure it is the reason.
>>>
>>> Thanks.
>>> Zhi-Qiang Ye
>>>
>>> 2008/6/11 Jason Stajich <jason at bioperl.org>:
>>>> What version of bioperl? It works for me using  this code I
>>> get 'CB271253'
>>>> printed out.
>>>>
>>>> #!/usr/bin/perl -w
>>>> use strict;
>>>> use Bio::SeqIO;
>>>> my $in = Bio::SeqIO->new(-format => 'embl', -file => shift);
>>>> while( my $seq = $in->next_seq ) {
>>>> print $seq->id,"\n";
>>>> }
>>>>
>>>> On Jun 10, 2008, at 4:43 AM, Zhi-Qiang Ye wrote:
>>>>
>>>>> That's weird. I also met this problem. I tried a
>>> embl-format file like
>>>>> this:
>>>>>
>>>>> ID   CB271253; SV 1; linear; mRNA; EST; INV; 591 BP.
>>>>> XX
>>>>> AC   CB271253;
>>>>> XX
>>>>> DT   24-FEB-2003 (Rel. 74, Created)
>>>>> DT   24-FEB-2003 (Rel. 74, Last updated, Version 1)
>>>>> XX
>>>>> DE   taa17c02.x2 Hydra EST -II Hydra magnipapillata cDNA
>>> 3' similar to
>>>>> DE   SW:OPSD_RABIT P49912 RHODOPSIN. ;, mRNA sequence.
>>>>>
>>>>> from:
>>> http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&id=CB271253&style=raw
>>>>>
>>>>> the $seq object's   ->id, ->display_id  are "unkown id" ...
>>>>>
>>>>>
>>>>>
>>>>> ZQ Ye
>>>>>
>>>>> 2008/6/9 Hilmar Lapp <hlapp at gmx.net>:
>>>>>>
>>>>>> If this is the case with the latest version of BioPerl it
>>> should be filed
>>>>>> as
>>>>>> a bug report for the embl parser. The ID ought to be reported in
>>>>>> $seq->get_secondary_accessions() (which returns an
>>> array). If it doesn't,
>>>>>> it
>>>>>> sounds like a bug to me.
>>>>>>
>>>>>>     -hilmar
>>>>>>
>>>>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>>>>
>>>>>>> Hi Wen,
>>>>>>> A dump of that sequence object (Data::Dumper is your
>>> friend !) reveals
>>>>>>> that the PA EMBL field is not saved into the object.
>>> However, you will
>>>>>>> find the string 'AB000170.1' in the embedded CDS
>>> feature, more precisely
>>>>>>> the seqid of the location object. I don't know whether
>>> that is always
>>>>>>> the case, but it is in your particular example.
>>>>>>> So, to get your hands on that value you have to do:
>>>>>>>
>>>>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'}
>>> $seq->get_SeqFeatures;
>>>>>>> my $parent_id = $cds->location->seq_id;
>>>>>>>
>>>>>>> HTH,
>>>>>>> Marc
>>>>>>>
>>>>>>> Marc Logghe
>>>>>>> Senior Bioinformatician
>>>>>>> Ablynx nv
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I have a EMBL file that I want to extract one of the line
>>>>>>>>
>>>>>>>> ###file###
>>>>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>>>>> XX
>>>>>>>> PA   AB000170.1
>>>>>>>> XX
>>>>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>>>>> XX
>>>>>>>> OS   Sus scrofa (pig)
>>>>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata;
>>> Vertebrata; Euteleostomi;
>>>>>>>> Mammalia;
>>>>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina;
>>> Suidae; Sus.
>>>>>>>> OX   NCBI_TaxID=9823;
>>>>>>>> .........
>>>>>>>>
>>>>>>>> I want the accession number in the line that starts
>>> with PA, AB000170
>>>>>>>> in this example.
>>>>>>>>
>>>>>>>> Can anybody kindly help, tell me which module and
>>> method I should use?
>>>>>>>> I tried various things like $seq_obj -> primary_id, display_id,
>>>>>>>> get_secondary_id, etc.. they did not work...
>>>>>>>>
>>>>>>>> Thanks a lot!
>>>>>>>>
>>>>>>>> Wen
>>>>>>>> _______________________________________________
>>> _______________________________________________
>>> Bioperl-l mailing list
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Sun Jun 15 01:17:10 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Sun, 15 Jun 2008 00:17:10 -0500
Subject: [Bioperl-l] EMBL format field
In-Reply-To: <AA4401CC-5EF2-4120-886C-82E8E57D6792@uiuc.edu>
References: <3A0B2CCF-6EA7-485D-ABC9-6A0F83B3F4B0@gmail.com>
	<03C512635899144083CADB0EE222018901C8072B@alpaca.lan.ablynx.com>
	<C7E355F0-CE8A-4BDA-894A-BD60600AEC6C@gmx.net>
	<34198fe40806100443g6c18f47dj881d68c0bf14ba8f@mail.gmail.com>
	<46E681F5-CB56-4ADA-BEB9-00083CFA78F9@bioperl.org>
	<34198fe40806120206i31cee6f5xfe6f57b3b9e2a84b@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B404F2B374@EX02.asurite.ad.asu.edu>
	<34198fe40806140639g1c2edc3aqe8fce6d03a102642@mail.gmail.com>
	<AA4401CC-5EF2-4120-886C-82E8E57D6792@uiuc.edu>
Message-ID: <1898E656-CC34-4BBE-8026-7266A6CC036D@uiuc.edu>

Um, should have attached a link there:

http://www.bioperl.org/wiki/FAQ#I_am_using_Ensembl.__How_do_I_do_XYZ.3F

chris

On Jun 14, 2008, at 9:25 PM, Chris Fields wrote:

> See this FAQ question, as well as the one following it.
>
> chris
>
> On Jun 14, 2008, at 8:39 AM, Zhi-Qiang Ye wrote:
>
>> Thank all of you.  I finally get the newest version of bioperl
>> installed and solved the problem.
>>
>> I noticed that ensembl API still uses bioperl-1.2.3, which
>> misleaded me that bioperl-1.4 is very up-to-date ...
>>
>>
>> Regards,
>> Zhi-Qiang
>>
>>
>> 2008/6/12 Kevin Brown <Kevin.M.Brown at asu.edu>:
>>> See the following links for where to get a more current version.   
>>> 1.4 is
>>> years old and lots of parts are non-functional due to website and  
>>> file
>>> format changes.
>>>
>>> http://www.bioperl.org/wiki/Installing_BioPerl
>>>
>>> http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>>>> Zhi-Qiang Ye
>>>> Sent: Thursday, June 12, 2008 2:07 AM
>>>> To: Jason Stajich
>>>> Cc: bioperl list
>>>> Subject: Re: [Bioperl-l] EMBL format field
>>>>
>>>> Hi, Jason
>>>>
>>>>  I used exactly your code, and the result is still 'unknown id'.
>>>> Where can I get the version of bioperl?
>>>> I used ubuntu gutsy, the version in ubuntu's package
>>>> management system is 1.4-1.
>>>>
>>>>  I installed BioPerl 1.4 on another computer, IA64 with redhat
>>>> linux.  It has the same problem.
>>>> In the process of installation using CPAN, make test always  
>>>> failed. So
>>>> I used 'force install ....'.
>>>> I am not sure it is the reason.
>>>>
>>>> Thanks.
>>>> Zhi-Qiang Ye
>>>>
>>>> 2008/6/11 Jason Stajich <jason at bioperl.org>:
>>>>> What version of bioperl? It works for me using  this code I
>>>> get 'CB271253'
>>>>> printed out.
>>>>>
>>>>> #!/usr/bin/perl -w
>>>>> use strict;
>>>>> use Bio::SeqIO;
>>>>> my $in = Bio::SeqIO->new(-format => 'embl', -file => shift);
>>>>> while( my $seq = $in->next_seq ) {
>>>>> print $seq->id,"\n";
>>>>> }
>>>>>
>>>>> On Jun 10, 2008, at 4:43 AM, Zhi-Qiang Ye wrote:
>>>>>
>>>>>> That's weird. I also met this problem. I tried a
>>>> embl-format file like
>>>>>> this:
>>>>>>
>>>>>> ID   CB271253; SV 1; linear; mRNA; EST; INV; 591 BP.
>>>>>> XX
>>>>>> AC   CB271253;
>>>>>> XX
>>>>>> DT   24-FEB-2003 (Rel. 74, Created)
>>>>>> DT   24-FEB-2003 (Rel. 74, Last updated, Version 1)
>>>>>> XX
>>>>>> DE   taa17c02.x2 Hydra EST -II Hydra magnipapillata cDNA
>>>> 3' similar to
>>>>>> DE   SW:OPSD_RABIT P49912 RHODOPSIN. ;, mRNA sequence.
>>>>>>
>>>>>> from:
>>>> http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&id=CB271253&style=raw
>>>>>>
>>>>>> the $seq object's   ->id, ->display_id  are "unkown id" ...
>>>>>>
>>>>>>
>>>>>>
>>>>>> ZQ Ye
>>>>>>
>>>>>> 2008/6/9 Hilmar Lapp <hlapp at gmx.net>:
>>>>>>>
>>>>>>> If this is the case with the latest version of BioPerl it
>>>> should be filed
>>>>>>> as
>>>>>>> a bug report for the embl parser. The ID ought to be reported in
>>>>>>> $seq->get_secondary_accessions() (which returns an
>>>> array). If it doesn't,
>>>>>>> it
>>>>>>> sounds like a bug to me.
>>>>>>>
>>>>>>>   -hilmar
>>>>>>>
>>>>>>> On Jun 9, 2008, at 4:47 AM, Marc Logghe wrote:
>>>>>>>>
>>>>>>>> Hi Wen,
>>>>>>>> A dump of that sequence object (Data::Dumper is your
>>>> friend !) reveals
>>>>>>>> that the PA EMBL field is not saved into the object.
>>>> However, you will
>>>>>>>> find the string 'AB000170.1' in the embedded CDS
>>>> feature, more precisely
>>>>>>>> the seqid of the location object. I don't know whether
>>>> that is always
>>>>>>>> the case, but it is in your particular example.
>>>>>>>> So, to get your hands on that value you have to do:
>>>>>>>>
>>>>>>>> my ($cds) = grep {$_->primary_tag eq 'CDS'}
>>>> $seq->get_SeqFeatures;
>>>>>>>> my $parent_id = $cds->location->seq_id;
>>>>>>>>
>>>>>>>> HTH,
>>>>>>>> Marc
>>>>>>>>
>>>>>>>> Marc Logghe
>>>>>>>> Senior Bioinformatician
>>>>>>>> Ablynx nv
>>>>>>>>>
>>>>>>>>> -----Original Message-----
>>>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>>>>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>>>>>>>>> Sent: Monday, June 09, 2008 5:28 AM
>>>>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>>>>> Subject: [Bioperl-l] EMBL format field
>>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> I have a EMBL file that I want to extract one of the line
>>>>>>>>>
>>>>>>>>> ###file###
>>>>>>>>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>>>>>>>>> XX
>>>>>>>>> PA   AB000170.1
>>>>>>>>> XX
>>>>>>>>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>>>>>>>>> XX
>>>>>>>>> OS   Sus scrofa (pig)
>>>>>>>>> OC   Eukaryota; Metazoa; Chordata; Craniata;
>>>> Vertebrata; Euteleostomi;
>>>>>>>>> Mammalia;
>>>>>>>>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina;
>>>> Suidae; Sus.
>>>>>>>>> OX   NCBI_TaxID=9823;
>>>>>>>>> .........
>>>>>>>>>
>>>>>>>>> I want the accession number in the line that starts
>>>> with PA, AB000170
>>>>>>>>> in this example.
>>>>>>>>>
>>>>>>>>> Can anybody kindly help, tell me which module and
>>>> method I should use?
>>>>>>>>> I tried various things like $seq_obj -> primary_id,  
>>>>>>>>> display_id,
>>>>>>>>> get_secondary_id, etc.. they did not work...
>>>>>>>>>
>>>>>>>>> Thanks a lot!
>>>>>>>>>
>>>>>>>>> Wen
>>>>>>>>> _______________________________________________
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From nsh9351 at rit.edu  Mon Jun 16 10:17:41 2008
From: nsh9351 at rit.edu (Nathan Haseley (RIT Student))
Date: Mon, 16 Jun 2008 10:17:41 -0400
Subject: [Bioperl-l] Limiting organism scope on bioperl BLAST searches
Message-ID: <7D75703BC8E1C149BF78A1E79AAAB169035BC511@svits28.main.ad.rit.edu>

Hello!
   I am trying to write a perl script comparing proteins from a group of mammals.  I am only interested in 5 organisms.  Is there a way to limit my bioperl BLAST search to specific genome databases?  Do you have any other suggestions for the most effective way to achieve this filtering?  Thanks!
Nathan



From akarger at CGR.Harvard.edu  Mon Jun 16 12:18:30 2008
From: akarger at CGR.Harvard.edu (Amir Karger)
Date: Mon, 16 Jun 2008 12:18:30 -0400
Subject: [Bioperl-l] Installing bioperl with Strawberry
Message-ID: <72AF30DC2881964CB911FD08E57157E7012188EE@lsdiv-msxbe-001.nucleus.harvard.edu>

I got a new Windows box and was going to install Bioperl.

Questions: has anyone had experience, positive or negative, with using
Strawberry Perl + Bioperl? I was thinking of going the Strawberry route
because they claim it acts more like UNIX Perl, which would be nice. But
if SP doesn't work with Bioperl, or is just generally horrible, I don't
want to install it.

SP claims it supports PPM, but I don't know whether I should use that or
the CPAN bioperl install.

Any thoughts?

-Amir Karger


From Kevin.M.Brown at asu.edu  Mon Jun 16 12:47:43 2008
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Mon, 16 Jun 2008 09:47:43 -0700
Subject: [Bioperl-l] Installing bioperl with Strawberry
In-Reply-To: <72AF30DC2881964CB911FD08E57157E7012188EE@lsdiv-msxbe-001.nucleus.harvard.edu>
References: <72AF30DC2881964CB911FD08E57157E7012188EE@lsdiv-msxbe-001.nucleus.harvard.edu>
Message-ID: <1A4207F8295607498283FE9E93B775B404FCCAB4@EX02.asurite.ad.asu.edu>

No experiences with SP, but if it supports PPM, then I would use those
rather than cpan for getting BioPerl installed on your system.

http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Amir Karger
> Sent: Monday, June 16, 2008 9:19 AM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] Installing bioperl with Strawberry
> 
> I got a new Windows box and was going to install Bioperl.
> 
> Questions: has anyone had experience, positive or negative, with using
> Strawberry Perl + Bioperl? I was thinking of going the 
> Strawberry route
> because they claim it acts more like UNIX Perl, which would 
> be nice. But
> if SP doesn't work with Bioperl, or is just generally 
> horrible, I don't
> want to install it.
> 
> SP claims it supports PPM, but I don't know whether I should 
> use that or
> the CPAN bioperl install.
> 
> Any thoughts?
> 
> -Amir Karger
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From David.Messina at sbc.su.se  Mon Jun 16 13:35:53 2008
From: David.Messina at sbc.su.se (Dave Messina)
Date: Mon, 16 Jun 2008 19:35:53 +0200
Subject: [Bioperl-l] Limiting organism scope on bioperl BLAST searches
In-Reply-To: <7D75703BC8E1C149BF78A1E79AAAB169035BC511@svits28.main.ad.rit.edu>
References: <AcjPu7zNJ9ADE66DSwup7L/Ivlp5Hg==>
	<7D75703BC8E1C149BF78A1E79AAAB169035BC511@svits28.main.ad.rit.edu>
Message-ID: <628aabb70806161035i57995291w935b3ae3904bdecc@mail.gmail.com>

Hi Nathan,

It's not clear from your script whether you are doing your BLAST search
locally with the database on your own computer or whether you're doing a
netblast (blastcl3) where the database is on the NCBI server.

If the latter, you can use the -u option to limit your search to the results
of an Entrez query. See the blastcl3 manual on NCBI's website for details; I
think there's even an example for this very purpose.

If the former, you could create a database with sequences from the 5
mammalian species. There are lots of ways to do that, but I usually do an
Entrez search crafted to my purpose and download the FASTA sequences. Or you
could do the same thing at Ensembl, either via the website or via the Perl
API.


Dave

From lamq at usal.es  Wed Jun 18 07:50:16 2008
From: lamq at usal.es (Luis A. M. Quintales)
Date: Wed, 18 Jun 2008 13:50:16 +0200
Subject: [Bioperl-l] bp_genbank2gff3 and method "binomial" problem
Message-ID: <4858F678.4070504@usal.es>

Hello!

I want to convert a set of EMBL files (genome of  S.pombe  version Sep 
04) to GFF files.

First I try
bp_genbank2gff3.pl --format EMBL chromosome1.contig.embl
and I obtain
Can't call method "binomial" on an undefined value at bp_genbank2gff3.pl 
line 674, <FH> line 103671

So, I convert the embl to genbank file using a perl program with 
Bio::SeqIO methods. This works. Then, I retry
bp_genbank2gff3.pl  chromosome1.gb
and ... I obtain again the same error
Can't call method "binomial" on an undefined value at bp_genbank2gff3.pl 
line 674, <FH> line 103496

Some help?
Thank you.

-- 
==================================================
 Luis Antonio Miguel Quintales
 Departamento de Inform?tica y Autom?tica
 Facultad de Ciencias
 Universidad de Salamanca
 Plaza de la Merced s/n
 37008-SALAMANCA
 SPAIN
==================================================
 Tel.: +34-923-294400(ext.1513)
 Fax.: +34-923-294584
 E-mail: lamq at usal.es
==================================================


From David.Messina at sbc.su.se  Wed Jun 18 09:20:10 2008
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 18 Jun 2008 15:20:10 +0200
Subject: [Bioperl-l] bp_genbank2gff3 and method "binomial" problem
In-Reply-To: <4858F678.4070504@usal.es>
References: <4858F678.4070504@usal.es>
Message-ID: <628aabb70806180620j6e8c6614sde2661b5cd0aee00@mail.gmail.com>

Hi Luis,

This is the line that you're dying on:
my ($species)= $seq->annotation->get_Annotations("species")
||      ( $seq->can('species') ?
   $seq->species()->binomial() : undef );


So it looks like there might be a problem with the species field in one of
the Genbank entries.

Could you extract from your input file the record that it is choking on? We
need it to reproduce the error.

And then, to help us keep track of the problem, could you submit a copy of
that record and your description of what happened to our bug tracker?

http://bugzilla.open-bio.org/


Please be sure to indicate which version of BioPerl you are using. Line 674
in the current version of genbank2gff3.pl is a comment (the above is line
672), so I suspect you may be using an outdated version. The problem may
already have been fixed in the current version.

More instructions here if needed:
http://www.bioperl.org/wiki/Bugs


Thanks,
Dave

From jajams at utu.fi  Wed Jun 18 18:52:47 2008
From: jajams at utu.fi (=?ISO-8859-15?Q?Joonas_J=E4msen?=)
Date: Thu, 19 Jun 2008 01:52:47 +0300
Subject: [Bioperl-l] hmmpfam
Message-ID: <485991BF.90307@utu.fi>

How to parse hmmpfam output to get gi/sequence of specified domain, 
score, E-value?

From heikki at sanbi.ac.za  Thu Jun 19 06:08:32 2008
From: heikki at sanbi.ac.za (Heikki Lehvaslaiho)
Date: Thu, 19 Jun 2008 12:08:32 +0200
Subject: [Bioperl-l] hmmpfam
In-Reply-To: <485991BF.90307@utu.fi>
References: <485991BF.90307@utu.fi>
Message-ID: <200806191208.33177.heikki@sanbi.ac.za>

Joonas,

I am not familiar with hmmpfam, but is is part of the HMMERtoolkit, so it 
should be possible to use Bio::SearchIO modules for parsing the output. In 
addition, it is possible to run HMMER programs directly from BioPerl (the 
bioperl-run repositoty is needed):

See:

http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bio/Tools/Run/Hmmer.html
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SearchIO/hmmer.html

for code examples, and

SearchIO HOWTO
http://bio.perl.org/wiki/HOWTO%3ASearchIO

for an introduction to Bio::SearchIO.

    -Heikki

On Thursday 19 June 2008 00:52:47 Joonas J?msen wrote:
> How to parse hmmpfam output to get gi/sequence of specified domain,
> score, E-value?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________


From bix at sendu.me.uk  Thu Jun 19 06:44:43 2008
From: bix at sendu.me.uk (Sendu Bala)
Date: Thu, 19 Jun 2008 11:44:43 +0100
Subject: [Bioperl-l] hmmpfam
In-Reply-To: <200806191208.33177.heikki@sanbi.ac.za>
References: <485991BF.90307@utu.fi> <200806191208.33177.heikki@sanbi.ac.za>
Message-ID: <485A389B.4000700@sendu.me.uk>

Heikki Lehvaslaiho wrote:
> Joonas,
> 
> I am not familiar with hmmpfam, but is is part of the HMMERtoolkit, so it 
> should be possible to use Bio::SearchIO modules for parsing the output. In 
> addition, it is possible to run HMMER programs directly from BioPerl (the 
> bioperl-run repositoty is needed):
> 
> See:
> 
> http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bio/Tools/Run/Hmmer.html
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SearchIO/hmmer.html

You may also prefer hmmer_pull:
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SearchIO/hmmer_pull.html
Which is faster and might behave more like you expect.

From govind.chandra at bbsrc.ac.uk  Thu Jun 19 09:42:23 2008
From: govind.chandra at bbsrc.ac.uk (Govind Chandra)
Date: Thu, 19 Jun 2008 14:42:23 +0100
Subject: [Bioperl-l] Bio::Ontology help solicited
In-Reply-To: <mailman.2779.1213637762.2759.bioperl-l@lists.open-bio.org>
References: <mailman.2779.1213637762.2759.bioperl-l@lists.open-bio.org>
Message-ID: <1213882943.7713.43.camel@jic51958.jic.bbsrc.ac.uk>

Hi,

In the code snippet below it seems I get the Bio::Ontology::Ontology
object $ontology but $ontology->find_terms is failing. It will help
greatly if someone points out what is wrong with this code and suggest a
correction. That the obo file is being read is obvious from the time it
takes from invocation to output.

I wrote another version of this script which read the "go" format and it
works fine. I cannot use the go format because it is deprecated and not
frequently updated. Even if I am willing to use the go format, the
process.ontology file (from geneontology.org) has an error in it which
causes Bio::OntologyIO->next_ontology() to fail. It will be best if I
could make the obo format work for me.

Cheers

Govind

### code begins ###

use strict;
use Bio::OntologyIO;

my $file='gene_ontology.1_2.obo';
my $parser = Bio::OntologyIO->new(
  -format => "obo",
  -file => $file
  );
my $ontology = $parser->next_ontology();
print(ref($ontology), "\n");
my ($term)=$ontology->find_terms(-name => "GO:0000072");
print($term->definition(), "\n");
print("$term\n");
print(ref($term),"\n");

### code ends ###

### output begins ###
Bio::Ontology::Ontology


Can't call method "definition" on an undefined value at
ontology_check.pl line 26, <GEN0> line 288014.
### output ends ###


Other Possibly relevant information:
------------------------------------

Perl is: v5.8.8 built for x86_64-linux-thread-multi

BioPerl is: bioperl-1.5.2_102 

Output of uname -a: Linux n61347 2.6.18-92.1.1.el5 #1 SMP Thu May 22
09:01:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux

Contents of /etc/redhat-release: Red Hat Enterprise Linux Server release
5.2 (Tikanga)




From byuhobbes85 at yahoo.com  Thu Jun 19 09:43:32 2008
From: byuhobbes85 at yahoo.com (byuhobbes)
Date: Thu, 19 Jun 2008 06:43:32 -0700 (PDT)
Subject: [Bioperl-l]  StandAloneBlast
Message-ID: <18009126.post@talk.nabble.com>


I'm running blastall with StandAloneBlast for the first time.  There is quite
a bit of documentation about how to run the blast, and how to get your blast
report object, but I am having trouble finding documentation on what values
you can retrieve from the report object and how you do so.

Any tips?

Thanks.

-----
--------------------
</byuhobbes>
-- 
View this message in context: http://www.nabble.com/StandAloneBlast-tp18009126p18009126.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From hlapp at gmx.net  Thu Jun 19 10:07:39 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu, 19 Jun 2008 10:07:39 -0400
Subject: [Bioperl-l] Bio::Ontology help solicited
In-Reply-To: <1213882943.7713.43.camel@jic51958.jic.bbsrc.ac.uk>
References: <mailman.2779.1213637762.2759.bioperl-l@lists.open-bio.org>
	<1213882943.7713.43.camel@jic51958.jic.bbsrc.ac.uk>
Message-ID: <39E954A9-72BB-466B-AEA3-1003B77CD49D@gmx.net>

I think you want to use -identifier rather than -name if you are  
querying by an identifier.

Let us know if that doesn't work either.

	-hilmar

On Jun 19, 2008, at 9:42 AM, Govind Chandra wrote:

> Hi,
>
> In the code snippet below it seems I get the Bio::Ontology::Ontology
> object $ontology but $ontology->find_terms is failing. It will help
> greatly if someone points out what is wrong with this code and  
> suggest a
> correction. That the obo file is being read is obvious from the time  
> it
> takes from invocation to output.
>
> I wrote another version of this script which read the "go" format  
> and it
> works fine. I cannot use the go format because it is deprecated and  
> not
> frequently updated. Even if I am willing to use the go format, the
> process.ontology file (from geneontology.org) has an error in it which
> causes Bio::OntologyIO->next_ontology() to fail. It will be best if I
> could make the obo format work for me.
>
> Cheers
>
> Govind
>
> ### code begins ###
>
> use strict;
> use Bio::OntologyIO;
>
> my $file='gene_ontology.1_2.obo';
> my $parser = Bio::OntologyIO->new(
>  -format => "obo",
>  -file => $file
>  );
> my $ontology = $parser->next_ontology();
> print(ref($ontology), "\n");
> my ($term)=$ontology->find_terms(-name => "GO:0000072");
> print($term->definition(), "\n");
> print("$term\n");
> print(ref($term),"\n");
>
> ### code ends ###
>
> ### output begins ###
> Bio::Ontology::Ontology
>
>
> Can't call method "definition" on an undefined value at
> ontology_check.pl line 26, <GEN0> line 288014.
> ### output ends ###
>
>
> Other Possibly relevant information:
> ------------------------------------
>
> Perl is: v5.8.8 built for x86_64-linux-thread-multi
>
> BioPerl is: bioperl-1.5.2_102
>
> Output of uname -a: Linux n61347 2.6.18-92.1.1.el5 #1 SMP Thu May 22
> 09:01:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
>
> Contents of /etc/redhat-release: Red Hat Enterprise Linux Server  
> release
> 5.2 (Tikanga)
>
>
>
> _______________________________________________
> 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 gmx dot net :
===========================================================




From govind.chandra at bbsrc.ac.uk  Thu Jun 19 10:27:21 2008
From: govind.chandra at bbsrc.ac.uk (Govind Chandra)
Date: Thu, 19 Jun 2008 15:27:21 +0100
Subject: [Bioperl-l] Bio::Ontology help solicited
In-Reply-To: <39E954A9-72BB-466B-AEA3-1003B77CD49D@gmx.net>
References: <mailman.2779.1213637762.2759.bioperl-l@lists.open-bio.org>
	<1213882943.7713.43.camel@jic51958.jic.bbsrc.ac.uk>
	<39E954A9-72BB-466B-AEA3-1003B77CD49D@gmx.net>
Message-ID: <1213885641.7713.54.camel@jic51958.jic.bbsrc.ac.uk>

Hi Hilmar,

Thanks for the very quick response.

I changed the line below 

my ($term)=$ontology->find_terms(-name => "GO:0000072");

to 

my ($term)=$ontology->find_terms(-identifier => "GO:0000072");

but it does not make any difference. From perldoc I gathered that -name
and -identifier should do the same thing anyway.

Cheers

Govind



On Thu, 2008-06-19 at 10:07 -0400, Hilmar Lapp wrote:
> I think you want to use -identifier rather than -name if you are  
> querying by an identifier.
> 
> Let us know if that doesn't work either.
> 
> 	-hilmar
> 
> On Jun 19, 2008, at 9:42 AM, Govind Chandra wrote:
> 
> > Hi,
> >
> > In the code snippet below it seems I get the Bio::Ontology::Ontology
> > object $ontology but $ontology->find_terms is failing. It will help
> > greatly if someone points out what is wrong with this code and  
> > suggest a
> > correction. That the obo file is being read is obvious from the time  
> > it
> > takes from invocation to output.
> >
> > I wrote another version of this script which read the "go" format  
> > and it
> > works fine. I cannot use the go format because it is deprecated and  
> > not
> > frequently updated. Even if I am willing to use the go format, the
> > process.ontology file (from geneontology.org) has an error in it which
> > causes Bio::OntologyIO->next_ontology() to fail. It will be best if I
> > could make the obo format work for me.
> >
> > Cheers
> >
> > Govind
> >
> > ### code begins ###
> >
> > use strict;
> > use Bio::OntologyIO;
> >
> > my $file='gene_ontology.1_2.obo';
> > my $parser = Bio::OntologyIO->new(
> >  -format => "obo",
> >  -file => $file
> >  );
> > my $ontology = $parser->next_ontology();
> > print(ref($ontology), "\n");
> > my ($term)=$ontology->find_terms(-name => "GO:0000072");
> > print($term->definition(), "\n");
> > print("$term\n");
> > print(ref($term),"\n");
> >
> > ### code ends ###
> >
> > ### output begins ###
> > Bio::Ontology::Ontology
> >
> >
> > Can't call method "definition" on an undefined value at
> > ontology_check.pl line 26, <GEN0> line 288014.
> > ### output ends ###
> >
> >
> > Other Possibly relevant information:
> > ------------------------------------
> >
> > Perl is: v5.8.8 built for x86_64-linux-thread-multi
> >
> > BioPerl is: bioperl-1.5.2_102
> >
> > Output of uname -a: Linux n61347 2.6.18-92.1.1.el5 #1 SMP Thu May 22
> > 09:01:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
> >
> > Contents of /etc/redhat-release: Red Hat Enterprise Linux Server  
> > release
> > 5.2 (Tikanga)
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From cjfields at uiuc.edu  Thu Jun 19 10:46:04 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 19 Jun 2008 09:46:04 -0500
Subject: [Bioperl-l] StandAloneBlast
In-Reply-To: <18009126.post@talk.nabble.com>
References: <18009126.post@talk.nabble.com>
Message-ID: <DA2E20B6-11C1-4951-9772-9AE766632022@uiuc.edu>

See the SearchIO HOWTO:

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

chris

On Jun 19, 2008, at 8:43 AM, byuhobbes wrote:

>
> I'm running blastall with StandAloneBlast for the first time.  There  
> is quite
> a bit of documentation about how to run the blast, and how to get  
> your blast
> report object, but I am having trouble finding documentation on what  
> values
> you can retrieve from the report object and how you do so.
>
> Any tips?
>
> Thanks.
>
> -----
> --------------------
> </byuhobbes>
> -- 
> View this message in context: http://www.nabble.com/StandAloneBlast-tp18009126p18009126.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

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From hlapp at gmx.net  Thu Jun 19 10:50:57 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu, 19 Jun 2008 10:50:57 -0400
Subject: [Bioperl-l] Bio::Ontology help solicited
In-Reply-To: <1213885641.7713.54.camel@jic51958.jic.bbsrc.ac.uk>
References: <mailman.2779.1213637762.2759.bioperl-l@lists.open-bio.org>
	<1213882943.7713.43.camel@jic51958.jic.bbsrc.ac.uk>
	<39E954A9-72BB-466B-AEA3-1003B77CD49D@gmx.net>
	<1213885641.7713.54.camel@jic51958.jic.bbsrc.ac.uk>
Message-ID: <5C819020-9094-416C-9B3B-DD085AB01602@gmx.net>


On Jun 19, 2008, at 10:27 AM, Govind Chandra wrote:

> I changed the line below
>
> my ($term)=$ontology->find_terms(-name => "GO:0000072");
>
> to
>
> my ($term)=$ontology->find_terms(-identifier => "GO:0000072");

That's odd. Did you convince yourself that a term with this identifier  
is indeed in the ontology? If you iterate over all terms (using e.g.  
$ontology->get_all_terms()), is there a term with this identifier?

E.g.: print join("\n", map { $_->identifier; }
                            (grep { $_->identifier =~ /0000072/; }
                                  $ontology->get_all_terms())),"\n";

Does this print anything?

> but it does not make any difference. From perldoc I gathered that - 
> name
> and -identifier should do the same thing anyway.


I'm not sure where you gathered that from. Could you point me to the  
location that says that?

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================




From bix at sendu.me.uk  Thu Jun 19 10:32:05 2008
From: bix at sendu.me.uk (Sendu Bala)
Date: Thu, 19 Jun 2008 15:32:05 +0100
Subject: [Bioperl-l] StandAloneBlast
In-Reply-To: <18009126.post@talk.nabble.com>
References: <18009126.post@talk.nabble.com>
Message-ID: <485A6DE5.4060503@sendu.me.uk>

byuhobbes wrote:
> I'm running blastall with StandAloneBlast for the first time.  There is quite
> a bit of documentation about how to run the blast, and how to get your blast
> report object, but I am having trouble finding documentation on what values
> you can retrieve from the report object and how you do so.

Look at the documentation for the objects you retrieve.

http://docs.bioperl.org/bioperl-live/Bio/SearchIO/blast.html

$searchio->next_result returns a Bio::Search::Result::ResultI, actually 
a Bio::Search::Result::BlastResult:

http://docs.bioperl.org/bioperl-live/Bio/Search/Result/BlastResult.html
which isa:
http://docs.bioperl.org/bioperl-live/Bio/Search/Result/GenericResult.html

These return $hit = $result->next_hit() Bio::Search::Hit::HitI objects:

http://docs.bioperl.org/bioperl-live/Bio/Search/Hit/BlastHit.html
http://docs.bioperl.org/bioperl-live/Bio/Search/Hit/GenericHit.html

which in turn will give you HSP objects:

http://docs.bioperl.org/bioperl-live/Bio/Search/HSP/BlastHSP.html
http://docs.bioperl.org/bioperl-live/Bio/Search/HSP/GenericHSP.html



From michael.watson at bbsrc.ac.uk  Thu Jun 19 10:51:41 2008
From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C))
Date: Thu, 19 Jun 2008 15:51:41 +0100
Subject: [Bioperl-l] Working with SeqWithQuality
Message-ID: <8975119BCD0AC5419D61A9CF1A923E9506D873FE@iahce2ksrv1.iah.bbsrc.ac.uk>

Hi

I have fasta files and separate quality fasta files.  I understand all
about constructing a SeqWithQuality object, that's the easy bit, but are
there no functions for actually manipulating the sequence based on the
quality values?  For example, trimming the ends where a moving window
average quality does not go above a certain value, or masking areas with
low quality?  

Thanks
Mick

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From michael.watson at bbsrc.ac.uk  Thu Jun 19 11:28:24 2008
From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C))
Date: Thu, 19 Jun 2008 16:28:24 +0100
Subject: [Bioperl-l] Working with SeqWithQuality
In-Reply-To: <485A7AAD.1010604@cam.ac.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9506D873FE@iahce2ksrv1.iah.bbsrc.ac.uk>
	<485A7AAD.1010604@cam.ac.uk>
Message-ID: <8975119BCD0AC5419D61A9CF1A923E9506D873FF@iahce2ksrv1.iah.bbsrc.ac.uk>

Hi Roy

That's exactly what I want, thanks, it just wasn't where I was expecting
it

Mick 

-----Original Message-----
From: Roy Chaudhuri [mailto:rrc22 at cam.ac.uk] 
Sent: 19 June 2008 16:27
To: michael watson (IAH-C)
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Working with SeqWithQuality

Hi Mick,

I think you want Bio::Tools::Alignment::Trim. There are lots of caveats 
in the POD but as I recall it works fine.

Here is a small script I wrote to return contigs over a certain length 
and a certain minimum quality (not exactly what you asked for but I'm 
sure it could be adapted).

#!/usr/bin/perl
use warnings;
use strict;
use Bio::SeqIO;
use Bio::Tools::Alignment::Trim;
use Getopt::Long;
die "Usage: trimqual fasta_file qual_file -qual 20 -window 10 -min 
500\n" unless $ARGV[1];
my $phred=20;
my $window=10;
my $min=500;
GetOptions ('phred|qual=i'=>\$phred,
             'window=i'=>\$window,
             'minimum=i'=>\$min) or die "Unrecognised option\n";
my $fasta=Bio::SeqIO->newFh(-file=>$ARGV[0], -format=>'fasta');
my $quality=Bio::SeqIO->newFh(-file=>$ARGV[1], -format=>'qual');
my $out=Bio::SeqIO->newFh(-format=>'fasta');
my $count=0;
while (<$fasta>) {
     my $seq=$_;
     my $qual=<$quality>;
     my $trim=Bio::Tools::Alignment::Trim->new(-phreds=>$phred,
                                               -windowsize=>$window);
     my ($start,$end) = @{$trim->trim_singlet($seq->seq,
                                              join(' ',@{$qual->qual}),
 
$seq->display_id,'singlet')};
     next if $end==0;
     my $trimmed_sequence=substr($seq->seq, $start, $end+1-$start);
     my $length=length $trimmed_sequence;
     print STDERR $seq->display_id, ": $start-$end [$length bp]";
     if ($length<$min) {
         print STDERR " - skipped\n";
         next;
     } else {
         print STDERR "\n";
     }
     my $trimseq=Bio::Seq->new(-seq=>$trimmed_sequence,
                               -id=>$seq->display_id);
     print $out $trimseq;
     $count++;
}
print STDERR "\nFinished. $count contigs larger than $min bp. were 
found.\n";


Cheers,
Roy.
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.


michael watson (IAH-C) wrote:
> Hi
> 
> I have fasta files and separate quality fasta files.  I understand all
> about constructing a SeqWithQuality object, that's the easy bit, but
are
> there no functions for actually manipulating the sequence based on the
> quality values?  For example, trimming the ends where a moving window
> average quality does not go above a certain value, or masking areas
with
> low quality?  
> 
> Thanks
> Mick
> 
> The information contained in this message may be confidential or
legally
> privileged and is intended solely for the addressee. If you have
> received this message in error please delete it & notify the
originator
> immediately.
> Unauthorised use, disclosure, copying or alteration of this message is
> forbidden & may be unlawful. 
> The contents of this e-mail are the views of the sender and do not
> necessarily represent the views of the Institute. 
> This email and associated attachments has been checked locally for
> viruses but we can accept no responsibility once it has left our
> systems.
> Communications on Institute computers are monitored to secure the
> effective operation of the systems and for other lawful purposes. 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From MEC at stowers-institute.org  Thu Jun 19 11:37:20 2008
From: MEC at stowers-institute.org (Cook, Malcolm)
Date: Thu, 19 Jun 2008 10:37:20 -0500
Subject: [Bioperl-l] Working with SeqWithQuality
In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9506D873FE@iahce2ksrv1.iah.bbsrc.ac.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9506D873FE@iahce2ksrv1.iah.bbsrc.ac.uk>
Message-ID: <BD62CBAC4395B94096109020651BE2EC129EC9C0B5@exchmb-02.stowers-institute.org>

Michael,

If you happen to be working abi chromatogram files you can use perl's Bio::Trace::ABIF (c.f. CPAN) to do this directly easily without need for SeqWIthQUality objects.

???

Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of michael watson (IAH-C)
Sent: Thursday, June 19, 2008 9:52 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Working with SeqWithQuality

Hi

I have fasta files and separate quality fasta files.  I understand all about constructing a SeqWithQuality object, that's the easy bit, but are there no functions for actually manipulating the sequence based on the quality values?  For example, trimming the ends where a moving window average quality does not go above a certain value, or masking areas with low quality?

Thanks
Mick

The information contained in this message may be confidential or legally privileged and is intended solely for the addressee. If you have received this message in error please delete it & notify the originator immediately.
Unauthorised use, disclosure, copying or alteration of this message is forbidden & may be unlawful.
The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Institute.
This email and associated attachments has been checked locally for viruses but we can accept no responsibility once it has left our systems.
Communications on Institute computers are monitored to secure the effective operation of the systems and for other lawful purposes.

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


From govind.chandra at bbsrc.ac.uk  Thu Jun 19 11:54:20 2008
From: govind.chandra at bbsrc.ac.uk (Govind Chandra)
Date: Thu, 19 Jun 2008 16:54:20 +0100
Subject: [Bioperl-l] Bio::Ontology help solicited
In-Reply-To: <5C819020-9094-416C-9B3B-DD085AB01602@gmx.net>
References: <mailman.2779.1213637762.2759.bioperl-l@lists.open-bio.org>
	<1213882943.7713.43.camel@jic51958.jic.bbsrc.ac.uk>
	<39E954A9-72BB-466B-AEA3-1003B77CD49D@gmx.net>
	<1213885641.7713.54.camel@jic51958.jic.bbsrc.ac.uk>
	<5C819020-9094-416C-9B3B-DD085AB01602@gmx.net>
Message-ID: <1213890860.7713.87.camel@jic51958.jic.bbsrc.ac.uk>

Hi Hilmar,

Below is an extract from perldoc Bio::Ontology::Ontology from which I
_wrongly_ concluded that -identifier and -name do the same thing.



       find_terms

        Title   : find_terms
        Usage   : ($term) = $oe->find_terms(-identifier => "SO:0000263");
        Function: Find term instances matching queries for their attributes.

                  An implementation may not support querying for arbitrary
                  attributes, but can generally be expected to accept
                  -identifier and -name as queries. If both are provided,
                  they are implicitly intersected.

        Example :
        Returns : an array of zero or more Bio::Ontology::TermI objects
        Args    : Named parameters. The following parameters should be recognized
                  by any implementations:

                     -identifier    query by the given identifier
                     -name          query by the given name



I had been messing with this script for a few hours before posting for
help and had tried various combinations of -identifier and -name. But
neither -identifier => "GO:0000072" nor -name => "M phase specific
microtubule process" work. I know that the GOid exists because I can
find it in the obo file. There is something more fundamentally wrong in
my script than just the syntax. Like you suggested, below, I
get_all_terms() but the list @allterms is empty.

### code begins ###
use strict;
use Bio::OntologyIO;

my $file='gene_ontology.1_2.obo';
my $parser = Bio::OntologyIO->new(
  -format => "obo",
  -file => $file
  );
my $ontology = $parser->next_ontology();
print(ref($ontology), "\n");
my @allterms = $ontology->get_all_terms();
print(scalar(@allterms), "\n");
my $limiter;
foreach my $term (@allterms) {
print($term->name(),"\n");
print($term->definition(),"\n");
if($limiter++ > 30) {last;}
}
exit;
### code ends ###

### output begins ###
Bio::Ontology::Ontology
0
### output ends ###

Given that the script works with the "go" format files (except
process.ontology in which case it complains and exits) I suspect the obo
file but am surprised that Bio::OntologyIO->next_ontology() does not
complain. Will it be asking for too much to request you to get the obo
file I am trying to parse from

ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology.1_2.obo

and see if it works for you?

Thanks

Govind





On Thu, 2008-06-19 at 10:50 -0400, Hilmar Lapp wrote:
> On Jun 19, 2008, at 10:27 AM, Govind Chandra wrote:
> 
> > I changed the line below
> >
> > my ($term)=$ontology->find_terms(-name => "GO:0000072");
> >
> > to
> >
> > my ($term)=$ontology->find_terms(-identifier => "GO:0000072");
> 
> That's odd. Did you convince yourself that a term with this identifier  
> is indeed in the ontology? If you iterate over all terms (using e.g.  
> $ontology->get_all_terms()), is there a term with this identifier?
> 
> E.g.: print join("\n", map { $_->identifier; }
>                             (grep { $_->identifier =~ /0000072/; }
>                                   $ontology->get_all_terms())),"\n";
> 
> Does this print anything?
> 
> > but it does not make any difference. From perldoc I gathered that - 
> > name
> > and -identifier should do the same thing anyway.
> 
> 
> I'm not sure where you gathered that from. Could you point me to the  
> location that says that?
> 
> 	-hilmar


From roy.chaudhuri at gmail.com  Thu Jun 19 11:44:37 2008
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Thu, 19 Jun 2008 16:44:37 +0100
Subject: [Bioperl-l] Working with SeqWithQuality
Message-ID: <485A7EE5.3090805@gmail.com>

Hi Mick,

I think you want Bio::Tools::Alignment::Trim. There are lots of caveats
in the POD but as I recall it works fine.

Here is a small script I wrote to return contigs over a certain length
and a certain minimum quality (not exactly what you asked for but I'm
sure it could be adapted).

#!/usr/bin/perl
use warnings;
use strict;
use Bio::SeqIO;
use Bio::Tools::Alignment::Trim;
use Getopt::Long;
die "Usage: trimqual fasta_file qual_file -qual 20 -window 10 -min
500\n" unless $ARGV[1];
my $phred=20;
my $window=10;
my $min=500;
GetOptions ('phred|qual=i'=>\$phred,
              'window=i'=>\$window,
              'minimum=i'=>\$min) or die "Unrecognised option\n";
my $fasta=Bio::SeqIO->newFh(-file=>$ARGV[0], -format=>'fasta');
my $quality=Bio::SeqIO->newFh(-file=>$ARGV[1], -format=>'qual');
my $out=Bio::SeqIO->newFh(-format=>'fasta');
my $count=0;
while (<$fasta>) {
      my $seq=$_;
      my $qual=<$quality>;
      my $trim=Bio::Tools::Alignment::Trim->new(-phreds=>$phred,
                                                -windowsize=>$window);
      my ($start,$end) = @{$trim->trim_singlet($seq->seq,
                                               join(' ',@{$qual->qual}),
                                               $seq->display_id,'singlet')};
      next if $end==0;
      my $trimmed_sequence=substr($seq->seq, $start, $end+1-$start);
      my $length=length $trimmed_sequence;
      print STDERR $seq->display_id, ": $start-$end [$length bp]";
      if ($length<$min) {
          print STDERR " - skipped\n";
          next;
      } else {
          print STDERR "\n";
      }
      my $trimseq=Bio::Seq->new(-seq=>$trimmed_sequence,
                                -id=>$seq->display_id);
      print $out $trimseq;
      $count++;
}
print STDERR "\nFinished. $count contigs larger than $min bp. were
found.\n";


Cheers,
Roy.
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.


michael watson (IAH-C) wrote:
> Hi
> 
> I have fasta files and separate quality fasta files.  I understand all
> about constructing a SeqWithQuality object, that's the easy bit, but are
> there no functions for actually manipulating the sequence based on the
> quality values?  For example, trimming the ends where a moving window
> average quality does not go above a certain value, or masking areas with
> low quality?  
> 
> Thanks
> Mick
> 
> The information contained in this message may be confidential or legally
> privileged and is intended solely for the addressee. If you have
> received this message in error please delete it & notify the originator
> immediately.
> Unauthorised use, disclosure, copying or alteration of this message is
> forbidden & may be unlawful. 
> The contents of this e-mail are the views of the sender and do not
> necessarily represent the views of the Institute. 
> This email and associated attachments has been checked locally for
> viruses but we can accept no responsibility once it has left our
> systems.
> Communications on Institute computers are monitored to secure the
> effective operation of the systems and for other lawful purposes. 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hlapp at gmx.net  Thu Jun 19 12:06:26 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu, 19 Jun 2008 12:06:26 -0400
Subject: [Bioperl-l] Bio::Ontology help solicited
In-Reply-To: <1213890860.7713.87.camel@jic51958.jic.bbsrc.ac.uk>
References: <mailman.2779.1213637762.2759.bioperl-l@lists.open-bio.org>
	<1213882943.7713.43.camel@jic51958.jic.bbsrc.ac.uk>
	<39E954A9-72BB-466B-AEA3-1003B77CD49D@gmx.net>
	<1213885641.7713.54.camel@jic51958.jic.bbsrc.ac.uk>
	<5C819020-9094-416C-9B3B-DD085AB01602@gmx.net>
	<1213890860.7713.87.camel@jic51958.jic.bbsrc.ac.uk>
Message-ID: <72EB057E-9E60-46B4-9E99-2117271AF135@gmx.net>

Hi Govind,

this looks like a bug (though it could indeed be a problem with the  
obo file - that has happened in the past too). Would you mind posting  
it at bugzilla.open-bio.org?

	-hilmar

On Jun 19, 2008, at 11:54 AM, Govind Chandra wrote:

> Hi Hilmar,
>
> Below is an extract from perldoc Bio::Ontology::Ontology from which I
> _wrongly_ concluded that -identifier and -name do the same thing.
>
>
>
>       find_terms
>
>        Title   : find_terms
>        Usage   : ($term) = $oe->find_terms(-identifier => "SO: 
> 0000263");
>        Function: Find term instances matching queries for their  
> attributes.
>
>                  An implementation may not support querying for  
> arbitrary
>                  attributes, but can generally be expected to accept
>                  -identifier and -name as queries. If both are  
> provided,
>                  they are implicitly intersected.
>
>        Example :
>        Returns : an array of zero or more Bio::Ontology::TermI objects
>        Args    : Named parameters. The following parameters should  
> be recognized
>                  by any implementations:
>
>                     -identifier    query by the given identifier
>                     -name          query by the given name
>
>
>
> I had been messing with this script for a few hours before posting for
> help and had tried various combinations of -identifier and -name. But
> neither -identifier => "GO:0000072" nor -name => "M phase specific
> microtubule process" work. I know that the GOid exists because I can
> find it in the obo file. There is something more fundamentally wrong  
> in
> my script than just the syntax. Like you suggested, below, I
> get_all_terms() but the list @allterms is empty.
>
> ### code begins ###
> use strict;
> use Bio::OntologyIO;
>
> my $file='gene_ontology.1_2.obo';
> my $parser = Bio::OntologyIO->new(
>  -format => "obo",
>  -file => $file
>  );
> my $ontology = $parser->next_ontology();
> print(ref($ontology), "\n");
> my @allterms = $ontology->get_all_terms();
> print(scalar(@allterms), "\n");
> my $limiter;
> foreach my $term (@allterms) {
> print($term->name(),"\n");
> print($term->definition(),"\n");
> if($limiter++ > 30) {last;}
> }
> exit;
> ### code ends ###
>
> ### output begins ###
> Bio::Ontology::Ontology
> 0
> ### output ends ###
>
> Given that the script works with the "go" format files (except
> process.ontology in which case it complains and exits) I suspect the  
> obo
> file but am surprised that Bio::OntologyIO->next_ontology() does not
> complain. Will it be asking for too much to request you to get the obo
> file I am trying to parse from
>
> ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology.1_2.obo
>
> and see if it works for you?
>
> Thanks
>
> Govind
>
>
>
>
>
> On Thu, 2008-06-19 at 10:50 -0400, Hilmar Lapp wrote:
>> On Jun 19, 2008, at 10:27 AM, Govind Chandra wrote:
>>
>>> I changed the line below
>>>
>>> my ($term)=$ontology->find_terms(-name => "GO:0000072");
>>>
>>> to
>>>
>>> my ($term)=$ontology->find_terms(-identifier => "GO:0000072");
>>
>> That's odd. Did you convince yourself that a term with this  
>> identifier
>> is indeed in the ontology? If you iterate over all terms (using e.g.
>> $ontology->get_all_terms()), is there a term with this identifier?
>>
>> E.g.: print join("\n", map { $_->identifier; }
>>                            (grep { $_->identifier =~ /0000072/; }
>>                                  $ontology->get_all_terms())),"\n";
>>
>> Does this print anything?
>>
>>> but it does not make any difference. From perldoc I gathered that -
>>> name
>>> and -identifier should do the same thing anyway.
>>
>>
>> I'm not sure where you gathered that from. Could you point me to the
>> location that says that?
>>
>> 	-hilmar

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================




From johnsonm at gmail.com  Thu Jun 19 15:38:32 2008
From: johnsonm at gmail.com (Mark Johnson)
Date: Thu, 19 Jun 2008 14:38:32 -0500
Subject: [Bioperl-l] Bio::FeatureIO::gff
Message-ID: <ebf5eb170806191238i20010583x37eed2952db06c20@mail.gmail.com>

I recently had to do some gff3 generation/munging, so I took a look at
Bio::FeatureIO::gff.  I ran into a few issues:

- The _handle_feature method (called by next_feature) attaches Dbxref
attributes using 'Dbxref' as the key.  However, _write_feature_3 uses
'dblink' for the key when looking for Dbxref attributes.  I changed
_handle_feature to use 'dblink' also, but I'm not sure that's any more
(or less) correct than changing _write_feature_3 to use 'Dbxref'.
Anybody have any strong opinions one way or the other?

- Sendu made some changes to _write_feature_25 and _write_feature_3,
but missed a line in _write_feature_3.  I think line 890 should be

  my $phase  = defined($feature->phase) ? (ref($feature->phase) ?
$feature->phase->value : $feature->phase) : '.';

instead of

  my $phase  = $feature->phase->value;

to be consistent.

- Also in _write_feature_3, the Dbxref attributes are wrapped in a
call to uri_escape().  This generates a mangled gff3 that Apollo, at
least, does not like.  Also, looking at the gff3 spec, I do not
believe this is correct behaviour.  Quoting
http://www.sequenceontology.org/gff3.shtml:

The value of both Ontology_term and Dbxref is the ID of the cross
referenced object in the form "DBTAG:ID".  The DBTAG indicates which
database the referenced object can be found in, and ID indicates the
identifier of the object within that database.  IDs can contain
unescaped colons but DBTAGs cannot, so parsing code should split on
the first colon encountered in the attribute value.

So the key (DBTAG) should be escaped, but not the value (ID).  The
code presently escapes both:

  my $vstring = join ',', map {uri_escape($_->database .':'.
$_->primary_id)} @v;

which should probably be something like

  my $vstring = join ',', map {uri_escape($_->database) .':'.
$_->primary_id} @v;


So, what are the plans for Bio::FeatureIO?  I find it kind of handy,
so unless it's going to be scrapped in favor of something else, any
objection to lobbing a ticket and patch at Bugzilla?

From sidd.basu at gmail.com  Thu Jun 19 15:55:10 2008
From: sidd.basu at gmail.com (Siddhartha Basu)
Date: Thu, 19 Jun 2008 14:55:10 -0500
Subject: [Bioperl-l]  Re: Bio::Ontology help solicited
In-Reply-To: <1213890860.7713.87.camel@jic51958.jic.bbsrc.ac.uk>
References: <mailman.2779.1213637762.2759.bioperl-l@lists.open-bio.org>
	<1213882943.7713.43.camel@jic51958.jic.bbsrc.ac.uk>
	<39E954A9-72BB-466B-AEA3-1003B77CD49D@gmx.net>
	<1213885641.7713.54.camel@jic51958.jic.bbsrc.ac.uk>
	<5C819020-9094-416C-9B3B-DD085AB01602@gmx.net>
	<1213890860.7713.87.camel@jic51958.jic.bbsrc.ac.uk>
Message-ID: <485ab9c6.3ff0220a.6b13.1589@mx.google.com>

Hi Govind,

There are few ways by which you could search and find the term...

On Thu, 19 Jun 2008, Govind Chandra wrote:

> Hi Hilmar,
> 
> Below is an extract from perldoc Bio::Ontology::Ontology from which I
> _wrongly_ concluded that -identifier and -name do the same thing.
> 
> 
> 
>        find_terms
> 
>         Title   : find_terms
>         Usage   : ($term) = $oe->find_terms(-identifier => "SO:0000263");
>         Function: Find term instances matching queries for their attributes.
> 
>                   An implementation may not support querying for arbitrary
>                   attributes, but can generally be expected to accept
>                   -identifier and -name as queries. If both are provided,
>                   they are implicitly intersected.
> 
>         Example :
>         Returns : an array of zero or more Bio::Ontology::TermI objects
>         Args    : Named parameters. The following parameters should be recognized
>                   by any implementations:
> 
>                      -identifier    query by the given identifier
>                      -name          query by the given name
> 
> 
> 
> I had been messing with this script for a few hours before posting for
> help and had tried various combinations of -identifier and -name. But
> neither -identifier => "GO:0000072" nor -name => "M phase specific
> microtubule process" work. I know that the GOid exists because I can
> find it in the obo file. There is something more fundamentally wrong in
> my script than just the syntax. Like you suggested, below, I
> get_all_terms() but the list @allterms is empty.
> 
> ### code begins ###
> use strict;
> use Bio::OntologyIO;
> 
> my $file='gene_ontology.1_2.obo';
> my $parser = Bio::OntologyIO->new(
>   -format => "obo",
>   -file => $file
>   );
> my $ontology = $parser->next_ontology();

1. You need to get the ontology object to which the term belongs. And if
you don't know if offhand then you have to search and get it. 

my $id = 'GO:0000072';
my $term;
ONT:
while ( my $ontrow = $parser->next_ontology() ) {
    my ($newterm) = $ontrow->find_terms( -identifier => $id );
    next ONT if !$newterm;
    $term = $newterm;
    last ONT;
}

if ($term) {
	print 'First try: ', $term->identifier, "\t", $term->name, "\t",
    $term->ontology->name(),
    "\n";
}

2. You know the ontology to which the term belong.

my $id = 'GO:0000072';
my $name = 'biological_process';
my $ont;

ONT:
while ( my $ontrow = $parser->next_ontology() ) {
	if ($ontrow->name() eq $name) {
		$ont = $ontrow;
		last ONT;
	}
}

my ($term) = $ont->find_terms(-identifier => $id);

if ($term) {
	print 'Second try: ', $term->identifier, "\t", $term->name, "\t",
    $term->ontology->name(),
    "\n";
}


3. Get the engine and search through it

my $id = 'GO:0000072';
my $eng = $parser->next_ontology->engine();
my ($term) = $eng->find_terms(-identifier => $id);
if ($term) {
	print 'Third try: ', $term->identifier, "\t", $term->name, "\t",
    $term->ontology->name(),
    "\n";
}

Hope that helps.

-siddhartha



> print(ref($ontology), "\n");
> my @allterms = $ontology->get_all_terms();
> print(scalar(@allterms), "\n");
> my $limiter;
> foreach my $term (@allterms) {
> print($term->name(),"\n");
> print($term->definition(),"\n");
> if($limiter++ > 30) {last;}
> }
> exit;
> ### code ends ###
> 
> ### output begins ###
> Bio::Ontology::Ontology
> 0
> ### output ends ###
> 
> Given that the script works with the "go" format files (except
> process.ontology in which case it complains and exits) I suspect the obo
> file but am surprised that Bio::OntologyIO->next_ontology() does not
> complain. Will it be asking for too much to request you to get the obo
> file I am trying to parse from
> 
> ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology.1_2.obo
> 
> and see if it works for you?
> 
> Thanks
> 
> Govind
> 
> 
> 
> 
> 
> On Thu, 2008-06-19 at 10:50 -0400, Hilmar Lapp wrote:
> > On Jun 19, 2008, at 10:27 AM, Govind Chandra wrote:
> > 
> > > I changed the line below
> > >
> > > my ($term)=$ontology->find_terms(-name => "GO:0000072");
> > >
> > > to
> > >
> > > my ($term)=$ontology->find_terms(-identifier => "GO:0000072");
> > 
> > That's odd. Did you convince yourself that a term with this identifier  
> > is indeed in the ontology? If you iterate over all terms (using e.g.  
> > $ontology->get_all_terms()), is there a term with this identifier?
> > 
> > E.g.: print join("\n", map { $_->identifier; }
> >                             (grep { $_->identifier =~ /0000072/; }
> >                                   $ontology->get_all_terms())),"\n";
> > 
> > Does this print anything?
> > 
> > > but it does not make any difference. From perldoc I gathered that - 
> > > name
> > > and -identifier should do the same thing anyway.
> > 
> > 
> > I'm not sure where you gathered that from. Could you point me to the  
> > location that says that?
> > 
> > 	-hilmar
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From cjfields at uiuc.edu  Thu Jun 19 16:19:13 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 19 Jun 2008 15:19:13 -0500
Subject: [Bioperl-l] Bio::FeatureIO::gff
In-Reply-To: <ebf5eb170806191238i20010583x37eed2952db06c20@mail.gmail.com>
References: <ebf5eb170806191238i20010583x37eed2952db06c20@mail.gmail.com>
Message-ID: <C3E239BB-70AF-47A5-BD08-558A8D7EF535@uiuc.edu>


On Jun 19, 2008, at 2:38 PM, Mark Johnson wrote:

> I recently had to do some gff3 generation/munging, so I took a look at
> Bio::FeatureIO::gff.  I ran into a few issues:
>
> - The _handle_feature method (called by next_feature) attaches Dbxref
> attributes using 'Dbxref' as the key.  However, _write_feature_3 uses
> 'dblink' for the key when looking for Dbxref attributes.  I changed
> _handle_feature to use 'dblink' also, but I'm not sure that's any more
> (or less) correct than changing _write_feature_3 to use 'Dbxref'.
> Anybody have any strong opinions one way or the other?
>
> - Sendu made some changes to _write_feature_25 and _write_feature_3,
> but missed a line in _write_feature_3.  I think line 890 should be
>
>  my $phase  = defined($feature->phase) ? (ref($feature->phase) ?
> $feature->phase->value : $feature->phase) : '.';
>
> instead of
>
>  my $phase  = $feature->phase->value;
>
> to be consistent.
>
> - Also in _write_feature_3, the Dbxref attributes are wrapped in a
> call to uri_escape().  This generates a mangled gff3 that Apollo, at
> least, does not like.  Also, looking at the gff3 spec, I do not
> believe this is correct behaviour.  Quoting
> http://www.sequenceontology.org/gff3.shtml:
>
> The value of both Ontology_term and Dbxref is the ID of the cross
> referenced object in the form "DBTAG:ID".  The DBTAG indicates which
> database the referenced object can be found in, and ID indicates the
> identifier of the object within that database.  IDs can contain
> unescaped colons but DBTAGs cannot, so parsing code should split on
> the first colon encountered in the attribute value.
>
> So the key (DBTAG) should be escaped, but not the value (ID).  The
> code presently escapes both:
>
>  my $vstring = join ',', map {uri_escape($_->database .':'.
> $_->primary_id)} @v;
>
> which should probably be something like
>
>  my $vstring = join ',', map {uri_escape($_->database) .':'.
> $_->primary_id} @v;
>
>
> So, what are the plans for Bio::FeatureIO?  I find it kind of handy,
> so unless it's going to be scrapped in favor of something else, any
> objection to lobbing a ticket and patch at Bugzilla?

I think the general idea of Bio::FeatureIO will remain (read/write  
feature data) but it will definitely undergo significant  
reimplementation.  The typed SeqFeatureI class  
(Bio::SeqFeature::Annotated) would be deprecated in favor of something  
more lightweight.

However, I don't see that happening until after 1.6 is released unless  
someone wants to take it on.

chris

From johnsonm at gmail.com  Thu Jun 19 16:47:57 2008
From: johnsonm at gmail.com (Mark Johnson)
Date: Thu, 19 Jun 2008 15:47:57 -0500
Subject: [Bioperl-l] Bio::FeatureIO::gff
In-Reply-To: <C3E239BB-70AF-47A5-BD08-558A8D7EF535@uiuc.edu>
References: <ebf5eb170806191238i20010583x37eed2952db06c20@mail.gmail.com>
	<C3E239BB-70AF-47A5-BD08-558A8D7EF535@uiuc.edu>
Message-ID: <ebf5eb170806191347tf1096cdve025832acdf735b3@mail.gmail.com>

On Thu, Jun 19, 2008 at 3:19 PM, Chris Fields <cjfields at uiuc.edu> wrote:

> I think the general idea of Bio::FeatureIO will remain (read/write feature
> data) but it will definitely undergo significant reimplementation.  The
> typed SeqFeatureI class (Bio::SeqFeature::Annotated) would be deprecated in
> favor of something more lightweight.
>
> However, I don't see that happening until after 1.6 is released unless
> someone wants to take it on.
>
> chris

I suspect the 'something' you mention is going to require a fair bit
of discussion and design.  The best time for that would be after 1.6.
Otherwise, we're likely to end up with something just as problematic
as Bio::SeqFeature::Annotated.

However, people are using Bio::FeatureIO as it stands.  Unless the
plan is to remove it from source control (as opposed to just not
packaging it up as part of the 1.6 release), would there be any
objection to patching up the existing implementation?  If nothing
else, it will be the starting point for the reimplementation.  Might
as well correct obvious defects, so they *don't* get reimplemented.

From mirhan at indiana.edu  Thu Jun 19 17:07:28 2008
From: mirhan at indiana.edu (Han, Mira)
Date: Thu, 19 Jun 2008 17:07:28 -0400
Subject: [Bioperl-l] Bio::Tree::AnnotatableNode
Message-ID: <C48042D0.9258%mirhan@indiana.edu>


Hi,
I have a few questions regarding the design of the AnnotatableNode.

1. add_tag_value or Annotation::SimpleValue?
I have property tags for nodes that can be defined by the user, that
contains generally simple scalar values,
I'm currently using the Annotation::SimpleValue to contain them in the node.
What I'm wondering is..
should I use the tag/value implementation already in NodeI for these
instead?

2. I have to also maintain a unique identifier for each node called
id_source.
First I was looking to use the internal_id to store the unique ids.
But now I realized that we cannot set the internal_id to arbitrary ids,
We can only get the values already determined.
So now I'm wondering again should I set this id as a tag/value? Or a
SimpleAnnotation?
Or can I modify the code so that we can set the internal_id?

Mira



From mirhan at indiana.edu  Thu Jun 19 17:23:40 2008
From: mirhan at indiana.edu (Han, Mira)
Date: Thu, 19 Jun 2008 17:23:40 -0400
Subject: [Bioperl-l] Bio::Tree::AnnotatableNode
In-Reply-To: <C48042D0.9258%mirhan@indiana.edu>
Message-ID: <C480469C.925D%mirhan@indiana.edu>


My current position is that
I will override the internal_id method to store the id_source ids instead of
the creation_id.
And I will use Annotation::SimpleValue instead of the _tags hash in the
Tree::Node
I guess in that case I'll have to implement the add_tag_value etc to use
Annotation::SimpleValue internally?

Another quick questions..
Which is the general style, to use hyphenated tags or just normal words for
keys like this?

Mira



On 6/19/08 5:07 PM, "Mira Han" <mirhan at indiana.edu> wrote:

>
> Hi,
> I have a few questions regarding the design of the AnnotatableNode.
>
> 1. add_tag_value or Annotation::SimpleValue?
> I have property tags for nodes that can be defined by the user, that contains
> generally simple scalar values,
> I'm currently using the Annotation::SimpleValue to contain them in the node.
> What I'm wondering is..
> should I use the tag/value implementation already in NodeI for these instead?
>
> 2. I have to also maintain a unique identifier for each node called id_source.
> First I was looking to use the internal_id to store the unique ids.
> But now I realized that we cannot set the internal_id to arbitrary ids,
> We can only get the values already determined.
> So now I'm wondering again should I set this id as a tag/value? Or a
> SimpleAnnotation?
> Or can I modify the code so that we can set the internal_id?
>
> Mira



From johnsonm at gmail.com  Thu Jun 19 17:29:01 2008
From: johnsonm at gmail.com (Mark Johnson)
Date: Thu, 19 Jun 2008 16:29:01 -0500
Subject: [Bioperl-l] Bio::Tools::Run::Genemark
Message-ID: <ebf5eb170806191429gc6b8866rf9fed515ee55c5d6@mail.gmail.com>

It seems that GeneMark.hmm returns 0 even when the license is expired.
 You can probably guess how I discovered this.  I created a bug and
attached a fix:

  http://bugzilla.open-bio.org/show_bug.cgi?id=2523

If you've built Bio::Tools::Run::Genemark into a gene prediction
pipeline (as I have), you really want this fix.  Otherwise, if your
license expires, you may not realize it until you wonder why GeneMark
has suddenly stopped predicting genes...

From cjfields at uiuc.edu  Thu Jun 19 17:29:45 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 19 Jun 2008 16:29:45 -0500
Subject: [Bioperl-l] Bio::FeatureIO::gff
In-Reply-To: <ebf5eb170806191347tf1096cdve025832acdf735b3@mail.gmail.com>
References: <ebf5eb170806191238i20010583x37eed2952db06c20@mail.gmail.com>
	<C3E239BB-70AF-47A5-BD08-558A8D7EF535@uiuc.edu>
	<ebf5eb170806191347tf1096cdve025832acdf735b3@mail.gmail.com>
Message-ID: <568794E1-29DE-4077-89CF-2FCB47BB8C1D@uiuc.edu>


On Jun 19, 2008, at 3:47 PM, Mark Johnson wrote:

> On Thu, Jun 19, 2008 at 3:19 PM, Chris Fields <cjfields at uiuc.edu>  
> wrote:
>
>> I think the general idea of Bio::FeatureIO will remain (read/write  
>> feature
>> data) but it will definitely undergo significant reimplementation.   
>> The
>> typed SeqFeatureI class (Bio::SeqFeature::Annotated) would be  
>> deprecated in
>> favor of something more lightweight.
>>
>> However, I don't see that happening until after 1.6 is released  
>> unless
>> someone wants to take it on.
>>
>> chris
>
> I suspect the 'something' you mention is going to require a fair bit
> of discussion and design.  The best time for that would be after 1.6.
> Otherwise, we're likely to end up with something just as problematic
> as Bio::SeqFeature::Annotated.
>
> However, people are using Bio::FeatureIO as it stands.  Unless the
> plan is to remove it from source control (as opposed to just not
> packaging it up as part of the 1.6 release), would there be any
> objection to patching up the existing implementation?  If nothing
> else, it will be the starting point for the reimplementation.  Might
> as well correct obvious defects, so they *don't* get reimplemented.

I think patching for the current implementation is fine.  We we plan  
on making changes we'll try posting plans on the wiki.

Speaking of, I need to look at the FeatureIO API to see what is  
expected.  Hopefully changes can occur with minimal to no API changes.

chris


From cjfields at uiuc.edu  Thu Jun 19 17:36:40 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 19 Jun 2008 16:36:40 -0500
Subject: [Bioperl-l] Bio::Tools::Run::Genemark
In-Reply-To: <ebf5eb170806191429gc6b8866rf9fed515ee55c5d6@mail.gmail.com>
References: <ebf5eb170806191429gc6b8866rf9fed515ee55c5d6@mail.gmail.com>
Message-ID: <E1740ABE-6637-4314-ABB9-80CDD199856D@uiuc.edu>

Just committed the patch to svn, so updating the local bioperl-run  
from subversion should work.

chris

On Jun 19, 2008, at 4:29 PM, Mark Johnson wrote:

> It seems that GeneMark.hmm returns 0 even when the license is expired.
> You can probably guess how I discovered this.  I created a bug and
> attached a fix:
>
>  http://bugzilla.open-bio.org/show_bug.cgi?id=2523
>
> If you've built Bio::Tools::Run::Genemark into a gene prediction
> pipeline (as I have), you really want this fix.  Otherwise, if your
> license expires, you may not realize it until you wonder why GeneMark
> has suddenly stopped predicting genes...
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at uiuc.edu  Thu Jun 19 18:24:21 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 19 Jun 2008 17:24:21 -0500
Subject: [Bioperl-l] Bio::Tree::AnnotatableNode
In-Reply-To: <C480469C.925D%mirhan@indiana.edu>
References: <C480469C.925D%mirhan@indiana.edu>
Message-ID: <6EE3DE6A-2EB0-4561-8CD1-9428A9D5AC88@uiuc.edu>

On Jun 19, 2008, at 4:23 PM, Han, Mira wrote:

> My current position is that
> I will override the internal_id method to store the id_source ids  
> instead of
> the creation_id.

It looks like you can set the internal_id() with the _creation_id()  
private method.

> And I will use Annotation::SimpleValue instead of the _tags hash in  
> the
> Tree::Node
> I guess in that case I'll have to implement the add_tag_value etc to  
> use
> Annotation::SimpleValue internally?

It makes sense as you wouldn't want a mixed bag of scalar tags and  
AnnotationI, though this sounds eerily similar to what I just rolled  
back in SeqFeature/Annotatable.  I think it's okay in this case.

With that in mind, you'll obviously need to reimplement the other  
'tag' methods similarly so they replicate behavior indicated in the  
NodeI API and Node implementation (i.e. if args are accepted or values  
returned they must be scalar values and not Annotation::SimpleValue).

> Another quick questions..
> Which is the general style, to use hyphenated tags or just normal  
> words for
> keys like this?
>
> Mira

Normal words, though documenting these is best.  For consistency you  
may want to see what other TreeIO parsers use for tag names and (if  
there are similarities) use the same tag names.

chris

> On 6/19/08 5:07 PM, "Mira Han" <mirhan at indiana.edu> wrote:
>
>>
>> Hi,
>> I have a few questions regarding the design of the AnnotatableNode.
>>
>> 1. add_tag_value or Annotation::SimpleValue?
>> I have property tags for nodes that can be defined by the user,  
>> that contains
>> generally simple scalar values,
>> I'm currently using the Annotation::SimpleValue to contain them in  
>> the node.
>> What I'm wondering is..
>> should I use the tag/value implementation already in NodeI for  
>> these instead?
>>
>> 2. I have to also maintain a unique identifier for each node called  
>> id_source.
>> First I was looking to use the internal_id to store the unique ids.
>> But now I realized that we cannot set the internal_id to arbitrary  
>> ids,
>> We can only get the values already determined.
>> So now I'm wondering again should I set this id as a tag/value? Or a
>> SimpleAnnotation?
>> Or can I modify the code so that we can set the internal_id?
>>
>> Mira
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From hlapp at gmx.net  Thu Jun 19 20:59:02 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu, 19 Jun 2008 20:59:02 -0400
Subject: [Bioperl-l] Bio::FeatureIO::gff
In-Reply-To: <ebf5eb170806191238i20010583x37eed2952db06c20@mail.gmail.com>
References: <ebf5eb170806191238i20010583x37eed2952db06c20@mail.gmail.com>
Message-ID: <513D9B7B-D5F0-43C0-8084-CEFBA3AE420D@gmx.net>


On Jun 19, 2008, at 3:38 PM, Mark Johnson wrote:

> So, what are the plans for Bio::FeatureIO?  I find it kind of handy,
> so unless it's going to be scrapped in favor of something else, any
> objection to lobbing a ticket and patch at Bugzilla?


Not at all, that would be great in fact. ChrisF mentioned the caveats  
due to the need for re-implementation, so before you go overboard with  
fixing design etc you may want to check here.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================




From koski at cenix-bioscience.com  Fri Jun 20 03:14:59 2008
From: koski at cenix-bioscience.com (Liisa Koski)
Date: Fri, 20 Jun 2008 09:14:59 +0200
Subject: [Bioperl-l] svn checkout error bioperl-live
Message-ID: <485B58F3.6000603@cenix-bioscience.com>

Hi,

I'm trying to checkout bioperl-live

svn co svn://open-bio.org/bioperl/bioperl-live/trunk bioperl-live

but get the following error:

svn: Can't connect to host 'open-bio.org': Connection refused

Any suggestions?

Thanks,
Liisa


From arareko at campus.iztacala.unam.mx  Fri Jun 20 11:04:16 2008
From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra)
Date: Fri, 20 Jun 2008 10:04:16 -0500
Subject: [Bioperl-l] svn checkout error bioperl-live
In-Reply-To: <485B58F3.6000603@cenix-bioscience.com>
References: <485B58F3.6000603@cenix-bioscience.com>
Message-ID: <485BC6F0.1040101@campus.iztacala.unam.mx>

Hi Lisa,

There was a problem in the server hosting the SVN service. ChrisD has 
fixed that and it should be working now, please try again.

Regards,
Mauricio.

Liisa Koski wrote:
> Hi,
> 
> I'm trying to checkout bioperl-live
> 
> svn co svn://open-bio.org/bioperl/bioperl-live/trunk bioperl-live
> 
> but get the following error:
> 
> svn: Can't connect to host 'open-bio.org': Connection refused
> 
> Any suggestions?
> 
> Thanks,
> Liisa
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM

From cjfields at uiuc.edu  Fri Jun 20 14:35:07 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 20 Jun 2008 13:35:07 -0500
Subject: [Bioperl-l] BioPerl Infernal tools
Message-ID: <F0C86F6D-2C60-4251-A915-2387EF681C3A@uiuc.edu>

For those interested,

The first release candidate for Infernal 1.0 (v 1.0rc1) is out now.  I  
am planning on updating all Infernal-related modules  
(Bio::SearchIO::infernal and Bio::Tools::Run::Infernal) to use the  
latest release, probably within the next couple of weeks.

It is possible I will need to drop support for pre-0.8 Infernal  
releases if discerning output between different versions becomes too  
problematic (you should probably be running the latest version anyway,  
but I digress...).  If so I will announce that when I commit the final  
changes.

chris

From jason at bioperl.org  Mon Jun 23 11:02:56 2008
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 23 Jun 2008 08:02:56 -0700
Subject: [Bioperl-l] Fwd: PAML through BIOPERL - parsing error
References: <263150.43884.qm@web36407.mail.mud.yahoo.com>
Message-ID: <10D5F46A-B9C3-4525-A66F-20B0D8786FB3@bioperl.org>

You'll have to report what version of BioPerl and PAML you are using,  
only certain versions work together because the report output from  
PAML changes in each version.  We have tried to fix it for PAML4 in  
the latest code in SVN and I believe PAML 3.15 should work with what  
is in 1.5.2 release of BioPerl  but I'm not sure.

Please direct your questions to the mailing list to insure someone  
has a chance to look at it.

-jason

Begin forwarded message:

> From: Tannistha <tannistha3 at yahoo.com>
> Date: June 22, 2008 10:43:41 PM PDT
> To: jason at bioperl.org
> Subject: PAML through BIOPERL - parsing error
> Reply-To: tannistha3 at yahoo.com
>
>
> Hi Jason,
>
> I am using PAML through BIOPERL. My input in multiple CDS sequence.  
> I am getting an error while parsing my codeml result.
> The error is:
> Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/ 
> site_perl/5.8.5/Bio/Tools/Phylo/PAML.pm line 615, <GEN2> line 90.
>
> Please suggest how to eliminate this error.
>
> Thanking you
>
> Regards
>
> Dr. Tannistha Nandi
> email: tannistha3 at yahoo.com
>
>


From nsh9351 at rit.edu  Mon Jun 23 15:32:08 2008
From: nsh9351 at rit.edu (Nathan Haseley (RIT Student))
Date: Mon, 23 Jun 2008 15:32:08 -0400
Subject: [Bioperl-l] BioPerl help with 2D arrays
Message-ID: <7D75703BC8E1C149BF78A1E79AAAB169035BC531@svits28.main.ad.rit.edu>

Hello,
   I am writing a script that returns an array of array references to  Bio::Search::HSP::GenericHSP objects (2D array of Bio::Search::HSP::GenericHSP objects).  Whenever I try to call functions such as ->num_identical I get an error message: 
Can't call method "num_identical" without a package or object reference.

Below are the segments of the code that are giving me problems to give you a general idea of what I'm doing.  Is there a way around this?  What am I doing wrong?  Thanks!
Sincerely,
Nathan

my $in = new Bio::SearchIO( -format => 'blast',
				    -file => $file );
my $ j = -1;
while( $result = $in->next_result and ref($result)) {
   ++$j;
   while( $has_species == 0) {
      if( my $hit = $result->next_hit) {
   	if( $hit -> description =~ /$species_names[$i]/i) {
       		$has_species = 1;
   		$temp[$i] = $hit->next_hsp;
       		$result->rewind;
        }
      }
     }   
  $homologs[$j] = [@temp];
.
.
.
return $homologs
.
.
. (eventually in a separate fucntion)
$temp = $homologs[$i]->[$j];
$temp->num_identical;








From jajams at utu.fi  Tue Jun 24 04:23:35 2008
From: jajams at utu.fi (=?iso-8859-1?Q?Joonas_J=E4msen?=)
Date: Tue, 24 Jun 2008 11:23:35 +0300
Subject: [Bioperl-l] hmmpfam
Message-ID: <fcc4f024596c.4860d937@utu.fi>

Hello,

Is it possible to just get the FASTA sequence of a specified domain (by name) above a certain threshold found with hmmpfam? I could not find this functionality in the packages I was referred to recently.

Joonas J?msen.


From David.Messina at sbc.su.se  Tue Jun 24 10:35:50 2008
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 24 Jun 2008 16:35:50 +0200
Subject: [Bioperl-l] BioPerl help with 2D arrays
In-Reply-To: <7D75703BC8E1C149BF78A1E79AAAB169035BC531@svits28.main.ad.rit.edu>
References: <7D75703BC8E1C149BF78A1E79AAAB169035BC531@svits28.main.ad.rit.edu>
Message-ID: <628aabb70806240735o60a4d292l93d620f1e829f92c@mail.gmail.com>

Hi Nathan,

I'm not sure, but I suspect that when you come back and try to examine one
of your saved objects, the class defining that object isn't loaded.

If you add the line

use Bio::Search::HSP::GenericHSP;

to the top of the file where you are getting the error, does that help?


Dave

From bix at sendu.me.uk  Tue Jun 24 11:23:50 2008
From: bix at sendu.me.uk (Sendu Bala)
Date: Tue, 24 Jun 2008 16:23:50 +0100
Subject: [Bioperl-l] BioPerl help with 2D arrays
In-Reply-To: <7D75703BC8E1C149BF78A1E79AAAB169035BC531@svits28.main.ad.rit.edu>
References: <7D75703BC8E1C149BF78A1E79AAAB169035BC531@svits28.main.ad.rit.edu>
Message-ID: <48611186.1020908@sendu.me.uk>

Nathan Haseley (RIT Student) wrote:
> Hello, I am writing a script that returns an array of array
> references to  Bio::Search::HSP::GenericHSP objects (2D array of
> Bio::Search::HSP::GenericHSP objects).  Whenever I try to call
> functions such as ->num_identical I get an error message: Can't call
> method "num_identical" without a package or object reference.
> 
> Below are the segments of the code that are giving me problems to
> give you a general idea of what I'm doing.  Is there a way around
> this?  What am I doing wrong?  Thanks! Sincerely, Nathan

I think we need to see more of your code. If I fill in enough of the 
missing blanks to make your example run, it works fine. So your problem 
is somewhere in your code that you haven't shown us.

Best thing to do is standard debugging to come up with a minimal but 
working script that demonstrates the problem, then give us that.

From cjfields at uiuc.edu  Tue Jun 24 11:39:47 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 24 Jun 2008 10:39:47 -0500
Subject: [Bioperl-l] BioPerl help with 2D arrays
In-Reply-To: <7D75703BC8E1C149BF78A1E79AAAB169035BC531@svits28.main.ad.rit.edu>
References: <7D75703BC8E1C149BF78A1E79AAAB169035BC531@svits28.main.ad.rit.edu>
Message-ID: <A4BF0CC5-F701-4074-A427-599967C04E52@uiuc.edu>

On Jun 23, 2008, at 2:32 PM, Nathan Haseley (RIT Student) wrote:

> Hello,
>   I am writing a script that returns an array of array references  
> to  Bio::Search::HSP::GenericHSP objects (2D array of  
> Bio::Search::HSP::GenericHSP objects).  Whenever I try to call  
> functions such as ->num_identical I get an error message:
> Can't call method "num_identical" without a package or object  
> reference.
>
> Below are the segments of the code that are giving me problems to  
> give you a general idea of what I'm doing.  Is there a way around  
> this?  What am I doing wrong?  Thanks!
> Sincerely,
> Nathan
>
> my $in = new Bio::SearchIO( -format => 'blast',
> 				    -file => $file );
> my $ j = -1;
> while( $result = $in->next_result and ref($result)) {

$result should always be assigned an object ref or undef, the latter  
which kills the loop, so '... and ref($result)' isn't needed.

>   ++$j;
>   while( $has_species == 0) {
>      if( my $hit = $result->next_hit) {
>   	if( $hit -> description =~ /$species_names[$i]/i) {
>       		$has_species = 1;
>   		$temp[$i] = $hit->next_hsp;
>       		$result->rewind;
>        }
>      }
>     }

I think you want to incorporate a simple hash construct for your  
species names.  However...

You have left out a significant bit of code, so I am finding it hard  
to determine what you are trying to accomplish.  For instance, from  
the above it seems you always want to always match to the same species  
name, as $i never changes (so $species_name[$i] also never changes).

The while loop as represented above is pretty dangerous, as you can  
feasibly enter an infinite loop unless you get both a hit AND the hit  
desc matches the regex.  Also, you're rewinding the main $result  
iterator ($result->rewind) while inside the $result iterator loop; not  
sure why you are doing that.

Note that '$hit->next_hsp;' can also be dangerous under some  
circumstances, as this can give you undef in cases where no HSP  
alignment is returned (e.g. the hit data is only in the hit table).   
May be one source of your problems.

>  $homologs[$j] = [@temp];

...

> return $homologs

Shouldn't that be @homologs?  You use '$homologs[$j]' above, which is  
a scalar in the array @homologs.

If you aren't 'use strict/warnings', this creates a local scalar  
$homologs then returns the value of $homologs (undef), which could be  
the problem.  Using 'strict/warnings' should catch that.

> .
> .
> . (eventually in a separate fucntion)
> $temp = $homologs[$i]->[$j];
> $temp->num_identical;

I would go about this by creating a lookup table (hash or array) of  
species names, then iterate through each BLAST report to either

(1) generically grab the species name generically and check it against  
the lookup table using 'exists',

%lookup = map {$_ => 1} ('species1', 'species2');
# if species is in brackets, match inside the brackets
if ($hit->description =~ /\[([^\]]+)\]/) {
    $sp = $1;
    if (exists $lookup{$sp}) {
       # do something
    } else { # do something on failure }
}

or (2) check each name (the key in the lookup table) against the  
description using a 'grep', such as:

%lookup = map {$_ => 1} ('species1', 'species2');
if (grep {$desc =~ /$_/} keys %lookup) {...} else {# do something on  
failure}
# could use array of names as a lookup as well

Depending on how the varied the descriptions are; it may only be  
feasible to try the latter one.

 From there you could store the HSP data in a hash, using the species  
name:

$temp{$species} = $hit->next_hsp || warn 'No HSP returned';

and store that by the report # or description:

# array of reports
push @reports, \%temp;

# hash of reports, by query name
$report{$result->query_name} = \%temp;

chris


From pmiguel at purdue.edu  Tue Jun 24 19:29:30 2008
From: pmiguel at purdue.edu (Phillip San Miguel)
Date: Tue, 24 Jun 2008 19:29:30 -0400
Subject: [Bioperl-l] The way to extract a segment of an EMBL record?
Message-ID: <4861835A.3010700@purdue.edu>

    When I use the trunc method to pull a segment of a sequence object 
derived from large EMBL file, the annotations are not propagated. Do I 
need to specify a heavy weight sequence object somehow for annotation in 
the EMBL file to be carried along?

Phillip

PS The code I'm talking about is below. This produces what appears to be 
a valid EMBL file, but only bare-bones annotation is carried along, or 
generated on the fly:

ID   NC_003070; SV 1; linear; unassigned DNA; STD; UNC; 70001 BP.
XX
AC   NC_003070;
XX
DE   Arabidopsis thaliana chromosome 1, complete sequence.
XX
XX
FH   Key             Location/Qualifiers
FH
XX
SQ   Sequence 70001 BP; 20783 A; 14173 C; 13896 G; 21149 T; 0 other;


Here is the code:

use Bio::SeqIO;
use Bio::Seq;

my $rh_opts =parseOptions();

#create input sequence object
my  $in  = Bio::SeqIO->new(-file => $rh_opts->{INFILE} , -format =>   
$rh_opts->{F_IN} );

#pull in sequence. (Ignores all but first sequence)
my $seq =   $in->next_seq()
    ||  die "Hey, $rh_opts-{INFILE} contains no sequence of format 
$rh_opts->{F_IN}!";
$in->close();

#xtract segment of sequence to output
my $end     =(defined $rh_opts->{END})
            ? $rh_opts->{END}
            : $seq->length();
my $begin   = $rh_opts->{BEGIN};
my $segment =$seq->trunc($begin, $end);

#create output object
my $out = Bio::SeqIO->new(-file => ">$rh_opts->{OUTFILE}" , -format => 
$rh_opts->{F_OUT});
$out->write_seq($segment);


From cjfields at uiuc.edu  Tue Jun 24 21:33:15 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 24 Jun 2008 20:33:15 -0500
Subject: [Bioperl-l] The way to extract a segment of an EMBL record?
In-Reply-To: <4861835A.3010700@purdue.edu>
References: <4861835A.3010700@purdue.edu>
Message-ID: <2EE95EFF-DF52-40DB-A9F6-EA9A5530CC94@uiuc.edu>

The trunc() methods are not completely implemented; Bio::Seq::trunc()  
doesn't carry over either annotations or seqfeatures AFAIK.  I think  
Bio::SeqUtils::trunc_with_features does this though.

chris

On Jun 24, 2008, at 6:29 PM, Phillip San Miguel wrote:

>   When I use the trunc method to pull a segment of a sequence object  
> derived from large EMBL file, the annotations are not propagated. Do  
> I need to specify a heavy weight sequence object somehow for  
> annotation in the EMBL file to be carried along?
>
> Phillip
>
> PS The code I'm talking about is below. This produces what appears  
> to be a valid EMBL file, but only bare-bones annotation is carried  
> along, or generated on the fly:
>
> ID   NC_003070; SV 1; linear; unassigned DNA; STD; UNC; 70001 BP.
> XX
> AC   NC_003070;
> XX
> DE   Arabidopsis thaliana chromosome 1, complete sequence.
> XX
> XX
> FH   Key             Location/Qualifiers
> FH
> XX
> SQ   Sequence 70001 BP; 20783 A; 14173 C; 13896 G; 21149 T; 0 other;
>
>
> Here is the code:
>
> use Bio::SeqIO;
> use Bio::Seq;
>
> my $rh_opts =parseOptions();
>
> #create input sequence object
> my  $in  = Bio::SeqIO->new(-file => $rh_opts->{INFILE} , -format  
> =>   $rh_opts->{F_IN} );
>
> #pull in sequence. (Ignores all but first sequence)
> my $seq =   $in->next_seq()
>   ||  die "Hey, $rh_opts-{INFILE} contains no sequence of format  
> $rh_opts->{F_IN}!";
> $in->close();
>
> #xtract segment of sequence to output
> my $end     =(defined $rh_opts->{END})
>           ? $rh_opts->{END}
>           : $seq->length();
> my $begin   = $rh_opts->{BEGIN};
> my $segment =$seq->trunc($begin, $end);
>
> #create output object
> my $out = Bio::SeqIO->new(-file => ">$rh_opts->{OUTFILE}" , -format  
> => $rh_opts->{F_OUT});
> $out->write_seq($segment);
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign





From jason at bioperl.org  Wed Jun 25 01:24:02 2008
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 25 Jun 2008 14:24:02 +0900
Subject: [Bioperl-l] Fwd:  hmmpfam
In-Reply-To: <8273f6c20806242223v4f6d1442n4a96233c6aff3112@mail.gmail.com>
References: <fcc4f024596c.4860d937@utu.fi>
	<8273f6c20806242223v4f6d1442n4a96233c6aff3112@mail.gmail.com>
Message-ID: <8273f6c20806242224g4d3b4579gd89619e34423358b@mail.gmail.com>

forgot to cc list

From: Jason Stajich <jason at bioperl.org>
Date: Jun 25, 2008 2:23 PM
Subject: Re: [Bioperl-l] hmmpfam
To: Joonas J?msen <jajams at utu.fi>

you can get the sequence as a string, but it will have the gaps and other
symbols inserted.

See the SEARCHIO Howto for getting query and hit sequence as a string or a
multiple-alignment of the query and hit pair (get_aln).
-jason


 On 6/24/08, Joonas J?msen <jajams at utu.fi> wrote:
>
> Hello,
>
> Is it possible to just get the FASTA sequence of a specified domain (by
> name) above a certain threshold found with hmmpfam? I could not find this
> functionality in the packages I was referred to recently.
>
> Joonas J?msen.
>
> _______________________________________________
> 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
http://bioperl.org/wiki/User:Jason

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki/User:Jason


From hlapp at gmx.net  Wed Jun 25 18:07:09 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Wed, 25 Jun 2008 18:07:09 -0400
Subject: [Bioperl-l] Problems when trying to persist a sequence in my
	BioSQL database using, BioPerl
In-Reply-To: <48611792.2060906@gmx.net>
References: <48611792.2060906@gmx.net>
Message-ID: <1DB86640-D4D5-4081-8DE5-E3181DD9D6A3@gmx.net>

Hi Gabrielle,

(note that I have changed the mailing list to bioperl - whoever  
replies please cut biosql from the cc list, assuming that this indeed  
isn't BioSQL's fault)

given the error message below, Bio::SeqIO::genbank can be found, but  
it fails to load because it requires Bio::Species, which in turn  
imports support for weak references from Scalar::Util. The last step  
fails, causing loading Bio::Species to fail, which in turn causes  
Bio::SeqIO::genbank to fail to load.

The real question is why your version of Perl doesn't seem to have  
support for weak references (the reason for Scalar::Util failing to  
load). Could you give details on your OS version and your version of  
Perl (output of 'perl -V').

The question for BioPerl is whether there is a fall-back mechanism we  
might want to support if weak references aren't supported, rather than  
rendering the genbank parser unusable. Sendu or Chris - any thoughts  
on this?

	-hilmar

On Jun 24, 2008, at 10:49 AM, Gabrielle Doan wrote:

> Hi all,
>
> I am new to BioPerl and BioSQL so please excuse me if my question is  
> a bit simple. I followed the installation files in the current  
> version of BioPerl very strictly (I used the Bioperl 1.5.2,  
> Developer Release from the bioperl website). After successful  
> installation I tried to persist a genbank file in my BioSQL  
> database, which runs on a database server and is accessible using  
> the mysql command shell. When using bioperl I receive the following  
> error message:
>
> ================
>
> $ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb -- 
> dbuser myuser --dbpass mypasswd --namespace GenBank /home/doan/db- 
> data/ref_chr1.gbk
> Loading /local/doan/db-daten/ref_chr1.gbk ...
> Bio::SeqIO: genbank cannot be found
> Exception ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Failed to load module Bio::SeqIO::genbank. Weak references are  
> not implemented in the version of perl at /usr/lib/perl5/site_perl/ 
> 5.8.8/Bio/Species.pm line 91
> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/ 
> Bio/Species.pm line 91.
> Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> SeqIO/genbank.pm line 172.
> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/ 
> Bio/SeqIO/genbank.pm line 172.
> Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm line 425.
>
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/ 
> Bio/Root/Root.pm:427
> STACK: Bio::SeqIO::_load_format_module /usr/lib/perl5/site_perl/ 
> 5.8.8/Bio/SeqIO.pm:555
> STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:376
> STACK: /usr/bin/bp_load_seqdatabase.pl:541
> -----------------------------------------------------------
>
> For more information about the SeqIO system please see the SeqIO docs.
> This includes ways of checking for formats at compile time, not run  
> time
> Can't call method "next_seq" on an undefined value at /usr/bin/ 
> bp_load_seqdatabase.pl line 565.
>
> ================
>
> Unfortunately, even Google does not provide any hints when searching  
> for the particular message. It seems that for some reason the path  
> to the Bio::SeqIO::genbank module cannot be found. I am greateful  
> for any hint!
>
> Cheers,
> Gabrielle
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================




From jason at bioperl.org  Thu Jun 26 00:37:41 2008
From: jason at bioperl.org (Jason Stajich)
Date: Thu, 26 Jun 2008 13:37:41 +0900
Subject: [Bioperl-l] hmmpfam
In-Reply-To: <4862A7B8.5020302@utu.fi>
References: <fcc4f024596c.4860d937@utu.fi>
	<8273f6c20806242223v4f6d1442n4a96233c6aff3112@mail.gmail.com>
	<8273f6c20806242224g4d3b4579gd89619e34423358b@mail.gmail.com>
	<4862A7B8.5020302@utu.fi>
Message-ID: <64CE7D40-9ED3-48F2-B46B-441368F201A6@bioperl.org>

yeah  - you get it as a string, you make a sequence object, you write  
it out as fasta. I'm sure someone on the list can help if you can't  
figure out how to do this.
Read the sequence howto, you want to use Bio::Seq to make the  
sequence and Bio::SeqIO to write the sequence.

  I don't know if you want the whole sequence or just what was  
matched by the profile search.
Please continue to reply to questions to the mailing list.

-jason
On Jun 26, 2008, at 5:16 AM, Joonas J?msen wrote:

> Thanks,
>
> Is there no way to get the sequence out in fasta format? I have  
> like 25000 sequences to extract. I have no clue as to how to do  
> this at the moment.
>
> Best regards,
> Joonas.
>
> Jason Stajich wrote:
>> forgot to cc list From: *Jason Stajich* <jason at bioperl.org  
>> <mailto:jason at bioperl.org>>
>> Date: Jun 25, 2008 2:23 PM
>> Subject: Re: [Bioperl-l] hmmpfam
>> To: Joonas J?msen <jajams at utu.fi <mailto:jajams at utu.fi>>
>> you can get the sequence as a string, but it will have the gaps  
>> and other symbols inserted.
>>  See the SEARCHIO Howto for getting query and hit sequence as a  
>> string or a multiple-alignment of the query and hit pair  
>> (get_aln). -jason
>>  On 6/24/08, *Joonas J?msen* <jajams at utu.fi  
>> <mailto:jajams at utu.fi>> wrote:
>>     Hello,
>>     Is it possible to just get the FASTA sequence of a specified  
>> domain
>>     (by name) above a certain threshold found with hmmpfam? I  
>> could not
>>     find this functionality in the packages I was referred to  
>> recently.
>>     Joonas J?msen.
>>     _______________________________________________
>>     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
>> -- 
>> Jason Stajich
>> jason at bioperl.org <mailto:jason at bioperl.org>
>> http://bioperl.org/wiki/User:Jason
>> -- 
>> Jason Stajich
>> jason at bioperl.org <mailto:jason at bioperl.org>
>> http://bioperl.org/wiki/User:Jason<jajams.vcf>



From bix at sendu.me.uk  Thu Jun 26 06:02:38 2008
From: bix at sendu.me.uk (Sendu Bala)
Date: Thu, 26 Jun 2008 11:02:38 +0100
Subject: [Bioperl-l] Problems when trying to persist a sequence in my
 BioSQL database using, BioPerl
In-Reply-To: <1DB86640-D4D5-4081-8DE5-E3181DD9D6A3@gmx.net>
References: <48611792.2060906@gmx.net>
	<1DB86640-D4D5-4081-8DE5-E3181DD9D6A3@gmx.net>
Message-ID: <4863693E.2080706@sendu.me.uk>

Hilmar Lapp wrote:
> The real question is why your version of Perl doesn't seem to have 
> support for weak references (the reason for Scalar::Util failing to 
> load). Could you give details on your OS version and your version of 
> Perl (output of 'perl -V').

Given that it seems to be perl 5.8.8, I'm guessing this is the 
RedHat/Fedora issue:

http://search.cpan.org/~adamk/Task-Weaken-1.02/lib/Task/Weaken.pm


Solutions:
First try installing the latest version of Scalar::Util yourself:

perl -MCPAN -e shell
force install Scalar::Util

(and see that it gets installed in a place that is checked before the 
Fedora version, or overwrites the Fedora version)

If that doesn't work, you'll have to download and compile Perl yourself 
from source (don't use Fedora's installation system).


> The question for BioPerl is whether there is a fall-back mechanism we 
> might want to support if weak references aren't supported, rather than 
> rendering the genbank parser unusable. Sendu or Chris - any thoughts on 
> this?

Firstly, Task::Weaken should get added to Build.pl as a requirement, so 
people get better error messages. If we do that, however, the whole of 
BioPerl doesn't get installed, never mind just the genbank parser not 
being usable.

As for a fall-back mechanism, I'm not really sure how that would work. 
The easiest thing to do would be to just not deal with the species lines 
if Bio::Species doesn't work. Is that an acceptable fall-back? If not, 
more thought and discussion is needed. Make a proposal: what would you 
want to happen?


> On Jun 24, 2008, at 10:49 AM, Gabrielle Doan wrote:
> 
>> Hi all,
>>
>> I am new to BioPerl and BioSQL so please excuse me if my question is a 
>> bit simple. I followed the installation files in the current version 
>> of BioPerl very strictly (I used the Bioperl 1.5.2, Developer Release 
>> from the bioperl website). After successful installation I tried to 
>> persist a genbank file in my BioSQL database, which runs on a database 
>> server and is accessible using the mysql command shell. When using 
>> bioperl I receive the following error message:
>>
>> ================
>>
>> $ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb 
>> --dbuser myuser --dbpass mypasswd --namespace GenBank 
>> /home/doan/db-data/ref_chr1.gbk
>> Loading /local/doan/db-daten/ref_chr1.gbk ...
>> Bio::SeqIO: genbank cannot be found
>> Exception ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Failed to load module Bio::SeqIO::genbank. Weak references are 
>> not implemented in the version of perl at 
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91

From cjfields at uiuc.edu  Thu Jun 26 08:44:52 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 26 Jun 2008 07:44:52 -0500
Subject: [Bioperl-l] Problems when trying to persist a sequence in my
	BioSQL database using, BioPerl
In-Reply-To: <1DB86640-D4D5-4081-8DE5-E3181DD9D6A3@gmx.net>
References: <48611792.2060906@gmx.net>
	<1DB86640-D4D5-4081-8DE5-E3181DD9D6A3@gmx.net>
Message-ID: <E43BA660-68C5-46DB-9C55-69DA77AA70AC@uiuc.edu>

We could change that in Bio::Species (maybe with DESTROY), but  
Scalar::Util is also used several other BioPerl modules and is used in  
a few BioPerl dependencies, I believe.

cjfields:bioperl-live cjfields$ ack Scalar::Util

Bio/DB/SeqFeature/Store.pm
231:use Scalar::Util 'blessed';

Bio/FeatureIO/bed.pm
71:use Scalar::Util qw(looks_like_number);

Bio/Map/Position.pm
89:use Scalar::Util qw(looks_like_number);

Bio/Map/PositionI.pm
81:use Scalar::Util qw(looks_like_number);

Bio/Map/Relative.pm
89:use Scalar::Util qw(looks_like_number);

Bio/SeqFeature/Gene/GeneStructure.pm
68:    eval "use Scalar::Util qw(weaken);";

Bio/Species.pm
91:use Scalar::Util qw(weaken isweak);

Bio/Tree/Node.pm
76:use Scalar::Util qw(weaken isweak);

chris

On Jun 25, 2008, at 5:07 PM, Hilmar Lapp wrote:

> Hi Gabrielle,
>
> (note that I have changed the mailing list to bioperl - whoever  
> replies please cut biosql from the cc list, assuming that this  
> indeed isn't BioSQL's fault)
>
> given the error message below, Bio::SeqIO::genbank can be found, but  
> it fails to load because it requires Bio::Species, which in turn  
> imports support for weak references from Scalar::Util. The last step  
> fails, causing loading Bio::Species to fail, which in turn causes  
> Bio::SeqIO::genbank to fail to load.
>
> The real question is why your version of Perl doesn't seem to have  
> support for weak references (the reason for Scalar::Util failing to  
> load). Could you give details on your OS version and your version of  
> Perl (output of 'perl -V').
>
> The question for BioPerl is whether there is a fall-back mechanism  
> we might want to support if weak references aren't supported, rather  
> than rendering the genbank parser unusable. Sendu or Chris - any  
> thoughts on this?
>
> 	-hilmar
>
> On Jun 24, 2008, at 10:49 AM, Gabrielle Doan wrote:
>
>> Hi all,
>>
>> I am new to BioPerl and BioSQL so please excuse me if my question  
>> is a bit simple. I followed the installation files in the current  
>> version of BioPerl very strictly (I used the Bioperl 1.5.2,  
>> Developer Release from the bioperl website). After successful  
>> installation I tried to persist a genbank file in my BioSQL  
>> database, which runs on a database server and is accessible using  
>> the mysql command shell. When using bioperl I receive the following  
>> error message:
>>
>> ================
>>
>> $ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb -- 
>> dbuser myuser --dbpass mypasswd --namespace GenBank /home/doan/db- 
>> data/ref_chr1.gbk
>> Loading /local/doan/db-daten/ref_chr1.gbk ...
>> Bio::SeqIO: genbank cannot be found
>> Exception ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Failed to load module Bio::SeqIO::genbank. Weak references are  
>> not implemented in the version of perl at /usr/lib/perl5/site_perl/ 
>> 5.8.8/Bio/Species.pm line 91
>> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/ 
>> Bio/Species.pm line 91.
>> Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/ 
>> SeqIO/genbank.pm line 172.
>> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/ 
>> Bio/SeqIO/genbank.pm line 172.
>> Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/ 
>> Root/Root.pm line 425.
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
>> Root/Root.pm:359
>> STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/ 
>> Bio/Root/Root.pm:427
>> STACK: Bio::SeqIO::_load_format_module /usr/lib/perl5/site_perl/ 
>> 5.8.8/Bio/SeqIO.pm:555
>> STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm: 
>> 376
>> STACK: /usr/bin/bp_load_seqdatabase.pl:541
>> -----------------------------------------------------------
>>
>> For more information about the SeqIO system please see the SeqIO  
>> docs.
>> This includes ways of checking for formats at compile time, not run  
>> time
>> Can't call method "next_seq" on an undefined value at /usr/bin/ 
>> bp_load_seqdatabase.pl line 565.
>>
>> ================
>>
>> Unfortunately, even Google does not provide any hints when  
>> searching for the particular message. It seems that for some reason  
>> the path to the Bio::SeqIO::genbank module cannot be found. I am  
>> greateful for any hint!
>>
>> Cheers,
>> Gabrielle
>>
>> _______________________________________________
>> BioSQL-l mailing list
>> BioSQL-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
Institute for Genomic Biology/College of Veterinary Medicine
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Thu Jun 26 10:58:29 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 26 Jun 2008 09:58:29 -0500
Subject: [Bioperl-l] Problems when trying to persist a sequence in my
	BioSQL database using, BioPerl
In-Reply-To: <4863693E.2080706@sendu.me.uk>
References: <48611792.2060906@gmx.net>
	<1DB86640-D4D5-4081-8DE5-E3181DD9D6A3@gmx.net>
	<4863693E.2080706@sendu.me.uk>
Message-ID: <1CECB9E9-1CB2-433D-9AE6-9A8EC3B26E63@uiuc.edu>


On Jun 26, 2008, at 5:02 AM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>> The real question is why your version of Perl doesn't seem to have  
>> support for weak references (the reason for Scalar::Util failing to  
>> load). Could you give details on your OS version and your version  
>> of Perl (output of 'perl -V').
>
> Given that it seems to be perl 5.8.8, I'm guessing this is the  
> RedHat/Fedora issue:
>
> http://search.cpan.org/~adamk/Task-Weaken-1.02/lib/Task/Weaken.pm
>
> Solutions:
> First try installing the latest version of Scalar::Util yourself:
>
> perl -MCPAN -e shell
> force install Scalar::Util
>
> (and see that it gets installed in a place that is checked before  
> the Fedora version, or overwrites the Fedora version)
>
> If that doesn't work, you'll have to download and compile Perl  
> yourself from source (don't use Fedora's installation system).

The last option isn't really viable.  BioPerl is hard enough to  
install w/o having to rebuild perl from scratch.

For the time being, we should add Task::Weaken to the requirements and  
describe the issue within the installation notes, or at least link to  
a reference to it.

>> The question for BioPerl is whether there is a fall-back mechanism  
>> we might want to support if weak references aren't supported,  
>> rather than rendering the genbank parser unusable. Sendu or Chris -  
>> any thoughts on this?
>
> Firstly, Task::Weaken should get added to Build.pl as a requirement,  
> so people get better error messages. If we do that, however, the  
> whole of BioPerl doesn't get installed, never mind just the genbank  
> parser not being usable.
>
> As for a fall-back mechanism, I'm not really sure how that would  
> work. The easiest thing to do would be to just not deal with the  
> species lines if Bio::Species doesn't work. Is that an acceptable  
> fall-back? If not, more thought and discussion is needed. Make a  
> proposal: what would you want to happen?

Skipping the Species isn't an option; it's an integral part of the  
main BioPerl core and would be a PITA to deal with in bioperl-live,  
let alone bioperl-db.  We would have to wrap every Species-related  
call in an eval{} and fallback to something else.  Could we just set  
DESTROY or a root cleanup callback to delete the child/parent node  
references?

chris

From ymc at shgc.stanford.edu  Thu Jun 26 14:13:04 2008
From: ymc at shgc.stanford.edu (Yee Man Chan)
Date: Thu, 26 Jun 2008 11:13:04 -0700 (PDT)
Subject: [Bioperl-l] IUPAC support for DNA alignment
Message-ID: <Pine.GSO.4.58.0806261108390.5533@gleam.stanford.edu>


Hi all

	I am the owner of Bio::Tools::dpAlign. A user emailed me to add
support for IUPAC nucleotide codes. I am ok to add this feature but I
would like to know what are the conventions to handle these IUPAC codes.

	Suppose match is +3 and mismatch is -1. Then what should be the
score when T matches with U, A with W, A with D, A with N and A with X?
Does anyone know the conventions?

Thanks a lot.
Yee Man

From bix at sendu.me.uk  Thu Jun 26 14:47:18 2008
From: bix at sendu.me.uk (Sendu Bala)
Date: Thu, 26 Jun 2008 19:47:18 +0100
Subject: [Bioperl-l] Problems when trying to persist a sequence in my
 BioSQL database using, BioPerl
In-Reply-To: <1CECB9E9-1CB2-433D-9AE6-9A8EC3B26E63@uiuc.edu>
References: <48611792.2060906@gmx.net>
	<1DB86640-D4D5-4081-8DE5-E3181DD9D6A3@gmx.net>
	<4863693E.2080706@sendu.me.uk>
	<1CECB9E9-1CB2-433D-9AE6-9A8EC3B26E63@uiuc.edu>
Message-ID: <4863E436.7020505@sendu.me.uk>

Chris Fields wrote:
>> As for a fall-back mechanism, I'm not really sure how that would work. 
>> The easiest thing to do would be to just not deal with the species 
>> lines if Bio::Species doesn't work. Is that an acceptable fall-back? 
>> If not, more thought and discussion is needed. Make a proposal: what 
>> would you want to happen?
> 
> Skipping the Species isn't an option; it's an integral part of the main 
> BioPerl core and would be a PITA to deal with in bioperl-live, let alone 
> bioperl-db.  We would have to wrap every Species-related call in an 
> eval{} and fallback to something else.  Could we just set DESTROY or a 
> root cleanup callback to delete the child/parent node references?

Just to remind everyone, this all first came up here:
http://thread.gmane.org/gmane.comp.lang.perl.bio.general/13623
And the associated bug report is here:
http://bugzilla.open-bio.org/show_bug.cgi?id=2149

I really can't remember now, but there might be problems with your 
suggestion. But by all means try your idea and see if it works. I'll 
take a look at it myself soon.

From cjfields at uiuc.edu  Thu Jun 26 16:41:08 2008
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 26 Jun 2008 15:41:08 -0500
Subject: [Bioperl-l] Problems when trying to persist a sequence in my
	BioSQL database using, BioPerl
In-Reply-To: <4863E436.7020505@sendu.me.uk>
References: <48611792.2060906@gmx.net>
	<1DB86640-D4D5-4081-8DE5-E3181DD9D6A3@gmx.net>
	<4863693E.2080706@sendu.me.uk>
	<1CECB9E9-1CB2-433D-9AE6-9A8EC3B26E63@uiuc.edu>
	<4863E436.7020505@sendu.me.uk>
Message-ID: <50497C21-4187-4D0E-B695-CA88862F5FD8@uiuc.edu>

On Jun 26, 2008, at 1:47 PM, Sendu Bala wrote:

> Chris Fields wrote:
>>> As for a fall-back mechanism, I'm not really sure how that would  
>>> work. The easiest thing to do would be to just not deal with the  
>>> species lines if Bio::Species doesn't work. Is that an acceptable  
>>> fall-back? If not, more thought and discussion is needed. Make a  
>>> proposal: what would you want to happen?
>> Skipping the Species isn't an option; it's an integral part of the  
>> main BioPerl core and would be a PITA to deal with in bioperl-live,  
>> let alone bioperl-db.  We would have to wrap every Species-related  
>> call in an eval{} and fallback to something else.  Could we just  
>> set DESTROY or a root cleanup callback to delete the child/parent  
>> node references?
>
> Just to remind everyone, this all first came up here:
> http://thread.gmane.org/gmane.comp.lang.perl.bio.general/13623
> And the associated bug report is here:
> http://bugzilla.open-bio.org/show_bug.cgi?id=2149
>
> I really can't remember now, but there might be problems with your  
> suggestion. But by all means try your idea and see if it works. I'll  
> take a look at it myself soon.

Double-checked, DESTROY wouldn't be called unless all references to  
the root node were removed.  weaken() is really the best option; it  
might be possible to wrap everything in a proxy object if weaken  
doesn't work (though it's a bit of a hack):

http://www.perl.com/pub/a/2002/08/07/proxyobject.html?page=3

chris

From apapanicolaou at ice.mpg.de  Fri Jun 27 06:02:08 2008
From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou)
Date: Fri, 27 Jun 2008 12:02:08 +0200
Subject: [Bioperl-l] IUPAC support for DNA alignment
In-Reply-To: <Pine.GSO.4.58.0806261108390.5533@gleam.stanford.edu>
References: <Pine.GSO.4.58.0806261108390.5533@gleam.stanford.edu>
Message-ID: <4864BAA0.1000103@ice.mpg.de>

Hello

I'm the user who asked for it. I don't know of any conventions but 
perhaps people can help on this?

I'm not an expert at all but here is my opinion:
If you don't know the codon position (or even if it is coding) then you 
can't estimate the codon degeneracy. If you don't know the frequency of 
the bases representated in the degenerate site then you can't model it 
either on the DNA level. So any solution will be ad-hoc.

Regarding 2 base degenerate positions: My suggestion is that in a 
situation of alignment between, say a polymorphic and non polymorphic 
population for that site, and the user is interested in the distance 
between the populations, it would make sense to have the score to the 
full match.

Regarding 3 bases: I don't really know (see N below) but I 'd go for a 
full match again, assuming the user build the consensus.

Regarding N:
I think this is more likely to be missing data. I doubt you can have a 
SNP occuring four times in the same position (three times are expected 
under infinite sites, too for that matter). Or the consensus is derived 
from very diverged sequences. I wouldn't score N therefore.

Regarding X:
That one shouldn't find in a DNA alignment unless it is a mask. I'd 
expect no score as well.

my /practical/ suggestion would be to have the user to define it, as you 
allow for the other options, perhaps even allowing 2fold and 3fold 
degenerate IUPAC codes to be given different scores. That might save you 
(the owner) some future work when the user wants it...

many thanks to anyone who can help,
alexie

ps. Yee Man had cleverly suggested a workaround: one can use the Protein 
Matrix to create a scoring matrix. Might require some caution, 
remembering resetting the alphabet though?



Yee Man Chan wrote:
> Hi all
>
> 	I am the owner of Bio::Tools::dpAlign. A user emailed me to add
> support for IUPAC nucleotide codes. I am ok to add this feature but I
> would like to know what are the conventions to handle these IUPAC codes.
>
> 	Suppose match is +3 and mismatch is -1. Then what should be the
> score when T matches with U, A with W, A with D, A with N and A with X?
> Does anyone know the conventions?
>
> Thanks a lot.
> Yee Man
>
>   

-- 
"You can't find a hermit to teach you herming, because of course that rather spoils the whole thing."

    -- (Terry Pratchett, Small Gods)

Alexie Papanicolaou
Department of Entomology,
Max Planck Institute for Chemical Ecology,
Hans-Knoell-Strasse 8,
D-07745 Jena, Germany.



From hlapp at gmx.net  Fri Jun 27 08:47:12 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 27 Jun 2008 08:47:12 -0400
Subject: [Bioperl-l] IUPAC support for DNA alignment
In-Reply-To: <4864BAA0.1000103@ice.mpg.de>
References: <Pine.GSO.4.58.0806261108390.5533@gleam.stanford.edu>
	<4864BAA0.1000103@ice.mpg.de>
Message-ID: <06F151CF-9994-42FD-BA8C-5F93AA285DF4@gmx.net>

Hi Alexie,

On Jun 27, 2008, at 6:02 AM, Alexie Papanicolaou wrote:

> Hello
>
> I'm the user who asked for it. I don't know of any conventions but  
> perhaps people can help on this?
>
> I'm not an expert at all but here is my opinion:
> If you don't know the codon position (or even if it is coding) then  
> you can't estimate the codon degeneracy. If you don't know the  
> frequency of the bases representated in the degenerate site then you  
> can't model it either on the DNA level. So any solution will be ad- 
> hoc.
>
> Regarding 2 base degenerate positions: My suggestion is that in a  
> situation of alignment between, say a polymorphic and non  
> polymorphic population for that site, and the user is interested in  
> the distance between the populations, it would make sense to have  
> the score to the full match.
>
> Regarding 3 bases: I don't really know (see N below) but I 'd go for  
> a full match again, assuming the user build the consensus.

are you suggesting that a determined and a degenerate site aligned  
pairwise should score as much as two determined sites?

My (possibly naive) default would be to average over all  
possibilities, each weighted by base frequency (if base frequencies  
are assumed unequal or independent), thus integrating out the  
uncertainty. (For standard matrices, I think this would also result in  
N receiving zero score.)

In the end though, maybe there should be an option for a user to just  
provide a substitution matrix?

	-hilmar

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================




From apapanicolaou at ice.mpg.de  Fri Jun 27 10:13:57 2008
From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou)
Date: Fri, 27 Jun 2008 16:13:57 +0200
Subject: [Bioperl-l] IUPAC support for DNA alignment
In-Reply-To: <06F151CF-9994-42FD-BA8C-5F93AA285DF4@gmx.net>
References: <Pine.GSO.4.58.0806261108390.5533@gleam.stanford.edu>
	<4864BAA0.1000103@ice.mpg.de>
	<06F151CF-9994-42FD-BA8C-5F93AA285DF4@gmx.net>
Message-ID: <4864F5A5.9000601@ice.mpg.de>

Hello

I guess I didn't give enough info... (also sorry Yee Man, forget to CC 
you before)

Scenario 1 - polymorphic allele vs non-polymorphic one. e.g.
Let [A/G] be SNP in two alleles in population A and the one fixed allele 
[G] is in population B.

In this scenario we want to calculate the distance between one locus 
between two populations ,thus a degenerate site is not the result of 
uncertaintly but of reality. Obviously the best method is to provide a 
matrix (if the user can be bothered) but Yee Man already allows this 
option. Personally, I wouldn't really using an alignment score to 
measure distance though... The application here is: we first want to 
align those two sequences and there should be no penalty because there 
is a SNP in one population (then estimate distance with another algorithm).

Scenario 2 - uncertainty
If the scenario is that [A/G] is the result of uncertainty then I gladly 
agree with you! I'm also perplexed how to score IUPAC codes allowing for 
three nucleotides (i.e. there might not be a SNP after all... but then 
again infinitite sites doesn't have to hold - in some species less than 
others...)

Scenario 3 - a type profile alignment to a consensus
In my particular case, I'm doing something different: I have the 
consensus of an alignment of multiple sequences (dozens to hundrends 
depending on dataset) with some mismatches including a SNP say [A/G]. A 
third sequence that I wish to align has A in that position. So 
obviously, it shouldn't be penalized.

So it really depends on application and the user should be able to 
decide in the end...  (Yee Man already provides the option for a protein 
substitution matrix). It would be nice if we had the option of 
specifying it though much more easily (a simple switch) so i can use for 
scenario 3.
a
ps. sorry, my english is going the drain...


Hilmar Lapp wrote:
> Hi Alexie,
>
> On Jun 27, 2008, at 6:02 AM, Alexie Papanicolaou wrote:
>
>> Hello
>>
>> I'm the user who asked for it. I don't know of any conventions but 
>> perhaps people can help on this?
>>
>> I'm not an expert at all but here is my opinion:
>> If you don't know the codon position (or even if it is coding) then 
>> you can't estimate the codon degeneracy. If you don't know the 
>> frequency of the bases representated in the degenerate site then you 
>> can't model it either on the DNA level. So any solution will be ad-hoc.
>>
>> Regarding 2 base degenerate positions: My suggestion is that in a 
>> situation of alignment between, say a polymorphic and non polymorphic 
>> population for that site, and the user is interested in the distance 
>> between the populations, it would make sense to have the score to the 
>> full match.
>>
>> Regarding 3 bases: I don't really know (see N below) but I 'd go for 
>> a full match again, assuming the user build the consensus.
>
> are you suggesting that a determined and a degenerate site aligned 
> pairwise should score as much as two determined sites?
>
> My (possibly naive) default would be to average over all 
> possibilities, each weighted by base frequency (if base frequencies 
> are assumed unequal or independent), thus integrating out the 
> uncertainty. (For standard matrices, I think this would also result in 
> N receiving zero score.)
>
> In the end though, maybe there should be an option for a user to just 
> provide a substitution matrix?
>
>     -hilmar
>

-- 
--
"Eppur si evolve" ("And yet it evolves")
-Galileo Jr (ca 21st century)

--
Alexie Papanicolaou
Entomology
Max Planck Institute for Chemical Ecology
Hans Knoell Str 8
Jena 07745
Germany
Email apapanicolaou at ice.mpg.de
Tel +493641571561


From hlapp at gmx.net  Fri Jun 27 13:33:46 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 27 Jun 2008 13:33:46 -0400
Subject: [Bioperl-l] IUPAC support for DNA alignment
In-Reply-To: <4864F5A5.9000601@ice.mpg.de>
References: <Pine.GSO.4.58.0806261108390.5533@gleam.stanford.edu>
	<4864BAA0.1000103@ice.mpg.de>
	<06F151CF-9994-42FD-BA8C-5F93AA285DF4@gmx.net>
	<4864F5A5.9000601@ice.mpg.de>
Message-ID: <F48D267D-BC4D-48F2-98FB-F238259EB9E1@gmx.net>

So instead of the user choosing a special matrix you would like to  
have a simple argument (that would probably under the hood do exactly  
that)?

BTW Scenarios #1 and #3 sound more or less the same to me (i.e., you  
believe the degenerate code to reflect site polymorphism, not sequence  
uncertainty).

	-hilmar

On Jun 27, 2008, at 10:13 AM, Alexie Papanicolaou wrote:

> Hello
>
> I guess I didn't give enough info... (also sorry Yee Man, forget to  
> CC you before)
>
> Scenario 1 - polymorphic allele vs non-polymorphic one. e.g.
> Let [A/G] be SNP in two alleles in population A and the one fixed  
> allele [G] is in population B.
>
> In this scenario we want to calculate the distance between one locus  
> between two populations ,thus a degenerate site is not the result of  
> uncertaintly but of reality. Obviously the best method is to provide  
> a matrix (if the user can be bothered) but Yee Man already allows  
> this option. Personally, I wouldn't really using an alignment score  
> to measure distance though... The application here is: we first want  
> to align those two sequences and there should be no penalty because  
> there is a SNP in one population (then estimate distance with  
> another algorithm).
>
> Scenario 2 - uncertainty
> If the scenario is that [A/G] is the result of uncertainty then I  
> gladly agree with you! I'm also perplexed how to score IUPAC codes  
> allowing for three nucleotides (i.e. there might not be a SNP after  
> all... but then again infinitite sites doesn't have to hold - in  
> some species less than others...)
>
> Scenario 3 - a type profile alignment to a consensus
> In my particular case, I'm doing something different: I have the  
> consensus of an alignment of multiple sequences (dozens to hundrends  
> depending on dataset) with some mismatches including a SNP say [A/ 
> G]. A third sequence that I wish to align has A in that position. So  
> obviously, it shouldn't be penalized.
>
> So it really depends on application and the user should be able to  
> decide in the end...  (Yee Man already provides the option for a  
> protein substitution matrix). It would be nice if we had the option  
> of specifying it though much more easily (a simple switch) so i can  
> use for scenario 3.
> a
> ps. sorry, my english is going the drain...
>
>
> Hilmar Lapp wrote:
>> Hi Alexie,
>>
>> On Jun 27, 2008, at 6:02 AM, Alexie Papanicolaou wrote:
>>
>>> Hello
>>>
>>> I'm the user who asked for it. I don't know of any conventions but  
>>> perhaps people can help on this?
>>>
>>> I'm not an expert at all but here is my opinion:
>>> If you don't know the codon position (or even if it is coding)  
>>> then you can't estimate the codon degeneracy. If you don't know  
>>> the frequency of the bases representated in the degenerate site  
>>> then you can't model it either on the DNA level. So any solution  
>>> will be ad-hoc.
>>>
>>> Regarding 2 base degenerate positions: My suggestion is that in a  
>>> situation of alignment between, say a polymorphic and non  
>>> polymorphic population for that site, and the user is interested  
>>> in the distance between the populations, it would make sense to  
>>> have the score to the full match.
>>>
>>> Regarding 3 bases: I don't really know (see N below) but I 'd go  
>>> for a full match again, assuming the user build the consensus.
>>
>> are you suggesting that a determined and a degenerate site aligned  
>> pairwise should score as much as two determined sites?
>>
>> My (possibly naive) default would be to average over all  
>> possibilities, each weighted by base frequency (if base frequencies  
>> are assumed unequal or independent), thus integrating out the  
>> uncertainty. (For standard matrices, I think this would also result  
>> in N receiving zero score.)
>>
>> In the end though, maybe there should be an option for a user to  
>> just provide a substitution matrix?
>>
>>    -hilmar
>>
>
> -- 
> --
> "Eppur si evolve" ("And yet it evolves")
> -Galileo Jr (ca 21st century)
>
> --
> Alexie Papanicolaou
> Entomology
> Max Planck Institute for Chemical Ecology
> Hans Knoell Str 8
> Jena 07745
> Germany
> Email apapanicolaou at ice.mpg.de
> Tel +493641571561

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================




From apapanicolaou at ice.mpg.de  Fri Jun 27 13:40:34 2008
From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou)
Date: Fri, 27 Jun 2008 19:40:34 +0200
Subject: [Bioperl-l] IUPAC support for DNA alignment
In-Reply-To: <F48D267D-BC4D-48F2-98FB-F238259EB9E1@gmx.net>
References: <Pine.GSO.4.58.0806261108390.5533@gleam.stanford.edu>
	<4864BAA0.1000103@ice.mpg.de>
	<06F151CF-9994-42FD-BA8C-5F93AA285DF4@gmx.net>
	<4864F5A5.9000601@ice.mpg.de>
	<F48D267D-BC4D-48F2-98FB-F238259EB9E1@gmx.net>
Message-ID: <48652612.2010709@ice.mpg.de>

Yes, I don't want to use a special scoring for what i'm doing now. The 
option would allow to score a C or A aligned with M the same score as 
specified in -match. I guess it would be quickier if I just made my own 
matrix but there is a TODO line on IUPAC codes so I thought I push it a bit.

Yes from a computation point of view Sc 1 & 3 are the same.

a


Hilmar Lapp wrote:
> So instead of the user choosing a special matrix you would like to 
> have a simple argument (that would probably under the hood do exactly 
> that)?
>
> BTW Scenarios #1 and #3 sound more or less the same to me (i.e., you 
> believe the degenerate code to reflect site polymorphism, not sequence 
> uncertainty).
>
>     -hilmar
>
> On Jun 27, 2008, at 10:13 AM, Alexie Papanicolaou wrote:
>
>> Hello
>>
>> I guess I didn't give enough info... (also sorry Yee Man, forget to 
>> CC you before)
>>
>> Scenario 1 - polymorphic allele vs non-polymorphic one. e.g.
>> Let [A/G] be SNP in two alleles in population A and the one fixed 
>> allele [G] is in population B.
>>
>> In this scenario we want to calculate the distance between one locus 
>> between two populations ,thus a degenerate site is not the result of 
>> uncertaintly but of reality. Obviously the best method is to provide 
>> a matrix (if the user can be bothered) but Yee Man already allows 
>> this option. Personally, I wouldn't really using an alignment score 
>> to measure distance though... The application here is: we first want 
>> to align those two sequences and there should be no penalty because 
>> there is a SNP in one population (then estimate distance with another 
>> algorithm).
>>
>> Scenario 2 - uncertainty
>> If the scenario is that [A/G] is the result of uncertainty then I 
>> gladly agree with you! I'm also perplexed how to score IUPAC codes 
>> allowing for three nucleotides (i.e. there might not be a SNP after 
>> all... but then again infinitite sites doesn't have to hold - in some 
>> species less than others...)
>>
>> Scenario 3 - a type profile alignment to a consensus
>> In my particular case, I'm doing something different: I have the 
>> consensus of an alignment of multiple sequences (dozens to hundrends 
>> depending on dataset) with some mismatches including a SNP say [A/G]. 
>> A third sequence that I wish to align has A in that position. So 
>> obviously, it shouldn't be penalized.
>>
>> So it really depends on application and the user should be able to 
>> decide in the end...  (Yee Man already provides the option for a 
>> protein substitution matrix). It would be nice if we had the option 
>> of specifying it though much more easily (a simple switch) so i can 
>> use for scenario 3.
>> a
>> ps. sorry, my english is going the drain...
>>
>>
>> Hilmar Lapp wrote:
>>> Hi Alexie,
>>>
>>> On Jun 27, 2008, at 6:02 AM, Alexie Papanicolaou wrote:
>>>
>>>> Hello
>>>>
>>>> I'm the user who asked for it. I don't know of any conventions but 
>>>> perhaps people can help on this?
>>>>
>>>> I'm not an expert at all but here is my opinion:
>>>> If you don't know the codon position (or even if it is coding) then 
>>>> you can't estimate the codon degeneracy. If you don't know the 
>>>> frequency of the bases representated in the degenerate site then 
>>>> you can't model it either on the DNA level. So any solution will be 
>>>> ad-hoc.
>>>>
>>>> Regarding 2 base degenerate positions: My suggestion is that in a 
>>>> situation of alignment between, say a polymorphic and non 
>>>> polymorphic population for that site, and the user is interested in 
>>>> the distance between the populations, it would make sense to have 
>>>> the score to the full match.
>>>>
>>>> Regarding 3 bases: I don't really know (see N below) but I 'd go 
>>>> for a full match again, assuming the user build the consensus.
>>>
>>> are you suggesting that a determined and a degenerate site aligned 
>>> pairwise should score as much as two determined sites?
>>>
>>> My (possibly naive) default would be to average over all 
>>> possibilities, each weighted by base frequency (if base frequencies 
>>> are assumed unequal or independent), thus integrating out the 
>>> uncertainty. (For standard matrices, I think this would also result 
>>> in N receiving zero score.)
>>>
>>> In the end though, maybe there should be an option for a user to 
>>> just provide a substitution matrix?
>>>
>>>    -hilmar
>>>
>>
>> -- 
>> -- 
>> "Eppur si evolve" ("And yet it evolves")
>> -Galileo Jr (ca 21st century)
>>
>> -- 
>> Alexie Papanicolaou
>> Entomology
>> Max Planck Institute for Chemical Ecology
>> Hans Knoell Str 8
>> Jena 07745
>> Germany
>> Email apapanicolaou at ice.mpg.de
>> Tel +493641571561
>

-- 
--
"Eppur si evolve" ("And yet it evolves")
-Galileo Jr (ca 21st century)

--
Alexie Papanicolaou
Entomology
Max Planck Institute for Chemical Ecology
Hans Knoell Str 8
Jena 07745
Germany
Email apapanicolaou at ice.mpg.de
Tel +493641571561


From aaron.j.mackey at gsk.com  Fri Jun 27 10:09:57 2008
From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com)
Date: Fri, 27 Jun 2008 10:09:57 -0400
Subject: [Bioperl-l] IUPAC support for DNA alignment
In-Reply-To: <Pine.GSO.4.58.0806261108390.5533@gleam.stanford.edu>
Message-ID: <OF9F336113.A5FE3A67-ON85257475.004D4A2A-85257475.004DD0E9@gsk.com>

You could replicate what they do here with EST_GENOME (re-engineered to 
accept ambiguity codes):

  http://www.genome.org/cgi/content/short/17/2/212

But I think the answer is user-dependent -- some might want the "full 
score" (as in the above case), others might want the "(probabilistically) 
averaged score", etc.  So, let the scoring matrix be subclass-able (or 
mix-able), so that users can specify the exact desired behavior via a 
handful of predefined (and useful) behaviors.

-Aaron


From ymc at shgc.stanford.edu  Fri Jun 27 13:35:39 2008
From: ymc at shgc.stanford.edu (Yee Man Chan)
Date: Fri, 27 Jun 2008 10:35:39 -0700 (PDT)
Subject: [Bioperl-l] IUPAC support for DNA alignment
In-Reply-To: <OF9F336113.A5FE3A67-ON85257475.004D4A2A-85257475.004DD0E9@gsk.com>
References: <OF9F336113.A5FE3A67-ON85257475.004D4A2A-85257475.004DD0E9@gsk.com>
Message-ID: <Pine.GSO.4.58.0806271029510.17516@gleam.stanford.edu>


Hi guys

	What about providing two switches; one for full score and one for
probabilistic score?

Assume match is +3 and mismatch -1

Full score version:
1) T - U = +3 (I assume U is the same as T for alignment purpose, right?)
2) A - W = +3
3) A - D = +3
4) A - N = +3
5) A - X = -1 (not so sure about this one)

Probabilistic score version:
1) T - U = +3
2) A - W = +3/2-1/2 = +1
3) A - D = +3/3-1*2/3 = +1/3
4) A - N = +3/4-1*3/4 = 0
5) A - X = -1

What do you think?

Yee Man

On Fri, 27 Jun 2008 aaron.j.mackey at gsk.com wrote:

> You could replicate what they do here with EST_GENOME (re-engineered to
> accept ambiguity codes):
>
>   http://www.genome.org/cgi/content/short/17/2/212
>
> But I think the answer is user-dependent -- some might want the "full
> score" (as in the above case), others might want the "(probabilistically)
> averaged score", etc.  So, let the scoring matrix be subclass-able (or
> mix-able), so that users can specify the exact desired behavior via a
> handful of predefined (and useful) behaviors.
>
> -Aaron
>

From hlapp at gmx.net  Fri Jun 27 17:31:55 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 27 Jun 2008 17:31:55 -0400
Subject: [Bioperl-l] IUPAC support for DNA alignment
In-Reply-To: <Pine.GSO.4.58.0806271029510.17516@gleam.stanford.edu>
References: <OF9F336113.A5FE3A67-ON85257475.004D4A2A-85257475.004DD0E9@gsk.com>
	<Pine.GSO.4.58.0806271029510.17516@gleam.stanford.edu>
Message-ID: <134AD76F-E008-4288-91BB-CBFA6042F54A@gmx.net>


On Jun 27, 2008, at 1:35 PM, Yee Man Chan wrote:

>
> Hi guys
>
> 	What about providing two switches; one for full score and one for
> probabilistic score?
>
> Assume match is +3 and mismatch -1
>
> Full score version:
> 1) T - U = +3 (I assume U is the same as T for alignment purpose,  
> right?)

Right.

>
> 2) A - W = +3
> 3) A - D = +3
> 4) A - N = +3
> 5) A - X = -1 (not so sure about this one)
>
> Probabilistic score version:
> 1) T - U = +3
> 2) A - W = +3/2-1/2 = +1
> 3) A - D = +3/3-1*2/3 = +1/3
> 4) A - N = +3/4-1*3/4 = 0
> 5) A - X = -1

Note that there are also M, R, V, and H, and their complements (which  
by definition would not match your example of 'A').

Note also that the above implicitly assumes 50% GC content or equal  
likelihood of the code-constituent bases, which in reality for most  
coding sequences is not true.

Also, if you have a known polymorphism at the site, for 3-letter  
ambiguities not all 3 may be equally likely. For example, if you have  
letter D for a [A/G] SNP, one may not want to give 1/3 of weight to  
possibility T.

I would at least allow for the possibility to assign expected base  
frequencies and weight the ambiguous possibilities by those.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================




From pmiguel at purdue.edu  Sun Jun 29 19:44:31 2008
From: pmiguel at purdue.edu (Phillip SanMiguel)
Date: Sun, 29 Jun 2008 19:44:31 -0400
Subject: [Bioperl-l] How to read seq and quals into Bio::Seq::Quality object?
Message-ID: <48681E5F.2090607@purdue.edu>

What would be the accepted method to read the seq and qual values in 
from two files (a fasta and a qual file) and put them into 
Bio::Seq::Quality object. Is there a Bio::SeqIO method that would do that?

Phillip

From pmiguel at purdue.edu  Mon Jun 30 15:13:47 2008
From: pmiguel at purdue.edu (Phillip San Miguel)
Date: Mon, 30 Jun 2008 15:13:47 -0400
Subject: [Bioperl-l] How to read seq and quals into Bio::Seq::Quality
 object?
In-Reply-To: <48681E5F.2090607@purdue.edu>
References: <48681E5F.2090607@purdue.edu>
Message-ID: <4869306B.1010503@purdue.edu>

    Anyone? Sorry if I'm being a jerk. But on the basis of the existence 
of Bio::Seq::Quality it seems Bio::Seq::SeqWithQuality was deprecated. 
But the latter has a clear methodology to get from .fasta and 
.fasta.qual files into a new object. Once the new object is populated, 
looks like the former might be superior to use.
    But at the moment the only way I'm seeing to populate the ::Quality 
object from two files is to bring each file in with SeqIO and then use 
the primary seq and primary qual objects.  Thus created I'd export their 
sequence and quals as text and use that create the ::Quality object. If 
that is the way to go, fine. But I feel like I must be missing something.

Phillip
Purdue Genomics Core Facility

Phillip SanMiguel wrote:
> What would be the accepted method to read the seq and qual values in 
> from two files (a fasta and a qual file) and put them into 
> Bio::Seq::Quality object. Is there a Bio::SeqIO method that would do 
> that?
>
> Phillip
> _______________________________________________
> 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 Jun 30 15:34:00 2008
From: florent.angly at gmail.com (Florent Angly)
Date: Mon, 30 Jun 2008 12:34:00 -0700
Subject: [Bioperl-l] How to read seq and quals into Bio::Seq::Quality
 object?
In-Reply-To: <4869306B.1010503@purdue.edu>
References: <48681E5F.2090607@purdue.edu> <4869306B.1010503@purdue.edu>
Message-ID: <48693528.1060700@gmail.com>

I have looked at the issue before and haven't found an existing way that 
import nicely a FASTA and QUAL file at the same time. It would be 
valuable in my opinion, but at the moment I think you have to create two 
SeqIO objects and go through all the sequence records in both of them 
simultaneously.
Florent


Phillip San Miguel wrote:
>    Anyone? Sorry if I'm being a jerk. But on the basis of the 
> existence of Bio::Seq::Quality it seems Bio::Seq::SeqWithQuality was 
> deprecated. But the latter has a clear methodology to get from .fasta 
> and .fasta.qual files into a new object. Once the new object is 
> populated, looks like the former might be superior to use.
>    But at the moment the only way I'm seeing to populate the ::Quality 
> object from two files is to bring each file in with SeqIO and then use 
> the primary seq and primary qual objects.  Thus created I'd export 
> their sequence and quals as text and use that create the ::Quality 
> object. If that is the way to go, fine. But I feel like I must be 
> missing something.
>
> Phillip
> Purdue Genomics Core Facility
>
> Phillip SanMiguel wrote:
>> What would be the accepted method to read the seq and qual values in 
>> from two files (a fasta and a qual file) and put them into 
>> Bio::Seq::Quality object. Is there a Bio::SeqIO method that would do 
>> that?
>>
>> Phillip
>> _______________________________________________
>> 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 hlapp at gmx.net  Mon Jun 30 17:25:32 2008
From: hlapp at gmx.net (Hilmar Lapp)
Date: Mon, 30 Jun 2008 17:25:32 -0400
Subject: [Bioperl-l] How to read seq and quals into Bio::Seq::Quality
	object?
In-Reply-To: <4869306B.1010503@purdue.edu>
References: <48681E5F.2090607@purdue.edu> <4869306B.1010503@purdue.edu>
Message-ID: <D5CA93FB-D14A-46B0-A262-65F10A55FE06@gmx.net>

Apologies if this is a stupid comment, but have you looked at the  
Bio::SeqIO::qual format parser? Purportedly, it returns  
Bio::Seq::Quality objects.

	-hilmar

On Jun 30, 2008, at 3:13 PM, Phillip San Miguel wrote:

>   Anyone? Sorry if I'm being a jerk. But on the basis of the  
> existence of Bio::Seq::Quality it seems Bio::Seq::SeqWithQuality was  
> deprecated. But the latter has a clear methodology to get  
> from .fasta and .fasta.qual files into a new object. Once the new  
> object is populated, looks like the former might be superior to use.
>   But at the moment the only way I'm seeing to populate  
> the ::Quality object from two files is to bring each file in with  
> SeqIO and then use the primary seq and primary qual objects.  Thus  
> created I'd export their sequence and quals as text and use that  
> create the ::Quality object. If that is the way to go, fine. But I  
> feel like I must be missing something.
>
> Phillip
> Purdue Genomics Core Facility
>
> Phillip SanMiguel wrote:
>> What would be the accepted method to read the seq and qual values  
>> in from two files (a fasta and a qual file) and put them into  
>> Bio::Seq::Quality object. Is there a Bio::SeqIO method that would  
>> do that?
>>
>> Phillip
>> _______________________________________________
>> 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

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================