From joel.klein at wur.nl  Wed Feb  1 09:32:19 2012
From: joel.klein at wur.nl (Bradyjoel)
Date: Wed, 1 Feb 2012 06:32:19 -0800 (PST)
Subject: [Bioperl-l] Running into problems
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
References: <33228400.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
Message-ID: <33243492.post@talk.nabble.com>


Thank you for your help! I think I'm almost there, but I still get 1 more
error when I run the script:

$ perl blast2.pl
Searching gi|146341649|ref|YP_001206697.1|
Undefined subroutine &main::hsp_filter called at
/usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm line 298, <GEN6>
line 71.
 


Smithies, Russell wrote:
> 
> I'd probably cheat a bit and optimise my blast parameters so there's less
> output to process.
> Also, are you sure an e-value of 100 is what you're after? I'd be aiming
> much lower - probably 1e-6.
> It also pays to mask repeats if you're blasting against a whole genome to
> cut down on the number of rubbish hits.
> 
> --Russell
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
>> Sent: Tuesday, 31 January 2012 12:21 a.m.
>> To: Bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Running into problems
>> 
>> 
>> HI all,
>> 
>> I'm quite new to bioperl and tried to write a script that creates a
>> database
>> from a newly sequenced genome and then preforms a tblastn against a
>> multiple protein fasta file and then creates a blast report were only the
>> results that only preservers identity scores above 98%. However my script
>> keeps returning numerous errors and problems and since I have only a
>> little
>> experience I cannot determine were I went wrong. I include the code that
>> I
>> got so far in the attachment. Hope someone can help.
>> Regards Joel
>> 
>> http://old.nabble.com/file/p33228400/blast1.pl blast1.pl
>> --
>> View this message in context: http://old.nabble.com/Running-into-
>> problems-tp33228400p33228400.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
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/Running-into-problems-tp33228400p33243492.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From joel.klein at wur.nl  Wed Feb  1 09:33:19 2012
From: joel.klein at wur.nl (Bradyjoel)
Date: Wed, 1 Feb 2012 06:33:19 -0800 (PST)
Subject: [Bioperl-l] Running into problems
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
References: <33228400.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
Message-ID: <33243494.post@talk.nabble.com>


Thank you for your help! I think I'm almost there, but I still get 1 more
error when I run the script:

$ perl blast2.pl
Searching gi|146341649|ref|YP_001206697.1|
Undefined subroutine &main::hsp_filter called at
/usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm line 298, <GEN6>
line 71.
 


Smithies, Russell wrote:
> 
> I'd probably cheat a bit and optimise my blast parameters so there's less
> output to process.
> Also, are you sure an e-value of 100 is what you're after? I'd be aiming
> much lower - probably 1e-6.
> It also pays to mask repeats if you're blasting against a whole genome to
> cut down on the number of rubbish hits.
> 
> --Russell
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
>> Sent: Tuesday, 31 January 2012 12:21 a.m.
>> To: Bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Running into problems
>> 
>> 
>> HI all,
>> 
>> I'm quite new to bioperl and tried to write a script that creates a
>> database
>> from a newly sequenced genome and then preforms a tblastn against a
>> multiple protein fasta file and then creates a blast report were only the
>> results that only preservers identity scores above 98%. However my script
>> keeps returning numerous errors and problems and since I have only a
>> little
>> experience I cannot determine were I went wrong. I include the code that
>> I
>> got so far in the attachment. Hope someone can help.
>> Regards Joel
>> 
>> http://old.nabble.com/file/p33228400/blast1.pl blast1.pl
>> --
>> View this message in context: http://old.nabble.com/Running-into-
>> problems-tp33228400p33228400.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
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/Running-into-problems-tp33228400p33243494.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From joel.klein at wur.nl  Wed Feb  1 09:33:33 2012
From: joel.klein at wur.nl (Bradyjoel)
Date: Wed, 1 Feb 2012 06:33:33 -0800 (PST)
Subject: [Bioperl-l] Running into problems
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
References: <33228400.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
Message-ID: <33243496.post@talk.nabble.com>


Thank you for your help! I think I'm almost there, but I still get 1 more
error when I run the script:

$ perl blast2.pl
Searching gi|146341649|ref|YP_001206697.1|
Undefined subroutine &main::hsp_filter called at
/usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm line 298, <GEN6>
line 71.
 

Smithies, Russell wrote:
> 
> I'd probably cheat a bit and optimise my blast parameters so there's less
> output to process.
> Also, are you sure an e-value of 100 is what you're after? I'd be aiming
> much lower - probably 1e-6.
> It also pays to mask repeats if you're blasting against a whole genome to
> cut down on the number of rubbish hits.
> 
> --Russell
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
>> Sent: Tuesday, 31 January 2012 12:21 a.m.
>> To: Bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Running into problems
>> 
>> 
>> HI all,
>> 
>> I'm quite new to bioperl and tried to write a script that creates a
>> database
>> from a newly sequenced genome and then preforms a tblastn against a
>> multiple protein fasta file and then creates a blast report were only the
>> results that only preservers identity scores above 98%. However my script
>> keeps returning numerous errors and problems and since I have only a
>> little
>> experience I cannot determine were I went wrong. I include the code that
>> I
>> got so far in the attachment. Hope someone can help.
>> Regards Joel
>> 
>> http://old.nabble.com/file/p33228400/blast1.pl blast1.pl
>> --
>> View this message in context: http://old.nabble.com/Running-into-
>> problems-tp33228400p33228400.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
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://old.nabble.com/Running-into-problems-tp33228400p33243496.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From vivekkrishnakumar at gmail.com  Wed Feb  1 10:14:05 2012
From: vivekkrishnakumar at gmail.com (Vivek Krishnakumar)
Date: Wed, 1 Feb 2012 10:14:05 -0500
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating to
 Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
Message-ID: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>

Hello,

I would like to state my problem: Previously, i was working with a
Bio::DB:GFF backend database and was able to retrieve features from the
database by feature name using the function 'get_feature_by_name()'. But
recently, when I made the switch to Bio::DB::SeqFeature::Store to store the
exact same data points as before in the new db, invoking the
'get_feature_by_name()' function returns nothing.

Please refer to the following code snippet which is supposed to retrieve a
certain gene "locus" feature from the backend database and use that to get
the 'start' and 'end' coordinate of the feature based on the 'strand' on
which it is present.

my ($locus_obj, $gene_models) = get_annotation_db_features($locus,
$gff_dbh);

sub get_annotation_db_features {
    my ($locus, $gff_dbh) = @_;

    my ($locus_obj) = $gff_dbh->get_feature_by_name('Gene' => '$locus');

    my ($end5, $end3) = $locus_obj->strand == 1
      ? ($locus_obj->start, $locus_obj->end)
      : ($locus_obj->end, $locus_obj->start);

    my $segment = $gff_dbh->segment($locus_obj->refseq, $end5, $end3);
    my @gene_models =
      $segment->features('processed_transcript:working_models', -attributes
=> { 'Gene' => $locus });

    #will have to sort the gene models
    return ($locus_obj, \@gene_models);
}

Also, here is a snippet of the GFF3 file that is used to populate the
backend database:
##gff-version 3
chr2    working_models  gene    30427563    30429139    .   -   .
ID=gene_35804;Note=Zinc transporter;Name=Medtr2g097580
chr2    working_models  mRNA    30427563    30429139    .   -   .
ID=mrna_36255;Parent=gene_35804;Name=Medtr2g097580.1;conf_class=F
chr2    working_models  exon    30428491    30429139    .   -   .
ID=exon_120028;Parent=mrna_36255
chr2    working_models  exon    30427563    30428147    .   -   .
ID=exon_120029;Parent=mrna_36255
chr2    working_models  CDS 30428491    30429109    .   -   0
ID=cds_120028;Parent=mrna_36255
chr2    working_models  CDS 30427756    30428147    .   -   2
ID=cds_120029;Parent=mrna_36255

Considering that this gene locus is unique in the entire GFF file, If this
above GFF is loaded into the SeqFeature::Store database, you would expect
that running the following query should yield a count of "1":

SELECT count(f.id) FROM feature as f, name as n WHERE
(n.id=f.id<https://owa.jcvi.org/OWA/redir.aspx?C=6752206bd7374e2483702b789422d7b3&URL=http%3a%2f%2ff.id%2f>
AND
n.name = 'Medtr2g097580' AND n.display_name > 0);

And in my case, it does yield "1".

But if I use the function *get_feature_by_name*, retrieve the locus object
and try to get the strand of this object, I get the following error:

[error] Can't call method "strand" on an undefined value at
get_db_features.pl line 910.

As specified earlier, I do not have any problems if the backend is
Bio::DB::GFF.

>From the SeqFeature::Store documentation, we know that
'get_feature_by_name()' is in place for backward compatibility, I even
tried modifying the code snippet to call 'get_features_by_name()' instead,
but no matter what, I do not get any locus object back from this subroutine!

Could someone please guide me in the right direction and let me know if I
am making any mistakes here when migrating from GFF2 to GFF3?
Thanks in advance.
~ Vivek

From lincoln.stein at gmail.com  Wed Feb  1 10:20:12 2012
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Wed, 1 Feb 2012 10:20:12 -0500
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
Message-ID: <CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>

Try not putting single quotation marks around $locus, as you are searching
for a gene named (literally) "$locus". If this doesn't work,
use $gff_dbh->get_features_by_name($locus) instead, as I'm not sure whether
the Class=>Identifier syntax is accepted by Bio::DB::SeqFeature::Store.

Lincoln

On Wed, Feb 1, 2012 at 10:14 AM, Vivek Krishnakumar <
vivekkrishnakumar at gmail.com> wrote:

> Hello,
>
> I would like to state my problem: Previously, i was working with a
> Bio::DB:GFF backend database and was able to retrieve features from the
> database by feature name using the function 'get_feature_by_name()'. But
> recently, when I made the switch to Bio::DB::SeqFeature::Store to store the
> exact same data points as before in the new db, invoking the
> 'get_feature_by_name()' function returns nothing.
>
> Please refer to the following code snippet which is supposed to retrieve a
> certain gene "locus" feature from the backend database and use that to get
> the 'start' and 'end' coordinate of the feature based on the 'strand' on
> which it is present.
>
> my ($locus_obj, $gene_models) = get_annotation_db_features($locus,
> $gff_dbh);
>
> sub get_annotation_db_features {
>    my ($locus, $gff_dbh) = @_;
>
>    my ($locus_obj) = $gff_dbh->get_feature_by_name('Gene' => '$locus');
>
>    my ($end5, $end3) = $locus_obj->strand == 1
>      ? ($locus_obj->start, $locus_obj->end)
>      : ($locus_obj->end, $locus_obj->start);
>
>    my $segment = $gff_dbh->segment($locus_obj->refseq, $end5, $end3);
>    my @gene_models =
>      $segment->features('processed_transcript:working_models', -attributes
> => { 'Gene' => $locus });
>
>    #will have to sort the gene models
>    return ($locus_obj, \@gene_models);
> }
>
> Also, here is a snippet of the GFF3 file that is used to populate the
> backend database:
> ##gff-version 3
> chr2    working_models  gene    30427563    30429139    .   -   .
> ID=gene_35804;Note=Zinc transporter;Name=Medtr2g097580
> chr2    working_models  mRNA    30427563    30429139    .   -   .
> ID=mrna_36255;Parent=gene_35804;Name=Medtr2g097580.1;conf_class=F
> chr2    working_models  exon    30428491    30429139    .   -   .
> ID=exon_120028;Parent=mrna_36255
> chr2    working_models  exon    30427563    30428147    .   -   .
> ID=exon_120029;Parent=mrna_36255
> chr2    working_models  CDS 30428491    30429109    .   -   0
> ID=cds_120028;Parent=mrna_36255
> chr2    working_models  CDS 30427756    30428147    .   -   2
> ID=cds_120029;Parent=mrna_36255
>
> Considering that this gene locus is unique in the entire GFF file, If this
> above GFF is loaded into the SeqFeature::Store database, you would expect
> that running the following query should yield a count of "1":
>
> SELECT count(f.id) FROM feature as f, name as n WHERE
> (n.id=f.id<
> https://owa.jcvi.org/OWA/redir.aspx?C=6752206bd7374e2483702b789422d7b3&URL=http%3a%2f%2ff.id%2f
> >
> AND
> n.name = 'Medtr2g097580' AND n.display_name > 0);
>
> And in my case, it does yield "1".
>
> But if I use the function *get_feature_by_name*, retrieve the locus object
> and try to get the strand of this object, I get the following error:
>
> [error] Can't call method "strand" on an undefined value at
> get_db_features.pl line 910.
>
> As specified earlier, I do not have any problems if the backend is
> Bio::DB::GFF.
>
> >From the SeqFeature::Store documentation, we know that
> 'get_feature_by_name()' is in place for backward compatibility, I even
> tried modifying the code snippet to call 'get_features_by_name()' instead,
> but no matter what, I do not get any locus object back from this
> subroutine!
>
> Could someone please guide me in the right direction and let me know if I
> am making any mistakes here when migrating from GFF2 to GFF3?
> Thanks in advance.
> ~ Vivek
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



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

From cjfields at illinois.edu  Wed Feb  1 10:37:06 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 1 Feb 2012 15:37:06 +0000
Subject: [Bioperl-l] Running into problems
In-Reply-To: <33243496.post@talk.nabble.com>
References: <33228400.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
	<33243496.post@talk.nabble.com>
Message-ID: <23334B19-0139-4279-A9ED-B442EED34052@illinois.edu>

That looks like a bug to me, but it's hard to say w/o having more information, such as the actual code you are using, the version of BioPerl, etc.  See the BioPerl FAQ to get the version number.

chris

On Feb 1, 2012, at 8:33 AM, Bradyjoel wrote:

> 
> Thank you for your help! I think I'm almost there, but I still get 1 more
> error when I run the script:
> 
> $ perl blast2.pl
> Searching gi|146341649|ref|YP_001206697.1|
> Undefined subroutine &main::hsp_filter called at
> /usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm line 298, <GEN6>
> line 71.
> 
> 
> Smithies, Russell wrote:
>> 
>> I'd probably cheat a bit and optimise my blast parameters so there's less
>> output to process.
>> Also, are you sure an e-value of 100 is what you're after? I'd be aiming
>> much lower - probably 1e-6.
>> It also pays to mask repeats if you're blasting against a whole genome to
>> cut down on the number of rubbish hits.
>> 
>> --Russell
>> 
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
>>> Sent: Tuesday, 31 January 2012 12:21 a.m.
>>> To: Bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] Running into problems
>>> 
>>> 
>>> HI all,
>>> 
>>> I'm quite new to bioperl and tried to write a script that creates a
>>> database
>>> from a newly sequenced genome and then preforms a tblastn against a
>>> multiple protein fasta file and then creates a blast report were only the
>>> results that only preservers identity scores above 98%. However my script
>>> keeps returning numerous errors and problems and since I have only a
>>> little
>>> experience I cannot determine were I went wrong. I include the code that
>>> I
>>> got so far in the attachment. Hope someone can help.
>>> Regards Joel
>>> 
>>> http://old.nabble.com/file/p33228400/blast1.pl blast1.pl
>>> --
>>> View this message in context: http://old.nabble.com/Running-into-
>>> problems-tp33228400p33228400.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
>> =======================================================================
>> Attention: The information contained in this message and/or attachments
>> from AgResearch Limited is intended only for the persons or entities
>> to which it is addressed and may contain confidential and/or privileged
>> material. Any review, retransmission, dissemination or other use of, or
>> taking of any action in reliance upon, this information by persons or
>> entities other than the intended recipients is prohibited by AgResearch
>> Limited. If you have received this message in error, please notify the
>> sender immediately.
>> =======================================================================
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> -- 
> View this message in context: http://old.nabble.com/Running-into-problems-tp33228400p33243496.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 vivekkrishnakumar at gmail.com  Wed Feb  1 10:50:43 2012
From: vivekkrishnakumar at gmail.com (Vivek Krishnakumar)
Date: Wed, 1 Feb 2012 07:50:43 -0800 (PST)
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
	<CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
Message-ID: <10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>

Hi Lincoln,

Thanks very much for your suggestions. Not sure how the single quotation 
marks appeared around the $locus variable. But looks like it was only in 
the email. Fortunately did not have quotes around the variable in my 
original code.

Now, when I switch over to 'get_features_by_name()', my script does not run 
to completion.

I want to mention that this snippet of code is part of a larger CGI script 
that interfaces with the SeqFeature backend DB. When I modify the function 
call to $gff_dbh->get_features_by_name($locus), the script just runs 
indefinitely and returns absolutely nothing. I did put in a warn statement 
to see if the correct locus ID is being passed to the function (I am able 
to see the warning message in my apache error log), which seems to be fine. 
But the moment it reaches the function call step, the CGI script freezes up 
and I am unable to do anything. It just ends up as a rogue process owned by 
the 'daemon' user and continues to use up a lot of memory.

I am using the following BioPerl modules in this CGI script:
use Bio::SeqIO;
use Bio::SearchIO;
use Bio::DB::SeqFeature::Store;
use Bio::SeqFeature::Generic;
use Bio::Graphics;
use Bio::Graphics::Feature;

Could any of these be interfering with get_features_by_name()?

Thank you.
Vivek

From vivekkrishnakumar at gmail.com  Wed Feb  1 10:50:43 2012
From: vivekkrishnakumar at gmail.com (Vivek Krishnakumar)
Date: Wed, 1 Feb 2012 07:50:43 -0800 (PST)
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
	<CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
Message-ID: <10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>

Hi Lincoln,

Thanks very much for your suggestions. Not sure how the single quotation 
marks appeared around the $locus variable. But looks like it was only in 
the email. Fortunately did not have quotes around the variable in my 
original code.

Now, when I switch over to 'get_features_by_name()', my script does not run 
to completion.

I want to mention that this snippet of code is part of a larger CGI script 
that interfaces with the SeqFeature backend DB. When I modify the function 
call to $gff_dbh->get_features_by_name($locus), the script just runs 
indefinitely and returns absolutely nothing. I did put in a warn statement 
to see if the correct locus ID is being passed to the function (I am able 
to see the warning message in my apache error log), which seems to be fine. 
But the moment it reaches the function call step, the CGI script freezes up 
and I am unable to do anything. It just ends up as a rogue process owned by 
the 'daemon' user and continues to use up a lot of memory.

I am using the following BioPerl modules in this CGI script:
use Bio::SeqIO;
use Bio::SearchIO;
use Bio::DB::SeqFeature::Store;
use Bio::SeqFeature::Generic;
use Bio::Graphics;
use Bio::Graphics::Feature;

Could any of these be interfering with get_features_by_name()?

Thank you.
Vivek

From scott at scottcain.net  Wed Feb  1 11:26:36 2012
From: scott at scottcain.net (Scott Cain)
Date: Wed, 1 Feb 2012 11:26:36 -0500
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
	<CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
	<10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>
Message-ID: <CA+JTaozJVAZZrmZuy6dfGr-56fVHcoOyJXdkPpZ2=_vhnJEzzg@mail.gmail.com>

Hi Vivek,

I responded to your original email and I suspect you may have missed
it.  I'll copy it below.  Another few things: how does $locus get
populated?  Are you sure what you expect to be there is?

Also, to answer your question about the other bioperl modules you're
using: no, I don't think that's interfering.

Scott

------------------------------------------------
Hello Vivek,

In your GFF3, you don't have any features of class "Gene".  In GFF2,
the class was the text string that started the ninth column, like
this:

chr2   .  gene    30427563    30429139    .   -   .  Gene 35804

where the class would be Gene and the name (also called group) would
be 35804.  Class is not a particularly well defined concept in GFF3,
so the easiest way to restore functionality to your script is to
change the call from this:

 my ($locus_obj) = $gff_dbh->get_feature_by_name('Gene' => $locus);

to this:

 my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus,
-type => 'gene');

I believe (though haven't tested it myself in a very long time) that
you can embed class in the name of the feature, like this:

chr2  .  gene    30427563    30429139    .   -   .  Name=Gene:Medtr2g097580

which may or may not be easier, depending on your data and your code base.

Scott


On Wed, Feb 1, 2012 at 10:50 AM, Vivek Krishnakumar
<vivekkrishnakumar at gmail.com> wrote:
> Hi Lincoln,
>
> Thanks very much for your suggestions. Not sure how the single quotation
> marks appeared around the $locus variable. But looks like it was only in
> the email. Fortunately did not have quotes around the variable in my
> original code.
>
> Now, when I switch over to 'get_features_by_name()', my script does not run
> to completion.
>
> I want to mention that this snippet of code is part of a larger CGI script
> that interfaces with the SeqFeature backend DB. When I modify the function
> call to $gff_dbh->get_features_by_name($locus), the script just runs
> indefinitely and returns absolutely nothing. I did put in a warn statement
> to see if the correct locus ID is being passed to the function (I am able
> to see the warning message in my apache error log), which seems to be fine.
> But the moment it reaches the function call step, the CGI script freezes up
> and I am unable to do anything. It just ends up as a rogue process owned by
> the 'daemon' user and continues to use up a lot of memory.
>
> I am using the following BioPerl modules in this CGI script:
> use Bio::SeqIO;
> use Bio::SearchIO;
> use Bio::DB::SeqFeature::Store;
> use Bio::SeqFeature::Generic;
> use Bio::Graphics;
> use Bio::Graphics::Feature;
>
> Could any of these be interfering with get_features_by_name()?
>
> Thank you.
> Vivek
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



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


From joel.klein at wur.nl  Wed Feb  1 11:47:14 2012
From: joel.klein at wur.nl (Bradyjoel)
Date: Wed, 1 Feb 2012 08:47:14 -0800 (PST)
Subject: [Bioperl-l] Running into problems
In-Reply-To: <23334B19-0139-4279-A9ED-B442EED34052@illinois.edu>
References: <33228400.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
	<33243496.post@talk.nabble.com>
	<23334B19-0139-4279-A9ED-B442EED34052@illinois.edu>
Message-ID: <33244172.post@talk.nabble.com>


the bioperl version that I have found with this command is:
$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
1.006901
$  perl -MBio::Root::Version -e 'printf "%vd\n",
$Bio::Root::Version::VERSION'
49.46.48.48.54.57.48.49

And I put the perl code that I'm currently using in the attachment. 



Fields, Christopher J wrote:
> 
> That looks like a bug to me, but it's hard to say w/o having more
> information, such as the actual code you are using, the version of
> BioPerl, etc.  See the BioPerl FAQ to get the version number.
> 
> chris
> 
> On Feb 1, 2012, at 8:33 AM, Bradyjoel wrote:
> 
>> 
>> Thank you for your help! I think I'm almost there, but I still get 1 more
>> error when I run the script:
>> 
>> $ perl blast2.pl
>> Searching gi|146341649|ref|YP_001206697.1|
>> Undefined subroutine &main::hsp_filter called at
>> /usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm line 298, <GEN6>
>> line 71.
>> 
>> 
>> Smithies, Russell wrote:
>>> 
>>> I'd probably cheat a bit and optimise my blast parameters so there's
>>> less
>>> output to process.
>>> Also, are you sure an e-value of 100 is what you're after? I'd be aiming
>>> much lower - probably 1e-6.
>>> It also pays to mask repeats if you're blasting against a whole genome
>>> to
>>> cut down on the number of rubbish hits.
>>> 
>>> --Russell
>>> 
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
>>>> Sent: Tuesday, 31 January 2012 12:21 a.m.
>>>> To: Bioperl-l at lists.open-bio.org
>>>> Subject: [Bioperl-l] Running into problems
>>>> 
>>>> 
>>>> HI all,
>>>> 
>>>> I'm quite new to bioperl and tried to write a script that creates a
>>>> database
>>>> from a newly sequenced genome and then preforms a tblastn against a
>>>> multiple protein fasta file and then creates a blast report were only
>>>> the
>>>> results that only preservers identity scores above 98%. However my
>>>> script
>>>> keeps returning numerous errors and problems and since I have only a
>>>> little
>>>> experience I cannot determine were I went wrong. I include the code
>>>> that
>>>> I
>>>> got so far in the attachment. Hope someone can help.
>>>> Regards Joel
>>>> 
>>>> http://old.nabble.com/file/p33228400/blast1.pl blast1.pl
>>>> --
>>>> View this message in context: http://old.nabble.com/Running-into-
>>>> problems-tp33228400p33228400.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
>>> =======================================================================
>>> Attention: The information contained in this message and/or attachments
>>> from AgResearch Limited is intended only for the persons or entities
>>> to which it is addressed and may contain confidential and/or privileged
>>> material. Any review, retransmission, dissemination or other use of, or
>>> taking of any action in reliance upon, this information by persons or
>>> entities other than the intended recipients is prohibited by AgResearch
>>> Limited. If you have received this message in error, please notify the
>>> sender immediately.
>>> =======================================================================
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>> 
>> -- 
>> View this message in context:
>> http://old.nabble.com/Running-into-problems-tp33228400p33243496.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://old.nabble.com/Running-into-problems-tp33228400p33244172.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From vivekkrishnakumar at gmail.com  Wed Feb  1 11:51:46 2012
From: vivekkrishnakumar at gmail.com (Vivek Krishnakumar)
Date: Wed, 1 Feb 2012 11:51:46 -0500
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <CA+JTaozJVAZZrmZuy6dfGr-56fVHcoOyJXdkPpZ2=_vhnJEzzg@mail.gmail.com>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
	<CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
	<10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>
	<CA+JTaozJVAZZrmZuy6dfGr-56fVHcoOyJXdkPpZ2=_vhnJEzzg@mail.gmail.com>
Message-ID: <CAHtOd9kt+L1xNQTREHGXkN13XwV0JRONe_hV_8Da2FBOn_9hxg@mail.gmail.com>

Hi Scott,

Thanks very much for your suggestions. Looks I did miss it somehow
(confusion was caused because I was using both bioperl-l at googlegroups and
bioperl-l at open-bio)

Anyway, I had modified my function exactly like your suggestion:
my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus, -type =>
'gene');

But doing so just returns the following error:

-------------------- EXCEPTION --------------------
MSG: segment() called in a scalar context but multiple features match.
Either call in a list context or narrow your search using the -types
or -class arguments

STACK Bio::DB::SeqFeature::Store::segment
/usr/local/packages/perl-5.10.1/lib/5.10.1/Bio/DB/SeqFeature/Store.pm:1322
STACK main::get_annotation_db_features
/opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:899
STACK main::structural_annotation
/opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:660
STACK toplevel /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:119
-------------------------------------------

which would suggest to oneself that there are several such features with
the same ID. But in fact, I was able to verify by querying the database
that I have only one such locus.

As for your question regarding how $locus is populated, it is populated
from a CGI parameter passed to the script. I know that I am only passing it
one locus ID. And as I mentioned earlier in this thread, the warning
statement I inserted before making the function call shows me that there is
only one ID in the $locus variable.

My last resort now is to try as you suggested and modify my GFF3 file and
embed the -class => 'Gene' into the "Name" attribute. While doing so,
should I also embed the 'mRNA' class into the "Name" attribute of the mRNA
feature like so:

chr2    working_models  mRNA    30427563    30429139    .   -   .
ID=mrna_36255;Parent=gene_35804;Name=mRNA:Medtr2g097580.1;conf_class=F

Subsequently, should I modify the function call to include the 'class':
my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus, -type =>
'gene', -class => 'Gene');

Thank you.
Vivek

On Wed, Feb 1, 2012 at 11:26 AM, Scott Cain <scott at scottcain.net> wrote:

> Hi Vivek,
>
> I responded to your original email and I suspect you may have missed
> it.  I'll copy it below.  Another few things: how does $locus get
> populated?  Are you sure what you expect to be there is?
>
> Also, to answer your question about the other bioperl modules you're
> using: no, I don't think that's interfering.
>
> Scott
>
> ------------------------------------------------
> Hello Vivek,
>
> In your GFF3, you don't have any features of class "Gene".  In GFF2,
> the class was the text string that started the ninth column, like
> this:
>
> chr2   .  gene    30427563    30429139    .   -   .  Gene 35804
>
> where the class would be Gene and the name (also called group) would
> be 35804.  Class is not a particularly well defined concept in GFF3,
> so the easiest way to restore functionality to your script is to
> change the call from this:
>
>  my ($locus_obj) = $gff_dbh->get_feature_by_name('Gene' => $locus);
>
> to this:
>
>  my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus,
> -type => 'gene');
>
> I believe (though haven't tested it myself in a very long time) that
> you can embed class in the name of the feature, like this:
>
> chr2  .  gene    30427563    30429139    .   -   .  Name=Gene:Medtr2g097580
>
> which may or may not be easier, depending on your data and your code base.
>
> Scott
>
>
> On Wed, Feb 1, 2012 at 10:50 AM, Vivek Krishnakumar
> <vivekkrishnakumar at gmail.com> wrote:
> > Hi Lincoln,
> >
> > Thanks very much for your suggestions. Not sure how the single quotation
> > marks appeared around the $locus variable. But looks like it was only in
> > the email. Fortunately did not have quotes around the variable in my
> > original code.
> >
> > Now, when I switch over to 'get_features_by_name()', my script does not
> run
> > to completion.
> >
> > I want to mention that this snippet of code is part of a larger CGI
> script
> > that interfaces with the SeqFeature backend DB. When I modify the
> function
> > call to $gff_dbh->get_features_by_name($locus), the script just runs
> > indefinitely and returns absolutely nothing. I did put in a warn
> statement
> > to see if the correct locus ID is being passed to the function (I am able
> > to see the warning message in my apache error log), which seems to be
> fine.
> > But the moment it reaches the function call step, the CGI script freezes
> up
> > and I am unable to do anything. It just ends up as a rogue process owned
> by
> > the 'daemon' user and continues to use up a lot of memory.
> >
> > I am using the following BioPerl modules in this CGI script:
> > use Bio::SeqIO;
> > use Bio::SearchIO;
> > use Bio::DB::SeqFeature::Store;
> > use Bio::SeqFeature::Generic;
> > use Bio::Graphics;
> > use Bio::Graphics::Feature;
> >
> > Could any of these be interfering with get_features_by_name()?
> >
> > Thank you.
> > Vivek
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

From cjfields at illinois.edu  Wed Feb  1 11:55:11 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 1 Feb 2012 16:55:11 +0000
Subject: [Bioperl-l] Running into problems
In-Reply-To: <33244172.post@talk.nabble.com>
References: <33228400.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
	<33243496.post@talk.nabble.com>
	<23334B19-0139-4279-A9ED-B442EED34052@illinois.edu>
	<33244172.post@talk.nabble.com>
Message-ID: <7622D0FC-5E84-461A-9966-2D6C713BC273@illinois.edu>

It's possible the attachment was scrubbed, can you send this to me directly?

chris

On Feb 1, 2012, at 10:47 AM, Bradyjoel wrote:

> 
> the bioperl version that I have found with this command is:
> $ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
> 1.006901
> $  perl -MBio::Root::Version -e 'printf "%vd\n",
> $Bio::Root::Version::VERSION'
> 49.46.48.48.54.57.48.49
> 
> And I put the perl code that I'm currently using in the attachment. 
> 
> 
> 
> Fields, Christopher J wrote:
>> 
>> That looks like a bug to me, but it's hard to say w/o having more
>> information, such as the actual code you are using, the version of
>> BioPerl, etc.  See the BioPerl FAQ to get the version number.
>> 
>> chris
>> 
>> On Feb 1, 2012, at 8:33 AM, Bradyjoel wrote:
>> 
>>> 
>>> Thank you for your help! I think I'm almost there, but I still get 1 more
>>> error when I run the script:
>>> 
>>> $ perl blast2.pl
>>> Searching gi|146341649|ref|YP_001206697.1|
>>> Undefined subroutine &main::hsp_filter called at
>>> /usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm line 298, <GEN6>
>>> line 71.
>>> 
>>> 
>>> Smithies, Russell wrote:
>>>> 
>>>> I'd probably cheat a bit and optimise my blast parameters so there's
>>>> less
>>>> output to process.
>>>> Also, are you sure an e-value of 100 is what you're after? I'd be aiming
>>>> much lower - probably 1e-6.
>>>> It also pays to mask repeats if you're blasting against a whole genome
>>>> to
>>>> cut down on the number of rubbish hits.
>>>> 
>>>> --Russell
>>>> 
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
>>>>> Sent: Tuesday, 31 January 2012 12:21 a.m.
>>>>> To: Bioperl-l at lists.open-bio.org
>>>>> Subject: [Bioperl-l] Running into problems
>>>>> 
>>>>> 
>>>>> HI all,
>>>>> 
>>>>> I'm quite new to bioperl and tried to write a script that creates a
>>>>> database
>>>>> from a newly sequenced genome and then preforms a tblastn against a
>>>>> multiple protein fasta file and then creates a blast report were only
>>>>> the
>>>>> results that only preservers identity scores above 98%. However my
>>>>> script
>>>>> keeps returning numerous errors and problems and since I have only a
>>>>> little
>>>>> experience I cannot determine were I went wrong. I include the code
>>>>> that
>>>>> I
>>>>> got so far in the attachment. Hope someone can help.
>>>>> Regards Joel
>>>>> 
>>>>> http://old.nabble.com/file/p33228400/blast1.pl blast1.pl
>>>>> --
>>>>> View this message in context: http://old.nabble.com/Running-into-
>>>>> problems-tp33228400p33228400.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
>>>> =======================================================================
>>>> Attention: The information contained in this message and/or attachments
>>>> from AgResearch Limited is intended only for the persons or entities
>>>> to which it is addressed and may contain confidential and/or privileged
>>>> material. Any review, retransmission, dissemination or other use of, or
>>>> taking of any action in reliance upon, this information by persons or
>>>> entities other than the intended recipients is prohibited by AgResearch
>>>> Limited. If you have received this message in error, please notify the
>>>> sender immediately.
>>>> =======================================================================
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
>>> 
>>> -- 
>>> View this message in context:
>>> http://old.nabble.com/Running-into-problems-tp33228400p33243496.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://old.nabble.com/Running-into-problems-tp33228400p33244172.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 vivekkrishnakumar at gmail.com  Wed Feb  1 12:37:47 2012
From: vivekkrishnakumar at gmail.com (Vivek Krishnakumar)
Date: Wed, 1 Feb 2012 12:37:47 -0500
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <CAHtOd9kt+L1xNQTREHGXkN13XwV0JRONe_hV_8Da2FBOn_9hxg@mail.gmail.com>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
	<CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
	<10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>
	<CA+JTaozJVAZZrmZuy6dfGr-56fVHcoOyJXdkPpZ2=_vhnJEzzg@mail.gmail.com>
	<CAHtOd9kt+L1xNQTREHGXkN13XwV0JRONe_hV_8Da2FBOn_9hxg@mail.gmail.com>
Message-ID: <CAHtOd9kicEM3MPjViFp-hV3FYT4+EfoJq_ZdWKT5kFbsh2j=eA@mail.gmail.com>

Hi Scott and Lincoln,

Thanks for all your suggestions. I figured out the mistake I was making.

Apart from switching to get_features_by_name(), I also need to switch from
$locus_obj->refseq to $locus_obj->seq_id to get the reference sequence
identifier. This was interfering with the $gff_dbh->segment() call.

Also, it looks like I do not need to embed the 'Gene' class in the GFF file
anymore.

Thanks again.
Regards,
~Vivek

On Wed, Feb 1, 2012 at 11:51 AM, Vivek Krishnakumar <
vivekkrishnakumar at gmail.com> wrote:

> Hi Scott,
>
> Thanks very much for your suggestions. Looks I did miss it somehow
> (confusion was caused because I was using both bioperl-l at googlegroups and
> bioperl-l at open-bio)
>
> Anyway, I had modified my function exactly like your suggestion:
>
> my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus, -type =>
> 'gene');
>
> But doing so just returns the following error:
>
> -------------------- EXCEPTION --------------------
> MSG: segment() called in a scalar context but multiple features match.
> Either call in a list context or narrow your search using the -types or -class arguments
>
> STACK Bio::DB::SeqFeature::Store::segment /usr/local/packages/perl-5.10.1/lib/5.10.1/Bio/DB/SeqFeature/Store.pm:1322
> STACK main::get_annotation_db_features /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:899
> STACK main::structural_annotation /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:660
> STACK toplevel /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:119
> -------------------------------------------
>
> which would suggest to oneself that there are several such features with
> the same ID. But in fact, I was able to verify by querying the database
> that I have only one such locus.
>
> As for your question regarding how $locus is populated, it is populated
> from a CGI parameter passed to the script. I know that I am only passing it
> one locus ID. And as I mentioned earlier in this thread, the warning
> statement I inserted before making the function call shows me that there is
> only one ID in the $locus variable.
>
> My last resort now is to try as you suggested and modify my GFF3 file and
> embed the -class => 'Gene' into the "Name" attribute. While doing so,
> should I also embed the 'mRNA' class into the "Name" attribute of the mRNA
> feature like so:
>
> chr2    working_models  mRNA    30427563    30429139    .   -   .
> ID=mrna_36255;Parent=gene_35804;Name=mRNA:Medtr2g097580.1;conf_class=F
>
> Subsequently, should I modify the function call to include the 'class':
> my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus, -type =>
> 'gene', -class => 'Gene');
>
> Thank you.
> Vivek
>
>
> On Wed, Feb 1, 2012 at 11:26 AM, Scott Cain <scott at scottcain.net> wrote:
>
>> Hi Vivek,
>>
>> I responded to your original email and I suspect you may have missed
>> it.  I'll copy it below.  Another few things: how does $locus get
>> populated?  Are you sure what you expect to be there is?
>>
>> Also, to answer your question about the other bioperl modules you're
>> using: no, I don't think that's interfering.
>>
>> Scott
>>
>> ------------------------------------------------
>> Hello Vivek,
>>
>> In your GFF3, you don't have any features of class "Gene".  In GFF2,
>> the class was the text string that started the ninth column, like
>> this:
>>
>> chr2   .  gene    30427563    30429139    .   -   .  Gene 35804
>>
>> where the class would be Gene and the name (also called group) would
>> be 35804.  Class is not a particularly well defined concept in GFF3,
>> so the easiest way to restore functionality to your script is to
>> change the call from this:
>>
>>  my ($locus_obj) = $gff_dbh->get_feature_by_name('Gene' => $locus);
>>
>> to this:
>>
>>  my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus,
>> -type => 'gene');
>>
>> I believe (though haven't tested it myself in a very long time) that
>> you can embed class in the name of the feature, like this:
>>
>> chr2  .  gene    30427563    30429139    .   -   .
>>  Name=Gene:Medtr2g097580
>>
>> which may or may not be easier, depending on your data and your code base.
>>
>> Scott
>>
>>
>> On Wed, Feb 1, 2012 at 10:50 AM, Vivek Krishnakumar
>> <vivekkrishnakumar at gmail.com> wrote:
>> > Hi Lincoln,
>> >
>> > Thanks very much for your suggestions. Not sure how the single quotation
>> > marks appeared around the $locus variable. But looks like it was only in
>> > the email. Fortunately did not have quotes around the variable in my
>> > original code.
>> >
>> > Now, when I switch over to 'get_features_by_name()', my script does not
>> run
>> > to completion.
>> >
>> > I want to mention that this snippet of code is part of a larger CGI
>> script
>> > that interfaces with the SeqFeature backend DB. When I modify the
>> function
>> > call to $gff_dbh->get_features_by_name($locus), the script just runs
>> > indefinitely and returns absolutely nothing. I did put in a warn
>> statement
>> > to see if the correct locus ID is being passed to the function (I am
>> able
>> > to see the warning message in my apache error log), which seems to be
>> fine.
>> > But the moment it reaches the function call step, the CGI script
>> freezes up
>> > and I am unable to do anything. It just ends up as a rogue process
>> owned by
>> > the 'daemon' user and continues to use up a lot of memory.
>> >
>> > I am using the following BioPerl modules in this CGI script:
>> > use Bio::SeqIO;
>> > use Bio::SearchIO;
>> > use Bio::DB::SeqFeature::Store;
>> > use Bio::SeqFeature::Generic;
>> > use Bio::Graphics;
>> > use Bio::Graphics::Feature;
>> >
>> > Could any of these be interfering with get_features_by_name()?
>> >
>> > Thank you.
>> > Vivek
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>
>

From lincoln.stein at gmail.com  Wed Feb  1 12:57:33 2012
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Wed, 1 Feb 2012 12:57:33 -0500
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <CAHtOd9kt+L1xNQTREHGXkN13XwV0JRONe_hV_8Da2FBOn_9hxg@mail.gmail.com>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
	<CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
	<10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>
	<CA+JTaozJVAZZrmZuy6dfGr-56fVHcoOyJXdkPpZ2=_vhnJEzzg@mail.gmail.com>
	<CAHtOd9kt+L1xNQTREHGXkN13XwV0JRONe_hV_8Da2FBOn_9hxg@mail.gmail.com>
Message-ID: <CAOS1dzzZnsa=F00FFSsLb6JFjnMvNR9gQvWvZ2Nc4ZGHbJ_DPA@mail.gmail.com>

Is this exception appearing at the get_features_by_name() call, or later on
in the script? I don't see how it can be generated in response to
get_features_by_name().

Lincoln

On Wed, Feb 1, 2012 at 11:51 AM, Vivek Krishnakumar <
vivekkrishnakumar at gmail.com> wrote:

> Hi Scott,
>
> Thanks very much for your suggestions. Looks I did miss it somehow
> (confusion was caused because I was using both bioperl-l at googlegroups and
> bioperl-l at open-bio)
>
> Anyway, I had modified my function exactly like your suggestion:
> my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus, -type =>
> 'gene');
>
> But doing so just returns the following error:
>
> -------------------- EXCEPTION --------------------
> MSG: segment() called in a scalar context but multiple features match.
> Either call in a list context or narrow your search using the -types
> or -class arguments
>
> STACK Bio::DB::SeqFeature::Store::segment
> /usr/local/packages/perl-5.10.1/lib/5.10.1/Bio/DB/SeqFeature/Store.pm:1322
> STACK main::get_annotation_db_features
> /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:899
> STACK main::structural_annotation
> /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:660
> STACK toplevel /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:119
> -------------------------------------------
>
> which would suggest to oneself that there are several such features with
> the same ID. But in fact, I was able to verify by querying the database
> that I have only one such locus.
>
> As for your question regarding how $locus is populated, it is populated
> from a CGI parameter passed to the script. I know that I am only passing it
> one locus ID. And as I mentioned earlier in this thread, the warning
> statement I inserted before making the function call shows me that there is
> only one ID in the $locus variable.
>
> My last resort now is to try as you suggested and modify my GFF3 file and
> embed the -class => 'Gene' into the "Name" attribute. While doing so,
> should I also embed the 'mRNA' class into the "Name" attribute of the mRNA
> feature like so:
>
> chr2    working_models  mRNA    30427563    30429139    .   -   .
> ID=mrna_36255;Parent=gene_35804;Name=mRNA:Medtr2g097580.1;conf_class=F
>
> Subsequently, should I modify the function call to include the 'class':
> my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus, -type =>
> 'gene', -class => 'Gene');
>
> Thank you.
> Vivek
>
> On Wed, Feb 1, 2012 at 11:26 AM, Scott Cain <scott at scottcain.net> wrote:
>
> > Hi Vivek,
> >
> > I responded to your original email and I suspect you may have missed
> > it.  I'll copy it below.  Another few things: how does $locus get
> > populated?  Are you sure what you expect to be there is?
> >
> > Also, to answer your question about the other bioperl modules you're
> > using: no, I don't think that's interfering.
> >
> > Scott
> >
> > ------------------------------------------------
> > Hello Vivek,
> >
> > In your GFF3, you don't have any features of class "Gene".  In GFF2,
> > the class was the text string that started the ninth column, like
> > this:
> >
> > chr2   .  gene    30427563    30429139    .   -   .  Gene 35804
> >
> > where the class would be Gene and the name (also called group) would
> > be 35804.  Class is not a particularly well defined concept in GFF3,
> > so the easiest way to restore functionality to your script is to
> > change the call from this:
> >
> >  my ($locus_obj) = $gff_dbh->get_feature_by_name('Gene' => $locus);
> >
> > to this:
> >
> >  my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus,
> > -type => 'gene');
> >
> > I believe (though haven't tested it myself in a very long time) that
> > you can embed class in the name of the feature, like this:
> >
> > chr2  .  gene    30427563    30429139    .   -   .
>  Name=Gene:Medtr2g097580
> >
> > which may or may not be easier, depending on your data and your code
> base.
> >
> > Scott
> >
> >
> > On Wed, Feb 1, 2012 at 10:50 AM, Vivek Krishnakumar
> > <vivekkrishnakumar at gmail.com> wrote:
> > > Hi Lincoln,
> > >
> > > Thanks very much for your suggestions. Not sure how the single
> quotation
> > > marks appeared around the $locus variable. But looks like it was only
> in
> > > the email. Fortunately did not have quotes around the variable in my
> > > original code.
> > >
> > > Now, when I switch over to 'get_features_by_name()', my script does not
> > run
> > > to completion.
> > >
> > > I want to mention that this snippet of code is part of a larger CGI
> > script
> > > that interfaces with the SeqFeature backend DB. When I modify the
> > function
> > > call to $gff_dbh->get_features_by_name($locus), the script just runs
> > > indefinitely and returns absolutely nothing. I did put in a warn
> > statement
> > > to see if the correct locus ID is being passed to the function (I am
> able
> > > to see the warning message in my apache error log), which seems to be
> > fine.
> > > But the moment it reaches the function call step, the CGI script
> freezes
> > up
> > > and I am unable to do anything. It just ends up as a rogue process
> owned
> > by
> > > the 'daemon' user and continues to use up a lot of memory.
> > >
> > > I am using the following BioPerl modules in this CGI script:
> > > use Bio::SeqIO;
> > > use Bio::SearchIO;
> > > use Bio::DB::SeqFeature::Store;
> > > use Bio::SeqFeature::Generic;
> > > use Bio::Graphics;
> > > use Bio::Graphics::Feature;
> > >
> > > Could any of these be interfering with get_features_by_name()?
> > >
> > > Thank you.
> > > Vivek
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                   scott at scottcain
> > dot net
> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > Ontario Institute for Cancer Research
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



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

From vivekkrishnakumar at gmail.com  Wed Feb  1 13:15:17 2012
From: vivekkrishnakumar at gmail.com (Vivek Krishnakumar)
Date: Wed, 1 Feb 2012 10:15:17 -0800 (PST)
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <CAOS1dzzZnsa=F00FFSsLb6JFjnMvNR9gQvWvZ2Nc4ZGHbJ_DPA@mail.gmail.com>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
	<CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
	<10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>
	<CA+JTaozJVAZZrmZuy6dfGr-56fVHcoOyJXdkPpZ2=_vhnJEzzg@mail.gmail.com>
	<CAHtOd9kt+L1xNQTREHGXkN13XwV0JRONe_hV_8Da2FBOn_9hxg@mail.gmail.com>
	<CAOS1dzzZnsa=F00FFSsLb6JFjnMvNR9gQvWvZ2Nc4ZGHbJ_DPA@mail.gmail.com>
Message-ID: <26948128.3288.1328120117492.JavaMail.geo-discussion-forums@vbto23>

Hi Lincoln,

This exception was NOT generated by the $gff_dbh->get_features_by_name() 
call.

It was later on in the script by the $gff_dbh->segment() call.
And the reason was because I was trying to get the reference seq_id by 
using $locus_obj->refseq, which seems to be deprecated in DB::SeqFeature. 
When I switched to $locus_obj->seq_id, everything worked fine.

Thanks again and sorry for the confusion.
Vivek

From vivekkrishnakumar at gmail.com  Wed Feb  1 13:15:17 2012
From: vivekkrishnakumar at gmail.com (Vivek Krishnakumar)
Date: Wed, 1 Feb 2012 10:15:17 -0800 (PST)
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <CAOS1dzzZnsa=F00FFSsLb6JFjnMvNR9gQvWvZ2Nc4ZGHbJ_DPA@mail.gmail.com>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
	<CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
	<10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>
	<CA+JTaozJVAZZrmZuy6dfGr-56fVHcoOyJXdkPpZ2=_vhnJEzzg@mail.gmail.com>
	<CAHtOd9kt+L1xNQTREHGXkN13XwV0JRONe_hV_8Da2FBOn_9hxg@mail.gmail.com>
	<CAOS1dzzZnsa=F00FFSsLb6JFjnMvNR9gQvWvZ2Nc4ZGHbJ_DPA@mail.gmail.com>
Message-ID: <26948128.3288.1328120117492.JavaMail.geo-discussion-forums@vbto23>

Hi Lincoln,

This exception was NOT generated by the $gff_dbh->get_features_by_name() 
call.

It was later on in the script by the $gff_dbh->segment() call.
And the reason was because I was trying to get the reference seq_id by 
using $locus_obj->refseq, which seems to be deprecated in DB::SeqFeature. 
When I switched to $locus_obj->seq_id, everything worked fine.

Thanks again and sorry for the confusion.
Vivek

From scott at scottcain.net  Wed Feb  1 14:43:56 2012
From: scott at scottcain.net (Scott Cain)
Date: Wed, 1 Feb 2012 14:43:56 -0500
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <CAHtOd9kt+L1xNQTREHGXkN13XwV0JRONe_hV_8Da2FBOn_9hxg@mail.gmail.com>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
	<CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
	<10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>
	<CA+JTaozJVAZZrmZuy6dfGr-56fVHcoOyJXdkPpZ2=_vhnJEzzg@mail.gmail.com>
	<CAHtOd9kt+L1xNQTREHGXkN13XwV0JRONe_hV_8Da2FBOn_9hxg@mail.gmail.com>
Message-ID: <CA+JTaoxPxaBTChB7stE+beKMwjQ=hE2Q5SSJu_Nfv960=Dij7w@mail.gmail.com>

Hi Vivek,

What I don't understand from the error stack that you copied in your
email is that it doesn't mention the get_features_by_name method,
rather it mentions the segment method--are you sure that the line
number reported in your get_annotation_db_features method corresponds
to the change you made in the get_features_by_name call?  I get the
feeling that it is dying somewhere else now.  I would say that
resorting to adding class to the feature names is unlikely to help.

Scott


On Wed, Feb 1, 2012 at 11:51 AM, Vivek Krishnakumar
<vivekkrishnakumar at gmail.com> wrote:
> Hi Scott,
>
> Thanks very much for your suggestions. Looks I did miss it somehow
> (confusion was caused because I was using both bioperl-l at googlegroups and
> bioperl-l at open-bio)
>
> Anyway, I had modified my function exactly like your suggestion:
>
> my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus, -type =>
> 'gene');
>
> But doing so just returns the following error:
>
> -------------------- EXCEPTION --------------------
> MSG: segment() called in a scalar context but multiple features match.
> Either call in a list context or narrow your search using the -types or
> -class arguments
>
> STACK Bio::DB::SeqFeature::Store::segment
> /usr/local/packages/perl-5.10.1/lib/5.10.1/Bio/DB/SeqFeature/Store.pm:1322
> STACK main::get_annotation_db_features
> /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:899
> STACK main::structural_annotation
> /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:660
> STACK toplevel /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:119
> -------------------------------------------
>
> which would suggest to oneself that there are several such features with the
> same ID. But in fact, I was able to verify by querying the database that I
> have only one such locus.
>
> As for your question regarding how $locus is populated, it is populated from
> a CGI parameter passed to the script. I know that I am only passing it one
> locus ID. And as I mentioned earlier in this thread, the warning statement I
> inserted before making the function call shows me that there is only one ID
> in the $locus variable.
>
> My last resort now is to try as you suggested and modify my GFF3 file and
> embed the -class => 'Gene' into the "Name" attribute. While doing so, should
> I also embed the 'mRNA' class into the "Name" attribute of the mRNA feature
> like so:
>
> chr2 ? ?working_models ?mRNA ? ?30427563 ? ?30429139 ? ?. ? - ? .
> ID=mrna_36255;Parent=gene_35804;Name=mRNA:Medtr2g097580.1;conf_class=F
>
> Subsequently, should I modify the function call to include the 'class':
> my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus, -type =>
> 'gene', -class => 'Gene');
>
> Thank you.
> Vivek
>
>
> On Wed, Feb 1, 2012 at 11:26 AM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Vivek,
>>
>> I responded to your original email and I suspect you may have missed
>> it. ?I'll copy it below. ?Another few things: how does $locus get
>> populated? ?Are you sure what you expect to be there is?
>>
>> Also, to answer your question about the other bioperl modules you're
>> using: no, I don't think that's interfering.
>>
>> Scott
>>
>> ------------------------------------------------
>> Hello Vivek,
>>
>> In your GFF3, you don't have any features of class "Gene". ?In GFF2,
>> the class was the text string that started the ninth column, like
>> this:
>>
>> chr2 ? . ?gene ? ?30427563 ? ?30429139 ? ?. ? - ? . ?Gene 35804
>>
>> where the class would be Gene and the name (also called group) would
>> be 35804. ?Class is not a particularly well defined concept in GFF3,
>> so the easiest way to restore functionality to your script is to
>> change the call from this:
>>
>> ?my ($locus_obj) = $gff_dbh->get_feature_by_name('Gene' => $locus);
>>
>> to this:
>>
>> ?my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus,
>> -type => 'gene');
>>
>> I believe (though haven't tested it myself in a very long time) that
>> you can embed class in the name of the feature, like this:
>>
>> chr2 ?. ?gene ? ?30427563 ? ?30429139 ? ?. ? - ? .
>> ?Name=Gene:Medtr2g097580
>>
>> which may or may not be easier, depending on your data and your code base.
>>
>> Scott
>>
>>
>> On Wed, Feb 1, 2012 at 10:50 AM, Vivek Krishnakumar
>> <vivekkrishnakumar at gmail.com> wrote:
>> > Hi Lincoln,
>> >
>> > Thanks very much for your suggestions. Not sure how the single quotation
>> > marks appeared around the $locus variable. But looks like it was only in
>> > the email. Fortunately did not have quotes around the variable in my
>> > original code.
>> >
>> > Now, when I switch over to 'get_features_by_name()', my script does not
>> > run
>> > to completion.
>> >
>> > I want to mention that this snippet of code is part of a larger CGI
>> > script
>> > that interfaces with the SeqFeature backend DB. When I modify the
>> > function
>> > call to $gff_dbh->get_features_by_name($locus), the script just runs
>> > indefinitely and returns absolutely nothing. I did put in a warn
>> > statement
>> > to see if the correct locus ID is being passed to the function (I am
>> > able
>> > to see the warning message in my apache error log), which seems to be
>> > fine.
>> > But the moment it reaches the function call step, the CGI script freezes
>> > up
>> > and I am unable to do anything. It just ends up as a rogue process owned
>> > by
>> > the 'daemon' user and continues to use up a lot of memory.
>> >
>> > I am using the following BioPerl modules in this CGI script:
>> > use Bio::SeqIO;
>> > use Bio::SearchIO;
>> > use Bio::DB::SeqFeature::Store;
>> > use Bio::SeqFeature::Generic;
>> > use Bio::Graphics;
>> > use Bio::Graphics::Feature;
>> >
>> > Could any of these be interfering with get_features_by_name()?
>> >
>> > Thank you.
>> > Vivek
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
>> Ontario Institute for Cancer Research
>
>



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


From scott at scottcain.net  Wed Feb  1 14:44:56 2012
From: scott at scottcain.net (Scott Cain)
Date: Wed, 1 Feb 2012 14:44:56 -0500
Subject: [Bioperl-l] `get_feature_by_name` not working after migrating
 to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
In-Reply-To: <CA+JTaoxPxaBTChB7stE+beKMwjQ=hE2Q5SSJu_Nfv960=Dij7w@mail.gmail.com>
References: <CAHtOd9=Jy-ZUKqs=WLq-vXZRXmtYp+qo-moo16c+5CG8OtNKUw@mail.gmail.com>
	<CAOS1dzwTRF5ctnQw=GTNg6CUAyfXt35UtuHPF3fDLjJnN95FJQ@mail.gmail.com>
	<10934743.3252.1328111443141.JavaMail.geo-discussion-forums@vbzs10>
	<CA+JTaozJVAZZrmZuy6dfGr-56fVHcoOyJXdkPpZ2=_vhnJEzzg@mail.gmail.com>
	<CAHtOd9kt+L1xNQTREHGXkN13XwV0JRONe_hV_8Da2FBOn_9hxg@mail.gmail.com>
	<CA+JTaoxPxaBTChB7stE+beKMwjQ=hE2Q5SSJu_Nfv960=Dij7w@mail.gmail.com>
Message-ID: <CA+JTaoziZDSTV=kLi5wRU4obN6j3pq72k8WjCzvkm9g8yHYyqg@mail.gmail.com>

/scott realizes he should refresh his mail client before sending
helpful emails :-)


On Wed, Feb 1, 2012 at 2:43 PM, Scott Cain <scott at scottcain.net> wrote:
> Hi Vivek,
>
> What I don't understand from the error stack that you copied in your
> email is that it doesn't mention the get_features_by_name method,
> rather it mentions the segment method--are you sure that the line
> number reported in your get_annotation_db_features method corresponds
> to the change you made in the get_features_by_name call? ?I get the
> feeling that it is dying somewhere else now. ?I would say that
> resorting to adding class to the feature names is unlikely to help.
>
> Scott
>
>
> On Wed, Feb 1, 2012 at 11:51 AM, Vivek Krishnakumar
> <vivekkrishnakumar at gmail.com> wrote:
>> Hi Scott,
>>
>> Thanks very much for your suggestions. Looks I did miss it somehow
>> (confusion was caused because I was using both bioperl-l at googlegroups and
>> bioperl-l at open-bio)
>>
>> Anyway, I had modified my function exactly like your suggestion:
>>
>> my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus, -type =>
>> 'gene');
>>
>> But doing so just returns the following error:
>>
>> -------------------- EXCEPTION --------------------
>> MSG: segment() called in a scalar context but multiple features match.
>> Either call in a list context or narrow your search using the -types or
>> -class arguments
>>
>> STACK Bio::DB::SeqFeature::Store::segment
>> /usr/local/packages/perl-5.10.1/lib/5.10.1/Bio/DB/SeqFeature/Store.pm:1322
>> STACK main::get_annotation_db_features
>> /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:899
>> STACK main::structural_annotation
>> /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:660
>> STACK toplevel /opt/www/medicago/cgi-bin/medicago/eucap/eucap.pl:119
>> -------------------------------------------
>>
>> which would suggest to oneself that there are several such features with the
>> same ID. But in fact, I was able to verify by querying the database that I
>> have only one such locus.
>>
>> As for your question regarding how $locus is populated, it is populated from
>> a CGI parameter passed to the script. I know that I am only passing it one
>> locus ID. And as I mentioned earlier in this thread, the warning statement I
>> inserted before making the function call shows me that there is only one ID
>> in the $locus variable.
>>
>> My last resort now is to try as you suggested and modify my GFF3 file and
>> embed the -class => 'Gene' into the "Name" attribute. While doing so, should
>> I also embed the 'mRNA' class into the "Name" attribute of the mRNA feature
>> like so:
>>
>> chr2 ? ?working_models ?mRNA ? ?30427563 ? ?30429139 ? ?. ? - ? .
>> ID=mrna_36255;Parent=gene_35804;Name=mRNA:Medtr2g097580.1;conf_class=F
>>
>> Subsequently, should I modify the function call to include the 'class':
>> my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus, -type =>
>> 'gene', -class => 'Gene');
>>
>> Thank you.
>> Vivek
>>
>>
>> On Wed, Feb 1, 2012 at 11:26 AM, Scott Cain <scott at scottcain.net> wrote:
>>>
>>> Hi Vivek,
>>>
>>> I responded to your original email and I suspect you may have missed
>>> it. ?I'll copy it below. ?Another few things: how does $locus get
>>> populated? ?Are you sure what you expect to be there is?
>>>
>>> Also, to answer your question about the other bioperl modules you're
>>> using: no, I don't think that's interfering.
>>>
>>> Scott
>>>
>>> ------------------------------------------------
>>> Hello Vivek,
>>>
>>> In your GFF3, you don't have any features of class "Gene". ?In GFF2,
>>> the class was the text string that started the ninth column, like
>>> this:
>>>
>>> chr2 ? . ?gene ? ?30427563 ? ?30429139 ? ?. ? - ? . ?Gene 35804
>>>
>>> where the class would be Gene and the name (also called group) would
>>> be 35804. ?Class is not a particularly well defined concept in GFF3,
>>> so the easiest way to restore functionality to your script is to
>>> change the call from this:
>>>
>>> ?my ($locus_obj) = $gff_dbh->get_feature_by_name('Gene' => $locus);
>>>
>>> to this:
>>>
>>> ?my ($locus_obj) = $gff_dbh->get_features_by_name(-name => $locus,
>>> -type => 'gene');
>>>
>>> I believe (though haven't tested it myself in a very long time) that
>>> you can embed class in the name of the feature, like this:
>>>
>>> chr2 ?. ?gene ? ?30427563 ? ?30429139 ? ?. ? - ? .
>>> ?Name=Gene:Medtr2g097580
>>>
>>> which may or may not be easier, depending on your data and your code base.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Feb 1, 2012 at 10:50 AM, Vivek Krishnakumar
>>> <vivekkrishnakumar at gmail.com> wrote:
>>> > Hi Lincoln,
>>> >
>>> > Thanks very much for your suggestions. Not sure how the single quotation
>>> > marks appeared around the $locus variable. But looks like it was only in
>>> > the email. Fortunately did not have quotes around the variable in my
>>> > original code.
>>> >
>>> > Now, when I switch over to 'get_features_by_name()', my script does not
>>> > run
>>> > to completion.
>>> >
>>> > I want to mention that this snippet of code is part of a larger CGI
>>> > script
>>> > that interfaces with the SeqFeature backend DB. When I modify the
>>> > function
>>> > call to $gff_dbh->get_features_by_name($locus), the script just runs
>>> > indefinitely and returns absolutely nothing. I did put in a warn
>>> > statement
>>> > to see if the correct locus ID is being passed to the function (I am
>>> > able
>>> > to see the warning message in my apache error log), which seems to be
>>> > fine.
>>> > But the moment it reaches the function call step, the CGI script freezes
>>> > up
>>> > and I am unable to do anything. It just ends up as a rogue process owned
>>> > by
>>> > the 'daemon' user and continues to use up a lot of memory.
>>> >
>>> > I am using the following BioPerl modules in this CGI script:
>>> > use Bio::SeqIO;
>>> > use Bio::SearchIO;
>>> > use Bio::DB::SeqFeature::Store;
>>> > use Bio::SeqFeature::Generic;
>>> > use Bio::Graphics;
>>> > use Bio::Graphics::Feature;
>>> >
>>> > Could any of these be interfering with get_features_by_name()?
>>> >
>>> > Thank you.
>>> > Vivek
>>> > _______________________________________________
>>> > Bioperl-l mailing list
>>> > Bioperl-l at lists.open-bio.org
>>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
>>> Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
> Ontario Institute for Cancer Research



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


From Russell.Smithies at agresearch.co.nz  Wed Feb  1 16:31:49 2012
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Thu, 2 Feb 2012 10:31:49 +1300
Subject: [Bioperl-l] Running into problems
In-Reply-To: <33243496.post@talk.nabble.com>
References: <33228400.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
	<33243496.post@talk.nabble.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF34BD33ADBC2@exchsth.agresearch.co.nz>

Sorry, typo.
Make sure you have your hsp_filter sub in there somewhere.

--Rusell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
> Sent: Thursday, 2 February 2012 3:34 a.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Running into problems
> 
> 
> Thank you for your help! I think I'm almost there, but I still get 1 more error
> when I run the script:
> 
> $ perl blast2.pl
> Searching gi|146341649|ref|YP_001206697.1| Undefined subroutine
> &main::hsp_filter called at
> /usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm line 298,
> <GEN6> line 71.
> 
> 
> Smithies, Russell wrote:
> >
> > I'd probably cheat a bit and optimise my blast parameters so there's
> > less output to process.
> > Also, are you sure an e-value of 100 is what you're after? I'd be
> > aiming much lower - probably 1e-6.
> > It also pays to mask repeats if you're blasting against a whole genome
> > to cut down on the number of rubbish hits.
> >
> > --Russell
> >
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
> >> Sent: Tuesday, 31 January 2012 12:21 a.m.
> >> To: Bioperl-l at lists.open-bio.org
> >> Subject: [Bioperl-l] Running into problems
> >>
> >>
> >> HI all,
> >>
> >> I'm quite new to bioperl and tried to write a script that creates a
> >> database from a newly sequenced genome and then preforms a tblastn
> >> against a multiple protein fasta file and then creates a blast report
> >> were only the results that only preservers identity scores above 98%.
> >> However my script keeps returning numerous errors and problems and
> >> since I have only a little experience I cannot determine were I went
> >> wrong. I include the code that I got so far in the attachment. Hope
> >> someone can help.
> >> Regards Joel
> >>
> >> http://old.nabble.com/file/p33228400/blast1.pl blast1.pl
> >> --
> >> View this message in context: http://old.nabble.com/Running-into-
> >> problems-tp33228400p33228400.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
> >
> ==========================================================
> ============
> > =
> > Attention: The information contained in this message and/or
> > attachments from AgResearch Limited is intended only for the persons
> > or entities to which it is addressed and may contain confidential
> > and/or privileged material. Any review, retransmission, dissemination
> > or other use of, or taking of any action in reliance upon, this
> > information by persons or entities other than the intended recipients
> > is prohibited by AgResearch Limited. If you have received this message
> > in error, please notify the sender immediately.
> >
> ==========================================================
> ============
> > =
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> 
> --
> View this message in context: http://old.nabble.com/Running-into-
> problems-tp33228400p33243496.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 adlai at refenestration.com  Wed Feb  1 16:43:37 2012
From: adlai at refenestration.com (Adlai Burman)
Date: Wed, 1 Feb 2012 22:43:37 +0100
Subject: [Bioperl-l] Lineage from GB files
In-Reply-To: <CAEiaqDnZAJWMpaV=xpjA9OFyCmGchmCV+vuWAqdm16J9GqGXog@mail.gmail.com>
References: <6CBCE402-E3C8-4FE0-BA57-4A7B82C3CF5F@refenestration.com>
	<CAEiaqDnZAJWMpaV=xpjA9OFyCmGchmCV+vuWAqdm16J9GqGXog@mail.gmail.com>
Message-ID: <C7B2658A-820C-4F5A-ABBD-3BA671BBE9BA@refenestration.com>

Thanks, Surya.
I'll give it a shot.
Adlai
On Jan 31, 2012, at 10:49 PM, Surya Saha wrote:

> Hi Adlai,
> 
> It really depends on what items are present the Genbank/EMBL. You can use the NCBI Taxonomy database and Taxonomy modules in CPAN to identify the taxonomic hierarchy of an accession, for e.g., you can map the GI to Taxonomy ID and extract the taxonomy using Bio::LITE::Taxonomy::NCBI. 
> 
> Here's a script (not authored by me) on Github that might get you started.
> 
> -Surya
> 
> 
> On Fri, Jan 27, 2012 at 6:27 AM, Adlai Burman <adlai at refenestration.com> wrote:
> Does anyone know if there is a way to batch extract taxa such as class, order in Perl from, e/g/ genbank, EMBL records? I know that genus/species and some of the higher taxa are easy to parse from gb records but the interior are inconsistent strings (e.g. element x sometimes is a subclass and sometimes a family.
> Any help would really be appreciated.
> 
> Thanks.
> Adlai
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From invite+2mkwrx5a at facebookmail.com  Wed Feb  1 22:16:52 2012
From: invite+2mkwrx5a at facebookmail.com (Puneet Kadimi)
Date: Wed, 1 Feb 2012 19:16:52 -0800
Subject: [Bioperl-l] Check out my photos on Facebook
Message-ID: <821a168884640d062e02ccd7a607c5ff@async.facebook.com>

Hi Bioperl-l,

I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile.

Thanks,
Puneet

To sign up for Facebook, follow the link below:
http://www.facebook.com/p.php?i=1646147841&k=AQBEf7iEx7uHcyAqQibbKMtZbUnyPj4MjFuGd4aBfXw2itCG-JcHfP9uwAy7Du4m2r2eHw&r

Already have an account? Add this email address to your account:
http://www.facebook.com/n/?merge_accounts.php&e=bioperl-l%40bioperl.org&c=AQDNbz0MpsGYMKLlzfTt1q_SQWUXniSEkqIU1W3otHmU8Q

=======================================
This message was sent to bioperl-l at bioperl.org. If you don't want to receive these emails from Facebook in the future, please follow the link below to unsubscribe.
http://www.facebook.com/o.php?k=24bbd2&u=1753461434&mid=593fd51G6883b2baG0G8
 Facebook, Inc. Attention: Department 415 P.O Box 10005 Palo Alto CA 94303 



From joel.klein at wur.nl  Thu Feb  2 05:29:11 2012
From: joel.klein at wur.nl (Bradyjoel)
Date: Thu, 2 Feb 2012 02:29:11 -0800 (PST)
Subject: [Bioperl-l] Running into problems
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF34BD33ADBC2@exchsth.agresearch.co.nz>
References: <33228400.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF34BD33ADBAB@exchsth.agresearch.co.nz>
	<33243496.post@talk.nabble.com>
	<18DF7D20DFEC044098A1062202F5FFF34BD33ADBC2@exchsth.agresearch.co.nz>
Message-ID: <33249286.post@talk.nabble.com>


That did the trick, its working now thank you all very much!



Smithies, Russell wrote:
> 
> Sorry, typo.
> Make sure you have your hsp_filter sub in there somewhere.
> 
> --Rusell
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
>> Sent: Thursday, 2 February 2012 3:34 a.m.
>> To: Bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] Running into problems
>> 
>> 
>> Thank you for your help! I think I'm almost there, but I still get 1 more
>> error
>> when I run the script:
>> 
>> $ perl blast2.pl
>> Searching gi|146341649|ref|YP_001206697.1| Undefined subroutine
>> &main::hsp_filter called at
>> /usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm line 298,
>> <GEN6> line 71.
>> 
>> 
>> Smithies, Russell wrote:
>> >
>> > I'd probably cheat a bit and optimise my blast parameters so there's
>> > less output to process.
>> > Also, are you sure an e-value of 100 is what you're after? I'd be
>> > aiming much lower - probably 1e-6.
>> > It also pays to mask repeats if you're blasting against a whole genome
>> > to cut down on the number of rubbish hits.
>> >
>> > --Russell
>> >
>> >> -----Original Message-----
>> >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> >> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
>> >> Sent: Tuesday, 31 January 2012 12:21 a.m.
>> >> To: Bioperl-l at lists.open-bio.org
>> >> Subject: [Bioperl-l] Running into problems
>> >>
>> >>
>> >> HI all,
>> >>
>> >> I'm quite new to bioperl and tried to write a script that creates a
>> >> database from a newly sequenced genome and then preforms a tblastn
>> >> against a multiple protein fasta file and then creates a blast report
>> >> were only the results that only preservers identity scores above 98%.
>> >> However my script keeps returning numerous errors and problems and
>> >> since I have only a little experience I cannot determine were I went
>> >> wrong. I include the code that I got so far in the attachment. Hope
>> >> someone can help.
>> >> Regards Joel
>> >>
>> >> http://old.nabble.com/file/p33228400/blast1.pl blast1.pl
>> >> --
>> >> View this message in context: http://old.nabble.com/Running-into-
>> >> problems-tp33228400p33228400.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
>> >
>> ==========================================================
>> ============
>> > =
>> > Attention: The information contained in this message and/or
>> > attachments from AgResearch Limited is intended only for the persons
>> > or entities to which it is addressed and may contain confidential
>> > and/or privileged material. Any review, retransmission, dissemination
>> > or other use of, or taking of any action in reliance upon, this
>> > information by persons or entities other than the intended recipients
>> > is prohibited by AgResearch Limited. If you have received this message
>> > in error, please notify the sender immediately.
>> >
>> ==========================================================
>> ============
>> > =
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>> >
>> 
>> --
>> View this message in context: http://old.nabble.com/Running-into-
>> problems-tp33228400p33243496.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://old.nabble.com/Running-into-problems-tp33228400p33249286.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From jw12 at sanger.ac.uk  Thu Feb  2 04:46:25 2012
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 2 Feb 2012 09:46:25 +0000
Subject: [Bioperl-l] Only 10 days left to register for DAS Workshop 2012
Message-ID: <A5AF83C7-323B-4858-AF0F-707C2406C401@sanger.ac.uk>

Only 10 days left to register for DAS Workshop 2012

DAS is currently being used to share annotations on genomes, protein
alignments, structural and interaction information.

If you are interested in sharing biological information the DAS workshop
below may be of interest to you.

Learn of and contribute to current developments in DAS such as: DAS in  
the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative  
annotation projects, DAS alternative formats.

Registration is open for the 2012 DAS workshop (27-29 February) at the
Genome Campus, Hinxton UK. If you are interested in attending, please
find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html 
  and
register via the web link at the bottom of the page. This workshop will
cater for novice to expert DAS users as each day is optional.

Please register early as places will be limited. Registration closes  
10 February 2012 - 12:00.

If you are interested in giving a 15 minute talk on the second day  
please email Jonathan Warren using jonathan.warren at sanger.ac.uk

Many thanks

The Sanger/EBI DAS team.

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314










-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From invite+2mkwrx5a at facebookmail.com  Wed Feb  1 22:18:14 2012
From: invite+2mkwrx5a at facebookmail.com (Puneet Kadimi)
Date: Wed, 1 Feb 2012 19:18:14 -0800
Subject: [Bioperl-l] Check out my photos on Facebook
Message-ID: <8864f9c408cc7de0cfa8b7ea40217bfc@async.facebook.com>

Hi Bioperl-l,

I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile.

Thanks,
Puneet

To sign up for Facebook, follow the link below:
http://www.facebook.com/p.php?i=1646147841&k=AQAVgAJy52mb1-PB2xQ61qhtO-fF4-23pEw0pLALyeJvw_fAgUtdIEMjZXJKwFERNxWSvA&r

Already have an account? Add this email address to your account:
http://www.facebook.com/n/?merge_accounts.php&e=bioperl-l%40bioperl.org&c=AQDNbz0MpsGYMKLlzfTt1q_SQWUXniSEkqIU1W3otHmU8Q

=======================================
This message was sent to bioperl-l at bioperl.org. If you don't want to receive these emails from Facebook in the future, please follow the link below to unsubscribe.
http://www.facebook.com/o.php?k=24bbd2&u=1753461434&mid=593fda3G6883b2baG0G8
 Facebook, Inc. Attention: Department 415 P.O Box 10005 Palo Alto CA 94303 



From dtorrente at javeriana.edu.co  Sun Feb  5 14:04:47 2012
From: dtorrente at javeriana.edu.co (DANIEL EDUARDO TORRENTE QUINTERO)
Date: Sun, 5 Feb 2012 19:04:47 +0000
Subject: [Bioperl-l] Bioperl parsing output file
Message-ID: <F3ED4577039E674FA8DA030DAF53EF21593848@SN2PRD0202MB155.namprd02.prod.outlook.com>

i need some help in this script


#!/usr/bin/perl
use Bio::SearchIO;

$report_obj = new Bio::SearchIO(-format => 'blast',
                     -file   => 'C:\blast-2.2.25+\Lib3_consensus_dbAt.xml');
    while( $result = $report_obj->next_result ) {
        while( $hit = $result->next_hit ) {
           while( $hsp = $hit->next_hsp ) {
              if ( $hsp->evalue <= 0.00001 ) {
                   print "Hit\t", $hit->name, "\n", "Length\t", $hsp->length('total'),
                   "\n", "Percent_id\t",
                   $hsp->percent_identity, "\n",$result>query_name(),;  }  } } }


I want to export the results of de perl script on a file but i dont know how..... i tried to use all the  Bio::SearchIO::Writer<http://www.bioperl.org/wiki/Module:Bio::SearchIO::Writer> methods but i cant make it work with this script.





From heikki.lehvaslaiho at gmail.com  Mon Feb  6 01:30:45 2012
From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho)
Date: Mon, 6 Feb 2012 09:30:45 +0300
Subject: [Bioperl-l] Bioperl parsing output file
In-Reply-To: <F3ED4577039E674FA8DA030DAF53EF21593848@SN2PRD0202MB155.namprd02.prod.outlook.com>
References: <F3ED4577039E674FA8DA030DAF53EF21593848@SN2PRD0202MB155.namprd02.prod.outlook.com>
Message-ID: <CAK=ukcayuBVAcPmtzQ+dn5F9-FEXrUbSggwj32APBkOq0qitwg@mail.gmail.com>

Daniel,

You are already printing the output to STDOUT which goes to the
terminal. You can redirect the output to a file using "prog > file"
syntax on the command line or read about the perl open function
(perldoc -f open) and print directly to a named file from within a
script.


? ?? -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho http://about.me/heikki
cell: +966 545 595 849? office: +966 2 808 2429

Computational Bioscience Research Center (CBRC), Building #2, Office #4337
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, Kingdom of Saudi Arabia



On 5 February 2012 22:04, DANIEL EDUARDO TORRENTE QUINTERO
<dtorrente at javeriana.edu.co> wrote:
> i need some help in this script
>
>
> #!/usr/bin/perl
> use Bio::SearchIO;
>
> $report_obj = new Bio::SearchIO(-format => 'blast',
> ? ? ? ? ? ? ? ? ? ? -file ? => 'C:\blast-2.2.25+\Lib3_consensus_dbAt.xml');
> ? ?while( $result = $report_obj->next_result ) {
> ? ? ? ?while( $hit = $result->next_hit ) {
> ? ? ? ? ? while( $hsp = $hit->next_hsp ) {
> ? ? ? ? ? ? ?if ( $hsp->evalue <= 0.00001 ) {
> ? ? ? ? ? ? ? ? ? print "Hit\t", $hit->name, "\n", "Length\t", $hsp->length('total'),
> ? ? ? ? ? ? ? ? ? "\n", "Percent_id\t",
> ? ? ? ? ? ? ? ? ? $hsp->percent_identity, "\n",$result>query_name(),; ?} ?} } }
>
>
> I want to export the results of de perl script on a file but i dont know how..... i tried to use all the ?Bio::SearchIO::Writer<http://www.bioperl.org/wiki/Module:Bio::SearchIO::Writer> methods but i cant make it work with this script.
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From florian.lajus at labri.fr  Tue Feb  7 14:49:02 2012
From: florian.lajus at labri.fr (florian lajus)
Date: Tue, 07 Feb 2012 20:49:02 +0100
Subject: [Bioperl-l] Question on seqfeature mapping
In-Reply-To: <054FEA92-8C5E-47D6-86AF-F71DEAFE2B63@illinois.edu>
References: <4F0C7017.90803@inria.fr>
	<CAKVJ-_7d_K6+MttpMvW7-kr9iYTL6u0TMDcM=GfW7sVFsrO6sQ@mail.gmail.com>
	<A9148EAE-8709-4944-8369-CC98E7B53263@illinois.edu>
	<4F0D83D8.90402@inria.fr> <4F0D8A18.1080606@inria.fr>
	<D2004971-6A32-4141-B446-D2A855FDB026@illinois.edu>
	<4F0EA69E.8040203@inria.fr>
	<49CC4A91-5E47-4866-AD63-62DC7F649CE6@drycafe.net>
	<4F0FF883.80109@inria.fr> <4F0FF8FF.6070706@inria.fr>
	<E0F6A75C-8902-44D5-BB5F-8C0A4060EF9B@drycafe.net>
	<4F199A27.8030408@inria.fr>
	<054FEA92-8C5E-47D6-86AF-F71DEAFE2B63@illinois.edu>
Message-ID: <4F31802E.9030002@labri.fr>

Hi,
I have a problem with bio queries: How can I retrieve from datadabse a seqfeature according to its annotation (tagname and value)?
The problem coming for value as we have "value"          =>  "=>{bioentry_qualifier_value,seqfeature_qualifier_value,location_qualifier_value}.value",
in the %slot_attribut_map of the base driver.
Do you know a solution?


From kasandrah at gmail.com  Tue Feb  7 11:11:57 2012
From: kasandrah at gmail.com (Casandra)
Date: Tue, 7 Feb 2012 17:11:57 +0100
Subject: [Bioperl-l] help!
Message-ID: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>

Hi,

I'm trying to install Bioperl but I'm a bit lost. I know I have perl  
installed becaused I have already write some scripts but I'm biologist  
so... not pretty sure about what messages say.

My perl version:
This is perl, v5.8.8 built for darwin-thread-multi-2level
My computer:
Mac OS X Vesion 10.5.8

I was following this preliminary steps:

--------------
PRELIMINARY PREPARATION

    This is optional, but regardless of your subsequent choice of
    installation method, it will help to carry out the following steps.
    They will increase the likelyhood of installation success
    (especially of optional dependencies).

      * Upgrade CPAN:

  >perl -MCPAN -e shell
  cpan>install Bundle::CPAN
  cpan>q				

      * Install/upgrade Module::Build, and make it your preferred
        installer:

  >cpan
  cpan>install Module::Build
  cpan>o conf prefer_installer MB
  cpan>o conf commit
  cpan>q

      * Install the expat library by whatever method is
        appropriate for your system.

      * If your expat library is installed in a non-standard location,
        tell CPAN about it:

  >cpan
  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib EXPATINCPATH=/ 
non-standard/include"
  cpan>o conf commit
--------------
And I think I did "Upgrade CPAN properly" but when I tried the next  
one it started asking too many things to me, and finally it stopped  
due to "some problems". In text file you can see the whole process.
What did I do wrong?


After solving these preliminary steps, what should I do? What  
exactly .tar or .whatever should I download to install?

I don't see the difference between installing it through "built.PL"  
or  CPAN. And I don't know if I should do this or that "Fink*" stuff  
for MAC.

* I went to Fink webpage and what I expected to see was "hello!  
download Bioperl simply clicking here!" but far from this, what it  
seems is that first I have to download some kinf of Fink-program  
before starting with Bioperl... is it something close to this?

I'm sorry, too many questions... But I really want to learn to use  
Bioperl but I have no people to ask it face to face.

Thank you so much,

Casandra
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20120207/cd487ef5/attachment.html>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: terminal.txt
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20120207/cd487ef5/attachment.txt>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20120207/cd487ef5/attachment-0001.html>

From limeyloos at gmail.com  Mon Feb  6 11:09:18 2012
From: limeyloos at gmail.com (Em Rich)
Date: Mon, 6 Feb 2012 08:09:18 -0800 (PST)
Subject: [Bioperl-l] Embedding hyperlinks in SVG files
Message-ID: <c59ef653-693a-424d-bda0-9ce610ca6b5f@bs8g2000vbb.googlegroups.com>

Hi,

I am currently using Bio::Graphics to render sequence images into SVG
format. As SVGs can inherently embed hyperlinks using the xlink
attribute I was wondering if there is a straight forward way of adding
this attribute type in Bio::Graphics rather than creating an image
map.

Thanks,

Emily

From scott at scottcain.net  Tue Feb  7 15:26:43 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 7 Feb 2012 15:26:43 -0500
Subject: [Bioperl-l] Embedding hyperlinks in SVG files
In-Reply-To: <c59ef653-693a-424d-bda0-9ce610ca6b5f@bs8g2000vbb.googlegroups.com>
References: <c59ef653-693a-424d-bda0-9ce610ca6b5f@bs8g2000vbb.googlegroups.com>
Message-ID: <CA+JTaowPcOpaK154HrzrNq1ezpAOYULhq7P8ibJ+X3J0sqmjwQ@mail.gmail.com>

Hi Emily,

I'm reasonably sure that it isn't supported.  GD::SVG was developed to
support creating hi-res images from GBrowse to be used in
documentation or publications, and so, supporting links wasn't on our
radar.  I imagine it wouldn't be very hard to add if you wanted to
send a patch to the author (Todd Harris, cc'ed here, so he can
contradict me if he wants).

Scott


On Mon, Feb 6, 2012 at 11:09 AM, Em Rich <limeyloos at gmail.com> wrote:
> Hi,
>
> I am currently using Bio::Graphics to render sequence images into SVG
> format. As SVGs can inherently embed hyperlinks using the xlink
> attribute I was wondering if there is a straight forward way of adding
> this attribute type in Bio::Graphics rather than creating an image
> map.
>
> Thanks,
>
> Emily
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



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


From scott at scottcain.net  Tue Feb  7 15:55:25 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 7 Feb 2012 15:55:25 -0500
Subject: [Bioperl-l] help!
In-Reply-To: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
Message-ID: <CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>

hi Cassandra,

I don't have an answer for you at the moment.  It seems to me that
using local::lib is a good idea, but I've never found a good tutorial
for using it, so I haven't.  Perhaps someone else on the list can
suggest one.

The other thing I just wanted to mention as the admin that approved
your message--I came very close to deleting it from the queue without
looking at it because it is not unusual for spam messages to have
generic subjects like "help!"  (just for future reference :-)

Scott


On Tue, Feb 7, 2012 at 11:11 AM, Casandra <kasandrah at gmail.com> wrote:
> Hi,
>
> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
> installed becaused I have already write some scripts but I'm biologist so...
> not pretty sure about what messages say.
>
> My perl version:
> This is perl, v5.8.8 built for darwin-thread-multi-2level
> My computer:
> Mac OS X Vesion 10.5.8
>
> I was following this preliminary steps:
>
> --------------
>
> PRELIMINARY PREPARATION
>
>    This is optional, but regardless of your subsequent choice of
>    installation method, it will help to carry out the following steps.
>    They will increase the likelyhood of installation success
>    (especially of optional dependencies).
>
>      * Upgrade CPAN:
>
>  >perl -MCPAN -e shell
>  cpan>install Bundle::CPAN
>  cpan>q				
>
>      * Install/upgrade Module::Build, and make it your preferred
>        installer:
>
>  >cpan
>  cpan>install Module::Build
>  cpan>o conf prefer_installer MB
>  cpan>o conf commit
>  cpan>q
>
>      * Install the expat library by whatever method is
>        appropriate for your system.
>
>      * If your expat library is installed in a non-standard location,
>        tell CPAN about it:
>
>  >cpan
>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
> EXPATINCPATH=/non-standard/include"
>  cpan>o conf commit
>
> --------------
>
> And I think I did "Upgrade CPAN properly" but when I tried the next one it
> started asking too many things to me, and finally it stopped due to "some
> problems". In text file you can see the whole process.
> What did I do wrong?
>
>
> After solving these preliminary steps, what should I do? What exactly .tar
> or .whatever should I download to install?
>
> I don't see the difference between installing it through "built.PL" or
> ?CPAN. And I don't know if I should do this or that "Fink*" stuff for MAC.
>
> * I went to Fink webpage and what I expected to see was "hello! download
> Bioperl simply clicking here!" but far from this, what it seems is that
> first I have to download some kinf of Fink-program before starting with
> Bioperl... is it something close to this?
>
> I'm sorry, too many questions... But I really want to learn to use Bioperl
> but I have no people to ask it face to face.
>
> Thank you so much,
>
> Casandra
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



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


From cjfields at illinois.edu  Tue Feb  7 16:02:50 2012
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 7 Feb 2012 15:02:50 -0600
Subject: [Bioperl-l] help!
In-Reply-To: <CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
Message-ID: <4F31917A.9030804@illinois.edu>

I guess one key question is where these CPAN installation instructions 
come from.  They're a bit odd, and if this is from the wiki we need to 
do some updating.

Re: local::lib, the docs on CPAN are pretty nice if one wants to use a 
single perl version.

https://metacpan.org/module/local::lib#The-bootstrapping-technique

In my case I use perlbrew (which is all local by default, and allows 
switching between perl versions).  Highly recommend using either simple 
local::lib or perlbrew in combination with cpanm.

https://metacpan.org/module/perlbrew
https://metacpan.org/module/cpanm

chris


On 02/07/2012 02:55 PM, Scott Cain wrote:
> hi Cassandra,
>
> I don't have an answer for you at the moment.  It seems to me that
> using local::lib is a good idea, but I've never found a good tutorial
> for using it, so I haven't.  Perhaps someone else on the list can
> suggest one.
>
> The other thing I just wanted to mention as the admin that approved
> your message--I came very close to deleting it from the queue without
> looking at it because it is not unusual for spam messages to have
> generic subjects like "help!"  (just for future reference :-)
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasandrah at gmail.com>  wrote:
>> Hi,
>>
>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>> installed becaused I have already write some scripts but I'm biologist so...
>> not pretty sure about what messages say.
>>
>> My perl version:
>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>> My computer:
>> Mac OS X Vesion 10.5.8
>>
>> I was following this preliminary steps:
>>
>> --------------
>>
>> PRELIMINARY PREPARATION
>>
>>     This is optional, but regardless of your subsequent choice of
>>     installation method, it will help to carry out the following steps.
>>     They will increase the likelyhood of installation success
>>     (especially of optional dependencies).
>>
>>       * Upgrade CPAN:
>>
>>   >perl -MCPAN -e shell
>>   cpan>install Bundle::CPAN
>>   cpan>q				
>>
>>       * Install/upgrade Module::Build, and make it your preferred
>>         installer:
>>
>>   >cpan
>>   cpan>install Module::Build
>>   cpan>o conf prefer_installer MB
>>   cpan>o conf commit
>>   cpan>q
>>
>>       * Install the expat library by whatever method is
>>         appropriate for your system.
>>
>>       * If your expat library is installed in a non-standard location,
>>         tell CPAN about it:
>>
>>   >cpan
>>   cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>> EXPATINCPATH=/non-standard/include"
>>   cpan>o conf commit
>>
>> --------------
>>
>> And I think I did "Upgrade CPAN properly" but when I tried the next one it
>> started asking too many things to me, and finally it stopped due to "some
>> problems". In text file you can see the whole process.
>> What did I do wrong?
>>
>>
>> After solving these preliminary steps, what should I do? What exactly .tar
>> or .whatever should I download to install?
>>
>> I don't see the difference between installing it through "built.PL" or
>>   CPAN. And I don't know if I should do this or that "Fink*" stuff for MAC.
>>
>> * I went to Fink webpage and what I expected to see was "hello! download
>> Bioperl simply clicking here!" but far from this, what it seems is that
>> first I have to download some kinf of Fink-program before starting with
>> Bioperl... is it something close to this?
>>
>> I'm sorry, too many questions... But I really want to learn to use Bioperl
>> but I have no people to ask it face to face.
>>
>> Thank you so much,
>>
>> Casandra
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>


From scott at scottcain.net  Tue Feb  7 16:12:19 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 7 Feb 2012 16:12:19 -0500
Subject: [Bioperl-l] help!
In-Reply-To: <4F31917A.9030804@illinois.edu>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
Message-ID: <CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>

Yes, but those doc don't address exactly the problem Cassandra is
having, that she wants to use local::lib, but there need to be some
prereqs installed, but they can't be because she chose to use
local::lib, and it's not installed.  That's all fine if you're not a
newbie and know how to properly install the prereqs before using the
cpan shell, but when following instructions that say "use local::lib",
I find that the instructions are completely insufficient in actually
getting the desired software installed.  Thus the need for a good
tutorial.

Scott


On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfields at illinois.edu> wrote:
> I guess one key question is where these CPAN installation instructions come
> from. ?They're a bit odd, and if this is from the wiki we need to do some
> updating.
>
> Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> single perl version.
>
> https://metacpan.org/module/local::lib#The-bootstrapping-technique
>
> In my case I use perlbrew (which is all local by default, and allows
> switching between perl versions). ?Highly recommend using either simple
> local::lib or perlbrew in combination with cpanm.
>
> https://metacpan.org/module/perlbrew
> https://metacpan.org/module/cpanm
>
> chris
>
>
>
> On 02/07/2012 02:55 PM, Scott Cain wrote:
>>
>> hi Cassandra,
>>
>> I don't have an answer for you at the moment. ?It seems to me that
>> using local::lib is a good idea, but I've never found a good tutorial
>> for using it, so I haven't. ?Perhaps someone else on the list can
>> suggest one.
>>
>> The other thing I just wanted to mention as the admin that approved
>> your message--I came very close to deleting it from the queue without
>> looking at it because it is not unusual for spam messages to have
>> generic subjects like "help!" ?(just for future reference :-)
>>
>> Scott
>>
>>
>> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasandrah at gmail.com> ?wrote:
>>>
>>> Hi,
>>>
>>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>>> installed becaused I have already write some scripts but I'm biologist
>>> so...
>>> not pretty sure about what messages say.
>>>
>>> My perl version:
>>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>> My computer:
>>> Mac OS X Vesion 10.5.8
>>>
>>> I was following this preliminary steps:
>>>
>>> --------------
>>>
>>> PRELIMINARY PREPARATION
>>>
>>> ? ?This is optional, but regardless of your subsequent choice of
>>> ? ?installation method, it will help to carry out the following steps.
>>> ? ?They will increase the likelyhood of installation success
>>> ? ?(especially of optional dependencies).
>>>
>>> ? ? ?* Upgrade CPAN:
>>>
>>> ?>perl -MCPAN -e shell
>>> ?cpan>install Bundle::CPAN
>>> ?cpan>q
>>>
>>> ? ? ?* Install/upgrade Module::Build, and make it your preferred
>>> ? ? ? ?installer:
>>>
>>> ?>cpan
>>> ?cpan>install Module::Build
>>> ?cpan>o conf prefer_installer MB
>>> ?cpan>o conf commit
>>> ?cpan>q
>>>
>>> ? ? ?* Install the expat library by whatever method is
>>> ? ? ? ?appropriate for your system.
>>>
>>> ? ? ?* If your expat library is installed in a non-standard location,
>>> ? ? ? ?tell CPAN about it:
>>>
>>> ?>cpan
>>> ?cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>>> EXPATINCPATH=/non-standard/include"
>>> ?cpan>o conf commit
>>>
>>> --------------
>>>
>>> And I think I did "Upgrade CPAN properly" but when I tried the next one
>>> it
>>> started asking too many things to me, and finally it stopped due to "some
>>> problems". In text file you can see the whole process.
>>> What did I do wrong?
>>>
>>>
>>> After solving these preliminary steps, what should I do? What exactly
>>> .tar
>>> or .whatever should I download to install?
>>>
>>> I don't see the difference between installing it through "built.PL" or
>>> ?CPAN. And I don't know if I should do this or that "Fink*" stuff for
>>> MAC.
>>>
>>> * I went to Fink webpage and what I expected to see was "hello! download
>>> Bioperl simply clicking here!" but far from this, what it seems is that
>>> first I have to download some kinf of Fink-program before starting with
>>> Bioperl... is it something close to this?
>>>
>>> I'm sorry, too many questions... But I really want to learn to use
>>> Bioperl
>>> but I have no people to ask it face to face.
>>>
>>> Thank you so much,
>>>
>>> Casandra
>>>
>>> _______________________________________________
>>> 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



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


From cjfields at illinois.edu  Tue Feb  7 16:27:38 2012
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 7 Feb 2012 15:27:38 -0600
Subject: [Bioperl-l] help!
In-Reply-To: <CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
	<CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
Message-ID: <4F31974A.8040804@illinois.edu>

Right, I see.  However, Casandra didn't mention using local::lib, just 
using CPAN in general (hence my initial question).

IIRC local::lib, if set up correctly, should take care of the 
installation paths for CPAN/cpanm/etc regardless whether it's bioperl or 
any other perl module.

Last I checked this didn't seem to be an issue with bioperl; I installed 
Bioperl, as well as any prereqs, Bio::DB::Sam/BigWig, Moose, 
DBD::SQLite, etc, on our local SGI using local::lib in a common project 
space (with perl 5.10.1) w/o a problem.  If there is a problem specific 
to BioPerl, we should probably try to fix it and clarify any workarounds 
in the meantime.

chris

On 02/07/2012 03:12 PM, Scott Cain wrote:
> Yes, but those doc don't address exactly the problem Cassandra is
> having, that she wants to use local::lib, but there need to be some
> prereqs installed, but they can't be because she chose to use
> local::lib, and it's not installed.  That's all fine if you're not a
> newbie and know how to properly install the prereqs before using the
> cpan shell, but when following instructions that say "use local::lib",
> I find that the instructions are completely insufficient in actually
> getting the desired software installed.  Thus the need for a good
> tutorial.
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields<cjfields at illinois.edu>  wrote:
>> I guess one key question is where these CPAN installation instructions come
>> from.  They're a bit odd, and if this is from the wiki we need to do some
>> updating.
>>
>> Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
>> single perl version.
>>
>> https://metacpan.org/module/local::lib#The-bootstrapping-technique
>>
>> In my case I use perlbrew (which is all local by default, and allows
>> switching between perl versions).  Highly recommend using either simple
>> local::lib or perlbrew in combination with cpanm.
>>
>> https://metacpan.org/module/perlbrew
>> https://metacpan.org/module/cpanm
>>
>> chris
>>
>>
>>
>> On 02/07/2012 02:55 PM, Scott Cain wrote:
>>>
>>> hi Cassandra,
>>>
>>> I don't have an answer for you at the moment.  It seems to me that
>>> using local::lib is a good idea, but I've never found a good tutorial
>>> for using it, so I haven't.  Perhaps someone else on the list can
>>> suggest one.
>>>
>>> The other thing I just wanted to mention as the admin that approved
>>> your message--I came very close to deleting it from the queue without
>>> looking at it because it is not unusual for spam messages to have
>>> generic subjects like "help!"  (just for future reference :-)
>>>
>>> Scott
>>>
>>>
>>> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasandrah at gmail.com>    wrote:
>>>>
>>>> Hi,
>>>>
>>>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>>>> installed becaused I have already write some scripts but I'm biologist
>>>> so...
>>>> not pretty sure about what messages say.
>>>>
>>>> My perl version:
>>>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>>> My computer:
>>>> Mac OS X Vesion 10.5.8
>>>>
>>>> I was following this preliminary steps:
>>>>
>>>> --------------
>>>>
>>>> PRELIMINARY PREPARATION
>>>>
>>>>     This is optional, but regardless of your subsequent choice of
>>>>     installation method, it will help to carry out the following steps.
>>>>     They will increase the likelyhood of installation success
>>>>     (especially of optional dependencies).
>>>>
>>>>       * Upgrade CPAN:
>>>>
>>>>   >perl -MCPAN -e shell
>>>>   cpan>install Bundle::CPAN
>>>>   cpan>q
>>>>
>>>>       * Install/upgrade Module::Build, and make it your preferred
>>>>         installer:
>>>>
>>>>   >cpan
>>>>   cpan>install Module::Build
>>>>   cpan>o conf prefer_installer MB
>>>>   cpan>o conf commit
>>>>   cpan>q
>>>>
>>>>       * Install the expat library by whatever method is
>>>>         appropriate for your system.
>>>>
>>>>       * If your expat library is installed in a non-standard location,
>>>>         tell CPAN about it:
>>>>
>>>>   >cpan
>>>>   cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>>>> EXPATINCPATH=/non-standard/include"
>>>>   cpan>o conf commit
>>>>
>>>> --------------
>>>>
>>>> And I think I did "Upgrade CPAN properly" but when I tried the next one
>>>> it
>>>> started asking too many things to me, and finally it stopped due to "some
>>>> problems". In text file you can see the whole process.
>>>> What did I do wrong?
>>>>
>>>>
>>>> After solving these preliminary steps, what should I do? What exactly
>>>> .tar
>>>> or .whatever should I download to install?
>>>>
>>>> I don't see the difference between installing it through "built.PL" or
>>>>   CPAN. And I don't know if I should do this or that "Fink*" stuff for
>>>> MAC.
>>>>
>>>> * I went to Fink webpage and what I expected to see was "hello! download
>>>> Bioperl simply clicking here!" but far from this, what it seems is that
>>>> first I have to download some kinf of Fink-program before starting with
>>>> Bioperl... is it something close to this?
>>>>
>>>> I'm sorry, too many questions... But I really want to learn to use
>>>> Bioperl
>>>> but I have no people to ask it face to face.
>>>>
>>>> Thank you so much,
>>>>
>>>> Casandra
>>>>
>>>> _______________________________________________
>>>> 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 guhli007 at umn.edu  Tue Feb  7 16:14:05 2012
From: guhli007 at umn.edu (Joseph Guhlin)
Date: Tue, 7 Feb 2012 15:14:05 -0600
Subject: [Bioperl-l] help!
In-Reply-To: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
Message-ID: <CANodYL=j5T7scCVm2NoZQziTvokWcVD78ZLqWJajPj7H2hUVrg@mail.gmail.com>

I wonder if this would work on your system?

http://www.sysarchitects.com/bioperl

Best,
--Joseph Guhlin

On Tue, Feb 7, 2012 at 10:11 AM, Casandra <kasandrah at gmail.com> wrote:

> Hi,
>
> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
> installed becaused I have already write some scripts but I'm biologist
> so... not pretty sure about what messages say.
>
> My perl version:
> This is perl, v5.8.8 built for darwin-thread-multi-2level
> My computer:
> Mac OS X Vesion 10.5.8
>
> I was following this preliminary steps:
>
> --------------
>
> PRELIMINARY PREPARATION
>
>    This is optional, but regardless of your subsequent choice of
>    installation method, it will help to carry out the following steps.
>    They will increase the likelyhood of installation success
>    (especially of optional dependencies).
>
>      * Upgrade CPAN:
>
>  >perl -MCPAN -e shell
>  cpan>install Bundle::CPAN
>  cpan>q				
>
>      * Install/upgrade Module::Build, and make it your preferred
>        installer:
>
>  >cpan
>  cpan>install Module::Build
>  cpan>o conf prefer_installer MB
>  cpan>o conf commit
>  cpan>q
>
>      * Install the expat library by whatever method is
>        appropriate for your system.
>
>      * If your expat library is installed in a non-standard location,
>        tell CPAN about it:
>
>  >cpan
>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib EXPATINCPATH=/non-standard/include"
>  cpan>o conf commit
>
> --------------
>
> And I think I did "Upgrade CPAN properly" but when I tried the next one it
> started asking too many things to me, and finally it stopped due to "some
> problems". In text file you can see the whole process.
> What did I do wrong?
>
>
> After solving these preliminary steps, what should I do? What exactly .tar
> or .whatever should I download to install?
>
> I don't see the difference between installing it through "built.PL" or
>  CPAN. And I don't know if I should do this or that "Fink*" stuff for MAC.
>
> * I went to Fink webpage and what I expected to see was "hello! download
> Bioperl simply clicking here!" but far from this, what it seems is that
> first I have to download some kinf of Fink-program before starting with
> Bioperl... is it something close to this?
>
> I'm sorry, too many questions... But I really want to learn to use Bioperl
> but I have no people to ask it face to face.
>
> Thank you so much,
>
> Casandra
>
> _______________________________________________
> 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  Tue Feb  7 16:38:12 2012
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 7 Feb 2012 22:38:12 +0100
Subject: [Bioperl-l] help!
In-Reply-To: <CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
	<CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
Message-ID: <CAM3TQQViA2jqp0qkLu+Cei30bq_=2afTESWTnUebkb1vLyrVJA@mail.gmail.com>

I will take the opportunity to shamelessly pimp my no-install install
instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
Casandra is just looking to get started with BioPerl, messing with external
libs and configs is probably overkill.

Best,
Dave



 There?s a quickie, ?zero-install? way to get BioPerl on your system.

    1) Okay, click here to download bioperl as a zip file:

    https://github.com/bioperl/bioperl-live/zipball/master


    when it's done downloading, unzip it if your computer hasn?t done it
automatically. On the
    command line, you would do:

         unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip

    or whatever the file is called. You should then have a folder with some
ugly name like

    bioperl-bioperl-live-558467a

    3) rename that to

    bioperl-live

    4) move that folder to wherever you want to keep it. I keep mine in a
directory called src in my
        home directory.

    So on my computer if I go to the command line and cd to that folder and
type pwd I get:

    /Users/dave/src/bioperl-live

    5) in the terminal, cd to your home directory.

    6) see if you have a file named .bash_profile by typing

    ls -l ~/.bash_profile

    7) if so, open that file in your favorite editor. if the file doesn't
exist, just create the file.

    8) put this line in your .bash_profile

             export PERL5LIB=/Users/dave/src/bioperl-live

    (obviously replacing my path info with wherever you chose to put
bioperl)

    9) save and close your .bash_profile

  10) open a new terminal window so that the change will take effect.

  11) on the command line of the new terminal, type

               perl -e "use Bio::SeqIO;"

    If that works, then you have "installed" bioperl. Yay!












On Tue, Feb 7, 2012 at 22:12, Scott Cain <scott at scottcain.net> wrote:

> Yes, but those doc don't address exactly the problem Cassandra is
> having, that she wants to use local::lib, but there need to be some
> prereqs installed, but they can't be because she chose to use
> local::lib, and it's not installed.  That's all fine if you're not a
> newbie and know how to properly install the prereqs before using the
> cpan shell, but when following instructions that say "use local::lib",
> I find that the instructions are completely insufficient in actually
> getting the desired software installed.  Thus the need for a good
> tutorial.
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfields at illinois.edu>
> wrote:
> > I guess one key question is where these CPAN installation instructions
> come
> > from.  They're a bit odd, and if this is from the wiki we need to do some
> > updating.
> >
> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> > single perl version.
> >
> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
> >
> > In my case I use perlbrew (which is all local by default, and allows
> > switching between perl versions).  Highly recommend using either simple
> > local::lib or perlbrew in combination with cpanm.
> >
> > https://metacpan.org/module/perlbrew
> > https://metacpan.org/module/cpanm
> >
> > chris
> >
> >
> >
> > On 02/07/2012 02:55 PM, Scott Cain wrote:
> >>
> >> hi Cassandra,
> >>
> >> I don't have an answer for you at the moment.  It seems to me that
> >> using local::lib is a good idea, but I've never found a good tutorial
> >> for using it, so I haven't.  Perhaps someone else on the list can
> >> suggest one.
> >>
> >> The other thing I just wanted to mention as the admin that approved
> >> your message--I came very close to deleting it from the queue without
> >> looking at it because it is not unusual for spam messages to have
> >> generic subjects like "help!"  (just for future reference :-)
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasandrah at gmail.com>  wrote:
> >>>
> >>> Hi,
> >>>
> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
> >>> installed becaused I have already write some scripts but I'm biologist
> >>> so...
> >>> not pretty sure about what messages say.
> >>>
> >>> My perl version:
> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
> >>> My computer:
> >>> Mac OS X Vesion 10.5.8
> >>>
> >>> I was following this preliminary steps:
> >>>
> >>> --------------
> >>>
> >>> PRELIMINARY PREPARATION
> >>>
> >>>    This is optional, but regardless of your subsequent choice of
> >>>    installation method, it will help to carry out the following steps.
> >>>    They will increase the likelyhood of installation success
> >>>    (especially of optional dependencies).
> >>>
> >>>      * Upgrade CPAN:
> >>>
> >>>  >perl -MCPAN -e shell
> >>>  cpan>install Bundle::CPAN
> >>>  cpan>q
> >>>
> >>>      * Install/upgrade Module::Build, and make it your preferred
> >>>        installer:
> >>>
> >>>  >cpan
> >>>  cpan>install Module::Build
> >>>  cpan>o conf prefer_installer MB
> >>>  cpan>o conf commit
> >>>  cpan>q
> >>>
> >>>      * Install the expat library by whatever method is
> >>>        appropriate for your system.
> >>>
> >>>      * If your expat library is installed in a non-standard location,
> >>>        tell CPAN about it:
> >>>
> >>>  >cpan
> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
> >>> EXPATINCPATH=/non-standard/include"
> >>>  cpan>o conf commit
> >>>
> >>> --------------
> >>>
> >>> And I think I did "Upgrade CPAN properly" but when I tried the next one
> >>> it
> >>> started asking too many things to me, and finally it stopped due to
> "some
> >>> problems". In text file you can see the whole process.
> >>> What did I do wrong?
> >>>
> >>>
> >>> After solving these preliminary steps, what should I do? What exactly
> >>> .tar
> >>> or .whatever should I download to install?
> >>>
> >>> I don't see the difference between installing it through "built.PL" or
> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff for
> >>> MAC.
> >>>
> >>> * I went to Fink webpage and what I expected to see was "hello!
> download
> >>> Bioperl simply clicking here!" but far from this, what it seems is that
> >>> first I have to download some kinf of Fink-program before starting with
> >>> Bioperl... is it something close to this?
> >>>
> >>> I'm sorry, too many questions... But I really want to learn to use
> >>> Bioperl
> >>> but I have no people to ask it face to face.
> >>>
> >>> Thank you so much,
> >>>
> >>> Casandra
> >>>
> >>> _______________________________________________
> >>> 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
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From mcasandrariera at gmail.com  Tue Feb  7 17:05:16 2012
From: mcasandrariera at gmail.com (casandra)
Date: Tue, 7 Feb 2012 23:05:16 +0100
Subject: [Bioperl-l] help!
In-Reply-To: <CAM3TQQViA2jqp0qkLu+Cei30bq_=2afTESWTnUebkb1vLyrVJA@mail.gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
	<CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
	<CAM3TQQViA2jqp0qkLu+Cei30bq_=2afTESWTnUebkb1vLyrVJA@mail.gmail.com>
Message-ID: <CAEFNBYBw6ZFGNRjYGQjqzGiGr6g+z09Nsk0y6c2hUDH5X0tQ=g@mail.gmail.com>

Ok, this is what happened. I guess this mean it worked, didn't it?

Last login: Tue Feb  7 22:47:16 on ttys000
maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
Can't locate Bio/SeqIO.pm in @INC (@INC contains:
/Users/mcasaandrariera/src/bioperl-live
/Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
/Network/Library/Perl/5.12/darwin-thread-multi-2level
/Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
/System/Library/Perl/5.12/darwin-thread-multi-2level
/System/Library/Perl/5.12
/System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.12 .) at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
maccasandra:bioperl-live mcasandrariera$

I took your src name (I hadn't any better suggestion, although I don't know
what src means... :P)

Thank you so much to all of you! I have to say that it was a big relief
reading Dave telling so simple things :D thanks!

Maybe it will be useless to explain it to me, but, why this method isn't
"installing" Bioperl? Why I didn't need to do all those preliminary steps,
use Fink, and so on? I mean, if I can finally do the same (using Bioperl).

And related to the previous method I tried, I read that you were discussing
"that she wants to use local::lib, but there need to be some prereqs
installed, but they can't be because she chose to use local::lib, and it's
not installed. " I really didn't "wanted" to use it, I chose it because it
was the default option, and, since I didn't know about the alternatives, I
thought that the default would be ok... But if what Dave said works, better
for me, I didn't really know what I was doing with thosesteps (but I want
to learn it soon! ;) )

Thank you all for your time ;)

Casandra

El 7 de febrero de 2012 22:38, Dave Messina <David.Messina at sbc.su.se>escribi?:

> I will take the opportunity to shamelessly pimp my no-install install
> instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
> Casandra is just looking to get started with BioPerl, messing with external
> libs and configs is probably overkill.
>
> Best,
> Dave
>
>
>
>  There?s a quickie, ?zero-install? way to get BioPerl on your system.
>
>     1) Okay, click here to download bioperl as a zip file:
>
>     https://github.com/bioperl/bioperl-live/zipball/master
>
>
>     when it's done downloading, unzip it if your computer hasn?t done it
> automatically. On the
>     command line, you would do:
>
>          unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
>
>     or whatever the file is called. You should then have a folder with
> some ugly name like
>
>     bioperl-bioperl-live-558467a
>
>     3) rename that to
>
>     bioperl-live
>
>     4) move that folder to wherever you want to keep it. I keep mine in a
> directory called src in my
>         home directory.
>
>     So on my computer if I go to the command line and cd to that folder
> and type pwd I get:
>
>     /Users/dave/src/bioperl-live
>
>     5) in the terminal, cd to your home directory.
>
>     6) see if you have a file named .bash_profile by typing
>
>     ls -l ~/.bash_profile
>
>     7) if so, open that file in your favorite editor. if the file doesn't
> exist, just create the file.
>
>     8) put this line in your .bash_profile
>
>              export PERL5LIB=/Users/dave/src/bioperl-live
>
>     (obviously replacing my path info with wherever you chose to put
> bioperl)
>
>     9) save and close your .bash_profile
>
>   10) open a new terminal window so that the change will take effect.
>
>   11) on the command line of the new terminal, type
>
>                perl -e "use Bio::SeqIO;"
>
>     If that works, then you have "installed" bioperl. Yay!
>
>
>
>
>
>
>
>
>
>
>
>
> On Tue, Feb 7, 2012 at 22:12, Scott Cain <scott at scottcain.net> wrote:
>
>> Yes, but those doc don't address exactly the problem Cassandra is
>> having, that she wants to use local::lib, but there need to be some
>> prereqs installed, but they can't be because she chose to use
>> local::lib, and it's not installed.  That's all fine if you're not a
>> newbie and know how to properly install the prereqs before using the
>> cpan shell, but when following instructions that say "use local::lib",
>> I find that the instructions are completely insufficient in actually
>> getting the desired software installed.  Thus the need for a good
>> tutorial.
>>
>> Scott
>>
>>
>> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfields at illinois.edu>
>> wrote:
>> > I guess one key question is where these CPAN installation instructions
>> come
>> > from.  They're a bit odd, and if this is from the wiki we need to do
>> some
>> > updating.
>> >
>> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
>> > single perl version.
>> >
>> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
>> >
>> > In my case I use perlbrew (which is all local by default, and allows
>> > switching between perl versions).  Highly recommend using either simple
>> > local::lib or perlbrew in combination with cpanm.
>> >
>> > https://metacpan.org/module/perlbrew
>> > https://metacpan.org/module/cpanm
>> >
>> > chris
>>
>> >
>> >
>> >
>> > On 02/07/2012 02:55 PM, Scott Cain wrote:
>> >>
>> >> hi Cassandra,
>> >>
>> >> I don't have an answer for you at the moment.  It seems to me that
>> >> using local::lib is a good idea, but I've never found a good tutorial
>> >> for using it, so I haven't.  Perhaps someone else on the list can
>> >> suggest one.
>> >>
>> >> The other thing I just wanted to mention as the admin that approved
>> >> your message--I came very close to deleting it from the queue without
>> >> looking at it because it is not unusual for spam messages to have
>> >> generic subjects like "help!"  (just for future reference :-)
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasandrah at gmail.com>  wrote:
>> >>>
>> >>> Hi,
>> >>>
>> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>> >>> installed becaused I have already write some scripts but I'm biologist
>> >>> so...
>> >>> not pretty sure about what messages say.
>> >>>
>> >>> My perl version:
>> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>> >>> My computer:
>> >>> Mac OS X Vesion 10.5.8
>> >>>
>> >>> I was following this preliminary steps:
>> >>>
>> >>> --------------
>> >>>
>> >>> PRELIMINARY PREPARATION
>> >>>
>> >>>    This is optional, but regardless of your subsequent choice of
>> >>>    installation method, it will help to carry out the following steps.
>> >>>    They will increase the likelyhood of installation success
>> >>>    (especially of optional dependencies).
>> >>>
>> >>>      * Upgrade CPAN:
>> >>>
>> >>>  >perl -MCPAN -e shell
>> >>>  cpan>install Bundle::CPAN
>> >>>  cpan>q
>> >>>
>> >>>      * Install/upgrade Module::Build, and make it your preferred
>> >>>        installer:
>> >>>
>> >>>  >cpan
>> >>>  cpan>install Module::Build
>> >>>  cpan>o conf prefer_installer MB
>> >>>  cpan>o conf commit
>> >>>  cpan>q
>> >>>
>> >>>      * Install the expat library by whatever method is
>> >>>        appropriate for your system.
>> >>>
>> >>>      * If your expat library is installed in a non-standard location,
>> >>>        tell CPAN about it:
>> >>>
>> >>>  >cpan
>> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>> >>> EXPATINCPATH=/non-standard/include"
>> >>>  cpan>o conf commit
>> >>>
>> >>> --------------
>> >>>
>> >>> And I think I did "Upgrade CPAN properly" but when I tried the next
>> one
>> >>> it
>> >>> started asking too many things to me, and finally it stopped due to
>> "some
>> >>> problems". In text file you can see the whole process.
>> >>> What did I do wrong?
>> >>>
>> >>>
>> >>> After solving these preliminary steps, what should I do? What exactly
>> >>> .tar
>> >>> or .whatever should I download to install?
>> >>>
>> >>> I don't see the difference between installing it through "built.PL" or
>> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff for
>> >>> MAC.
>> >>>
>> >>> * I went to Fink webpage and what I expected to see was "hello!
>> download
>> >>> Bioperl simply clicking here!" but far from this, what it seems is
>> that
>> >>> first I have to download some kinf of Fink-program before starting
>> with
>> >>> Bioperl... is it something close to this?
>> >>>
>> >>> I'm sorry, too many questions... But I really want to learn to use
>> >>> Bioperl
>> >>> but I have no people to ask it face to face.
>> >>>
>> >>> Thank you so much,
>> >>>
>> >>> Casandra
>> >>>
>> >>> _______________________________________________
>> >>> 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
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>


-- 
Casandra Riera
+34 629774181
Barcelona, Spain.

mcasandrariera at gmail.com
http://terrainsalo.blogspot.com/


From wkretzsch at gmail.com  Tue Feb  7 17:30:37 2012
From: wkretzsch at gmail.com (Warren W. Kretzschmar)
Date: Tue, 7 Feb 2012 22:30:37 +0000
Subject: [Bioperl-l] help!
In-Reply-To: <CAEFNBYBw6ZFGNRjYGQjqzGiGr6g+z09Nsk0y6c2hUDH5X0tQ=g@mail.gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
	<CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
	<CAM3TQQViA2jqp0qkLu+Cei30bq_=2afTESWTnUebkb1vLyrVJA@mail.gmail.com>
	<CAEFNBYBw6ZFGNRjYGQjqzGiGr6g+z09Nsk0y6c2hUDH5X0tQ=g@mail.gmail.com>
Message-ID: <CA+1yJLESsxCkA+bGuaDy36r1ZQP6H9vGhLpb84N08Zkm1X0-gw@mail.gmail.com>

Hi Cassandra,
Do make sure you follow steps 6-10 (below) because bioperl is not in your
include path yet.  Without adding bioperl to your include path, bioperl
will only work when you are running programs while in the bioperl-live
dir.  This is because the current dir is usually added to the perl include
list.

   6) see if you have a file named .bash_profile by typing

   ls -l ~/.bash_profile

   7) if so, open that file in your favorite editor. if the file doesn't
exist, just create the file.

   8) put this line in your .bash_profile

            export PERL5LIB=/Users/dave/src/
bioperl-live

   (obviously replacing my path info with wherever you chose to put
bioperl)

   9) save and close your .bash_profile

 10) open a new terminal window so that the change will take effect.

Warren
--
In God we trust, all others bring data. - William Edwards Deming


On Tue, Feb 7, 2012 at 10:05 PM, casandra <mcasandrariera at gmail.com> wrote:

> Ok, this is what happened. I guess this mean it worked, didn't it?
>
> Last login: Tue Feb  7 22:47:16 on ttys000
> maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
> Can't locate Bio/SeqIO.pm in @INC (@INC contains:
> /Users/mcasaandrariera/src/bioperl-live
> /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
> /Network/Library/Perl/5.12/darwin-thread-multi-2level
> /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
> /System/Library/Perl/5.12/darwin-thread-multi-2level
> /System/Library/Perl/5.12
> /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.12 .) at -e line 1.
> BEGIN failed--compilation aborted at -e line 1.
> maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
> maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
> maccasandra:bioperl-live mcasandrariera$
>
> I took your src name (I hadn't any better suggestion, although I don't know
> what src means... :P)
>
> Thank you so much to all of you! I have to say that it was a big relief
> reading Dave telling so simple things :D thanks!
>
> Maybe it will be useless to explain it to me, but, why this method isn't
> "installing" Bioperl? Why I didn't need to do all those preliminary steps,
> use Fink, and so on? I mean, if I can finally do the same (using Bioperl).
>
> And related to the previous method I tried, I read that you were discussing
> "that she wants to use local::lib, but there need to be some prereqs
> installed, but they can't be because she chose to use local::lib, and it's
> not installed. " I really didn't "wanted" to use it, I chose it because it
> was the default option, and, since I didn't know about the alternatives, I
> thought that the default would be ok... But if what Dave said works, better
> for me, I didn't really know what I was doing with thosesteps (but I want
> to learn it soon! ;) )
>
> Thank you all for your time ;)
>
> Casandra
>
> El 7 de febrero de 2012 22:38, Dave Messina <David.Messina at sbc.su.se
> >escribi?:
>
> > I will take the opportunity to shamelessly pimp my no-install install
> > instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
> > Casandra is just looking to get started with BioPerl, messing with
> external
> > libs and configs is probably overkill.
> >
> > Best,
> > Dave
> >
> >
> >
> >  There?s a quickie, ?zero-install? way to get BioPerl on your system.
> >
> >     1) Okay, click here to download bioperl as a zip file:
> >
> >     https://github.com/bioperl/bioperl-live/zipball/master
> >
> >
> >     when it's done downloading, unzip it if your computer hasn?t done it
> > automatically. On the
> >     command line, you would do:
> >
> >          unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
> >
> >     or whatever the file is called. You should then have a folder with
> > some ugly name like
> >
> >     bioperl-bioperl-live-558467a
> >
> >     3) rename that to
> >
> >     bioperl-live
> >
> >     4) move that folder to wherever you want to keep it. I keep mine in a
> > directory called src in my
> >         home directory.
> >
> >     So on my computer if I go to the command line and cd to that folder
> > and type pwd I get:
> >
> >     /Users/dave/src/bioperl-live
> >
> >     5) in the terminal, cd to your home directory.
> >
> >     6) see if you have a file named .bash_profile by typing
> >
> >     ls -l ~/.bash_profile
> >
> >     7) if so, open that file in your favorite editor. if the file doesn't
> > exist, just create the file.
> >
> >     8) put this line in your .bash_profile
> >
> >              export PERL5LIB=/Users/dave/src/bioperl-live
> >
> >     (obviously replacing my path info with wherever you chose to put
> > bioperl)
> >
> >     9) save and close your .bash_profile
> >
> >   10) open a new terminal window so that the change will take effect.
> >
> >   11) on the command line of the new terminal, type
> >
> >                perl -e "use Bio::SeqIO;"
> >
> >     If that works, then you have "installed" bioperl. Yay!
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On Tue, Feb 7, 2012 at 22:12, Scott Cain <scott at scottcain.net> wrote:
> >
> >> Yes, but those doc don't address exactly the problem Cassandra is
> >> having, that she wants to use local::lib, but there need to be some
> >> prereqs installed, but they can't be because she chose to use
> >> local::lib, and it's not installed.  That's all fine if you're not a
> >> newbie and know how to properly install the prereqs before using the
> >> cpan shell, but when following instructions that say "use local::lib",
> >> I find that the instructions are completely insufficient in actually
> >> getting the desired software installed.  Thus the need for a good
> >> tutorial.
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfields at illinois.edu>
> >> wrote:
> >> > I guess one key question is where these CPAN installation instructions
> >> come
> >> > from.  They're a bit odd, and if this is from the wiki we need to do
> >> some
> >> > updating.
> >> >
> >> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> >> > single perl version.
> >> >
> >> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
> >> >
> >> > In my case I use perlbrew (which is all local by default, and allows
> >> > switching between perl versions).  Highly recommend using either
> simple
> >> > local::lib or perlbrew in combination with cpanm.
> >> >
> >> > https://metacpan.org/module/perlbrew
> >> > https://metacpan.org/module/cpanm
> >> >
> >> > chris
> >>
> >> >
> >> >
> >> >
> >> > On 02/07/2012 02:55 PM, Scott Cain wrote:
> >> >>
> >> >> hi Cassandra,
> >> >>
> >> >> I don't have an answer for you at the moment.  It seems to me that
> >> >> using local::lib is a good idea, but I've never found a good tutorial
> >> >> for using it, so I haven't.  Perhaps someone else on the list can
> >> >> suggest one.
> >> >>
> >> >> The other thing I just wanted to mention as the admin that approved
> >> >> your message--I came very close to deleting it from the queue without
> >> >> looking at it because it is not unusual for spam messages to have
> >> >> generic subjects like "help!"  (just for future reference :-)
> >> >>
> >> >> Scott
> >> >>
> >> >>
> >> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasandrah at gmail.com>
>  wrote:
> >> >>>
> >> >>> Hi,
> >> >>>
> >> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
> >> >>> installed becaused I have already write some scripts but I'm
> biologist
> >> >>> so...
> >> >>> not pretty sure about what messages say.
> >> >>>
> >> >>> My perl version:
> >> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
> >> >>> My computer:
> >> >>> Mac OS X Vesion 10.5.8
> >> >>>
> >> >>> I was following this preliminary steps:
> >> >>>
> >> >>> --------------
> >> >>>
> >> >>> PRELIMINARY PREPARATION
> >> >>>
> >> >>>    This is optional, but regardless of your subsequent choice of
> >> >>>    installation method, it will help to carry out the following
> steps.
> >> >>>    They will increase the likelyhood of installation success
> >> >>>    (especially of optional dependencies).
> >> >>>
> >> >>>      * Upgrade CPAN:
> >> >>>
> >> >>>  >perl -MCPAN -e shell
> >> >>>  cpan>install Bundle::CPAN
> >> >>>  cpan>q
> >> >>>
> >> >>>      * Install/upgrade Module::Build, and make it your preferred
> >> >>>        installer:
> >> >>>
> >> >>>  >cpan
> >> >>>  cpan>install Module::Build
> >> >>>  cpan>o conf prefer_installer MB
> >> >>>  cpan>o conf commit
> >> >>>  cpan>q
> >> >>>
> >> >>>      * Install the expat library by whatever method is
> >> >>>        appropriate for your system.
> >> >>>
> >> >>>      * If your expat library is installed in a non-standard
> location,
> >> >>>        tell CPAN about it:
> >> >>>
> >> >>>  >cpan
> >> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
> >> >>> EXPATINCPATH=/non-standard/include"
> >> >>>  cpan>o conf commit
> >> >>>
> >> >>> --------------
> >> >>>
> >> >>> And I think I did "Upgrade CPAN properly" but when I tried the next
> >> one
> >> >>> it
> >> >>> started asking too many things to me, and finally it stopped due to
> >> "some
> >> >>> problems". In text file you can see the whole process.
> >> >>> What did I do wrong?
> >> >>>
> >> >>>
> >> >>> After solving these preliminary steps, what should I do? What
> exactly
> >> >>> .tar
> >> >>> or .whatever should I download to install?
> >> >>>
> >> >>> I don't see the difference between installing it through "built.PL"
> or
> >> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff
> for
> >> >>> MAC.
> >> >>>
> >> >>> * I went to Fink webpage and what I expected to see was "hello!
> >> download
> >> >>> Bioperl simply clicking here!" but far from this, what it seems is
> >> that
> >> >>> first I have to download some kinf of Fink-program before starting
> >> with
> >> >>> Bioperl... is it something close to this?
> >> >>>
> >> >>> I'm sorry, too many questions... But I really want to learn to use
> >> >>> Bioperl
> >> >>> but I have no people to ask it face to face.
> >> >>>
> >> >>> Thank you so much,
> >> >>>
> >> >>> Casandra
> >> >>>
> >> >>> _______________________________________________
> >> >>> 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
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> Ontario Institute for Cancer Research
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
>
>
> --
> Casandra Riera
> +34 629774181
> Barcelona, Spain.
>
> mcasandrariera at gmail.com
> http://terrainsalo.blogspot.com/
>
> _______________________________________________
> 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  Tue Feb  7 17:39:48 2012
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 7 Feb 2012 23:39:48 +0100
Subject: [Bioperl-l] help!
In-Reply-To: <CAEFNBYBw6ZFGNRjYGQjqzGiGr6g+z09Nsk0y6c2hUDH5X0tQ=g@mail.gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
	<CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
	<CAM3TQQViA2jqp0qkLu+Cei30bq_=2afTESWTnUebkb1vLyrVJA@mail.gmail.com>
	<CAEFNBYBw6ZFGNRjYGQjqzGiGr6g+z09Nsk0y6c2hUDH5X0tQ=g@mail.gmail.com>
Message-ID: <CAM3TQQWaRg=nscktwV45TVrw5dbAPbq6BY=1cQ7rXbp8+fdbyg@mail.gmail.com>

Hi Casandra,

(Wayne already answered this much more succinctly than me, but here is my
answer anyway.)


I think you're almost there.

The fact that you get no error message when you type
perl -e "use Bio::SeqIO;"

in the directory src/bioperl-live/ tells me that probably Perl doesn't
"see" where you put BioPerl. That's what the PERL5LIB variable does; it
tells Perl that it should look for Perl modules in the directories named in
the environmental variable PERL5LIB.

If you type

printenv PERL5LIB

do you see

/Users/mcasandrariera/src/bioperl-live

?

If not, then redo steps 5-10 and then try typing
printenv PERL5LIB

again. Make sure that in step 8, instead of

export PERL5LIB=/Users/dave/src/bioperl-live

you type

export PERL5LIB=/Users/mcasandrariera/src/bioperl-live


To answer your other questions:

although I don't know what src means...


src is just a directory name. It's short for "source", which itself is
really short for "source code". src the name of the directory where I keep
all of my source code libraries like BioPerl.


Maybe it will be useless to explain it to me, but, why this method isn't
> "installing" Bioperl? Why I didn't need to do all those preliminary steps,
> use Fink, and so on? I mean, if I can finally do the same (using Bioperl).
>

The short answer is that by following the zero-install instructions, you
won't be able use some parts of BioPerl (which I'm betting you won't need
right away).

Chris and Scott's advice is correct and the right way to go in the long
run. Once you've gotten your feet wet a bit and become more familiar with
Perl and BioPerl, you may want to come back to their approach and try it
again.


Best,
Dave






On Tue, Feb 7, 2012 at 23:05, casandra <mcasandrariera at gmail.com> wrote:

> Ok, this is what happened. I guess this mean it worked, didn't it?
>
> Last login: Tue Feb  7 22:47:16 on ttys000
> maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
> Can't locate Bio/SeqIO.pm in @INC (@INC contains:
> /Users/mcasaandrariera/src/bioperl-live
> /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
> /Network/Library/Perl/5.12/darwin-thread-multi-2level
> /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
> /System/Library/Perl/5.12/darwin-thread-multi-2level
> /System/Library/Perl/5.12
> /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.12 .) at -e line 1.
> BEGIN failed--compilation aborted at -e line 1.
> maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
> maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
> maccasandra:bioperl-live mcasandrariera$
>
> I took your src name (I hadn't any better suggestion, although I don't
> know what src means... :P)
>
> Thank you so much to all of you! I have to say that it was a big relief
> reading Dave telling so simple things :D thanks!
>
> Maybe it will be useless to explain it to me, but, why this method isn't
> "installing" Bioperl? Why I didn't need to do all those preliminary steps,
> use Fink, and so on? I mean, if I can finally do the same (using Bioperl).
>
> And related to the previous method I tried, I read that you were
> discussing "that she wants to use local::lib, but there need to be
> some prereqs installed, but they can't be because she chose to
> use local::lib, and it's not installed. " I really didn't "wanted" to use
> it, I chose it because it was the default option, and, since I didn't know
> about the alternatives, I thought that the default would be ok... But if
> what Dave said works, better for me, I didn't really know what I was doing
> with thosesteps (but I want to learn it soon! ;) )
>
> Thank you all for your time ;)
>
> Casandra
>
> El 7 de febrero de 2012 22:38, Dave Messina <David.Messina at sbc.su.se>escribi?:
>
> I will take the opportunity to shamelessly pimp my no-install install
>> instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
>> Casandra is just looking to get started with BioPerl, messing with external
>> libs and configs is probably overkill.
>>
>> Best,
>> Dave
>>
>>
>>
>>  There?s a quickie, ?zero-install? way to get BioPerl on your system.
>>
>>     1) Okay, click here to download bioperl as a zip file:
>>
>>     https://github.com/bioperl/bioperl-live/zipball/master
>>
>>
>>     when it's done downloading, unzip it if your computer hasn?t done it
>> automatically. On the
>>     command line, you would do:
>>
>>          unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
>>
>>     or whatever the file is called. You should then have a folder with
>> some ugly name like
>>
>>     bioperl-bioperl-live-558467a
>>
>>     3) rename that to
>>
>>     bioperl-live
>>
>>     4) move that folder to wherever you want to keep it. I keep mine in a
>> directory called src in my
>>         home directory.
>>
>>     So on my computer if I go to the command line and cd to that folder
>> and type pwd I get:
>>
>>     /Users/dave/src/bioperl-live
>>
>>     5) in the terminal, cd to your home directory.
>>
>>     6) see if you have a file named .bash_profile by typing
>>
>>     ls -l ~/.bash_profile
>>
>>     7) if so, open that file in your favorite editor. if the file doesn't
>> exist, just create the file.
>>
>>     8) put this line in your .bash_profile
>>
>>              export PERL5LIB=/Users/dave/src/bioperl-live
>>
>>     (obviously replacing my path info with wherever you chose to put
>> bioperl)
>>
>>     9) save and close your .bash_profile
>>
>>   10) open a new terminal window so that the change will take effect.
>>
>>   11) on the command line of the new terminal, type
>>
>>                perl -e "use Bio::SeqIO;"
>>
>>     If that works, then you have "installed" bioperl. Yay!
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Feb 7, 2012 at 22:12, Scott Cain <scott at scottcain.net> wrote:
>>
>>> Yes, but those doc don't address exactly the problem Cassandra is
>>> having, that she wants to use local::lib, but there need to be some
>>> prereqs installed, but they can't be because she chose to use
>>> local::lib, and it's not installed.  That's all fine if you're not a
>>> newbie and know how to properly install the prereqs before using the
>>> cpan shell, but when following instructions that say "use local::lib",
>>> I find that the instructions are completely insufficient in actually
>>> getting the desired software installed.  Thus the need for a good
>>> tutorial.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfields at illinois.edu>
>>> wrote:
>>> > I guess one key question is where these CPAN installation instructions
>>> come
>>> > from.  They're a bit odd, and if this is from the wiki we need to do
>>> some
>>> > updating.
>>> >
>>> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
>>> > single perl version.
>>> >
>>> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
>>> >
>>> > In my case I use perlbrew (which is all local by default, and allows
>>> > switching between perl versions).  Highly recommend using either simple
>>> > local::lib or perlbrew in combination with cpanm.
>>> >
>>> > https://metacpan.org/module/perlbrew
>>> > https://metacpan.org/module/cpanm
>>> >
>>> > chris
>>>
>>> >
>>> >
>>> >
>>> > On 02/07/2012 02:55 PM, Scott Cain wrote:
>>> >>
>>> >> hi Cassandra,
>>> >>
>>> >> I don't have an answer for you at the moment.  It seems to me that
>>> >> using local::lib is a good idea, but I've never found a good tutorial
>>> >> for using it, so I haven't.  Perhaps someone else on the list can
>>> >> suggest one.
>>> >>
>>> >> The other thing I just wanted to mention as the admin that approved
>>> >> your message--I came very close to deleting it from the queue without
>>> >> looking at it because it is not unusual for spam messages to have
>>> >> generic subjects like "help!"  (just for future reference :-)
>>> >>
>>> >> Scott
>>> >>
>>> >>
>>> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasandrah at gmail.com>
>>>  wrote:
>>> >>>
>>> >>> Hi,
>>> >>>
>>> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>>> >>> installed becaused I have already write some scripts but I'm
>>> biologist
>>> >>> so...
>>> >>> not pretty sure about what messages say.
>>> >>>
>>> >>> My perl version:
>>> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>> >>> My computer:
>>> >>> Mac OS X Vesion 10.5.8
>>> >>>
>>> >>> I was following this preliminary steps:
>>> >>>
>>> >>> --------------
>>> >>>
>>> >>> PRELIMINARY PREPARATION
>>> >>>
>>> >>>    This is optional, but regardless of your subsequent choice of
>>> >>>    installation method, it will help to carry out the following
>>> steps.
>>> >>>    They will increase the likelyhood of installation success
>>> >>>    (especially of optional dependencies).
>>> >>>
>>> >>>      * Upgrade CPAN:
>>> >>>
>>> >>>  >perl -MCPAN -e shell
>>> >>>  cpan>install Bundle::CPAN
>>> >>>  cpan>q
>>> >>>
>>> >>>      * Install/upgrade Module::Build, and make it your preferred
>>> >>>        installer:
>>> >>>
>>> >>>  >cpan
>>> >>>  cpan>install Module::Build
>>> >>>  cpan>o conf prefer_installer MB
>>> >>>  cpan>o conf commit
>>> >>>  cpan>q
>>> >>>
>>> >>>      * Install the expat library by whatever method is
>>> >>>        appropriate for your system.
>>> >>>
>>> >>>      * If your expat library is installed in a non-standard location,
>>> >>>        tell CPAN about it:
>>> >>>
>>> >>>  >cpan
>>> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>>> >>> EXPATINCPATH=/non-standard/include"
>>> >>>  cpan>o conf commit
>>> >>>
>>> >>> --------------
>>> >>>
>>> >>> And I think I did "Upgrade CPAN properly" but when I tried the next
>>> one
>>> >>> it
>>> >>> started asking too many things to me, and finally it stopped due to
>>> "some
>>> >>> problems". In text file you can see the whole process.
>>> >>> What did I do wrong?
>>> >>>
>>> >>>
>>> >>> After solving these preliminary steps, what should I do? What exactly
>>> >>> .tar
>>> >>> or .whatever should I download to install?
>>> >>>
>>> >>> I don't see the difference between installing it through "built.PL"
>>> or
>>> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff for
>>> >>> MAC.
>>> >>>
>>> >>> * I went to Fink webpage and what I expected to see was "hello!
>>> download
>>> >>> Bioperl simply clicking here!" but far from this, what it seems is
>>> that
>>> >>> first I have to download some kinf of Fink-program before starting
>>> with
>>> >>> Bioperl... is it something close to this?
>>> >>>
>>> >>> I'm sorry, too many questions... But I really want to learn to use
>>> >>> Bioperl
>>> >>> but I have no people to ask it face to face.
>>> >>>
>>> >>> Thank you so much,
>>> >>>
>>> >>> Casandra
>>> >>>
>>> >>> _______________________________________________
>>> >>> 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
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>
>
> --
> Casandra Riera
> +34 629774181
> Barcelona, Spain.
>
> mcasandrariera at gmail.com
> http://terrainsalo.blogspot.com/
>
>


From mcasandrariera at gmail.com  Tue Feb  7 17:46:42 2012
From: mcasandrariera at gmail.com (casandra)
Date: Tue, 7 Feb 2012 23:46:42 +0100
Subject: [Bioperl-l] help!
In-Reply-To: <CAM3TQQWaRg=nscktwV45TVrw5dbAPbq6BY=1cQ7rXbp8+fdbyg@mail.gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
	<CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
	<CAM3TQQViA2jqp0qkLu+Cei30bq_=2afTESWTnUebkb1vLyrVJA@mail.gmail.com>
	<CAEFNBYBw6ZFGNRjYGQjqzGiGr6g+z09Nsk0y6c2hUDH5X0tQ=g@mail.gmail.com>
	<CAM3TQQWaRg=nscktwV45TVrw5dbAPbq6BY=1cQ7rXbp8+fdbyg@mail.gmail.com>
Message-ID: <CAEFNBYD46Xh0G57krKVa14ZmLyDjBQB59wfMwTL20g=S753qxw@mail.gmail.com>

Thank you both,
before I received Dave's email I was answering the following:

Hello Warren,

I've repeated those steps just in case, here I show you:

maccasandra:~ mcasandrariera$ vi .bash_profile
maccasandra:~ mcasandrariera$ more .bash_profile
export PERL5LIB=/Users/mcasandrariera/src/bioperl-live
maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
maccasandra:bioperl-live mcasandrariera$

I get the same "result". Am I supposed to get something different?"

And now I tried what Dave ask me:

maccasandra:bioperl-live mcasandrariera$ printenv PERL5LIB
/Users/mcasandrariera/src/bioperl-live
maccasandra:bioperl-live mcasandrariera$

I have to say it's very nice from you to help me, specially you, Dave, who
translates all this into casandra's-super-dummie language..

Cas.

El 7 de febrero de 2012 23:39, Dave Messina <David.Messina at sbc.su.se>escribi?:

> Hi Casandra,
>
> (Wayne already answered this much more succinctly than me, but here is my
> answer anyway.)
>
>
> I think you're almost there.
>
> The fact that you get no error message when you type
>  perl -e "use Bio::SeqIO;"
>
> in the directory src/bioperl-live/ tells me that probably Perl doesn't
> "see" where you put BioPerl. That's what the PERL5LIB variable does; it
> tells Perl that it should look for Perl modules in the directories named in
> the environmental variable PERL5LIB.
>
> If you type
>
> printenv PERL5LIB
>
> do you see
>
> /Users/mcasandrariera/src/bioperl-live
>
> ?
>
> If not, then redo steps 5-10 and then try typing
> printenv PERL5LIB
>
> again. Make sure that in step 8, instead of
>
> export PERL5LIB=/Users/dave/src/bioperl-live
>
> you type
>
> export PERL5LIB=/Users/mcasandrariera/src/bioperl-live
>
>
> To answer your other questions:
>
> although I don't know what src means...
>
>
> src is just a directory name. It's short for "source", which itself is
> really short for "source code". src the name of the directory where I keep
> all of my source code libraries like BioPerl.
>
>
> Maybe it will be useless to explain it to me, but, why this method isn't
>> "installing" Bioperl? Why I didn't need to do all those preliminary steps,
>> use Fink, and so on? I mean, if I can finally do the same (using Bioperl).
>>
>
> The short answer is that by following the zero-install instructions, you
> won't be able use some parts of BioPerl (which I'm betting you won't need
> right away).
>
> Chris and Scott's advice is correct and the right way to go in the long
> run. Once you've gotten your feet wet a bit and become more familiar with
> Perl and BioPerl, you may want to come back to their approach and try it
> again.
>
>
> Best,
> Dave
>
>
>
>
>
>
> On Tue, Feb 7, 2012 at 23:05, casandra <mcasandrariera at gmail.com> wrote:
>
>> Ok, this is what happened. I guess this mean it worked, didn't it?
>>
>> Last login: Tue Feb  7 22:47:16 on ttys000
>> maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
>> Can't locate Bio/SeqIO.pm in @INC (@INC contains:
>> /Users/mcasaandrariera/src/bioperl-live
>> /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
>> /Network/Library/Perl/5.12/darwin-thread-multi-2level
>> /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
>> /System/Library/Perl/5.12/darwin-thread-multi-2level
>> /System/Library/Perl/5.12
>> /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
>> /System/Library/Perl/Extras/5.12 .) at -e line 1.
>> BEGIN failed--compilation aborted at -e line 1.
>> maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
>> maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
>> maccasandra:bioperl-live mcasandrariera$
>>
>> I took your src name (I hadn't any better suggestion, although I don't
>> know what src means... :P)
>>
>> Thank you so much to all of you! I have to say that it was a big relief
>> reading Dave telling so simple things :D thanks!
>>
>> Maybe it will be useless to explain it to me, but, why this method isn't
>> "installing" Bioperl? Why I didn't need to do all those preliminary steps,
>> use Fink, and so on? I mean, if I can finally do the same (using Bioperl).
>>
>> And related to the previous method I tried, I read that you were
>> discussing "that she wants to use local::lib, but there need to be
>> some prereqs installed, but they can't be because she chose to
>> use local::lib, and it's not installed. " I really didn't "wanted" to use
>> it, I chose it because it was the default option, and, since I didn't know
>> about the alternatives, I thought that the default would be ok... But if
>> what Dave said works, better for me, I didn't really know what I was doing
>> with thosesteps (but I want to learn it soon! ;) )
>>
>> Thank you all for your time ;)
>>
>> Casandra
>>
>> El 7 de febrero de 2012 22:38, Dave Messina <David.Messina at sbc.su.se>escribi?:
>>
>> I will take the opportunity to shamelessly pimp my no-install install
>>> instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
>>> Casandra is just looking to get started with BioPerl, messing with external
>>> libs and configs is probably overkill.
>>>
>>> Best,
>>> Dave
>>>
>>>
>>>
>>>  There?s a quickie, ?zero-install? way to get BioPerl on your system.
>>>
>>>     1) Okay, click here to download bioperl as a zip file:
>>>
>>>     https://github.com/bioperl/bioperl-live/zipball/master
>>>
>>>
>>>     when it's done downloading, unzip it if your computer hasn?t done it
>>> automatically. On the
>>>     command line, you would do:
>>>
>>>          unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
>>>
>>>     or whatever the file is called. You should then have a folder with
>>> some ugly name like
>>>
>>>     bioperl-bioperl-live-558467a
>>>
>>>     3) rename that to
>>>
>>>     bioperl-live
>>>
>>>     4) move that folder to wherever you want to keep it. I keep mine in
>>> a directory called src in my
>>>         home directory.
>>>
>>>     So on my computer if I go to the command line and cd to that folder
>>> and type pwd I get:
>>>
>>>     /Users/dave/src/bioperl-live
>>>
>>>     5) in the terminal, cd to your home directory.
>>>
>>>     6) see if you have a file named .bash_profile by typing
>>>
>>>     ls -l ~/.bash_profile
>>>
>>>     7) if so, open that file in your favorite editor. if the file
>>> doesn't exist, just create the file.
>>>
>>>     8) put this line in your .bash_profile
>>>
>>>              export PERL5LIB=/Users/dave/src/bioperl-live
>>>
>>>     (obviously replacing my path info with wherever you chose to put
>>> bioperl)
>>>
>>>     9) save and close your .bash_profile
>>>
>>>   10) open a new terminal window so that the change will take effect.
>>>
>>>   11) on the command line of the new terminal, type
>>>
>>>                perl -e "use Bio::SeqIO;"
>>>
>>>     If that works, then you have "installed" bioperl. Yay!
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Tue, Feb 7, 2012 at 22:12, Scott Cain <scott at scottcain.net> wrote:
>>>
>>>> Yes, but those doc don't address exactly the problem Cassandra is
>>>> having, that she wants to use local::lib, but there need to be some
>>>> prereqs installed, but they can't be because she chose to use
>>>> local::lib, and it's not installed.  That's all fine if you're not a
>>>> newbie and know how to properly install the prereqs before using the
>>>> cpan shell, but when following instructions that say "use local::lib",
>>>> I find that the instructions are completely insufficient in actually
>>>> getting the desired software installed.  Thus the need for a good
>>>> tutorial.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfields at illinois.edu>
>>>> wrote:
>>>> > I guess one key question is where these CPAN installation
>>>> instructions come
>>>> > from.  They're a bit odd, and if this is from the wiki we need to do
>>>> some
>>>> > updating.
>>>> >
>>>> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
>>>> > single perl version.
>>>> >
>>>> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
>>>> >
>>>> > In my case I use perlbrew (which is all local by default, and allows
>>>> > switching between perl versions).  Highly recommend using either
>>>> simple
>>>> > local::lib or perlbrew in combination with cpanm.
>>>> >
>>>> > https://metacpan.org/module/perlbrew
>>>> > https://metacpan.org/module/cpanm
>>>> >
>>>> > chris
>>>>
>>>> >
>>>> >
>>>> >
>>>> > On 02/07/2012 02:55 PM, Scott Cain wrote:
>>>> >>
>>>> >> hi Cassandra,
>>>> >>
>>>> >> I don't have an answer for you at the moment.  It seems to me that
>>>> >> using local::lib is a good idea, but I've never found a good tutorial
>>>> >> for using it, so I haven't.  Perhaps someone else on the list can
>>>> >> suggest one.
>>>> >>
>>>> >> The other thing I just wanted to mention as the admin that approved
>>>> >> your message--I came very close to deleting it from the queue without
>>>> >> looking at it because it is not unusual for spam messages to have
>>>> >> generic subjects like "help!"  (just for future reference :-)
>>>> >>
>>>> >> Scott
>>>> >>
>>>> >>
>>>> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasandrah at gmail.com>
>>>>  wrote:
>>>> >>>
>>>> >>> Hi,
>>>> >>>
>>>> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>>>> >>> installed becaused I have already write some scripts but I'm
>>>> biologist
>>>> >>> so...
>>>> >>> not pretty sure about what messages say.
>>>> >>>
>>>> >>> My perl version:
>>>> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>>> >>> My computer:
>>>> >>> Mac OS X Vesion 10.5.8
>>>> >>>
>>>> >>> I was following this preliminary steps:
>>>> >>>
>>>> >>> --------------
>>>> >>>
>>>> >>> PRELIMINARY PREPARATION
>>>> >>>
>>>> >>>    This is optional, but regardless of your subsequent choice of
>>>> >>>    installation method, it will help to carry out the following
>>>> steps.
>>>> >>>    They will increase the likelyhood of installation success
>>>> >>>    (especially of optional dependencies).
>>>> >>>
>>>> >>>      * Upgrade CPAN:
>>>> >>>
>>>> >>>  >perl -MCPAN -e shell
>>>> >>>  cpan>install Bundle::CPAN
>>>> >>>  cpan>q
>>>> >>>
>>>> >>>      * Install/upgrade Module::Build, and make it your preferred
>>>> >>>        installer:
>>>> >>>
>>>> >>>  >cpan
>>>> >>>  cpan>install Module::Build
>>>> >>>  cpan>o conf prefer_installer MB
>>>> >>>  cpan>o conf commit
>>>> >>>  cpan>q
>>>> >>>
>>>> >>>      * Install the expat library by whatever method is
>>>> >>>        appropriate for your system.
>>>> >>>
>>>> >>>      * If your expat library is installed in a non-standard
>>>> location,
>>>> >>>        tell CPAN about it:
>>>> >>>
>>>> >>>  >cpan
>>>> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>>>> >>> EXPATINCPATH=/non-standard/include"
>>>> >>>  cpan>o conf commit
>>>> >>>
>>>> >>> --------------
>>>> >>>
>>>> >>> And I think I did "Upgrade CPAN properly" but when I tried the next
>>>> one
>>>> >>> it
>>>> >>> started asking too many things to me, and finally it stopped due to
>>>> "some
>>>> >>> problems". In text file you can see the whole process.
>>>> >>> What did I do wrong?
>>>> >>>
>>>> >>>
>>>> >>> After solving these preliminary steps, what should I do? What
>>>> exactly
>>>> >>> .tar
>>>> >>> or .whatever should I download to install?
>>>> >>>
>>>> >>> I don't see the difference between installing it through "built.PL"
>>>> or
>>>> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff
>>>> for
>>>> >>> MAC.
>>>> >>>
>>>> >>> * I went to Fink webpage and what I expected to see was "hello!
>>>> download
>>>> >>> Bioperl simply clicking here!" but far from this, what it seems is
>>>> that
>>>> >>> first I have to download some kinf of Fink-program before starting
>>>> with
>>>> >>> Bioperl... is it something close to this?
>>>> >>>
>>>> >>> I'm sorry, too many questions... But I really want to learn to use
>>>> >>> Bioperl
>>>> >>> but I have no people to ask it face to face.
>>>> >>>
>>>> >>> Thank you so much,
>>>> >>>
>>>> >>> Casandra
>>>> >>>
>>>> >>> _______________________________________________
>>>> >>> 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
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>> dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>
>>
>> --
>> Casandra Riera
>> +34 629774181
>> Barcelona, Spain.
>>
>> mcasandrariera at gmail.com
>> http://terrainsalo.blogspot.com/
>>
>>
>


-- 
Casandra Riera
+34 629774181
Barcelona, Spain.

mcasandrariera at gmail.com
http://terrainsalo.blogspot.com/


From cjfields at illinois.edu  Tue Feb  7 17:50:29 2012
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 7 Feb 2012 16:50:29 -0600
Subject: [Bioperl-l] help!
In-Reply-To: <CAM3TQQWaRg=nscktwV45TVrw5dbAPbq6BY=1cQ7rXbp8+fdbyg@mail.gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
	<CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
	<CAM3TQQViA2jqp0qkLu+Cei30bq_=2afTESWTnUebkb1vLyrVJA@mail.gmail.com>
	<CAEFNBYBw6ZFGNRjYGQjqzGiGr6g+z09Nsk0y6c2hUDH5X0tQ=g@mail.gmail.com>
	<CAM3TQQWaRg=nscktwV45TVrw5dbAPbq6BY=1cQ7rXbp8+fdbyg@mail.gmail.com>
Message-ID: <4F31AAB5.5010201@illinois.edu>

The catch with a PERL5LIB approach for a new installation is the very
possibility that non-core dependencies will not be installed.  We'll 
have a response down the road for 'why did Bio::Foo fail with the 
following error', with an obvious missing dependency being the problem.

We've been discussing this on IRC (scott, leont and I). I tend to think 
the best solution for new users is to set them up with both local::lib 
and cpanm initially, either by simply documenting this or by getting a 
script up and running for them.  This will resolve down-stream problems 
(for instance, if the distribution is split up).

chris


On 02/07/2012 04:39 PM, Dave Messina wrote:
> Hi Casandra,
>
> (Wayne already answered this much more succinctly than me, but here is
> my answer anyway.)
>
>
> I think you're almost there.
>
> The fact that you get no error message when you type
> perl -e "use Bio::SeqIO;"
>
> in the directory src/bioperl-live/ tells me that probably Perl doesn't
> "see" where you put BioPerl. That's what the PERL5LIB variable does; it
> tells Perl that it should look for Perl modules in the directories named
> in the environmental variable PERL5LIB.
>
> If you type
>
> printenv PERL5LIB
>
> do you see
>
> /Users/mcasandrariera/src/bioperl-live
>
> ?
>
> If not, then redo steps 5-10 and then try typing
> printenv PERL5LIB
>
> again. Make sure that in step 8, instead of
>
> export PERL5LIB=/Users/dave/src/bioperl-live
>
> you type
>
> export PERL5LIB=/Users/mcasandrariera/src/bioperl-live
>
>
> To answer your other questions:
>
>     although I don't know what src means...
>
>
> src is just a directory name. It's short for "source", which itself is
> really short for "source code". src the name of the directory where I
> keep all of my source code libraries like BioPerl.
>
>
>     Maybe it will be useless to explain it to me, but, why this method
>     isn't "installing" Bioperl? Why I didn't need to do all those
>     preliminary steps, use Fink, and so on? I mean, if I can finally do
>     the same (using Bioperl).
>
>
> The short answer is that by following the zero-install instructions, you
> won't be able use some parts of BioPerl (which I'm betting you won't
> need right away).
>
> Chris and Scott's advice is correct and the right way to go in the long
> run. Once you've gotten your feet wet a bit and become more familiar
> with Perl and BioPerl, you may want to come back to their approach and
> try it again.
>
>
> Best,
> Dave
>
>
>
>
>
> On Tue, Feb 7, 2012 at 23:05, casandra <mcasandrariera at gmail.com
> <mailto:mcasandrariera at gmail.com>> wrote:
>
>     Ok, this is what happened. I guess this mean it worked, didn't it?
>
>     Last login: Tue Feb 7 22:47:16 on ttys000
>     maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
>     Can't locate Bio/SeqIO.pm in @INC (@INC contains:
>     /Users/mcasaandrariera/src/bioperl-live
>     /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
>     /Network/Library/Perl/5.12/darwin-thread-multi-2level
>     /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
>     /System/Library/Perl/5.12/darwin-thread-multi-2level
>     /System/Library/Perl/5.12
>     /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
>     /System/Library/Perl/Extras/5.12 .) at -e line 1.
>     BEGIN failed--compilation aborted at -e line 1.
>     maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
>     maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
>     maccasandra:bioperl-live mcasandrariera$
>
>     I took your src name (I hadn't any better suggestion, although I
>     don't know what src means... :P)
>
>     Thank you so much to all of you! I have to say that it was a big
>     relief reading Dave telling so simple things :D thanks!
>
>     Maybe it will be useless to explain it to me, but, why this method
>     isn't "installing" Bioperl? Why I didn't need to do all those
>     preliminary steps, use Fink, and so on? I mean, if I can finally do
>     the same (using Bioperl).
>
>     And related to the previous method I tried, I read that you were
>     discussing "that she wants to use local::lib, but there need to be
>     some prereqs installed, but they can't be because she chose to use
>     local::lib, and it's not installed. " I really didn't "wanted" to
>     use it, I chose it because it was the default option, and, since I
>     didn't know about the alternatives, I thought that the default would
>     be ok... But if what Dave said works, better for me, I didn't really
>     know what I was doing with thosesteps (but I want to learn it soon! ;) )
>
>     Thank you all for your time ;)
>
>     Casandra
>
>     El 7 de febrero de 2012 22:38, Dave Messina <David.Messina at sbc.su.se
>     <mailto:David.Messina at sbc.su.se>> escribi?:
>
>         I will take the opportunity to shamelessly pimp my no-install
>         install instructions (below and
>         http://seqxml.org/xml/BioPerl.html). IMHO if Casandra is just
>         looking to get started with BioPerl, messing with external libs
>         and configs is probably overkill.
>
>         Best,
>         Dave
>
>
>
>         There?s a quickie, ?zero-install? way to get BioPerl on your system.
>         1) Okay, click here to download bioperl as a zip file:
>
>         https://github.com/bioperl/bioperl-live/zipball/master
>
>
>         when it's done downloading, unzip it if your computer hasn?t
>         done it automatically. On the
>         command line, you would do:
>
>         unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
>
>         or whatever the file is called. You should then have a folder
>         with some ugly name like
>
>         bioperl-bioperl-live-558467a
>
>         3) rename that to
>
>         bioperl-live
>
>         4) move that folder to wherever you want to keep it. I keep mine
>         in a directory called src in my
>         home directory.
>
>         So on my computer if I go to the command line and cd to that
>         folder and type pwd I get:
>
>         /Users/dave/src/bioperl-live
>
>         5) in the terminal, cd to your home directory.
>
>         6) see if you have a file named .bash_profile by typing
>
>         ls -l ~/.bash_profile
>
>         7) if so, open that file in your favorite editor. if the file
>         doesn't exist, just create the file.
>
>         8) put this line in your .bash_profile
>
>         export PERL5LIB=/Users/dave/src/bioperl-live
>
>         (obviously replacing my path info with wherever you chose to put
>         bioperl)
>
>         9) save and close your .bash_profile
>
>         10) open a new terminal window so that the change will take effect.
>
>         11) on the command line of the new terminal, type
>
>         perl -e "use Bio::SeqIO;"
>
>         If that works, then you have "installed" bioperl. Yay!
>
>
>
>
>
>
>
>
>
>
>
>
>         On Tue, Feb 7, 2012 at 22:12, Scott Cain <scott at scottcain.net
>         <mailto:scott at scottcain.net>> wrote:
>
>             Yes, but those doc don't address exactly the problem
>             Cassandra is
>             having, that she wants to use local::lib, but there need to
>             be some
>             prereqs installed, but they can't be because she chose to use
>             local::lib, and it's not installed. That's all fine if
>             you're not a
>             newbie and know how to properly install the prereqs before
>             using the
>             cpan shell, but when following instructions that say "use
>             local::lib",
>             I find that the instructions are completely insufficient in
>             actually
>             getting the desired software installed. Thus the need for a good
>             tutorial.
>
>             Scott
>
>
>             On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields
>             <cjfields at illinois.edu <mailto:cjfields at illinois.edu>> wrote:
>              > I guess one key question is where these CPAN installation
>             instructions come
>              > from. They're a bit odd, and if this is from the wiki we
>             need to do some
>              > updating.
>              >
>              > Re: local::lib, the docs on CPAN are pretty nice if one
>             wants to use a
>              > single perl version.
>              >
>              >
>             https://metacpan.org/module/local::lib#The-bootstrapping-technique
>              >
>              > In my case I use perlbrew (which is all local by default,
>             and allows
>              > switching between perl versions). Highly recommend using
>             either simple
>              > local::lib or perlbrew in combination with cpanm.
>              >
>              > https://metacpan.org/module/perlbrew
>              > https://metacpan.org/module/cpanm
>              >
>              > chris
>
>              >
>              >
>              >
>              > On 02/07/2012 02:55 PM, Scott Cain wrote:
>              >>
>              >> hi Cassandra,
>              >>
>              >> I don't have an answer for you at the moment. It seems
>             to me that
>              >> using local::lib is a good idea, but I've never found a
>             good tutorial
>              >> for using it, so I haven't. Perhaps someone else on the
>             list can
>              >> suggest one.
>              >>
>              >> The other thing I just wanted to mention as the admin
>             that approved
>              >> your message--I came very close to deleting it from the
>             queue without
>              >> looking at it because it is not unusual for spam
>             messages to have
>              >> generic subjects like "help!" (just for future reference :-)
>              >>
>              >> Scott
>              >>
>              >>
>              >> On Tue, Feb 7, 2012 at 11:11 AM,
>             Casandra<kasandrah at gmail.com <mailto:kasandrah at gmail.com>>
>             wrote:
>              >>>
>              >>> Hi,
>              >>>
>              >>> I'm trying to install Bioperl but I'm a bit lost. I
>             know I have perl
>              >>> installed becaused I have already write some scripts
>             but I'm biologist
>              >>> so...
>              >>> not pretty sure about what messages say.
>              >>>
>              >>> My perl version:
>              >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>              >>> My computer:
>              >>> Mac OS X Vesion 10.5.8
>              >>>
>              >>> I was following this preliminary steps:
>              >>>
>              >>> --------------
>              >>>
>              >>> PRELIMINARY PREPARATION
>              >>>
>              >>> This is optional, but regardless of your subsequent
>             choice of
>              >>> installation method, it will help to carry out the
>             following steps.
>              >>> They will increase the likelyhood of installation success
>              >>> (especially of optional dependencies).
>              >>>
>              >>> * Upgrade CPAN:
>              >>>
>              >>> >perl -MCPAN -e shell
>              >>> cpan>install Bundle::CPAN
>              >>> cpan>q
>              >>>
>              >>> * Install/upgrade Module::Build, and make it your preferred
>              >>> installer:
>              >>>
>              >>> >cpan
>              >>> cpan>install Module::Build
>              >>> cpan>o conf prefer_installer MB
>              >>> cpan>o conf commit
>              >>> cpan>q
>              >>>
>              >>> * Install the expat library by whatever method is
>              >>> appropriate for your system.
>              >>>
>              >>> * If your expat library is installed in a non-standard
>             location,
>              >>> tell CPAN about it:
>              >>>
>              >>> >cpan
>              >>> cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>              >>> EXPATINCPATH=/non-standard/include"
>              >>> cpan>o conf commit
>              >>>
>              >>> --------------
>              >>>
>              >>> And I think I did "Upgrade CPAN properly" but when I
>             tried the next one
>              >>> it
>              >>> started asking too many things to me, and finally it
>             stopped due to "some
>              >>> problems". In text file you can see the whole process.
>              >>> What did I do wrong?
>              >>>
>              >>>
>              >>> After solving these preliminary steps, what should I
>             do? What exactly
>              >>> .tar
>              >>> or .whatever should I download to install?
>              >>>
>              >>> I don't see the difference between installing it
>             through "built.PL" or
>              >>> CPAN. And I don't know if I should do this or that
>             "Fink*" stuff for
>              >>> MAC.
>              >>>
>              >>> * I went to Fink webpage and what I expected to see was
>             "hello! download
>              >>> Bioperl simply clicking here!" but far from this, what
>             it seems is that
>              >>> first I have to download some kinf of Fink-program
>             before starting with
>              >>> Bioperl... is it something close to this?
>              >>>
>              >>> I'm sorry, too many questions... But I really want to
>             learn to use
>              >>> Bioperl
>              >>> but I have no people to ask it face to face.
>              >>>
>              >>> Thank you so much,
>              >>>
>              >>> Casandra
>              >>>
>              >>> _______________________________________________
>              >>> 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
>              >>
>              >>
>              >>
>              >>
>              >
>              > _______________________________________________
>              > 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
>
>
>
>             --
>             ------------------------------------------------------------------------
>             Scott Cain, Ph. D. scott at scottcain dot net
>             GMOD Coordinator (http://gmod.org/) 216-392-3087
>             <tel:216-392-3087>
>             Ontario Institute for Cancer Research
>
>             _______________________________________________
>             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
>
>
>
>
>
>     --
>     Casandra Riera
>     +34 629774181 <tel:%2B34%20629774181>
>     Barcelona, Spain.
>
>     mcasandrariera at gmail.com <mailto:mcasandrariera at gmail.com>
>     http://terrainsalo.blogspot.com/
>
>


From David.Messina at sbc.su.se  Tue Feb  7 18:33:34 2012
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 8 Feb 2012 00:33:34 +0100
Subject: [Bioperl-l] help!
In-Reply-To: <4F31AAB5.5010201@illinois.edu>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
	<CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
	<CAM3TQQViA2jqp0qkLu+Cei30bq_=2afTESWTnUebkb1vLyrVJA@mail.gmail.com>
	<CAEFNBYBw6ZFGNRjYGQjqzGiGr6g+z09Nsk0y6c2hUDH5X0tQ=g@mail.gmail.com>
	<CAM3TQQWaRg=nscktwV45TVrw5dbAPbq6BY=1cQ7rXbp8+fdbyg@mail.gmail.com>
	<4F31AAB5.5010201@illinois.edu>
Message-ID: <CAM3TQQWAAG7KucRdkW_mZVP4E5q4QpAWoU0o_tz9YiMAaX00ZQ@mail.gmail.com>

Ah right, that's a good point. Well, don't I feel like the asshole. :)

Once local::lib and cpanm are installed, it's possible to run cpanm on the
tarball downloaded from github, right?

i.e.
cpanm bioperl-live-bioperl-release-**1-5-1-rc4-4318-g342e587.zip

And that should take care of dependencies, then, correct?


either by simply documenting this or by getting a script up and running for
> them.  This will resolve down-stream problems (for instance, if the
> distribution is split up).


Agreed, that's a great idea.


Best,
Dave




On Tue, Feb 7, 2012 at 23:50, Chris Fields <cjfields at illinois.edu> wrote:

> The catch with a PERL5LIB approach for a new installation is the very
> possibility that non-core dependencies will not be installed.  We'll have
> a response down the road for 'why did Bio::Foo fail with the following
> error', with an obvious missing dependency being the problem.
>
> We've been discussing this on IRC (scott, leont and I). I tend to think
> the best solution for new users is to set them up with both local::lib and
> cpanm initially, either by simply documenting this or by getting a script
> up and running for them.  This will resolve down-stream problems (for
> instance, if the distribution is split up).
>
> chris
>
>
>
> On 02/07/2012 04:39 PM, Dave Messina wrote:
>
>> Hi Casandra,
>>
>> (Wayne already answered this much more succinctly than me, but here is
>> my answer anyway.)
>>
>>
>> I think you're almost there.
>>
>> The fact that you get no error message when you type
>> perl -e "use Bio::SeqIO;"
>>
>> in the directory src/bioperl-live/ tells me that probably Perl doesn't
>> "see" where you put BioPerl. That's what the PERL5LIB variable does; it
>> tells Perl that it should look for Perl modules in the directories named
>> in the environmental variable PERL5LIB.
>>
>> If you type
>>
>> printenv PERL5LIB
>>
>> do you see
>>
>> /Users/mcasandrariera/src/**bioperl-live
>>
>> ?
>>
>> If not, then redo steps 5-10 and then try typing
>> printenv PERL5LIB
>>
>> again. Make sure that in step 8, instead of
>>
>> export PERL5LIB=/Users/dave/src/**bioperl-live
>>
>> you type
>>
>> export PERL5LIB=/Users/**mcasandrariera/src/bioperl-**live
>>
>>
>> To answer your other questions:
>>
>>    although I don't know what src means...
>>
>>
>> src is just a directory name. It's short for "source", which itself is
>> really short for "source code". src the name of the directory where I
>> keep all of my source code libraries like BioPerl.
>>
>>
>>    Maybe it will be useless to explain it to me, but, why this method
>>    isn't "installing" Bioperl? Why I didn't need to do all those
>>    preliminary steps, use Fink, and so on? I mean, if I can finally do
>>    the same (using Bioperl).
>>
>>
>> The short answer is that by following the zero-install instructions, you
>> won't be able use some parts of BioPerl (which I'm betting you won't
>> need right away).
>>
>> Chris and Scott's advice is correct and the right way to go in the long
>> run. Once you've gotten your feet wet a bit and become more familiar
>> with Perl and BioPerl, you may want to come back to their approach and
>> try it again.
>>
>>
>> Best,
>> Dave
>>
>>
>>
>>
>>
>> On Tue, Feb 7, 2012 at 23:05, casandra <mcasandrariera at gmail.com
>> <mailto:mcasandrariera at gmail.**com <mcasandrariera at gmail.com>>> wrote:
>>
>>    Ok, this is what happened. I guess this mean it worked, didn't it?
>>
>>    Last login: Tue Feb 7 22:47:16 on ttys000
>>    maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
>>    Can't locate Bio/SeqIO.pm in @INC (@INC contains:
>>    /Users/mcasaandrariera/src/**bioperl-live
>>    /Library/Perl/5.12/darwin-**thread-multi-2level /Library/Perl/5.12
>>    /Network/Library/Perl/5.12/**darwin-thread-multi-2level
>>    /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
>>    /System/Library/Perl/5.12/**darwin-thread-multi-2level
>>    /System/Library/Perl/5.12
>>    /System/Library/Perl/Extras/5.**12/darwin-thread-multi-2level
>>    /System/Library/Perl/Extras/5.**12 .) at -e line 1.
>>    BEGIN failed--compilation aborted at -e line 1.
>>    maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
>>    maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
>>    maccasandra:bioperl-live mcasandrariera$
>>
>>    I took your src name (I hadn't any better suggestion, although I
>>    don't know what src means... :P)
>>
>>    Thank you so much to all of you! I have to say that it was a big
>>    relief reading Dave telling so simple things :D thanks!
>>
>>    Maybe it will be useless to explain it to me, but, why this method
>>    isn't "installing" Bioperl? Why I didn't need to do all those
>>    preliminary steps, use Fink, and so on? I mean, if I can finally do
>>    the same (using Bioperl).
>>
>>    And related to the previous method I tried, I read that you were
>>    discussing "that she wants to use local::lib, but there need to be
>>    some prereqs installed, but they can't be because she chose to use
>>    local::lib, and it's not installed. " I really didn't "wanted" to
>>    use it, I chose it because it was the default option, and, since I
>>    didn't know about the alternatives, I thought that the default would
>>    be ok... But if what Dave said works, better for me, I didn't really
>>    know what I was doing with thosesteps (but I want to learn it soon! ;)
>> )
>>
>>    Thank you all for your time ;)
>>
>>    Casandra
>>
>>    El 7 de febrero de 2012 22:38, Dave Messina <David.Messina at sbc.su.se
>>    <mailto:David.Messina at sbc.su.**se <David.Messina at sbc.su.se>>>
>> escribi?:
>>
>>
>>        I will take the opportunity to shamelessly pimp my no-install
>>        install instructions (below and
>>        http://seqxml.org/xml/BioPerl.**html<http://seqxml.org/xml/BioPerl.html>).
>> IMHO if Casandra is just
>>        looking to get started with BioPerl, messing with external libs
>>        and configs is probably overkill.
>>
>>        Best,
>>        Dave
>>
>>
>>
>>        There?s a quickie, ?zero-install? way to get BioPerl on your
>> system.
>>        1) Okay, click here to download bioperl as a zip file:
>>
>>        https://github.com/bioperl/**bioperl-live/zipball/master<https://github.com/bioperl/bioperl-live/zipball/master>
>>
>>
>>        when it's done downloading, unzip it if your computer hasn?t
>>        done it automatically. On the
>>        command line, you would do:
>>
>>        unzip bioperl-live-bioperl-release-**1-5-1-rc4-4318-g342e587.zip
>>
>>        or whatever the file is called. You should then have a folder
>>        with some ugly name like
>>
>>        bioperl-bioperl-live-558467a
>>
>>        3) rename that to
>>
>>        bioperl-live
>>
>>        4) move that folder to wherever you want to keep it. I keep mine
>>        in a directory called src in my
>>        home directory.
>>
>>        So on my computer if I go to the command line and cd to that
>>        folder and type pwd I get:
>>
>>        /Users/dave/src/bioperl-live
>>
>>        5) in the terminal, cd to your home directory.
>>
>>        6) see if you have a file named .bash_profile by typing
>>
>>        ls -l ~/.bash_profile
>>
>>        7) if so, open that file in your favorite editor. if the file
>>        doesn't exist, just create the file.
>>
>>        8) put this line in your .bash_profile
>>
>>        export PERL5LIB=/Users/dave/src/**bioperl-live
>>
>>        (obviously replacing my path info with wherever you chose to put
>>        bioperl)
>>
>>        9) save and close your .bash_profile
>>
>>        10) open a new terminal window so that the change will take effect.
>>
>>        11) on the command line of the new terminal, type
>>
>>        perl -e "use Bio::SeqIO;"
>>
>>        If that works, then you have "installed" bioperl. Yay!
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>        On Tue, Feb 7, 2012 at 22:12, Scott Cain <scott at scottcain.net
>>        <mailto:scott at scottcain.net>> wrote:
>>
>>            Yes, but those doc don't address exactly the problem
>>            Cassandra is
>>            having, that she wants to use local::lib, but there need to
>>            be some
>>            prereqs installed, but they can't be because she chose to use
>>            local::lib, and it's not installed. That's all fine if
>>            you're not a
>>            newbie and know how to properly install the prereqs before
>>            using the
>>            cpan shell, but when following instructions that say "use
>>            local::lib",
>>            I find that the instructions are completely insufficient in
>>            actually
>>            getting the desired software installed. Thus the need for a
>> good
>>            tutorial.
>>
>>            Scott
>>
>>
>>            On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields
>>            <cjfields at illinois.edu <mailto:cjfields at illinois.edu>**>
>> wrote:
>>             > I guess one key question is where these CPAN installation
>>            instructions come
>>             > from. They're a bit odd, and if this is from the wiki we
>>            need to do some
>>             > updating.
>>             >
>>             > Re: local::lib, the docs on CPAN are pretty nice if one
>>            wants to use a
>>             > single perl version.
>>             >
>>             >
>>            https://metacpan.org/module/**local::lib#The-bootstrapping-**
>> technique<https://metacpan.org/module/local::lib#The-bootstrapping-technique>
>>             >
>>             > In my case I use perlbrew (which is all local by default,
>>            and allows
>>             > switching between perl versions). Highly recommend using
>>            either simple
>>             > local::lib or perlbrew in combination with cpanm.
>>             >
>>             > https://metacpan.org/module/**perlbrew<https://metacpan.org/module/perlbrew>
>>             > https://metacpan.org/module/**cpanm<https://metacpan.org/module/cpanm>
>>             >
>>             > chris
>>
>>             >
>>             >
>>             >
>>             > On 02/07/2012 02:55 PM, Scott Cain wrote:
>>             >>
>>             >> hi Cassandra,
>>             >>
>>             >> I don't have an answer for you at the moment. It seems
>>            to me that
>>             >> using local::lib is a good idea, but I've never found a
>>            good tutorial
>>             >> for using it, so I haven't. Perhaps someone else on the
>>            list can
>>             >> suggest one.
>>             >>
>>             >> The other thing I just wanted to mention as the admin
>>            that approved
>>             >> your message--I came very close to deleting it from the
>>            queue without
>>             >> looking at it because it is not unusual for spam
>>            messages to have
>>             >> generic subjects like "help!" (just for future reference
>> :-)
>>             >>
>>             >> Scott
>>             >>
>>             >>
>>             >> On Tue, Feb 7, 2012 at 11:11 AM,
>>            Casandra<kasandrah at gmail.com <mailto:kasandrah at gmail.com>>
>>
>>            wrote:
>>             >>>
>>             >>> Hi,
>>             >>>
>>             >>> I'm trying to install Bioperl but I'm a bit lost. I
>>            know I have perl
>>             >>> installed becaused I have already write some scripts
>>            but I'm biologist
>>             >>> so...
>>             >>> not pretty sure about what messages say.
>>             >>>
>>             >>> My perl version:
>>             >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>             >>> My computer:
>>             >>> Mac OS X Vesion 10.5.8
>>             >>>
>>             >>> I was following this preliminary steps:
>>             >>>
>>             >>> --------------
>>             >>>
>>             >>> PRELIMINARY PREPARATION
>>             >>>
>>             >>> This is optional, but regardless of your subsequent
>>            choice of
>>             >>> installation method, it will help to carry out the
>>            following steps.
>>             >>> They will increase the likelyhood of installation success
>>             >>> (especially of optional dependencies).
>>             >>>
>>             >>> * Upgrade CPAN:
>>             >>>
>>             >>> >perl -MCPAN -e shell
>>             >>> cpan>install Bundle::CPAN
>>             >>> cpan>q
>>             >>>
>>             >>> * Install/upgrade Module::Build, and make it your
>> preferred
>>             >>> installer:
>>             >>>
>>             >>> >cpan
>>             >>> cpan>install Module::Build
>>             >>> cpan>o conf prefer_installer MB
>>             >>> cpan>o conf commit
>>             >>> cpan>q
>>             >>>
>>             >>> * Install the expat library by whatever method is
>>             >>> appropriate for your system.
>>             >>>
>>             >>> * If your expat library is installed in a non-standard
>>            location,
>>             >>> tell CPAN about it:
>>             >>>
>>             >>> >cpan
>>             >>> cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/**lib
>>             >>> EXPATINCPATH=/non-standard/**include"
>>             >>> cpan>o conf commit
>>             >>>
>>             >>> --------------
>>             >>>
>>             >>> And I think I did "Upgrade CPAN properly" but when I
>>            tried the next one
>>             >>> it
>>             >>> started asking too many things to me, and finally it
>>            stopped due to "some
>>             >>> problems". In text file you can see the whole process.
>>             >>> What did I do wrong?
>>             >>>
>>             >>>
>>             >>> After solving these preliminary steps, what should I
>>            do? What exactly
>>             >>> .tar
>>             >>> or .whatever should I download to install?
>>             >>>
>>             >>> I don't see the difference between installing it
>>            through "built.PL" or
>>             >>> CPAN. And I don't know if I should do this or that
>>            "Fink*" stuff for
>>             >>> MAC.
>>             >>>
>>             >>> * I went to Fink webpage and what I expected to see was
>>            "hello! download
>>             >>> Bioperl simply clicking here!" but far from this, what
>>            it seems is that
>>             >>> first I have to download some kinf of Fink-program
>>            before starting with
>>             >>> Bioperl... is it something close to this?
>>             >>>
>>             >>> I'm sorry, too many questions... But I really want to
>>            learn to use
>>             >>> Bioperl
>>             >>> but I have no people to ask it face to face.
>>             >>>
>>             >>> Thank you so much,
>>             >>>
>>             >>> Casandra
>>             >>>
>>             >>> ______________________________**_________________
>>             >>> Bioperl-l mailing list
>>             >>> Bioperl-l at lists.open-bio.org
>>            <mailto:Bioperl-l at lists.open-**bio.org<Bioperl-l at lists.open-bio.org>
>> >
>>
>>             >>> http://lists.open-bio.org/**mailman/listinfo/bioperl-l<http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>             >>
>>             >>
>>             >>
>>             >>
>>             >
>>             > ______________________________**_________________
>>             > Bioperl-l mailing list
>>             > Bioperl-l at lists.open-bio.org
>>            <mailto:Bioperl-l at lists.open-**bio.org<Bioperl-l at lists.open-bio.org>
>> >
>>
>>             > http://lists.open-bio.org/**mailman/listinfo/bioperl-l<http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>
>>
>>
>>            --
>>            ------------------------------**------------------------------
>> **------------
>>            Scott Cain, Ph. D. scott at scottcain dot net
>>            GMOD Coordinator (http://gmod.org/) 216-392-3087
>>            <tel:216-392-3087>
>>
>>            Ontario Institute for Cancer Research
>>
>>            ______________________________**_________________
>>            Bioperl-l mailing list
>>            Bioperl-l at lists.open-bio.org
>>            <mailto:Bioperl-l at lists.open-**bio.org<Bioperl-l at lists.open-bio.org>
>> >
>>
>>            http://lists.open-bio.org/**mailman/listinfo/bioperl-l<http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>
>>
>>
>>
>>
>>    --
>>    Casandra Riera
>>    +34 629774181 <tel:%2B34%20629774181>
>>    Barcelona, Spain.
>>
>>    mcasandrariera at gmail.com <mailto:mcasandrariera at gmail.**com<mcasandrariera at gmail.com>
>> >
>>    http://terrainsalo.blogspot.**com/ <http://terrainsalo.blogspot.com/>
>>
>>
>>
>


From cjfields at illinois.edu  Tue Feb  7 21:25:12 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 8 Feb 2012 02:25:12 +0000
Subject: [Bioperl-l] help!
In-Reply-To: <CAM3TQQWAAG7KucRdkW_mZVP4E5q4QpAWoU0o_tz9YiMAaX00ZQ@mail.gmail.com>
References: <8DFE8929-F3F7-4D0A-AD9E-A11983020EDF@gmail.com>
	<CA+JTaox--hBLMDb6Fe=b5p0yC-ZMTGzjxfe1c-DxqM8FVQnKOQ@mail.gmail.com>
	<4F31917A.9030804@illinois.edu>
	<CA+JTaowDXGvvCJz=Jm8DbOk6urcFrzNc+4rRUKO4zqAzZRV1EA@mail.gmail.com>
	<CAM3TQQViA2jqp0qkLu+Cei30bq_=2afTESWTnUebkb1vLyrVJA@mail.gmail.com>
	<CAEFNBYBw6ZFGNRjYGQjqzGiGr6g+z09Nsk0y6c2hUDH5X0tQ=g@mail.gmail.com>
	<CAM3TQQWaRg=nscktwV45TVrw5dbAPbq6BY=1cQ7rXbp8+fdbyg@mail.gmail.com>
	<4F31AAB5.5010201@illinois.edu>
	<CAM3TQQWAAG7KucRdkW_mZVP4E5q4QpAWoU0o_tz9YiMAaX00ZQ@mail.gmail.com>
Message-ID: <704AA15E-13F6-4498-9519-DC6986191A09@illinois.edu>

On Feb 7, 2012, at 5:33 PM, Dave Messina wrote:

> Ah right, that's a good point. Well, don't I feel like the asshole. :)

Nah.  It's something we've done for quite a while, but we probably should adopt something that works better in the long run.

> Once local::lib and cpanm are installed, it's possible to run cpanm on the tarball downloaded from github, right?
> 
> i.e.
> cpanm bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
> 
> And that should take care of dependencies, then, correct?

Yep.  One can install from a URL as well:

cpanm http://example.org/LDS/CGI.pm-3.20.tar.gz

> either by simply documenting this or by getting a script up and running for them.  This will resolve down-stream problems (for instance, if the distribution is split up).
> 
> Agreed, that's a great idea.
> 
> 
> Best,
> Dave

chris

From hlapp at drycafe.net  Tue Feb  7 23:37:32 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Tue, 7 Feb 2012 23:37:32 -0500
Subject: [Bioperl-l] Question on seqfeature mapping
In-Reply-To: <4F31802E.9030002@labri.fr>
References: <4F0C7017.90803@inria.fr>
	<CAKVJ-_7d_K6+MttpMvW7-kr9iYTL6u0TMDcM=GfW7sVFsrO6sQ@mail.gmail.com>
	<A9148EAE-8709-4944-8369-CC98E7B53263@illinois.edu>
	<4F0D83D8.90402@inria.fr> <4F0D8A18.1080606@inria.fr>
	<D2004971-6A32-4141-B446-D2A855FDB026@illinois.edu>
	<4F0EA69E.8040203@inria.fr>
	<49CC4A91-5E47-4866-AD63-62DC7F649CE6@drycafe.net>
	<4F0FF883.80109@inria.fr> <4F0FF8FF.6070706@inria.fr>
	<E0F6A75C-8902-44D5-BB5F-8C0A4060EF9B@drycafe.net>
	<4F199A27.8030408@inria.fr>
	<054FEA92-8C5E-47D6-86AF-F71DEAFE2B63@illinois.edu>
	<4F31802E.9030002@labri.fr>
Message-ID: <33DA4F1D-3575-4925-A123-F6A77EAE753D@drycafe.net>

Hi Florian,

Are you asking about the Bio::DB::Query::BioQuery interface, or an object persistence adaptor in Bio/DB/BioSQL? Either way, the code resolves which table to use by the association that needs to be queried. How these map to association tables is in the %association_entity_map mapping. You'll see that there is one for term => seqfeature, which is mapped to seqfeature_qualifier_value, for example. So if the association is between seqfeature and term, the adaptor will then use that table to access the value column.

Does that make sense?

	-hilmar
 
On Feb 7, 2012, at 2:49 PM, florian lajus wrote:

> Hi,
> I have a problem with bio queries: How can I retrieve from datadabse a seqfeature according to its annotation (tagname and value)?
> The problem coming for value as we have "value"          =>  "=>{bioentry_qualifier_value,seqfeature_qualifier_value,location_qualifier_value}.value",
> in the %slot_attribut_map of the base driver.
> Do you know a solution?
> 

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






From adsj at novozymes.com  Wed Feb  8 07:28:11 2012
From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=)
Date: Wed, 08 Feb 2012 13:28:11 +0100
Subject: [Bioperl-l] Memory leak in
	Bio::SeqIO::staden::read->staden_read_trace() ?
Message-ID: <87wr7xv7ac.fsf@topper.koldfront.dk>

  Hi.

I am using Bio::SeqIO(staden::read) to read .ab1 files in a long lived
(daemon) process, and I have noticed that memory usage keeps growing
somewhat rapidly.

I have thrown together a small script that illustrates what I am seeing:

#!/usr/bin/perl

# test.pl - illustrate possible memory leak in Bio::SeqIO::staden::read->staden_read_trace
#           Example .ab1 file found via first hit on Google: http://www.elimbio.com/Forms/pGEM.zip

use strict;
use warnings;

use Bio::SeqIO;

while (1) {
    print "Reading 100 times\n";
    for my $i (1 .. 100) {
        my $in=Bio::SeqIO->new(-file=>'pGEM_(ABI)_A01.ab1', -format=>'abi');
        my $seq=$in->next_seq(); # This seems to leak memory
    }
    print "Sleeping\n";
    sleep 5;
}

Running this, and running 'while (( 1 )); do ps fauxww | grep [t]est.pl;
sleep 2; done;' I see an increase of memory usage by ~30MB per 100 read
cycle; e.g. 108660, 140260, 171860, 203460, 235064, 266676 bytes.

I would have expected the number to level out as $seq goes out of scope
and memory is returned to Perls internal pool for reuse.

If I comment out the $self->staden_read_trace() in L104 of
Bio::SeqIO::staden::read then memory usage stays constant, which leads
me to believe that it might be leaking (rather than some circular
reference I'm overlooking).

I am wondering if anyone can reproduce this problem, or if it is a local
thing (I had to do some gymnastics to build bioperl-ext way-back-when,
so it isn't entirely impossible); if anyone could try it and report
back, that would be a great help.

I am using BioPerl 1.6.1, bioperl-ext 1.5.1 and perl 5.10.1 on Ubuntu
10.04.03 lucid amd64.

  Best regards,

    Adam

-- 
                                                          Adam Sj?gren
                                                    adsj at novozymes.com


From flajus at labri.fr  Wed Feb  8 03:02:32 2012
From: flajus at labri.fr (Lajus Florian)
Date: Wed, 08 Feb 2012 09:02:32 +0100
Subject: [Bioperl-l] Question on seqfeature mapping
In-Reply-To: <33DA4F1D-3575-4925-A123-F6A77EAE753D@drycafe.net>
References: <4F0C7017.90803@inria.fr>
	<CAKVJ-_7d_K6+MttpMvW7-kr9iYTL6u0TMDcM=GfW7sVFsrO6sQ@mail.gmail.com>
	<A9148EAE-8709-4944-8369-CC98E7B53263@illinois.edu>
	<4F0D83D8.90402@inria.fr> <4F0D8A18.1080606@inria.fr>
	<D2004971-6A32-4141-B446-D2A855FDB026@illinois.edu>
	<4F0EA69E.8040203@inria.fr>
	<49CC4A91-5E47-4866-AD63-62DC7F649CE6@drycafe.net>
	<4F0FF883.80109@inria.fr> <4F0FF8FF.6070706@inria.fr>
	<E0F6A75C-8902-44D5-BB5F-8C0A4060EF9B@drycafe.net>
	<4F199A27.8030408@inria.fr>
	<054FEA92-8C5E-47D6-86AF-F71DEAFE2B63@illinois.edu>
	<4F31802E.9030002@labri.fr>
	<33DA4F1D-3575-4925-A123-F6A77EAE753D@drycafe.net>
Message-ID: <4F322C18.7010103@labri.fr>

I'm talking about the interface. I'm far from understanding all the way 
the association is done but for a query like this: my $query = 
Bio::DB::Query::BioQuery->new(				-datacollections => 
["Bio::Annotation::SimpleValue=>Bio::SeqFeatureI qv"],
-where => ["qv::value = \'$value\'"]);

according to the sql generator I have this:
SELECT * FROM seqfeature, term qv WHERE seqfeature.term_id = qv.term_id 
AND qv.=>{bioentry_qualifier_value,seqfeature_qualifier_value}.value = 
'Samatha Carter'

Le 08/02/2012 05:37, Hilmar Lapp a ?crit :
> Hi Florian,
>
> Are you asking about the Bio::DB::Query::BioQuery interface, or an object persistence adaptor in Bio/DB/BioSQL? Either way, the code resolves which table to use by the association that needs to be queried. How these map to association tables is in the %association_entity_map mapping. You'll see that there is one for term =>  seqfeature, which is mapped to seqfeature_qualifier_value, for example. So if the association is between seqfeature and term, the adaptor will then use that table to access the value column.
>
> Does that make sense?
>
> 	-hilmar
>
> On Feb 7, 2012, at 2:49 PM, florian lajus wrote:
>
>> Hi,
>> I have a problem with bio queries: How can I retrieve from datadabse a seqfeature according to its annotation (tagname and value)?
>> The problem coming for value as we have "value"          =>   "=>{bioentry_qualifier_value,seqfeature_qualifier_value,location_qualifier_value}.value",
>> in the %slot_attribut_map of the base driver.
>> Do you know a solution?
>>
>


From flajus at labri.fr  Wed Feb  8 04:52:04 2012
From: flajus at labri.fr (Lajus Florian)
Date: Wed, 08 Feb 2012 10:52:04 +0100
Subject: [Bioperl-l] Question on seqfeature mapping
In-Reply-To: <4F322C18.7010103@labri.fr>
References: <4F0C7017.90803@inria.fr>
	<CAKVJ-_7d_K6+MttpMvW7-kr9iYTL6u0TMDcM=GfW7sVFsrO6sQ@mail.gmail.com>
	<A9148EAE-8709-4944-8369-CC98E7B53263@illinois.edu>
	<4F0D83D8.90402@inria.fr> <4F0D8A18.1080606@inria.fr>
	<D2004971-6A32-4141-B446-D2A855FDB026@illinois.edu>
	<4F0EA69E.8040203@inria.fr>
	<49CC4A91-5E47-4866-AD63-62DC7F649CE6@drycafe.net>
	<4F0FF883.80109@inria.fr> <4F0FF8FF.6070706@inria.fr>
	<E0F6A75C-8902-44D5-BB5F-8C0A4060EF9B@drycafe.net>
	<4F199A27.8030408@inria.fr>
	<054FEA92-8C5E-47D6-86AF-F71DEAFE2B63@illinois.edu>
	<4F31802E.9030002@labri.fr>
	<33DA4F1D-3575-4925-A123-F6A77EAE753D@drycafe.net>
	<4F322C18.7010103@labri.fr>
Message-ID: <4F3245C4.9040506@labri.fr>

Never mind. It works much better if write: 
"Bio::Annotation::SimpleValue<=>Bio::SeqFeatureI instead.

The problem is if we also want to find by primary_tag:
my $query = Bio::DB::Query::BioQuery->new(
-datacollections => ["Bio::Annotation::SimpleValue<=>Bio::SeqFeatureI qv"],
-where => ["Bio::Annotation::SimpleValue::tagname = \'$tag\'","qv.value 
= \'$value\'","Bio::SeqFeatureI.primary_tag = ".$term_primary_key]);

The slot type_term_id is not mapped to column for table seqfeature

Le 08/02/2012 09:02, Lajus Florian a ?crit :
> I'm talking about the interface. I'm far from understanding all the way
> the association is done but for a query like this: my $query =
> Bio::DB::Query::BioQuery->new( -datacollections =>
> ["Bio::Annotation::SimpleValue=>Bio::SeqFeatureI qv"],
> -where => ["qv::value = \'$value\'"]);
>
> according to the sql generator I have this:
> SELECT * FROM seqfeature, term qv WHERE seqfeature.term_id = qv.term_id
> AND qv.=>{bioentry_qualifier_value,seqfeature_qualifier_value}.value =
> 'Samatha Carter'
>
> Le 08/02/2012 05:37, Hilmar Lapp a ?crit :
>> Hi Florian,
>>
>> Are you asking about the Bio::DB::Query::BioQuery interface, or an
>> object persistence adaptor in Bio/DB/BioSQL? Either way, the code
>> resolves which table to use by the association that needs to be
>> queried. How these map to association tables is in the
>> %association_entity_map mapping. You'll see that there is one for term
>> => seqfeature, which is mapped to seqfeature_qualifier_value, for
>> example. So if the association is between seqfeature and term, the
>> adaptor will then use that table to access the value column.
>>
>> Does that make sense?
>>
>> -hilmar
>>
>> On Feb 7, 2012, at 2:49 PM, florian lajus wrote:
>>
>>> Hi,
>>> I have a problem with bio queries: How can I retrieve from datadabse
>>> a seqfeature according to its annotation (tagname and value)?
>>> The problem coming for value as we have "value" =>
>>> "=>{bioentry_qualifier_value,seqfeature_qualifier_value,location_qualifier_value}.value",
>>>
>>> in the %slot_attribut_map of the base driver.
>>> Do you know a solution?
>>>
>>
>


From cjfields at illinois.edu  Wed Feb  8 14:24:00 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 8 Feb 2012 19:24:00 +0000
Subject: [Bioperl-l] bioperl-guts filtering
Message-ID: <206492C2-3C71-4CD6-A619-57C25E91D207@illinois.edu>

Just noticed a huge backlog of spam as well as lots of github commits caught up on the bioperl-guts-l listserv.  There is also some buildbot stuff coming in, we need to change the sender to something other than bioperl-guts-l (spoofing the sender to be the same as the recipient is a common spam mechanism).

I am setting the default non-member to simply reject incoming email for that list and to hold member posts, along with a message to post bioperl questions to bioperl-l.  Any complaints on that?  Seems like we should be keeping the posts to automated stuff anyway?

chris

From David.Messina at sbc.su.se  Wed Feb  8 14:45:01 2012
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 8 Feb 2012 20:45:01 +0100
Subject: [Bioperl-l] bioperl-guts filtering
In-Reply-To: <206492C2-3C71-4CD6-A619-57C25E91D207@illinois.edu>
References: <206492C2-3C71-4CD6-A619-57C25E91D207@illinois.edu>
Message-ID: <CAM3TQQXSNQR0bty0xO4oxHh3m+3g+n+-GOptQGUfT93nXMaipw@mail.gmail.com>

Sounds good to me.

D


On Wed, Feb 8, 2012 at 20:24, Fields, Christopher J
<cjfields at illinois.edu>wrote:

> Just noticed a huge backlog of spam as well as lots of github commits
> caught up on the bioperl-guts-l listserv.  There is also some buildbot
> stuff coming in, we need to change the sender to something other than
> bioperl-guts-l (spoofing the sender to be the same as the recipient is a
> common spam mechanism).
>
> I am setting the default non-member to simply reject incoming email for
> that list and to hold member posts, along with a message to post bioperl
> questions to bioperl-l.  Any complaints on that?  Seems like we should be
> keeping the posts to automated stuff anyway?
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From aminmom at hotmail.com  Thu Feb  9 16:23:19 2012
From: aminmom at hotmail.com (Amin Momin)
Date: Fri, 10 Feb 2012 02:53:19 +0530
Subject: [Bioperl-l] parsing swissprot using SeqIO::swiss
In-Reply-To: <mailman.19.1328806807.22049.bioperl-l@lists.open-bio.org>
References: <mailman.19.1328806807.22049.bioperl-l@lists.open-bio.org>
Message-ID: <BAY171-W5700847FC723E1D0C4DD0EAB7B0@phx.gbl>


Hi

I am trying to parse the swissprot text files to capture the feature (FT) information. However I cant find any documentation to get the information from the functions _print_swissprot_FTHelper and _read_swissprot_FTHelper that capture the feature table. Can someone give any suggestions.

Thanks,
 Amin
 		 	   		  

From bosborne11 at verizon.net  Thu Feb  9 16:37:17 2012
From: bosborne11 at verizon.net (Brian Osborne)
Date: Thu, 09 Feb 2012 16:37:17 -0500
Subject: [Bioperl-l] parsing swissprot using SeqIO::swiss
In-Reply-To: <BAY171-W5700847FC723E1D0C4DD0EAB7B0@phx.gbl>
References: <mailman.19.1328806807.22049.bioperl-l@lists.open-bio.org>
	<BAY171-W5700847FC723E1D0C4DD0EAB7B0@phx.gbl>
Message-ID: <115DCF0A-A787-44FA-AA87-6B333B13BD73@verizon.net>

Amin,

I'm not sure why you want use these methods. You should not have to use them if all you want to do is get features from SwissProt files. Have you taken a look at the HOWTO?

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

Brian O.



On Feb 9, 2012, at 4:23 PM, Amin Momin wrote:

> 
> Hi
> 
> I am trying to parse the swissprot text files to capture the feature (FT) information. However I cant find any documentation to get the information from the functions _print_swissprot_FTHelper and _read_swissprot_FTHelper that capture the feature table. Can someone give any suggestions.
> 
> Thanks,
> Amin
> 		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From avilella at gmail.com  Fri Feb 10 09:42:18 2012
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 10 Feb 2012 14:42:18 +0000
Subject: [Bioperl-l] blast2sam
In-Reply-To: <CACsenP6VUG5GXDLxDL_Gu=OkT26+0im+MxtdhKva3JaLPn8VVQ@mail.gmail.com>
References: <CACsenP6VUG5GXDLxDL_Gu=OkT26+0im+MxtdhKva3JaLPn8VVQ@mail.gmail.com>
Message-ID: <CAG0+gRPajsPzVVqoYMqT9XQWMA2Ed21_0yKtyqn3o9V-sp9HnQ@mail.gmail.com>

I just created a ticket:
https://redmine.open-bio.org/issues/3324

For this blast2sam request I did a while ago:
http://bioperl.org/pipermail/bioperl-l/2011-June/035229.html

Thanks,

Albert.

From rbuels at gmail.com  Fri Feb 10 12:35:57 2012
From: rbuels at gmail.com (Robert Buels)
Date: Fri, 10 Feb 2012 12:35:57 -0500
Subject: [Bioperl-l] call for project ideas - Google Summer of Code
Message-ID: <4F35557D.6090405@gmail.com>

Hi all,

Google's Summer of Code is coming round again, very soon now (mentoring 
organization applications are due this week).  We need to update our 
project ideas for prospective Summer of Code interns.  The rest of the 
page also needs updates, changing dates and such.

There's a page on the BioPerl wiki, please have a look and add your 
ideas for intern projects.

For more on Google Summer of Code, what it is and how it works, see 
their FAQ at 
http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2012/faqs

I'm sure you all can think of plenty of ideas!

Here's the page: http://www.bioperl.org/wiki/Google_Summer_of_Code

Please have a look, add your project ideas, and/or delete ones that have 
already been done, are no longer relevant, or no longer have a mentor 
available.

Rob


From shalabh.sharma7 at gmail.com  Fri Feb 10 13:30:46 2012
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 10 Feb 2012 13:30:46 -0500
Subject: [Bioperl-l] downloading 16s from NCBI
Message-ID: <CAA7rn9f7zM42EcaieikfFVA+Hmm=-pWO24OWOGxtOZKvsYRoWg@mail.gmail.com>

Hi,
    Is it possible to download all 16s sequences from NCBI?
I tried to look at Bio::DB::GenBank, but i am not sure if u can do it for
all 16s .

I would really appreciate if anyone can help me out.

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

From florent.angly at gmail.com  Fri Feb 10 19:26:40 2012
From: florent.angly at gmail.com (Florent Angly)
Date: Sat, 11 Feb 2012 10:26:40 +1000
Subject: [Bioperl-l] downloading 16s from NCBI
In-Reply-To: <CAA7rn9f7zM42EcaieikfFVA+Hmm=-pWO24OWOGxtOZKvsYRoWg@mail.gmail.com>
References: <CAA7rn9f7zM42EcaieikfFVA+Hmm=-pWO24OWOGxtOZKvsYRoWg@mail.gmail.com>
Message-ID: <4F35B5C0.50704@gmail.com>

Hi Shalabh,
There are specialized databases that contain only 16S rRNA genes, namely 
GreenGenes, RDP, Silva. You should have a look.
Regards.
Florent


On 11/02/12 04:30, shalabh sharma wrote:
> Hi,
>      Is it possible to download all 16s sequences from NCBI?
> I tried to look at Bio::DB::GenBank, but i am not sure if u can do it for
> all 16s .
>
> I would really appreciate if anyone can help me out.
>
> Thanks
> Shalabh
>
>


From thomas.sharpton at gmail.com  Fri Feb 10 19:42:58 2012
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Fri, 10 Feb 2012 16:42:58 -0800
Subject: [Bioperl-l] downloading 16s from NCBI
In-Reply-To: <4F35B5C0.50704@gmail.com>
References: <CAA7rn9f7zM42EcaieikfFVA+Hmm=-pWO24OWOGxtOZKvsYRoWg@mail.gmail.com>
	<4F35B5C0.50704@gmail.com>
Message-ID: <D176529F-BD5E-4BC9-B234-939A8A6464E3@gmail.com>

Hi Shalabh,

Florent is correct about the specialized databases - they are great  
resources.

To answer your specific question about all 16S sequences in GenBank,  
see this webpage, which contains a 16S database download link:

http://www.ncbi.nlm.nih.gov/books/NBK82331/#Nov11.New_BLAST_16S_Prokaryotic_Ribosoma

Best,
Tom

On Feb 10, 2012, at 4:26 PM, Florent Angly wrote:

> Hi Shalabh,
> There are specialized databases that contain only 16S rRNA genes,  
> namely GreenGenes, RDP, Silva. You should have a look.
> Regards.
> Florent
>
>
> On 11/02/12 04:30, shalabh sharma wrote:
>> Hi,
>>     Is it possible to download all 16s sequences from NCBI?
>> I tried to look at Bio::DB::GenBank, but i am not sure if u can do  
>> it for
>> all 16s .
>>
>> I would really appreciate if anyone can help me out.
>>
>> Thanks
>> Shalabh
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From hlapp at drycafe.net  Sat Feb 11 17:24:01 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Sat, 11 Feb 2012 17:24:01 -0500
Subject: [Bioperl-l] Question on seqfeature mapping
In-Reply-To: <4F3245C4.9040506@labri.fr>
References: <4F0C7017.90803@inria.fr>
	<CAKVJ-_7d_K6+MttpMvW7-kr9iYTL6u0TMDcM=GfW7sVFsrO6sQ@mail.gmail.com>
	<A9148EAE-8709-4944-8369-CC98E7B53263@illinois.edu>
	<4F0D83D8.90402@inria.fr> <4F0D8A18.1080606@inria.fr>
	<D2004971-6A32-4141-B446-D2A855FDB026@illinois.edu>
	<4F0EA69E.8040203@inria.fr>
	<49CC4A91-5E47-4866-AD63-62DC7F649CE6@drycafe.net>
	<4F0FF883.80109@inria.fr> <4F0FF8FF.6070706@inria.fr>
	<E0F6A75C-8902-44D5-BB5F-8C0A4060EF9B@drycafe.net>
	<4F199A27.8030408@inria.fr>
	<054FEA92-8C5E-47D6-86AF-F71DEAFE2B63@illinois.edu>
	<4F31802E.9030002@labri.fr>
	<33DA4F1D-3575-4925-A123-F6A77EAE753D@drycafe.net>
	<4F322C18.7010103@labri.fr> <4F3245C4.9040506@labri.fr>
Message-ID: <FE2B9674-33A3-4C60-9623-008E6B0F23C4@drycafe.net>


On Feb 8, 2012, at 4:52 AM, Lajus Florian wrote:

> Never mind. It works much better if write: "Bio::Annotation::SimpleValue<=>Bio::SeqFeatureI instead.

Yes indeed, for n-n associations you need to use "<=>".

> The problem is if we also want to find by primary_tag:
> my $query = Bio::DB::Query::BioQuery->new(
> -datacollections => ["Bio::Annotation::SimpleValue<=>Bio::SeqFeatureI qv"],
> -where => ["Bio::Annotation::SimpleValue::tagname = \'$tag\'","qv.value = \'$value\'","Bio::SeqFeatureI.primary_tag = ".$term_primary_key]);
> 
> The slot type_term_id is not mapped to column for table seqfeature

It is actually - both the mapping for term and for seqfeature have the mapping of primary_tag to type_term_id. What error are you getting?

And shouldn't Bio::SeqFeatureI.primary_tag have a double colon instead of the dot? (Also, BTW, you should be able to say "qv.tagname" instead of "Bio::Annotation::SimpleValue::tagname", just as you do for the value column - have you tried that and found it not to work? Either way, what you have for that part looks correct.) 

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






From dan.bolser at gmail.com  Mon Feb 13 07:53:43 2012
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 13 Feb 2012 12:53:43 +0000
Subject: [Bioperl-l] Fwd: Interested in Variation?
In-Reply-To: <CAPBO=2m9=h6PJvmikVsZ785BChhgfTuQ6Kb1psvTeaHpD8PNJw@mail.gmail.com>
References: <CAPBO=2=FfmY70b0_u6cVk9Bv5RH7Lt5Lg7huE1-1s_Keu_bNRQ@mail.gmail.com>
	<CAPBO=2m9=h6PJvmikVsZ785BChhgfTuQ6Kb1psvTeaHpD8PNJw@mail.gmail.com>
Message-ID: <CAPBO=2=uR-aTe=qsjTnRwmvgMFzXzDuuJgfhfW87iAT4qoAyEg@mail.gmail.com>

Job at the EBI:

"... the primary responsibility of the post-holder will be the
development of pipelines and storage solutions for variation data
deriving from whole genome re-sequencing."

http://goo.gl/eQrRu or

http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=LktVsYDaNlCOtQqCli&jobid=47627,4187528723&key=45520467&c=126152212583&pagestamp=dbnjwyufpgvrmyvkmt


Cheers,
Dan.

From rondonbio at yahoo.com.br  Wed Feb 15 13:59:15 2012
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Wed, 15 Feb 2012 10:59:15 -0800 (PST)
Subject: [Bioperl-l] Bio::SearchIO::XML::BlastHandler problems
Message-ID: <1329332355.18626.YahooMailNeo@web130206.mail.mud.yahoo.com>

Hello everybody,
unffortunally I'm having problems with Bio::SearchIO, that I wasn't having before. Perl is returning this to me:
" Can't locate object method "_eventHandler" via package "Bio::SearchIO::XML::BlastHandler" at /usr/local/share/perl/5.10.1/Bio/SearchIO/blastxml.pm line 151. "

I believe it's happening because I installed a genome assembler that use a different version of Bio::SearchIO that I have before.


thank you,

Rondon

the subroutine that use this module is above:

sub nucleotide_coverage{
#Bio::SearchIO dependent
#This subroutine returns a Hash and a file with nucleotide coverage
#for each query in an blast alignment xlm file. The input is the
#alignment file and the name of output (just the index).
#USAGE::: ?$ref = nucleotide_coverage("blast.xml", "gene_family");

? ? ? ? my ($alignment_file, $gene_family) = @_;


? ? ? ? my $alignment = new Bio::SearchIO ( -format => 'blastxml',
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -file ? => $alignment_file );

? ? ? ? print "Parseando o resultado do BLAST\n";
? ? ? ? my %positions;
? ? ? ? my @used_reads;
? ? ? ? open OUT, ">reads_per_CDS.txt";
? ? ? ? while (my $result = $alignment->next_result) {
? ? ? ? ? ? ? ? my $query_name = $result->query_name();
? ? ? ? ? ? ? ? my $tam = $result -> query_length();
? ? ? ? ? ? ? ? for (0..$tam-1){ ${$positions{$query_name}}[$_] = 0 }
? ? ? ? ? ? ? ? while (my $hit = $result->next_hit) {
? ? ? ? ? ? ? ? ? ? ? ? my $hit_name = $hit->name;
? ? ? ? ? ? ? ? ? ? ? ? LABEL:
? ? ? ? ? ? ? ? ? ? ? ? foreach my $read (@used_reads) {
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? if ( $read eq $hit_name ) {
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? next LABEL;
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }
? ? ? ? ? ? ? ? ? ? ? ? }
? ? ? ? ? ? ? ? ? ? ? ? print OUT "$query_name\t$hit_name\n";
? ? ? ? ? ? ? ? ? ? ? ? while (my $hsp = $hit->next_hsp) {
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? my $query_name = $result->query_name();
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? my @pos = $hsp->seq_inds('query','identical');
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? foreach my $num (@pos) {
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ${$positions{$query_name}}[$num-1]++;
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }
? ? ? ? ? ? ? ? ? ? ? ? }
? ? ? ? ? ? ? ? push (@used_reads, $hit_name);
? ? ? ? ? ? ? ? }
? ? ? ? }
? ? ? ? close OUT;

? ? ? ? my $outfile = "nucleotide_coverage.txt";
? ? ? ? open OUT, ">$outfile" or die $!;
? ? ? ? foreach my $key (keys %positions){

? ? ? ? ? ? ? ? print OUT "$key\t@{$positions{$key}}\n";
? ? ? ? }

? ? ? ? close OUT;

? ? ? ? return \%positions;

}


From rondonbio at yahoo.com.br  Wed Feb 15 14:43:48 2012
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Wed, 15 Feb 2012 11:43:48 -0800 (PST)
Subject: [Bioperl-l] Bio::SearchIO::XML::BlastHandler problems
In-Reply-To: <1329335001.11066.YahooMailNeo@web130202.mail.mud.yahoo.com>
References: <1329332355.18626.YahooMailNeo@web130206.mail.mud.yahoo.com>
	<1329335001.11066.YahooMailNeo@web130202.mail.mud.yahoo.com>
Message-ID: <1329335028.66134.YahooMailNeo@web130206.mail.mud.yahoo.com>

sorry, I didn't ask anything. So..


Can anyone help me to solve it?

thanks again

Rondon



________________________________
 De: Rondon Neto <rondonbio at yahoo.com.br>
Para: "Bioperl-l at lists.open-bio.org" <Bioperl-l at lists.open-bio.org> 
Enviadas: Quarta-feira, 15 de Fevereiro de 2012 16:59
Assunto: [Bioperl-l] Bio::SearchIO::XML::BlastHandler problems
 
Hello everybody,
unffortunally I'm having problems with Bio::SearchIO, that I wasn't having before. Perl is returning this to me:
" Can't locate object method "_eventHandler" via package "Bio::SearchIO::XML::BlastHandler" at /usr/local/share/perl/5.10.1/Bio/SearchIO/blastxml.pm line 151. "

I believe it's happening because I installed a genome assembler that use a different version of Bio::SearchIO that I have before.


thank you,

Rondon

the subroutine that use this module is above:

sub nucleotide_coverage{
#Bio::SearchIO dependent
#This subroutine returns a Hash and a file with nucleotide coverage
#for each query in an blast alignment xlm file. The input is the
#alignment file and the name of output (just the index).
#USAGE::: ?$ref = nucleotide_coverage("blast.xml",
 "gene_family");

? ? ? ? my ($alignment_file, $gene_family) = @_;


? ? ? ? my $alignment = new Bio::SearchIO ( -format => 'blastxml',
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -file ? => $alignment_file );

? ? ? ? print "Parseando o resultado do BLAST\n";
? ? ? ? my %positions;
? ? ? ? my @used_reads;
? ? ? ? open OUT, ">reads_per_CDS.txt";
? ? ? ? while (my $result = $alignment->next_result) {
? ? ? ? ? ? ? ? my $query_name = $result->query_name();
? ? ? ? ? ? ? ? my $tam = $result -> query_length();
? ? ? ? ? ? ? ?
 for (0..$tam-1){ ${$positions{$query_name}}[$_] = 0 }
? ? ? ? ? ? ? ? while (my $hit = $result->next_hit) {
? ? ? ? ? ? ? ? ? ? ? ? my $hit_name = $hit->name;
? ? ? ? ? ? ? ? ? ? ? ? LABEL:
? ? ? ? ? ? ? ? ? ? ? ? foreach my $read (@used_reads) {
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? if ( $read eq $hit_name ) {
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? next LABEL;
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? }
? ? ? ? ? ? ? ? ?
 ? ? ? }
? ? ? ? ? ? ? ? ? ? ? ? print OUT "$query_name\t$hit_name\n";
? ? ? ? ? ? ? ? ? ? ? ? while (my $hsp = $hit->next_hsp) {
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? my $query_name = $result->query_name();
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? my @pos = $hsp->seq_inds('query','identical');
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? foreach my $num (@pos) {
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ${$positions{$query_name}}[$num-1]++;
? ? ? ? ? ?
 ? ? ? ? ? ? ? ? ? ? }
? ? ? ? ? ? ? ? ? ? ? ? }
? ? ? ? ? ? ? ? push (@used_reads, $hit_name);
? ? ? ? ? ? ? ? }
? ? ? ? }
? ? ? ? close OUT;

? ? ? ? my $outfile = "nucleotide_coverage.txt";
? ? ? ? open OUT, ">$outfile" or die $!;
? ? ? ? foreach my $key (keys %positions){

? ? ? ? ? ? ? ? print OUT "$key\t@{$positions{$key}}\n";
? ? ? ? }

? ? ? ? close OUT;

? ? ? ? return \%positions;

}

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

From flajus at labri.fr  Wed Feb 15 03:04:24 2012
From: flajus at labri.fr (Lajus Florian)
Date: Wed, 15 Feb 2012 09:04:24 +0100
Subject: [Bioperl-l] Question on seqfeature mapping
In-Reply-To: <FE2B9674-33A3-4C60-9623-008E6B0F23C4@drycafe.net>
References: <4F0C7017.90803@inria.fr>
	<CAKVJ-_7d_K6+MttpMvW7-kr9iYTL6u0TMDcM=GfW7sVFsrO6sQ@mail.gmail.com>
	<A9148EAE-8709-4944-8369-CC98E7B53263@illinois.edu>
	<4F0D83D8.90402@inria.fr> <4F0D8A18.1080606@inria.fr>
	<D2004971-6A32-4141-B446-D2A855FDB026@illinois.edu>
	<4F0EA69E.8040203@inria.fr>
	<49CC4A91-5E47-4866-AD63-62DC7F649CE6@drycafe.net>
	<4F0FF883.80109@inria.fr> <4F0FF8FF.6070706@inria.fr>
	<E0F6A75C-8902-44D5-BB5F-8C0A4060EF9B@drycafe.net>
	<4F199A27.8030408@inria.fr>
	<054FEA92-8C5E-47D6-86AF-F71DEAFE2B63@illinois.edu>
	<4F31802E.9030002@labri.fr>
	<33DA4F1D-3575-4925-A123-F6A77EAE753D@drycafe.net>
	<4F322C18.7010103@labri.fr> <4F3245C4.9040506@labri.fr>
	<FE2B9674-33A3-4C60-9623-008E6B0F23C4@drycafe.net>
Message-ID: <4F3B6708.9090307@labri.fr>

In fact, the query works fine. I don't understand why it didn't work 
when I wrote the mail...
Le 11/02/2012 23:24, Hilmar Lapp a ?crit :
>
> On Feb 8, 2012, at 4:52 AM, Lajus Florian wrote:
>
>> Never mind. It works much better if write: "Bio::Annotation::SimpleValue<=>Bio::SeqFeatureI instead.
>
> Yes indeed, for n-n associations you need to use "<=>".
>
>> The problem is if we also want to find by primary_tag:
>> my $query = Bio::DB::Query::BioQuery->new(
>> -datacollections =>  ["Bio::Annotation::SimpleValue<=>Bio::SeqFeatureI qv"],
>> -where =>  ["Bio::Annotation::SimpleValue::tagname = \'$tag\'","qv.value = \'$value\'","Bio::SeqFeatureI.primary_tag = ".$term_primary_key]);
>>
>> The slot type_term_id is not mapped to column for table seqfeature
>
> It is actually - both the mapping for term and for seqfeature have the mapping of primary_tag to type_term_id. What error are you getting?
>
> And shouldn't Bio::SeqFeatureI.primary_tag have a double colon instead of the dot? (Also, BTW, you should be able to say "qv.tagname" instead of "Bio::Annotation::SimpleValue::tagname", just as you do for the value column - have you tried that and found it not to work? Either way, what you have for that part looks correct.)
>
> 	-hilmar


From tarakaramji at gmail.com  Thu Feb 16 14:17:37 2012
From: tarakaramji at gmail.com (tarakaramji M)
Date: Fri, 17 Feb 2012 00:47:37 +0530
Subject: [Bioperl-l] Query regarding retrieval sequences
Message-ID: <CAN53njc7FuiTemAnE+PBPdMm7ks2qP4-EPG1XmFa-1KqS-uxoQ@mail.gmail.com>

hi,
i wander if we can retrieve sequences together at once of reuired genes. in
more simple words i have set of gene or EST IDs for which i have get the
sequence from database together?

-- 
tarakaramji

From admin at yapcna.org  Thu Feb 16 16:45:46 2012
From: admin at yapcna.org (JT Smith)
Date: Thu, 16 Feb 2012 15:45:46 -0600
Subject: [Bioperl-l] YAPC::NA & BioPerl
Message-ID: <9E03C4BE-C93F-4EB8-9BC5-24F9492C23E3@yapcna.org>

I'd like to run a BioPerl track at YAPC::NA 2012. Our theme this year is "Perl in the Wild", which is all about real-world applications of Perl. I can't imagine anything more real-world than what you folks do with Perl. 

If you are interested in giving a talk, you can submit one here: http://act.yapcna.org/2012/newtalk

If we get enough submissions, I'll set aside an entire room just for BioPerl talks. 

Likewise, if you want to run a mini-workshop to get people bootstrapped on BioPerl, I'd love to have that as well. I just need someone to submit that as a talk. We have our workshops limited to 2 hours, but if you need more time than that, you can submit multiple sessions and I'll schedule them back to back. 

If there's anything else I can do to make YAPC::NA 2012 a good destination for BioPerl, please let me know.

For those of you who don't know, YAPC::NA 2012 will be held June 13-15 in Madison, WI. Madison is a big BioTech town, so I'm sure many of you are familiar with it, and even have colleagues who work here.

JT Smith
Director, YAPC::NA 2012
http://www.yapcna.org



From l.m.timmermans at students.uu.nl  Fri Feb 17 08:02:21 2012
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Fri, 17 Feb 2012 14:02:21 +0100
Subject: [Bioperl-l] YAPC::NA & BioPerl
In-Reply-To: <9E03C4BE-C93F-4EB8-9BC5-24F9492C23E3@yapcna.org>
References: <9E03C4BE-C93F-4EB8-9BC5-24F9492C23E3@yapcna.org>
Message-ID: <CAC1jpXBYPfUmaXUDn90DZcc-XBFDy9TtQxDNUGijwH4SVP_9fg@mail.gmail.com>

On Thu, Feb 16, 2012 at 10:45 PM, JT Smith <admin at yapcna.org> wrote:

> I'd like to run a BioPerl track at YAPC::NA 2012. Our theme this year is
> "Perl in the Wild", which is all about real-world applications of Perl. I
> can't imagine anything more real-world than what you folks do with Perl.
>
> If you are interested in giving a talk, you can submit one here:
> http://act.yapcna.org/2012/newtalk
>
> If we get enough submissions, I'll set aside an entire room just for
> BioPerl talks.
>
> Likewise, if you want to run a mini-workshop to get people bootstrapped on
> BioPerl, I'd love to have that as well. I just need someone to submit that
> as a talk. We have our workshops limited to 2 hours, but if you need more
> time than that, you can submit multiple sessions and I'll schedule them
> back to back.
>
> If there's anything else I can do to make YAPC::NA 2012 a good destination
> for BioPerl, please let me know.
>
> For those of you who don't know, YAPC::NA 2012 will be held June 13-15 in
> Madison, WI. Madison is a big BioTech town, so I'm sure many of you are
> familiar with it, and even have colleagues who work here.
>

I think that's be an excellent idea. Anything that would bring the
bioinformatics community closer to the open source community would be a
good thing; they often seem rather absent at conferences and the like in my
experience.

Leon

From hlapp at drycafe.net  Fri Feb 17 09:45:51 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Fri, 17 Feb 2012 09:45:51 -0500
Subject: [Bioperl-l] YAPC::NA & BioPerl
In-Reply-To: <CAC1jpXBYPfUmaXUDn90DZcc-XBFDy9TtQxDNUGijwH4SVP_9fg@mail.gmail.com>
References: <9E03C4BE-C93F-4EB8-9BC5-24F9492C23E3@yapcna.org>
	<CAC1jpXBYPfUmaXUDn90DZcc-XBFDy9TtQxDNUGijwH4SVP_9fg@mail.gmail.com>
Message-ID: <039387B1-114D-47E1-B86B-7057FCF6216C@drycafe.net>


On Feb 17, 2012, at 8:02 AM, Leon Timmermans wrote:

> I think that's be an excellent idea. Anything that would bring the
> bioinformatics community closer to the open source community would be a
> good thing; they often seem rather absent at conferences and the like in my
> experience.

+1 

I agree very much. Attending the pure open-source conferences has been a challenge for me, frankly - I've wanted to go to YAPC::NA or OSCON for years, but finding both the time and budget among the science conferences that I more or less have to attend already is real difficult. I'd imagine that others face similar challenges. So any efforts at cross-fertilization are good.

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






From cjfields at illinois.edu  Fri Feb 17 10:30:54 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 Feb 2012 15:30:54 +0000
Subject: [Bioperl-l] YAPC::NA & BioPerl
In-Reply-To: <039387B1-114D-47E1-B86B-7057FCF6216C@drycafe.net>
References: <9E03C4BE-C93F-4EB8-9BC5-24F9492C23E3@yapcna.org>
	<CAC1jpXBYPfUmaXUDn90DZcc-XBFDy9TtQxDNUGijwH4SVP_9fg@mail.gmail.com>
	<039387B1-114D-47E1-B86B-7057FCF6216C@drycafe.net>
Message-ID: <3C915E17-46A8-4385-87E2-834F2F68CAFF@illinois.edu>

On Feb 17, 2012, at 8:45 AM, Hilmar Lapp wrote:

> On Feb 17, 2012, at 8:02 AM, Leon Timmermans wrote:
> 
>> I think that's be an excellent idea. Anything that would bring the
>> bioinformatics community closer to the open source community would be a
>> good thing; they often seem rather absent at conferences and the like in my
>> experience.
> 
> +1 
> 
> I agree very much. Attending the pure open-source conferences has been a challenge for me, frankly - I've wanted to go to YAPC::NA or OSCON for years, but finding both the time and budget among the science conferences that I more or less have to attend already is real difficult. I'd imagine that others face similar challenges. So any efforts at cross-fertilization are good.
> 
> 	-hilmar

Yes, this is a significant problem for me as well (not to mention the constraints I have in my current job), so committing to anything right now is a bit tricky.  

I do think a 'warts-and-all' bioperl talk would be good, mainly to emphasize the point that we do cover a lot of graound in the toolkit but that there are definitely areas that could be improved within the code, the distribution, etc.  A mini version of this could also be used at BOSC I suppose.

chris

From cjfields at illinois.edu  Fri Feb 17 10:47:29 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 Feb 2012 15:47:29 +0000
Subject: [Bioperl-l] YAPC::NA & BioPerl
In-Reply-To: <3C915E17-46A8-4385-87E2-834F2F68CAFF@illinois.edu>
References: <9E03C4BE-C93F-4EB8-9BC5-24F9492C23E3@yapcna.org>
	<CAC1jpXBYPfUmaXUDn90DZcc-XBFDy9TtQxDNUGijwH4SVP_9fg@mail.gmail.com>
	<039387B1-114D-47E1-B86B-7057FCF6216C@drycafe.net>
	<3C915E17-46A8-4385-87E2-834F2F68CAFF@illinois.edu>
Message-ID: <C1DC9D1A-CEE7-4883-BE46-206C1CC7DAAD@illinois.edu>

On Feb 17, 2012, at 9:30 AM, Fields, Christopher J wrote:

> On Feb 17, 2012, at 8:45 AM, Hilmar Lapp wrote:
> 
>> On Feb 17, 2012, at 8:02 AM, Leon Timmermans wrote:
>> 
>>> I think that's be an excellent idea. Anything that would bring the
>>> bioinformatics community closer to the open source community would be a
>>> good thing; they often seem rather absent at conferences and the like in my
>>> experience.
>> 
>> +1 
>> 
>> I agree very much. Attending the pure open-source conferences has been a challenge for me, frankly - I've wanted to go to YAPC::NA or OSCON for years, but finding both the time and budget among the science conferences that I more or less have to attend already is real difficult. I'd imagine that others face similar challenges. So any efforts at cross-fertilization are good.
>> 
>> 	-hilmar
> 
> Yes, this is a significant problem for me as well (not to mention the constraints I have in my current job), so committing to anything right now is a bit tricky.  
> 
> I do think a 'warts-and-all' bioperl talk would be good, mainly to emphasize the point that we do cover a lot of graound in the toolkit but that there are definitely areas that could be improved within the code, the distribution, etc.  A mini version of this could also be used at BOSC I suppose.
> 
> chris

Reread that and it gives a more positive expectation than I realized.  I just want to re-emphasize the bit above about committing so everyone's expectations are tempered; I am really constrained on time commitments (particularly those involving travel) until fall.  However, I fully support anyone giving a talk at YAPC, though, and I can help out in whatever way possible, including coding.  

chris



From dcmertens.perl at gmail.com  Fri Feb 17 12:20:43 2012
From: dcmertens.perl at gmail.com (David Mertens)
Date: Fri, 17 Feb 2012 11:20:43 -0600
Subject: [Bioperl-l] YAPC::NA & BioPerl
Message-ID: <CA+4ieYUUAkAQPST5_LMjazELh9BLT6yqsYSoVgxuM011aUO=+Q@mail.gmail.com>

Hey folks -

I would really like to see BioPerl have a presence at YAPC. For what it's
worth, I have submitted a couple of talks about PDL at YAPC this year, one
of them being an introduction to PDL. Even if the talk isn't accepted, I
will be more than happy to meet up with anybody who has questions about
PDL. As for BioPerl at YAPC, I know very little about BioPerl but would
really like to learn more. I would be *thrilled* if somebody could give a
min-workshop! This would make for a very scientific YAPC: an intro to PDL
*and* an intro to BioPerl. :-D

David

-- 
 "Debugging is twice as hard as writing the code in the first place.
  Therefore, if you write the code as cleverly as possible, you are,
  by definition, not smart enough to debug it." -- Brian Kernighan

From jason.stajich at gmail.com  Fri Feb 17 12:42:29 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Fri, 17 Feb 2012 09:42:29 -0800
Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [BioPerl - Bug #3328] (New)
	segregating sites calculation fails on gapped sequences
References: <redmine.issue-3328.20120217173941@redmine.open-bio.org>
Message-ID: <B37A51B6-5A19-4EBC-91E3-2F104D26F2BD@gmail.com>


This should be an easy bug for someone to fix -- I am pretty sure the solution is to ignore gapped columns but I haven't looked deeper and I don't have any time right now to work on bioperl fixes so be great if someone wanted to help out here.

The redmine bug info is appended below.

Jason

Begin forwarded message:

> From: redmine at redmine.open-bio.org
> Subject: [Bioperl-guts-l] [BioPerl - Bug #3328] (New) segregating sites calculation fails on gapped sequences
> Date: February 17, 2012 9:39:42 AM PST
> To: bioperl-guts-l at lists.open-bio.org
> 
> 
> Issue #3328 has been reported by Jason Stajich.
> 
> ----------------------------------------
> Bug #3328: segregating sites calculation fails on gapped sequences
> https://redmine.open-bio.org/issues/3328
> 
> Author: Jason Stajich
> Status: New
> Priority: Normal
> Assignee: Bioperl Guts
> Category: Bio::PopGen
> Target version: 
> URL: 
> 
> 
> 
>   I am Cheng-Ruei Lee, a graduate student in Duke Biology. I'm analyzing many DNA alignments of a plant species.
>   I first used (Bio::PopGen::Utilities -> aln_to_population()) to read in the fasta format alignment, and then use Bio::PopGen::Statistics to calculate some statistics without outgroup. Most gene work fine, but I think a bug happened when it meets alignments like this:
> 
>> Genotype1
> ATGATCGTAGCTGATGCTGTGATCGATCGCTAGCTAGCTCGA
>> Genotype2
> ------------GATGCTGTGATCGATCGCTAGCTAGCTCGA
>> Genotype3
> ------------GATGCTGTGATCGATCGCTAGCTAGCTCGA
>> Genotype4
> ------------GATGCTGTGATCGATCGCTAGCTAGCTCGA
> 
>   I get this data set from other people. I guess due to the annotation program people used, the definition of coding sequence is much longer in genotype 1 than in other genotypes. This creates a long stretch of gap in the very beginning. Whenever Bio::PopGen meets this kind of genes, the number of singleton counts boost a lot - seems like the long stretch of sites with gap is also counted as singletons. Also, some Fu & Li statistics boosted. The "number of segregation sites" seems not to be affected. (And therefore, there are genes with hundreds of singleton sites but only a few total segregating sites.)
>   May be a possible bug in Bio::PopGen::Utilities when reading in the data? Or when calculating singletons?
> 
> Sincerely,
> Cheng-Ruei Lee <cl134 at duke.edu>
> 
> 
> -- 
> You have received this notification because you have either subscribed to it, or are involved in it.
> To change your notification preferences, please click here and login: http://redmine.open-bio.org
> 
> _______________________________________________
> Bioperl-guts-l mailing list
> Bioperl-guts-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org



From admin at yapcna.org  Fri Feb 17 13:51:36 2012
From: admin at yapcna.org (JT Smith)
Date: Fri, 17 Feb 2012 12:51:36 -0600
Subject: [Bioperl-l] YAPC::NA & BioPerl
In-Reply-To: <CA+4ieYUUAkAQPST5_LMjazELh9BLT6yqsYSoVgxuM011aUO=+Q@mail.gmail.com>
References: <CA+4ieYUUAkAQPST5_LMjazELh9BLT6yqsYSoVgxuM011aUO=+Q@mail.gmail.com>
Message-ID: <2B17B64F-70F2-4C40-90CE-35C3A6953DCA@yapcna.org>

I'm also going to get a PDL track started at YAPC. I'll be announcing that next week.

JT Smith
Director, YAPC::NA 2012
http://www.yapcna.org

PS 

Another way you can support Perl is by adding a link to the bottom of your web site, or on your credits / thank you page to http://www.perl.org
	

On Feb 17, 2012, at 11:20 AM, David Mertens wrote:

> Hey folks -
> 
> I would really like to see BioPerl have a presence at YAPC. For what it's
> worth, I have submitted a couple of talks about PDL at YAPC this year, one
> of them being an introduction to PDL. Even if the talk isn't accepted, I
> will be more than happy to meet up with anybody who has questions about
> PDL. As for BioPerl at YAPC, I know very little about BioPerl but would
> really like to learn more. I would be *thrilled* if somebody could give a
> min-workshop! This would make for a very scientific YAPC: an intro to PDL
> *and* an intro to BioPerl. :-D
> 
> David
> 
> -- 
> "Debugging is twice as hard as writing the code in the first place.
>  Therefore, if you write the code as cleverly as possible, you are,
>  by definition, not smart enough to debug it." -- Brian Kernighan
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Fri Feb 17 14:11:48 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 Feb 2012 19:11:48 +0000
Subject: [Bioperl-l] Bio::SearchIO::XML::BlastHandler problems
In-Reply-To: <1329335028.66134.YahooMailNeo@web130206.mail.mud.yahoo.com>
References: <1329332355.18626.YahooMailNeo@web130206.mail.mud.yahoo.com>
	<1329335001.11066.YahooMailNeo@web130202.mail.mud.yahoo.com>
	<1329335028.66134.YahooMailNeo@web130206.mail.mud.yahoo.com>
Message-ID: <3F5F0A6E-C51E-4DF9-A293-924A5AA5245B@illinois.edu>

I'm not sure what you mean. Do you mean the installed assembler is using a specific version of BioPerl than what you have installed elsewhere (e.g. there are two local versions)?  

If so, it's possible the two versions are somehow getting mixed up (odd that it would happen, though).  You can probably add a 'use lib PATH' directive in the script to be more explicit.

BLAST XML parsing requires two different parsing mechanisms based upon the type of BLAST run (PSI-BLAST or normal BLAST); older versions of bioperl prior to 1.6 lacked this, though it's possible the last release in the 1.5 series did have it, not sure.

chris

On Feb 15, 2012, at 1:43 PM, Rondon Neto wrote:

> sorry, I didn't ask anything. So..
> 
> 
> Can anyone help me to solve it?
> 
> thanks again
> 
> Rondon
> 
> 
> 
> ________________________________
> De: Rondon Neto <rondonbio at yahoo.com.br>
> Para: "Bioperl-l at lists.open-bio.org" <Bioperl-l at lists.open-bio.org> 
> Enviadas: Quarta-feira, 15 de Fevereiro de 2012 16:59
> Assunto: [Bioperl-l] Bio::SearchIO::XML::BlastHandler problems
> 
> Hello everybody,
> unffortunally I'm having problems with Bio::SearchIO, that I wasn't having before. Perl is returning this to me:
> " Can't locate object method "_eventHandler" via package "Bio::SearchIO::XML::BlastHandler" at /usr/local/share/perl/5.10.1/Bio/SearchIO/blastxml.pm line 151. "
> 
> I believe it's happening because I installed a genome assembler that use a different version of Bio::SearchIO that I have before.
> 
> 
> thank you,
> 
> Rondon
> 
> the subroutine that use this module is above:
> 
> sub nucleotide_coverage{
> #Bio::SearchIO dependent
> #This subroutine returns a Hash and a file with nucleotide coverage
> #for each query in an blast alignment xlm file. The input is the
> #alignment file and the name of output (just the index).
> #USAGE:::  $ref = nucleotide_coverage("blast.xml",
> "gene_family");
> 
>         my ($alignment_file, $gene_family) = @_;
> 
> 
>         my $alignment = new Bio::SearchIO ( -format => 'blastxml',
>                                             -file   => $alignment_file );
> 
>         print "Parseando o resultado do BLAST\n";
>         my %positions;
>         my @used_reads;
>         open OUT, ">reads_per_CDS.txt";
>         while (my $result = $alignment->next_result) {
>                 my $query_name = $result->query_name();
>                 my $tam = $result -> query_length();
>                
> for (0..$tam-1){ ${$positions{$query_name}}[$_] = 0 }
>                 while (my $hit = $result->next_hit) {
>                         my $hit_name = $hit->name;
>                         LABEL:
>                         foreach my $read (@used_reads) {
>                                 if ( $read eq $hit_name ) {
>                                         next LABEL;
>                                 }
>                  
>       }
>                         print OUT "$query_name\t$hit_name\n";
>                         while (my $hsp = $hit->next_hsp) {
>                                 my $query_name = $result->query_name();
>                                 my @pos = $hsp->seq_inds('query','identical');
>                                 foreach my $num (@pos) {
>                                         ${$positions{$query_name}}[$num-1]++;
>            
>                     }
>                         }
>                 push (@used_reads, $hit_name);
>                 }
>         }
>         close OUT;
> 
>         my $outfile = "nucleotide_coverage.txt";
>         open OUT, ">$outfile" or die $!;
>         foreach my $key (keys %positions){
> 
>                 print OUT "$key\t@{$positions{$key}}\n";
>         }
> 
>         close OUT;
> 
>         return \%positions;
> 
> }
> 
> _______________________________________________
> 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 p.j.a.cock at googlemail.com  Fri Feb 17 17:40:29 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 17 Feb 2012 22:40:29 +0000
Subject: [Bioperl-l] Fwd: [Utilities-announce] NCBI E-Utilities Update
In-Reply-To: <A9D8BF3D8A74DF4A925FB541C0F39D2A165D643674@NIHMLBX15.nih.gov>
References: <A9D8BF3D8A74DF4A925FB541C0F39D2A165D643674@NIHMLBX15.nih.gov>
Message-ID: <CAKVJ-_7SyXQ_snA5U6zkRx0W-wcJi6iG+HdhmTPuv9z-47+3bQ@mail.gmail.com>

Hi all,

Just FYI, the following was also changed in this week's Entrez
update to EFetch 2.0 (see forwarded email below).

This was breaking some Biopython scripts - depending on how
they passed in the id parameters. It turns out we relied on the
undocumented and now withdrawn form in one of our examples,
so some users had copied this style. Biopython 1.59 will solve
this.

I know BioJava is looking at the more publicised changes to
retmode - I don't know if BioPerl or BioRuby was affected.

Regards,

Peter

---------- Forwarded message ----------
From:  <utilities-announce at ncbi.nlm.nih.gov>
Date: Fri, Feb 17, 2012 at 7:09 PM
Subject: [Utilities-announce] NCBI E-Utilities Update
To: NLM/NCBI List utilities-announce <utilities-announce at ncbi.nlm.nih.gov>


The most recent NCBI E-Utilities update includes a more stringent
check for correct URL parameters.



EFetch URLs with multiple IDs must be entered as: id=1,2,3



EFetch no longer accepts invalid URL parameters, e.g., id=1&id=2&id=3



Please see the online E-Utilities help for additional information:

http://www.ncbi.nlm.nih.gov/books/NBK25500/



EFetch online help:

http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch



Thank you.




_______________________________________________
Utilities-announce mailing list
http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce

From cjfields at illinois.edu  Fri Feb 17 21:54:44 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 18 Feb 2012 02:54:44 +0000
Subject: [Bioperl-l] Fwd: [Utilities-announce] NCBI E-Utilities Update
In-Reply-To: <CAKVJ-_7SyXQ_snA5U6zkRx0W-wcJi6iG+HdhmTPuv9z-47+3bQ@mail.gmail.com>
References: <A9D8BF3D8A74DF4A925FB541C0F39D2A165D643674@NIHMLBX15.nih.gov>
	<CAKVJ-_7SyXQ_snA5U6zkRx0W-wcJi6iG+HdhmTPuv9z-47+3bQ@mail.gmail.com>
Message-ID: <F3AE560F-4CFB-47B9-ABD2-B117F8E63452@illinois.edu>

On Feb 17, 2012, at 4:40 PM, Peter Cock wrote:

> Hi all,
> 
> Just FYI, the following was also changed in this week's Entrez
> update to EFetch 2.0 (see forwarded email below).
> 
> This was breaking some Biopython scripts - depending on how
> they passed in the id parameters. It turns out we relied on the
> undocumented and now withdrawn form in one of our examples,
> so some users had copied this style. Biopython 1.59 will solve
> this.
> 
> I know BioJava is looking at the more publicised changes to
> retmode - I don't know if BioPerl or BioRuby was affected.

No, I checked the BioPerl modules against regression tests today after seeing the announcement.  Seems everything is fine; the main issue on NCBI's end that seemed to break things was how multiple IDs were joined.

> Regards,
> 
> Peter

chris

From jalevine at email.arizona.edu  Fri Feb 17 21:03:14 2012
From: jalevine at email.arizona.edu (Joshua Levine)
Date: Fri, 17 Feb 2012 19:03:14 -0700
Subject: [Bioperl-l] Can't get bioperl to install
Message-ID: <CABCMFNjDZTURmhyZ-1JEaDYFRk_uJwpEG=e2XqnA4tROPRhDHA@mail.gmail.com>

Hello,

I used to have bioperl working just fine on my machine (MacBook Pro,
running OS X v10.6.8).  I tried installing some new perl modules ( DBI &
DBD::mysql) and have not gotten them to work yet, but when I went back to
run a script that uses bioperl, I got this error message:

Can't locate Bio/SeqIO.pm in @INC...

Now I just want to get bioperl working again, even if I can't also get DBI
& DBD:mysql working.

Any help would be greatly appreciated
-Josh


-- 
Joshua A. Levine

Graduate Student
University of Arizona
Ecology and Evolutionary Biology
BioScience West 121
jalevine at email.arizona.edu

From cjfields at illinois.edu  Fri Feb 17 22:16:18 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Sat, 18 Feb 2012 03:16:18 +0000
Subject: [Bioperl-l] Can't get bioperl to install
In-Reply-To: <CABCMFNjDZTURmhyZ-1JEaDYFRk_uJwpEG=e2XqnA4tROPRhDHA@mail.gmail.com>
References: <CABCMFNjDZTURmhyZ-1JEaDYFRk_uJwpEG=e2XqnA4tROPRhDHA@mail.gmail.com>
Message-ID: <3B75BC6C-B624-4FF2-AF91-8D3146E4259D@illinois.edu>

The error indicates that BioPerl isn't in your @INC (paths where perl searches for modules).  There are a number of things that could cause this, namely changing the version of perl you are using, upgrades to the OS, changes in local configuration, e.g. missing PERL5LIB.  In short, anything that can possibly modify the search path.

You could possibly try adding the bioperl directory to PERL5LIB locally.  What you *don't* want to do is attempt to add a version-specific path (say, a directory for an older version of perl in the system perl library).  

See this for more details on @INC:

http://stackoverflow.com/questions/2526804/how-is-perls-inc-constructed-aka-what-are-all-the-ways-of-affecting-where-pe

chris

On Feb 17, 2012, at 8:03 PM, Joshua Levine wrote:

> Hello,
> 
> I used to have bioperl working just fine on my machine (MacBook Pro,
> running OS X v10.6.8).  I tried installing some new perl modules ( DBI &
> DBD::mysql) and have not gotten them to work yet, but when I went back to
> run a script that uses bioperl, I got this error message:
> 
> Can't locate Bio/SeqIO.pm in @INC...
> 
> Now I just want to get bioperl working again, even if I can't also get DBI
> & DBD:mysql working.
> 
> Any help would be greatly appreciated
> -Josh
> 
> 
> -- 
> Joshua A. Levine
> 
> Graduate Student
> University of Arizona
> Ecology and Evolutionary Biology
> BioScience West 121
> jalevine at email.arizona.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Mon Feb 20 19:44:16 2012
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 21 Feb 2012 00:44:16 +0000
Subject: [Bioperl-l] Search for sequence inside sequence
Message-ID: <CAPOrs_1xViz-6YKF2XWXh+2kPzYR6a_B=hSPXHnxsAP=QCDZ4Q@mail.gmail.com>

Hi everyone

is there a method to check if a sequence exists inside another one? I
have a sequence object and a small string of a sequence. I'd like to
know if it's present? Currently I only have

say "Found on $file" if $seq->seq =~ /$string/i;

It solves my problem but this doesn't look very smart to me. Is there
a better way? Maybe even something that would also accept S to match
against [G|C] for example?

Thanks in advance,
Carn?


From Kevin.M.Brown at asu.edu  Mon Feb 20 20:12:33 2012
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Mon, 20 Feb 2012 18:12:33 -0700
Subject: [Bioperl-l] Search for sequence inside sequence
In-Reply-To: <CAPOrs_1xViz-6YKF2XWXh+2kPzYR6a_B=hSPXHnxsAP=QCDZ4Q@mail.gmail.com>
References: <CAPOrs_1xViz-6YKF2XWXh+2kPzYR6a_B=hSPXHnxsAP=QCDZ4Q@mail.gmail.com>
Message-ID: <1A4207F8295607498283FE9E93B775B408219A7A@EX02.asurite.ad.asu.edu>

Build up the Regexp outside of that line and then use it in there.

$string = "[GC]TAAGGACAA[AC]...";
print "Found in $file" if $seq->seq =~ /$string/I;

If you want your code to do substitution for the extra characters, then you'll need to interpret them into their regex equivalents. Such as reading in the string desired, and doing s/s/\[gc\]/I, etc...

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Carn? Draug
Sent: Monday, February 20, 2012 5:44 PM
To: bioperl mailing list
Subject: [Bioperl-l] Search for sequence inside sequence

Hi everyone

is there a method to check if a sequence exists inside another one? I have a sequence object and a small string of a sequence. I'd like to know if it's present? Currently I only have

say "Found on $file" if $seq->seq =~ /$string/i;

It solves my problem but this doesn't look very smart to me. Is there a better way? Maybe even something that would also accept S to match against [G|C] for example?

Thanks in advance,
Carn?

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


From cjfields at illinois.edu  Mon Feb 20 21:28:03 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 21 Feb 2012 02:28:03 +0000
Subject: [Bioperl-l] Search for sequence inside sequence
In-Reply-To: <1A4207F8295607498283FE9E93B775B408219A7A@EX02.asurite.ad.asu.edu>
References: <CAPOrs_1xViz-6YKF2XWXh+2kPzYR6a_B=hSPXHnxsAP=QCDZ4Q@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B408219A7A@EX02.asurite.ad.asu.edu>
Message-ID: <16F7B63A-5F72-41F3-94AE-63B7E53FD50A@illinois.edu>

There is a BioPerl-ish way of doing this, namely Bio::Tools::SeqPattern.  Might be worth a look (though a simple regex should also suffice).

chris

On Feb 20, 2012, at 7:12 PM, Kevin Brown wrote:

> Build up the Regexp outside of that line and then use it in there.
> 
> $string = "[GC]TAAGGACAA[AC]...";
> print "Found in $file" if $seq->seq =~ /$string/I;
> 
> If you want your code to do substitution for the extra characters, then you'll need to interpret them into their regex equivalents. Such as reading in the string desired, and doing s/s/\[gc\]/I, etc...
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Carn? Draug
> Sent: Monday, February 20, 2012 5:44 PM
> To: bioperl mailing list
> Subject: [Bioperl-l] Search for sequence inside sequence
> 
> Hi everyone
> 
> is there a method to check if a sequence exists inside another one? I have a sequence object and a small string of a sequence. I'd like to know if it's present? Currently I only have
> 
> say "Found on $file" if $seq->seq =~ /$string/i;
> 
> It solves my problem but this doesn't look very smart to me. Is there a better way? Maybe even something that would also accept S to match against [G|C] for example?
> 
> Thanks in advance,
> Carn?
> 
> _______________________________________________
> 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 carandraug+dev at gmail.com  Tue Feb 21 05:18:37 2012
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Tue, 21 Feb 2012 10:18:37 +0000
Subject: [Bioperl-l] Search for sequence inside sequence
In-Reply-To: <16F7B63A-5F72-41F3-94AE-63B7E53FD50A@illinois.edu>
References: <CAPOrs_1xViz-6YKF2XWXh+2kPzYR6a_B=hSPXHnxsAP=QCDZ4Q@mail.gmail.com>
	<1A4207F8295607498283FE9E93B775B408219A7A@EX02.asurite.ad.asu.edu>
	<16F7B63A-5F72-41F3-94AE-63B7E53FD50A@illinois.edu>
Message-ID: <CAPOrs_06-KZPJ8eZXPYZyBe_KSz2QqSKUezbzV1O+r9D+QgMHg@mail.gmail.com>

On 21 February 2012 02:28, Fields, Christopher J <cjfields at illinois.edu> wrote:
> There is a BioPerl-ish way of doing this, namely Bio::Tools::SeqPattern. ?Might be worth a look (though a simple regex should also suffice).

Thank you both.

I looked into this class and into the code in
examples/tools/seq_pattern.pl. It seems this module is more to create
a regexp from other string which can then be used on a normal regexp.

$pattern = "SS";
$regex = new Bio::Tools::SeqPattern(-seq =>$pattern, -type =>'Dna');

print "Found in $file" if $seq->seq =~ /$regex->expand/i;
print "Found in $file" if $seq->seq =~ /$regex->revcom(1)->str/i;
## to also search on the revcom

Do you think it is acceptable to add a method that would allow for:

say "Found in $file" if $seq->match(-seq-> $pattern );

maybe have an extra option that will also check the revcom of:

say "Found in $file" if $seq->match(-seq-> $pattern -revcom-> 1);

Carn?


From arlett.wrona at c-lecta.de  Tue Feb 21 06:14:14 2012
From: arlett.wrona at c-lecta.de (Enzyme)
Date: Tue, 21 Feb 2012 03:14:14 -0800 (PST)
Subject: [Bioperl-l]  BLAST example doesn't work
Message-ID: <33362540.post@talk.nabble.com>


Hi,

i'm new to BioPerl and wanna use it for BLAST. But the example doesn't work.
I tried some possible solutions and at the moment i don't know if the code
is wrong or my bio perl package don't work how it should:

use Bio::Tools::Run::StandAloneBlast;
my $factory = Bio::Tools::Run::StandAloneBlast->new(p => 'blastn',
                                                    d => 'nr',
                                                    e => '1e-5');
my $seq = Bio::PrimarySeq->new(-id => 'test1',
                               -seq => 'AGATCAGTAGATGATAGGGGTAGA');
my $report = $factory->blastall($seq); # get back a {{PM|Bio::SearchIO}}
report

I get this error:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Command 'run' not registered
STACK: Error::throw
STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::set_parameters
C:/Perl/site/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:1203
STACK: Bio::Tools::Run::WrapperBase::new
C:/Perl/site/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:505
STACK: Bio::Tools::Run::StandAloneBlast::new
C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:366
STACK: Bio::Tools::Run::StandAloneNCBIBlast::new
C:/Perl/site/lib/Bio\Tools\Run\StandAloneNCBIBlast.pm:166
STACK: C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:382

Any ideas?
I downloaded the database "nr" correctly. The environment paths were
created.

Thanks! Enzyme
-- 
View this message in context: http://old.nabble.com/BLAST-example-doesn%27t-work-tp33362540p33362540.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From fossandonc at hotmail.com  Wed Feb 22 13:55:23 2012
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Wed, 22 Feb 2012 15:55:23 -0300
Subject: [Bioperl-l] Fasta sequence width question
Message-ID: <BLU0-SMTP225B3D87620D5BC0691B940CF640@phx.gbl>

Hello,
I have a question about the width used by Bioperl in the Fasta format. This
format recommends that lines of text be shorter than 80 characters, but
there is no really fixed length for the sequence lines.
http://en.wikipedia.org/wiki/FASTA_format
http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml

I usually download sequences from NCBI and their Fasta sequences always use
a sequence line width of 70 characters (like
http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while Bioperl
uses a default of 60 to write in Fasta format using Bio::SeqIO::Fasta
("BEGIN { $WIDTH = 60}"). Is there a particular reason to set the width at
60 characters?? Or maybe it could be changed to 70 to match NCBI??

Cheers,

Francisco J. Ossandon



From bosborne11 at verizon.net  Wed Feb 22 14:28:12 2012
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 22 Feb 2012 14:28:12 -0500
Subject: [Bioperl-l] Fasta sequence width question
In-Reply-To: <BLU0-SMTP225B3D87620D5BC0691B940CF640@phx.gbl>
References: <BLU0-SMTP225B3D87620D5BC0691B940CF640@phx.gbl>
Message-ID: <871478E1-15CD-4F3D-B95E-71193723D593@verizon.net>

Francis,

You can set this yourself.

http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width

Brian O.


On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:

> Hello,
> I have a question about the width used by Bioperl in the Fasta format. This
> format recommends that lines of text be shorter than 80 characters, but
> there is no really fixed length for the sequence lines.
> http://en.wikipedia.org/wiki/FASTA_format
> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> 
> I usually download sequences from NCBI and their Fasta sequences always use
> a sequence line width of 70 characters (like
> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while Bioperl
> uses a default of 60 to write in Fasta format using Bio::SeqIO::Fasta
> ("BEGIN { $WIDTH = 60}"). Is there a particular reason to set the width at
> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> 
> Cheers,
> 
> Francisco J. Ossandon
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From fossandonc at hotmail.com  Wed Feb 22 16:37:42 2012
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Wed, 22 Feb 2012 18:37:42 -0300
Subject: [Bioperl-l] Fasta sequence width question
In-Reply-To: <871478E1-15CD-4F3D-B95E-71193723D593@verizon.net>
References: <BLU0-SMTP225B3D87620D5BC0691B940CF640@phx.gbl>
	<871478E1-15CD-4F3D-B95E-71193723D593@verizon.net>
Message-ID: <BLU0-SMTP324801F8A32A12FE1700ED0CF640@phx.gbl>

Yes, I know about the method to change the width myself, thanks. =)
My question was more about if there was an specific reason to choose that
default value (60) instead of the NCBI value (70). And if it should be
changed to 70 to match NCBI or not.

Cheers,
 
Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Brian Osborne
Enviado el: mi?rcoles, 22 de febrero de 2012 16:28
Para: Francisco J. Ossand?n
CC: Bioperl-l at lists.open-bio.org
Asunto: Re: [Bioperl-l] Fasta sequence width question

Francis,

You can set this yourself.

http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width

Brian O.


On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:

> Hello,
> I have a question about the width used by Bioperl in the Fasta format. 
> This format recommends that lines of text be shorter than 80 
> characters, but there is no really fixed length for the sequence lines.
> http://en.wikipedia.org/wiki/FASTA_format
> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> 
> I usually download sequences from NCBI and their Fasta sequences 
> always use a sequence line width of 70 characters (like 
> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while 
> Bioperl uses a default of 60 to write in Fasta format using 
> Bio::SeqIO::Fasta ("BEGIN { $WIDTH = 60}"). Is there a particular 
> reason to set the width at
> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> 
> Cheers,
> 
> Francisco J. Ossandon
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


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



From cjfields at illinois.edu  Wed Feb 22 17:42:04 2012
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 22 Feb 2012 16:42:04 -0600
Subject: [Bioperl-l] Fasta sequence width question
In-Reply-To: <BLU0-SMTP324801F8A32A12FE1700ED0CF640@phx.gbl>
References: <BLU0-SMTP225B3D87620D5BC0691B940CF640@phx.gbl>
	<871478E1-15CD-4F3D-B95E-71193723D593@verizon.net>
	<BLU0-SMTP324801F8A32A12FE1700ED0CF640@phx.gbl>
Message-ID: <4F456F3C.4070903@illinois.edu>

No reason, beyond legacy and possibly a fear that changing it could 
cause unforeseen consequences down the road.

chris

On 02/22/2012 03:37 PM, Francisco J. Ossand?n wrote:
> Yes, I know about the method to change the width myself, thanks. =)
> My question was more about if there was an specific reason to choose that
> default value (60) instead of the NCBI value (70). And if it should be
> changed to 70 to match NCBI or not.
>
> Cheers,
>
> Francisco J. Ossandon
>
> -----Mensaje original-----
> De: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Brian Osborne
> Enviado el: mi?rcoles, 22 de febrero de 2012 16:28
> Para: Francisco J. Ossand?n
> CC: Bioperl-l at lists.open-bio.org
> Asunto: Re: [Bioperl-l] Fasta sequence width question
>
> Francis,
>
> You can set this yourself.
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width
>
> Brian O.
>
>
> On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:
>
>> Hello,
>> I have a question about the width used by Bioperl in the Fasta format.
>> This format recommends that lines of text be shorter than 80
>> characters, but there is no really fixed length for the sequence lines.
>> http://en.wikipedia.org/wiki/FASTA_format
>> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
>>
>> I usually download sequences from NCBI and their Fasta sequences
>> always use a sequence line width of 70 characters (like
>> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while
>> Bioperl uses a default of 60 to write in Fasta format using
>> Bio::SeqIO::Fasta ("BEGIN { $WIDTH = 60}"). Is there a particular
>> reason to set the width at
>> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
>>
>> Cheers,
>>
>> Francisco J. Ossandon
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From bosborne11 at verizon.net  Wed Feb 22 16:50:58 2012
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 22 Feb 2012 16:50:58 -0500
Subject: [Bioperl-l] Fasta sequence width question
In-Reply-To: <BLU0-SMTP324801F8A32A12FE1700ED0CF640@phx.gbl>
References: <BLU0-SMTP225B3D87620D5BC0691B940CF640@phx.gbl>
	<871478E1-15CD-4F3D-B95E-71193723D593@verizon.net>
	<BLU0-SMTP324801F8A32A12FE1700ED0CF640@phx.gbl>
Message-ID: <9A106184-4082-4E23-B91B-6DBCCE0B319E@verizon.net>

Francis,

There's has never been a decision, to my knowledge, to base "global" Bioperl defaults on NCBI's conventions. Yes, there are tools in Bioperl that access NCBI in various ways but Bioperl does not generally refer to NCBI for its definitions.

Brian O.

On Feb 22, 2012, at 4:37 PM, Francisco J. Ossand?n wrote:

> Yes, I know about the method to change the width myself, thanks. =)
> My question was more about if there was an specific reason to choose that
> default value (60) instead of the NCBI value (70). And if it should be
> changed to 70 to match NCBI or not.
> 
> Cheers,
> 
> Francisco J. Ossandon
> 
> -----Mensaje original-----
> De: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Brian Osborne
> Enviado el: mi?rcoles, 22 de febrero de 2012 16:28
> Para: Francisco J. Ossand?n
> CC: Bioperl-l at lists.open-bio.org
> Asunto: Re: [Bioperl-l] Fasta sequence width question
> 
> Francis,
> 
> You can set this yourself.
> 
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width
> 
> Brian O.
> 
> 
> On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:
> 
>> Hello,
>> I have a question about the width used by Bioperl in the Fasta format. 
>> This format recommends that lines of text be shorter than 80 
>> characters, but there is no really fixed length for the sequence lines.
>> http://en.wikipedia.org/wiki/FASTA_format
>> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
>> 
>> I usually download sequences from NCBI and their Fasta sequences 
>> always use a sequence line width of 70 characters (like 
>> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while 
>> Bioperl uses a default of 60 to write in Fasta format using 
>> Bio::SeqIO::Fasta ("BEGIN { $WIDTH = 60}"). Is there a particular 
>> reason to set the width at
>> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
>> 
>> Cheers,
>> 
>> Francisco J. Ossandon
>> 
>> 
>> _______________________________________________
>> 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 adlai at refenestration.com  Thu Feb 23 19:43:41 2012
From: adlai at refenestration.com (Adlai Burman)
Date: Fri, 24 Feb 2012 01:43:41 +0100
Subject: [Bioperl-l] Navigating a genbank file
Message-ID: <3F92E96A-2A69-4F6F-AA92-AAA7A2122BD8@refenestration.com>

I am struggling with Bioperl to do something which I know is simple (I stumbled on it before, but it was just by dumb luck and I forgot how it is done). Basically what I am trying to do is, given a target gene symbol extract the intergenic region between that CDS and the next one 3'. One ugly way I could do this would be:
 (1) Make an array of all of the CDSs in each gb file
(2) Make a second run through the file using either the symbol prior or post the target symbol (depending on the strand of the target symbol).

This is, of course, cumbersome and unnecessary but I can't figure out how it should be done.
Here is a skeletal version of what I understand about getting feature info with bioperl.
Can anyone help me figure out how to access the CDS features on either side?
Please?
Thank you,

Adlai

#!/usr/bin/perl                                                                                                     
use strict;
use warnings;
use IO::String;
use Bio::Perl;
use Bio::SeqIO;
use IO::String;


my $target_sym = shift;
my $file = "../Dropbox/local_gb/*";

my $seqio = Bio::SeqIO-> new(
                             -file     => $file,
                             -format => 'GenBank',
    );

my $seq = $seqio->next_seq;
for my $feats ($seq->get_SeqFeatures){
if ($feats->primary_tag eq "CDS"){
  my $start = $feats->location->start;
my $end = $feats->location->end;
my $strand = $feats->strand;
 if ($feats->has_tag('gene')) {
     for my $val ($feats->get_tag_values('gene')){
if ($val eq $target_sym){
print $start."\n";
print "$val\n";
  }

}
}
}
}

From abhishek.vit at gmail.com  Thu Feb 23 19:55:02 2012
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Thu, 23 Feb 2012 16:55:02 -0800
Subject: [Bioperl-l] fetching all alignments from a sam/bam by read header
	in perl
Message-ID: <CAJbA1KCpjhWALG1KYJTNKexnt8ba7vfGpPm0q8kUr0SBvRe73w@mail.gmail.com>

I am wondering if there is a slick way access all the possible
alignments for a read present in sam or bam file given the read
header. Since the existing codebase is in perl I would prefer
something which can be done in/via perl.

By default BAM's are indexed by location so the inbuilt samtools
indexing wont work I guess.

I should also say the input bam file will have in the order of 500
million total alignments and many reads are expected to be aligned to
more than one place in the genome. Given the size of the data loading
it all in one big hash is not turning out to be memory friendly.

PS:  I also posted this earlier on Biostar.

Thanks!
-Abhi

From mcoyne at channing.harvard.edu  Thu Feb 23 21:01:51 2012
From: mcoyne at channing.harvard.edu (Michael Coyne)
Date: Thu, 23 Feb 2012 21:01:51 -0500
Subject: [Bioperl-l] Bioperl-l Digest, Vol 106, Issue 18
In-Reply-To: <mailman.15.1330016406.16682.bioperl-l@lists.open-bio.org>
References: <mailman.15.1330016406.16682.bioperl-l@lists.open-bio.org>
Message-ID: <CAJBUCCUS8RbRgnr6Gmq4VmJtzSqvKZ1TYWiPMi44HdbSTE5nsg@mail.gmail.com>

Sixty is evenly divisible by three (20 codons), while 70 is not...?

On Thu, Feb 23, 2012 at 12:00 PM, <bioperl-l-request at lists.open-bio.org>wrote:

> Send Bioperl-l mailing list submissions to
>        bioperl-l at lists.open-bio.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://lists.open-bio.org/mailman/listinfo/bioperl-l
> or, via email, send a message with subject or body 'help' to
>        bioperl-l-request at lists.open-bio.org
>
> You can reach the person managing the list at
>        bioperl-l-owner at lists.open-bio.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioperl-l digest..."
>
>
> Today's Topics:
>
>   1.  Fasta sequence width question ( Francisco J. Ossand?n )
>   2. Re:  Fasta sequence width question (Brian Osborne)
>   3. Re:  Fasta sequence width question ( Francisco J. Ossand?n )
>   4. Re:  Fasta sequence width question (Chris Fields)
>   5. Re:  Fasta sequence width question (Brian Osborne)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 22 Feb 2012 15:55:23 -0300
> From: " Francisco J. Ossand?n " <fossandonc at hotmail.com>
> Subject: [Bioperl-l] Fasta sequence width question
> To: <Bioperl-l at lists.open-bio.org>
> Message-ID: <BLU0-SMTP225B3D87620D5BC0691B940CF640 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
> I have a question about the width used by Bioperl in the Fasta format. This
> format recommends that lines of text be shorter than 80 characters, but
> there is no really fixed length for the sequence lines.
> http://en.wikipedia.org/wiki/FASTA_format
> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
>
> I usually download sequences from NCBI and their Fasta sequences always use
> a sequence line width of 70 characters (like
> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while Bioperl
> uses a default of 60 to write in Fasta format using Bio::SeqIO::Fasta
> ("BEGIN { $WIDTH = 60}"). Is there a particular reason to set the width at
> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
>
> Cheers,
>
> Francisco J. Ossandon
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 22 Feb 2012 14:28:12 -0500
> From: Brian Osborne <bosborne11 at verizon.net>
> Subject: Re: [Bioperl-l] Fasta sequence width question
> To: Francisco J. Ossand?n <fossandonc at hotmail.com>
> Cc: Bioperl-l at lists.open-bio.org
> Message-ID: <871478E1-15CD-4F3D-B95E-71193723D593 at verizon.net>
> Content-Type: text/plain; charset=iso-8859-1
>
> Francis,
>
> You can set this yourself.
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width
>
> Brian O.
>
>
> On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:
>
> > Hello,
> > I have a question about the width used by Bioperl in the Fasta format.
> This
> > format recommends that lines of text be shorter than 80 characters, but
> > there is no really fixed length for the sequence lines.
> > http://en.wikipedia.org/wiki/FASTA_format
> > http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> >
> > I usually download sequences from NCBI and their Fasta sequences always
> use
> > a sequence line width of 70 characters (like
> > http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while
> Bioperl
> > uses a default of 60 to write in Fasta format using Bio::SeqIO::Fasta
> > ("BEGIN { $WIDTH = 60}"). Is there a particular reason to set the width
> at
> > 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> >
> > Cheers,
> >
> > Francisco J. Ossandon
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 22 Feb 2012 18:37:42 -0300
> From: " Francisco J. Ossand?n " <fossandonc at hotmail.com>
> Subject: Re: [Bioperl-l] Fasta sequence width question
> To: "'Brian Osborne'" <bosborne11 at verizon.net>
> Cc: Bioperl-l at lists.open-bio.org
> Message-ID: <BLU0-SMTP324801F8A32A12FE1700ED0CF640 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Yes, I know about the method to change the width myself, thanks. =)
> My question was more about if there was an specific reason to choose that
> default value (60) instead of the NCBI value (70). And if it should be
> changed to 70 to match NCBI or not.
>
> Cheers,
>
> Francisco J. Ossandon
>
> -----Mensaje original-----
> De: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Brian Osborne
> Enviado el: mi?rcoles, 22 de febrero de 2012 16:28
> Para: Francisco J. Ossand?n
> CC: Bioperl-l at lists.open-bio.org
> Asunto: Re: [Bioperl-l] Fasta sequence width question
>
> Francis,
>
> You can set this yourself.
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width
>
> Brian O.
>
>
> On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:
>
> > Hello,
> > I have a question about the width used by Bioperl in the Fasta format.
> > This format recommends that lines of text be shorter than 80
> > characters, but there is no really fixed length for the sequence lines.
> > http://en.wikipedia.org/wiki/FASTA_format
> > http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> >
> > I usually download sequences from NCBI and their Fasta sequences
> > always use a sequence line width of 70 characters (like
> > http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while
> > Bioperl uses a default of 60 to write in Fasta format using
> > Bio::SeqIO::Fasta ("BEGIN { $WIDTH = 60}"). Is there a particular
> > reason to set the width at
> > 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> >
> > Cheers,
> >
> > Francisco J. Ossandon
> >
> >
> > _______________________________________________
> > 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
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 22 Feb 2012 16:42:04 -0600
> From: Chris Fields <cjfields at illinois.edu>
> Subject: Re: [Bioperl-l] Fasta sequence width question
> To: bioperl-l at lists.open-bio.org
> Message-ID: <4F456F3C.4070903 at illinois.edu>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> No reason, beyond legacy and possibly a fear that changing it could
> cause unforeseen consequences down the road.
>
> chris
>
> On 02/22/2012 03:37 PM, Francisco J. Ossand?n wrote:
> > Yes, I know about the method to change the width myself, thanks. =)
> > My question was more about if there was an specific reason to choose that
> > default value (60) instead of the NCBI value (70). And if it should be
> > changed to 70 to match NCBI or not.
> >
> > Cheers,
> >
> > Francisco J. Ossandon
> >
> > -----Mensaje original-----
> > De: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Brian Osborne
> > Enviado el: mi?rcoles, 22 de febrero de 2012 16:28
> > Para: Francisco J. Ossand?n
> > CC: Bioperl-l at lists.open-bio.org
> > Asunto: Re: [Bioperl-l] Fasta sequence width question
> >
> > Francis,
> >
> > You can set this yourself.
> >
> >
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width
> >
> > Brian O.
> >
> >
> > On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:
> >
> >> Hello,
> >> I have a question about the width used by Bioperl in the Fasta format.
> >> This format recommends that lines of text be shorter than 80
> >> characters, but there is no really fixed length for the sequence lines.
> >> http://en.wikipedia.org/wiki/FASTA_format
> >> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> >>
> >> I usually download sequences from NCBI and their Fasta sequences
> >> always use a sequence line width of 70 characters (like
> >> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while
> >> Bioperl uses a default of 60 to write in Fasta format using
> >> Bio::SeqIO::Fasta ("BEGIN { $WIDTH = 60}"). Is there a particular
> >> reason to set the width at
> >> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> >>
> >> Cheers,
> >>
> >> Francisco J. Ossandon
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 22 Feb 2012 16:50:58 -0500
> From: Brian Osborne <bosborne11 at verizon.net>
> Subject: Re: [Bioperl-l] Fasta sequence width question
> To: Francisco J. Ossand?n <fossandonc at hotmail.com>
> Cc: Bioperl-l at lists.open-bio.org
> Message-ID: <9A106184-4082-4E23-B91B-6DBCCE0B319E at verizon.net>
> Content-Type: text/plain; charset=iso-8859-1
>
> Francis,
>
> There's has never been a decision, to my knowledge, to base "global"
> Bioperl defaults on NCBI's conventions. Yes, there are tools in Bioperl
> that access NCBI in various ways but Bioperl does not generally refer to
> NCBI for its definitions.
>
> Brian O.
>
> On Feb 22, 2012, at 4:37 PM, Francisco J. Ossand?n wrote:
>
> > Yes, I know about the method to change the width myself, thanks. =)
> > My question was more about if there was an specific reason to choose that
> > default value (60) instead of the NCBI value (70). And if it should be
> > changed to 70 to match NCBI or not.
> >
> > Cheers,
> >
> > Francisco J. Ossandon
> >
> > -----Mensaje original-----
> > De: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Brian Osborne
> > Enviado el: mi?rcoles, 22 de febrero de 2012 16:28
> > Para: Francisco J. Ossand?n
> > CC: Bioperl-l at lists.open-bio.org
> > Asunto: Re: [Bioperl-l] Fasta sequence width question
> >
> > Francis,
> >
> > You can set this yourself.
> >
> >
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width
> >
> > Brian O.
> >
> >
> > On Feb 22, 2012, at 1:55 PM, Francisco J. Ossand?n wrote:
> >
> >> Hello,
> >> I have a question about the width used by Bioperl in the Fasta format.
> >> This format recommends that lines of text be shorter than 80
> >> characters, but there is no really fixed length for the sequence lines.
> >> http://en.wikipedia.org/wiki/FASTA_format
> >> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> >>
> >> I usually download sequences from NCBI and their Fasta sequences
> >> always use a sequence line width of 70 characters (like
> >> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while
> >> Bioperl uses a default of 60 to write in Fasta format using
> >> Bio::SeqIO::Fasta ("BEGIN { $WIDTH = 60}"). Is there a particular
> >> reason to set the width at
> >> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> >>
> >> Cheers,
> >>
> >> Francisco J. Ossandon
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> End of Bioperl-l Digest, Vol 106, Issue 18
> ******************************************
>

From jason.stajich at gmail.com  Fri Feb 24 01:49:38 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 23 Feb 2012 22:49:38 -0800
Subject: [Bioperl-l] Navigating a genbank file
In-Reply-To: <3F92E96A-2A69-4F6F-AA92-AAA7A2122BD8@refenestration.com>
References: <3F92E96A-2A69-4F6F-AA92-AAA7A2122BD8@refenestration.com>
Message-ID: <F7FE7024-F054-4617-A3A5-F02DB2098DE8@gmail.com>

You just need a $last_CDS variable.
Here's code that does this for genes retrieved from Bio::DB::SeqFeature but the concept is the same.

https://github.com/hyphaltip/genome-scripts/blob/master/seqfeature/get_intergenic_seq.pl

On Feb 23, 2012, at 4:43 PM, Adlai Burman wrote:

> I am struggling with Bioperl to do something which I know is simple (I stumbled on it before, but it was just by dumb luck and I forgot how it is done). Basically what I am trying to do is, given a target gene symbol extract the intergenic region between that CDS and the next one 3'. One ugly way I could do this would be:
> (1) Make an array of all of the CDSs in each gb file
> (2) Make a second run through the file using either the symbol prior or post the target symbol (depending on the strand of the target symbol).
> 
> This is, of course, cumbersome and unnecessary but I can't figure out how it should be done.
> Here is a skeletal version of what I understand about getting feature info with bioperl.
> Can anyone help me figure out how to access the CDS features on either side?
> Please?
> Thank you,
> 
> Adlai
> 
> #!/usr/bin/perl                                                                                                     
> use strict;
> use warnings;
> use IO::String;
> use Bio::Perl;
> use Bio::SeqIO;
> use IO::String;
> 
> 
> my $target_sym = shift;
> my $file = "../Dropbox/local_gb/*";
> 
> my $seqio = Bio::SeqIO-> new(
>                             -file     => $file,
>                             -format => 'GenBank',
>    );
> 
> my $seq = $seqio->next_seq;
> for my $feats ($seq->get_SeqFeatures){
> if ($feats->primary_tag eq "CDS"){
>  my $start = $feats->location->start;
> my $end = $feats->location->end;
> my $strand = $feats->strand;
> if ($feats->has_tag('gene')) {
>     for my $val ($feats->get_tag_values('gene')){
> if ($val eq $target_sym){
> print $start."\n";
> print "$val\n";
>  }
> 
> }
> }
> }
> }
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org



From p.j.a.cock at googlemail.com  Fri Feb 24 04:24:35 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 24 Feb 2012 09:24:35 +0000
Subject: [Bioperl-l] fetching all alignments from a sam/bam by read
 header in perl
In-Reply-To: <CAJbA1KCpjhWALG1KYJTNKexnt8ba7vfGpPm0q8kUr0SBvRe73w@mail.gmail.com>
References: <CAJbA1KCpjhWALG1KYJTNKexnt8ba7vfGpPm0q8kUr0SBvRe73w@mail.gmail.com>
Message-ID: <CAKVJ-_4vLDHcUmhAFn2Mw0oy=sjdgn1TQrj47AhO25kcwy=oaQ@mail.gmail.com>

On Fri, Feb 24, 2012 at 12:55 AM, Abhishek Pratap
<abhishek.vit at gmail.com> wrote:
> I am wondering if there is a slick way access all the possible
> alignments for a read present in sam or bam file given the read
> header. Since the existing codebase is in perl I would prefer
> something which can be done in/via perl.
>
> By default BAM's are indexed by location so the inbuilt samtools
> indexing wont work I guess.
>
> I should also say the input bam file will have in the order of 500
> million total alignments and many reads are expected to be aligned to
> more than one place in the genome. Given the size of the data loading
> it all in one big hash is not turning out to be memory friendly.

Are you asking for SAM/BAM read lookup by read name?

> PS: ?I also posted this earlier on Biostar.

Link?

Peter


From briano at bioteam.net  Fri Feb 24 09:58:58 2012
From: briano at bioteam.net (Brian Osborne)
Date: Fri, 24 Feb 2012 09:58:58 -0500
Subject: [Bioperl-l] Can't locate object method "seq" via package
	"Bio::DB::Query::GenBank"
In-Reply-To: <7716984D-CB98-4CC0-9E1A-69D696FB6745@gmail.com>
References: <7716984D-CB98-4CC0-9E1A-69D696FB6745@gmail.com>
Message-ID: <8664C24D-786A-4268-9917-9D630C58D9B4@bioteam.net>

Casandra,

BioPerl questions should be directed to the bioperl-l mailing list, that's where they will get the most attention. I'm CC'ing the list here.

Brian O.



On Feb 24, 2012, at 7:07 AM, Casandra wrote:

> Hi, 
> I was training with "Retrieving multiple sequences from a database" 
> use Bio::DB::Query::GenBank;
>  
> $query = "Arabidopsis[ORGN] AND topoisomerase[TITL] and 0:3000[SLEN]";
> $query_obj = Bio::DB::Query::GenBank->new(-db    => 'nucleotide', -query => $query )
> but I'm stuck in the print step. This is what I wrote:
> 
> #!/bin/perl -w
> 
> use Bio::DB::Query::GenBank;
> use Bio::Seq;
> use Bio::SeqIO;
> 
> $query = "Arabidopsis[ORGN] AND topoisomerase[TITL]";
> $query_obj = Bio::DB::Query::GenBank->new(-db =>'nucleotide', -query => $query);
> 
> #$seqio_obj = Bio::SeqIO->new(-file =>'>Arab46.gb', -format =>'genbank');
> #$seqio_obj->write_seq($query_obj);
> 
> print $query_obj->accession_number,"\n";
> 
> I've tried to print it to a file with seqio and to print it through terminal with the following:
> print $query_obj->accession_number,"\n";
> print $query_obj->seq,"\n";
> print $query_obj->division,"\n";
> 
> But the error message I get when I try to print it to a file is:
> --------------------- WARNING ---------------------
> MSG:  Bio::DB::Query::GenBank=HASH(0x965010) is not a SeqI compliant module. Attempting to dump, but may fail!
> ---------------------------------------------------
> Can't locate object method "seq" via package "Bio::DB::Query::GenBank" at /Library/Perl/5.8.8/Bio/SeqIO/genbank.pm line 760.
> 
> And when I try to print it normally:
> Can't locate object method "seq" via package "Bio::DB::Query::GenBank" at bp_seq4.pl line 15.
> 
> 
> I went to cpan to check for this module 
> Bio::DB::Query::GenBank
> I install Bioperl again the one that was following "Bio::DB::Query::GenBank".
> But no change in the message error.
> 
> could you help me?
> 
> Thank you very much.

Brian O.
--
Brian Osborne, PhD
BioTeam: http://bioteam.net
email: briano at bioteam.net
mobile: 978-317-3101



From abhishek.vit at gmail.com  Fri Feb 24 09:58:33 2012
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Fri, 24 Feb 2012 06:58:33 -0800
Subject: [Bioperl-l] fetching all alignments from a sam/bam by read
 header in perl
In-Reply-To: <CAKVJ-_4vLDHcUmhAFn2Mw0oy=sjdgn1TQrj47AhO25kcwy=oaQ@mail.gmail.com>
References: <CAJbA1KCpjhWALG1KYJTNKexnt8ba7vfGpPm0q8kUr0SBvRe73w@mail.gmail.com>
	<CAKVJ-_4vLDHcUmhAFn2Mw0oy=sjdgn1TQrj47AhO25kcwy=oaQ@mail.gmail.com>
Message-ID: <CAJbA1KBifpnFJS_fu5T5quODvK3gs5TsP9Z=9xXJLn85Wm_2Tg@mail.gmail.com>

Hi Peter

You got it right.

Here is the link :
http://biostar.stackexchange.com/questions/17787/fetching-all-alignments-from-a-sam-bam-by-read-header-in-perl



-A

On Fri, Feb 24, 2012 at 1:24 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Fri, Feb 24, 2012 at 12:55 AM, Abhishek Pratap
> <abhishek.vit at gmail.com> wrote:
>> I am wondering if there is a slick way access all the possible
>> alignments for a read present in sam or bam file given the read
>> header. Since the existing codebase is in perl I would prefer
>> something which can be done in/via perl.
>>
>> By default BAM's are indexed by location so the inbuilt samtools
>> indexing wont work I guess.
>>
>> I should also say the input bam file will have in the order of 500
>> million total alignments and many reads are expected to be aligned to
>> more than one place in the genome. Given the size of the data loading
>> it all in one big hash is not turning out to be memory friendly.
>
> Are you asking for SAM/BAM read lookup by read name?
>
>> PS: ?I also posted this earlier on Biostar.
>
> Link?
>
> Peter


From sami.kilpinen at medisapiens.com  Thu Feb 23 02:20:10 2012
From: sami.kilpinen at medisapiens.com (Sami Kilpinen)
Date: Thu, 23 Feb 2012 09:20:10 +0200
Subject: [Bioperl-l] Problem with Bio::GeneMapper
Message-ID: <6EDB646F-017F-4BA1-BA32-70A7F0972BB2@medisapiens.com>

Hello,

I have been trying to solve following issues with GeneMapper.
1) ->to_string(); throws an error
2) Mapper doesn't seem to do much of anything


Bioperl 1.6.1 in use and relevant parts of the code are as follows:
---------------------------------------------------
use Bio::Coordinate::GeneMapper;
use Bio::Location::Split;
use Bio::Location::Simple;

# get a Bio::Location::Split or an array of Bio::LocationI objects
# holding the start, end and strand of all the exons in chromosomal
# (or entry) coordinates
my $splits = Bio::Location::Split->new();

# $exons come from mongodb, not relevant here as data is printed to screen for debug purposes

while ( my $exon = $exons->next ) {
	my $e_start=$exon->{'start'};
	my $e_end=$exon->{'end'};
	my $e_strand=$exon->{'strand'};
	print "Exon_start,Exon-end,Exon-strand\n";
	print $e_start,",",$e_end,",",$e_strand,"\n";
	$splits->add_sub_Location(Bio::Location::Simple->new(-start=>$e_start,-end=>$e_end,-strand=>$e_strand));
}

print  "Location::Split object string dump\n";
print $splits->to_FTstring(),"\n";

# get a Bio::RangeI representing the start, end and strand of the CDS
# in chromosomal (or entry) coordinates
my $cds = Bio::Location::Simple->new(-start => 752890, -end => 753369, -strand => 1 );

# create a gene mapper and set it to map from chromosomal to cds coordinates
my $gene = Bio::Coordinate::GeneMapper->new(-in   =>'chr',
				      -out  =>'cds',
				      -cds  =>$cds,
				      -exons=>$splits
				     );

# get a a Bio::Location or sequence feature in input (chr) coordinates
my $loc = Bio::Location::Simple->new(-start => 753584, -end => 753584, -strand => 1 );

# Trying to set strict boundaries
$gene->strict('cds');

# map the location into output coordinates and get a new location object
my $newloc = $gene->map($loc);

print "new location in cds coordinates\n";
print  $newloc->start(),"\n";

print "Mapper internal data in human readable format\n";
my $tmp=$gene->to_string();

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

And the result of running this are:
==========================
Exon_start,Exon-end,Exon-strand
752751,753582,1
Exon_start,Exon-end,Exon-strand
754103,755214,1
Location::Split object string dump
join(752751..753582,754103..755214)
new location in cds coordinates
695
Mapper internal data in human readable format
----------------------------------------

     chr-gene     (1-2)
                gene offset: 752889 (753368)
                gene strand: 1

     gene-intron  (2-5)
Can't call method "each_mapper" on an undefined value at /usr/local/share/perl/5.10.1/Bio/Coordinate/GeneMapper.pm line 1013.
==========================

Thus here we have two exons and cds situating completely in the first exon. GeneMapper calculates (correctly) that chr coordinate 752892 is nucleotide 2 from the start of cds (752890) but then throws an error about each_mapper. Then, if I ask for cds coordinate for chr coordinate (753769) which is between the exons and beyond the end of the cds (753369) it returns me value 880 and same error (why it even claims that such an cds coordinate exists? cds is 479 long...). I have tried to test some more complex genes where cds contains >1 exons and if I ask chr=>cds coordinate mapping when the chr coordinate situates in exon 2 it seems that it does not take the intron into account.. it just returns the "asked chr coordinate"-"cds start coordinate". This simple calculation is all that this module does for me... 

What I would like to do in this more complex cases is that it calculates the length of all exon nucleotides between cds start and the asked chr coordinate. In other words ("asked chr coordinate"-"cds start in chr coordinates")-length of all introns between those. Isn't this what GeneMapper is supposed to do?

I would highly appreciate any help with this issue.

Regards,
Sami Kilpinen




From arlett.wrona at c-lecta.de  Tue Feb 21 04:16:21 2012
From: arlett.wrona at c-lecta.de (Enzyme)
Date: Tue, 21 Feb 2012 01:16:21 -0800 (PST)
Subject: [Bioperl-l]  BLAST example doesn't work
Message-ID: <33362540.post@talk.nabble.com>


Hi,

i'm new to BioPerl and wanna use it for BLAST. But the example doesn't work.
I tried some possible solutions and at the moment i don't know if the code
is wrong or my bio perl package don't work how it should:

use Bio::Tools::Run::StandAloneBlast;
my $factory = Bio::Tools::Run::StandAloneBlast->new(p => 'blastn',
                                                    d => 'nr',
                                                    e => '1e-5');
my $seq = Bio::PrimarySeq->new(-id => 'test1',
                               -seq => 'AGATCAGTAGATGATAGGGGTAGA');
my $report = $factory->blastall($seq); # get back a {{PM|Bio::SearchIO}}
report

I get this error:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Command 'run' not registered
STACK: Error::throw
STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::set_parameters
C:/Perl/site/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:1203
STACK: Bio::Tools::Run::WrapperBase::new
C:/Perl/site/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:505
STACK: Bio::Tools::Run::StandAloneBlast::new
C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:366
STACK: Bio::Tools::Run::StandAloneNCBIBlast::new
C:/Perl/site/lib/Bio\Tools\Run\StandAloneNCBIBlast.pm:166
STACK: C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:382

Any ideas?
I downloaded the database "nr" correctly. The environment paths were
created.

Thanks! Enzyme
-- 
View this message in context: http://old.nabble.com/BLAST-example-doesn%27t-work-tp33362540p33362540.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From kasandrah at gmail.com  Fri Feb 24 10:24:05 2012
From: kasandrah at gmail.com (Casandra)
Date: Fri, 24 Feb 2012 16:24:05 +0100
Subject: [Bioperl-l] Can't locate object method "seq" via package
	"Bio::DB::Query::GenBank"
In-Reply-To: <8664C24D-786A-4268-9917-9D630C58D9B4@bioteam.net>
References: <7716984D-CB98-4CC0-9E1A-69D696FB6745@gmail.com>
	<8664C24D-786A-4268-9917-9D630C58D9B4@bioteam.net>
Message-ID: <6AE6A02D-BF93-498D-8FCC-34FE40E13143@gmail.com>

I saw my mistake but thank you anyway : )


El 24/02/2012, a las 15:58, Brian Osborne escribi?:

> Casandra,
>
> BioPerl questions should be directed to the bioperl-l mailing list,  
> that's where they will get the most attention. I'm CC'ing the list  
> here.
>
> Brian O.
>
>
>
> On Feb 24, 2012, at 7:07 AM, Casandra wrote:
>
>> Hi,
>> I was training with "Retrieving multiple sequences from a database"
>> use Bio::DB::Query::GenBank;
>>
>> $query = "Arabidopsis[ORGN] AND topoisomerase[TITL] and  
>> 0:3000[SLEN]";
>> $query_obj = Bio::DB::Query::GenBank->new(-db    => 'nucleotide', - 
>> query => $query )
>> but I'm stuck in the print step. This is what I wrote:
>>
>> #!/bin/perl -w
>>
>> use Bio::DB::Query::GenBank;
>> use Bio::Seq;
>> use Bio::SeqIO;
>>
>> $query = "Arabidopsis[ORGN] AND topoisomerase[TITL]";
>> $query_obj = Bio::DB::Query::GenBank->new(-db =>'nucleotide', - 
>> query => $query);
>>
>> #$seqio_obj = Bio::SeqIO->new(-file =>'>Arab46.gb', -format  
>> =>'genbank');
>> #$seqio_obj->write_seq($query_obj);
>>
>> print $query_obj->accession_number,"\n";
>>
>> I've tried to print it to a file with seqio and to print it through  
>> terminal with the following:
>> print $query_obj->accession_number,"\n";
>> print $query_obj->seq,"\n";
>> print $query_obj->division,"\n";
>>
>> But the error message I get when I try to print it to a file is:
>> --------------------- WARNING ---------------------
>> MSG:  Bio::DB::Query::GenBank=HASH(0x965010) is not a SeqI  
>> compliant module. Attempting to dump, but may fail!
>> ---------------------------------------------------
>> Can't locate object method "seq" via package  
>> "Bio::DB::Query::GenBank" at /Library/Perl/5.8.8/Bio/SeqIO/ 
>> genbank.pm line 760.
>>
>> And when I try to print it normally:
>> Can't locate object method "seq" via package  
>> "Bio::DB::Query::GenBank" at bp_seq4.pl line 15.
>>
>>
>> I went to cpan to check for this module
>> Bio::DB::Query::GenBank
>> I install Bioperl again the one that was following  
>> "Bio::DB::Query::GenBank".
>> But no change in the message error.
>>
>> could you help me?
>>
>> Thank you very much.
>
> Brian O.
> --
> Brian Osborne, PhD
> BioTeam: http://bioteam.net
> email: briano at bioteam.net
> mobile: 978-317-3101
>



From adlai at refenestration.com  Fri Feb 24 14:24:18 2012
From: adlai at refenestration.com (Adlai Burman)
Date: Fri, 24 Feb 2012 20:24:18 +0100
Subject: [Bioperl-l] Navigating a genbank file
In-Reply-To: <F7FE7024-F054-4617-A3A5-F02DB2098DE8@gmail.com>
References: <3F92E96A-2A69-4F6F-AA92-AAA7A2122BD8@refenestration.com>
	<F7FE7024-F054-4617-A3A5-F02DB2098DE8@gmail.com>
Message-ID: <D4EAC040-8A94-4DA5-AF25-7F71DA93F951@refenestration.com>

Thanks, Jason.
Your code looks elegant and should do the trick. Unfortunately it is a little over my quasi (perl) newbie head. I'm sure I will learn a lot from trying to figure out how to implement it. Who would have guessed that grabbing intergenic regions could be such a nosebleed (for perl flat-foots that is)?
In the meantime if you, or anybody else, can help me out with this in a more neophyte digestible way it would be excruciatingly appreciated.

Regards, 
Adlai
On Feb 24, 2012, at 7:49 AM, Jason Stajich wrote:

> You just need a $last_CDS variable.
> Here's code that does this for genes retrieved from Bio::DB::SeqFeature but the concept is the same.
> 
> https://github.com/hyphaltip/genome-scripts/blob/master/seqfeature/get_intergenic_seq.pl
> 
> On Feb 23, 2012, at 4:43 PM, Adlai Burman wrote:
> 
>> I am struggling with Bioperl to do something which I know is simple (I stumbled on it before, but it was just by dumb luck and I forgot how it is done). Basically what I am trying to do is, given a target gene symbol extract the intergenic region between that CDS and the next one 3'. One ugly way I could do this would be:
>> (1) Make an array of all of the CDSs in each gb file
>> (2) Make a second run through the file using either the symbol prior or post the target symbol (depending on the strand of the target symbol).
>> 
>> This is, of course, cumbersome and unnecessary but I can't figure out how it should be done.
>> Here is a skeletal version of what I understand about getting feature info with bioperl.
>> Can anyone help me figure out how to access the CDS features on either side?
>> Please?
>> Thank you,
>> 
>> Adlai
>> 
>> #!/usr/bin/perl                                                                                                     
>> use strict;
>> use warnings;
>> use IO::String;
>> use Bio::Perl;
>> use Bio::SeqIO;
>> use IO::String;
>> 
>> 
>> my $target_sym = shift;
>> my $file = "../Dropbox/local_gb/*";
>> 
>> my $seqio = Bio::SeqIO-> new(
>>                             -file     => $file,
>>                             -format => 'GenBank',
>>    );
>> 
>> my $seq = $seqio->next_seq;
>> for my $feats ($seq->get_SeqFeatures){
>> if ($feats->primary_tag eq "CDS"){
>>  my $start = $feats->location->start;
>> my $end = $feats->location->end;
>> my $strand = $feats->strand;
>> if ($feats->has_tag('gene')) {
>>     for my $val ($feats->get_tag_values('gene')){
>> if ($val eq $target_sym){
>> print $start."\n";
>> print "$val\n";
>>  }
>> 
>> }
>> }
>> }
>> }
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 



From adlai at refenestration.com  Fri Feb 24 15:43:40 2012
From: adlai at refenestration.com (Adlai Burman)
Date: Fri, 24 Feb 2012 21:43:40 +0100
Subject: [Bioperl-l] Odd problem with get_tag_values
Message-ID: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>

I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:

#!/usr/bin/perl                                                                                                     
use strict;
use warnings;
use IO::String;
use Bio::Perl;
use Bio::SeqIO;
use IO::String;

my @files = </Users/adlai/Dropbox/atrsh/*>;
foreach my $file(@files){


my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
.
.
.
#do nifty stuff
}

For some files this approach works just fine.
For others the script dies immediately with the error message:

------------- EXCEPTION -------------
MSG: asking for tag value that does not exist gene
STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
STACK toplevel tosend.pl:16
-------------------------------------

The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
Does anyone know why this is a problem and what can be done to circumvent it?

Thanks,
Adlai



From jason.stajich at gmail.com  Fri Feb 24 16:21:07 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Fri, 24 Feb 2012 13:21:07 -0800
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
Message-ID: <D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>

not all CDS will be annotated with a 'gene' tag, this is due to variation in how annotation is done and that there is not a requirement that there be a gene tag for all CDS features.

You can protect your query - we often do this when dealing with data from the wild by testing for has_tag first.

my %strands;
for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
 if( $cds->has_tag('gene') ) {
	my ($gene) = $cds->get_tag_values('gene'); # get the 1st one, this returns a list
	$strands{$gene} = $cds->strand; 
 } else { # look in alternative places for a name, e.g. locus, 
  ...
 }
}

An alternative is to loop through your list of tags in order of preference

my %strands;
for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
 for my $tag ( qw(gene locus name product accession note) ) {  
   if( $cds->has_tag($tag) ) {
	my ($name) = $cds->get_tag_values($tag); # get the 1st one, this returns a list
	$strands{$name} = $cds->strand;
        $seen = 1;
        last;
 }
 if( ! $seen ) { 
	warn("not tag found for feature at ", $cds->location->to_FTstring, "\n");
 }
}

On Feb 24, 2012, at 12:43 PM, Adlai Burman wrote:

> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
> 
> #!/usr/bin/perl                                                                                                     
> use strict;
> use warnings;
> use IO::String;
> use Bio::Perl;
> use Bio::SeqIO;
> use IO::String;
> 
> my @files = </Users/adlai/Dropbox/atrsh/*>;
> foreach my $file(@files){
> 
> 
> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
> .
> .
> .
> #do nifty stuff
> }
> 
> For some files this approach works just fine.
> For others the script dies immediately with the error message:
> 
> ------------- EXCEPTION -------------
> MSG: asking for tag value that does not exist gene
> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
> STACK toplevel tosend.pl:16
> -------------------------------------
> 
> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
> Does anyone know why this is a problem and what can be done to circumvent it?
> 
> Thanks,
> Adlai
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org



From adlai at refenestration.com  Fri Feb 24 16:22:09 2012
From: adlai at refenestration.com (Adlai Burman)
Date: Fri, 24 Feb 2012 22:22:09 +0100
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <1840B7A6-D949-44CA-8CDE-1313F06CD0CD@verizon.net>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
	<1840B7A6-D949-44CA-8CDE-1313F06CD0CD@verizon.net>
Message-ID: <68A216EA-2175-45C1-98CE-E4F949C565FC@refenestration.com>

Hey, Brian.
No, I am not absolutely sure about that but I am checking now. In the process of checking this I found out that one of the files that successfully parsed (NC_015139) had NO Features tags (other that "source"). No "CDS", no "gene" etc...
ok, now I am sure. I checked one record that didn't parse and and all the CDS's have "gene" tags. Go figure. 
Regarding your suggestion: I agree, checking for the existence of a tag is an important thing to do and everything parses great in a script I wrote which uses that. This, however, might be problematic for two reasons:
(1) The fact that the aforementioned featureless record parses and one of the crashers does have a full complement of properly placed "genes" suggest that this might not address the problem, and
(2) On a more humbling note, I don't know how to embed such a check into the one line hash generator, my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; , which wold be perfect for what I am coding now.

Thanks for your response,
Adlai
On Feb 24, 2012, at 10:03 PM, Brian Osborne wrote:

> Adlai,
> 
> You are absolutely sure that every single CDS feature has a "gene" tag inside it?
> 
> If this is not the case then you have to use the "if ($cds_feature->has_tag("gene")) ?" type of logic.
> 
> Brian O.
> 
> On Feb 24, 2012, at 3:43 PM, Adlai Burman wrote:
> 
>> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
>> 
>> #!/usr/bin/perl                                                                                                     
>> use strict;
>> use warnings;
>> use IO::String;
>> use Bio::Perl;
>> use Bio::SeqIO;
>> use IO::String;
>> 
>> my @files = </Users/adlai/Dropbox/atrsh/*>;
>> foreach my $file(@files){
>> 
>> 
>> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
>> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
>> .
>> .
>> .
>> #do nifty stuff
>> }
>> 
>> For some files this approach works just fine.
>> For others the script dies immediately with the error message:
>> 
>> ------------- EXCEPTION -------------
>> MSG: asking for tag value that does not exist gene
>> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>> STACK toplevel tosend.pl:16
>> -------------------------------------
>> 
>> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
>> Does anyone know why this is a problem and what can be done to circumvent it?
>> 
>> Thanks,
>> Adlai
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From adlai at refenestration.com  Fri Feb 24 16:27:19 2012
From: adlai at refenestration.com (Adlai Burman)
Date: Fri, 24 Feb 2012 22:27:19 +0100
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <1840B7A6-D949-44CA-8CDE-1313F06CD0CD@verizon.net>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
	<1840B7A6-D949-44CA-8CDE-1313F06CD0CD@verizon.net>
Message-ID: <E4BA5CAE-1086-4360-9873-B58B173C82F4@refenestration.com>

P.S. In case anyone is interested (and I hope they are), here is an example of one record that fails here and one that doesn't:

NC_015820 parses and NC_012927 fails. Unlike what I said earlier, some of the good ones have exons and some of the crashers don't.

On Feb 24, 2012, at 10:03 PM, Brian Osborne wrote:

> Adlai,
> 
> You are absolutely sure that every single CDS feature has a "gene" tag inside it?
> 
> If this is not the case then you have to use the "if ($cds_feature->has_tag("gene")) ?" type of logic.
> 
> Brian O.
> 
> On Feb 24, 2012, at 3:43 PM, Adlai Burman wrote:
> 
>> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
>> 
>> #!/usr/bin/perl                                                                                                     
>> use strict;
>> use warnings;
>> use IO::String;
>> use Bio::Perl;
>> use Bio::SeqIO;
>> use IO::String;
>> 
>> my @files = </Users/adlai/Dropbox/atrsh/*>;
>> foreach my $file(@files){
>> 
>> 
>> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
>> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
>> .
>> .
>> .
>> #do nifty stuff
>> }
>> 
>> For some files this approach works just fine.
>> For others the script dies immediately with the error message:
>> 
>> ------------- EXCEPTION -------------
>> MSG: asking for tag value that does not exist gene
>> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>> STACK toplevel tosend.pl:16
>> -------------------------------------
>> 
>> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
>> Does anyone know why this is a problem and what can be done to circumvent it?
>> 
>> Thanks,
>> Adlai
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From cjfields at illinois.edu  Fri Feb 24 16:28:52 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 24 Feb 2012 21:28:52 +0000
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
Message-ID: <63416EB7-8C06-4904-8E36-84D6A655B6CD@illinois.edu>

On 02/24/2012 02:43 PM, Adlai Burman wrote:
> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
> 
> #!/usr/bin/perl
> use strict;
> use warnings;
> use IO::String;
> use Bio::Perl;
> use Bio::SeqIO;
> use IO::String;
> 
> my @files =</Users/adlai/Dropbox/atrsh/*>;
> foreach my $file(@files){
> 
> 
> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file =>  $file)->next_seq->get_SeqFeatures;
> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit.
> .
> .
> .
> #do nifty stuff
> }
> 
> For some files this approach works just fine.
> For others the script dies immediately with the error message:
> 
> ------------- EXCEPTION -------------
> MSG: asking for tag value that does not exist gene
> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
> STACK toplevel tosend.pl:16
> -------------------------------------

There are two possibilities:

1) There is at least one feature w/o a 'gene' tag for those files.
2) This is a bug.

Either way it's hard to tell b/c we don't have the example data you are checking.

I would note this is *not* the way to screen for features with specific tags, though, at least with the current API.  You have to actually check for the presence of the tag first with has_tag('gene').  You could do that within the grep:

{ $_->primary_tag eq 'CDS' && $_->has_tag('gene') }

> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
> Does anyone know why this is a problem and what can be done to circumvent it?
> 
> Thanks,
> Adlai

chris



From adlai at refenestration.com  Fri Feb 24 16:33:31 2012
From: adlai at refenestration.com (Adlai Burman)
Date: Fri, 24 Feb 2012 22:33:31 +0100
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
	<D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>
Message-ID: <C1EE8D29-1480-4DF0-BCBE-400F202A6210@refenestration.com>

Thanks so much, Jason.
I will give that a try in after I get a few hours of much needed sleep :-)


On Feb 24, 2012, at 10:21 PM, Jason Stajich wrote:

> not all CDS will be annotated with a 'gene' tag, this is due to variation in how annotation is done and that there is not a requirement that there be a gene tag for all CDS features.
> 
> You can protect your query - we often do this when dealing with data from the wild by testing for has_tag first.
> 
> my %strands;
> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
> if( $cds->has_tag('gene') ) {
> 	my ($gene) = $cds->get_tag_values('gene'); # get the 1st one, this returns a list
> 	$strands{$gene} = $cds->strand; 
> } else { # look in alternative places for a name, e.g. locus, 
>  ...
> }
> }
> 
> An alternative is to loop through your list of tags in order of preference
> 
> my %strands;
> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
> for my $tag ( qw(gene locus name product accession note) ) {  
>   if( $cds->has_tag($tag) ) {
> 	my ($name) = $cds->get_tag_values($tag); # get the 1st one, this returns a list
> 	$strands{$name} = $cds->strand;
>        $seen = 1;
>        last;
> }
> if( ! $seen ) { 
> 	warn("not tag found for feature at ", $cds->location->to_FTstring, "\n");
> }
> }
> 
> On Feb 24, 2012, at 12:43 PM, Adlai Burman wrote:
> 
>> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
>> 
>> #!/usr/bin/perl                                                                                                     
>> use strict;
>> use warnings;
>> use IO::String;
>> use Bio::Perl;
>> use Bio::SeqIO;
>> use IO::String;
>> 
>> my @files = </Users/adlai/Dropbox/atrsh/*>;
>> foreach my $file(@files){
>> 
>> 
>> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
>> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
>> .
>> .
>> .
>> #do nifty stuff
>> }
>> 
>> For some files this approach works just fine.
>> For others the script dies immediately with the error message:
>> 
>> ------------- EXCEPTION -------------
>> MSG: asking for tag value that does not exist gene
>> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>> STACK toplevel tosend.pl:16
>> -------------------------------------
>> 
>> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
>> Does anyone know why this is a problem and what can be done to circumvent it?
>> 
>> Thanks,
>> Adlai
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
> 



From cjfields at illinois.edu  Fri Feb 24 16:46:55 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 24 Feb 2012 21:46:55 +0000
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <C1EE8D29-1480-4DF0-BCBE-400F202A6210@refenestration.com>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
	<D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>
	<C1EE8D29-1480-4DF0-BCBE-400F202A6210@refenestration.com>
Message-ID: <A97AF018-3476-4E42-8190-A2E8AD7B782A@illinois.edu>

Using has_tag('gene') as a pre-screen works for me for both example seqs.

chris

On Feb 24, 2012, at 3:33 PM, Adlai Burman wrote:

> Thanks so much, Jason.
> I will give that a try in after I get a few hours of much needed sleep :-)
> 
> 
> On Feb 24, 2012, at 10:21 PM, Jason Stajich wrote:
> 
>> not all CDS will be annotated with a 'gene' tag, this is due to variation in how annotation is done and that there is not a requirement that there be a gene tag for all CDS features.
>> 
>> You can protect your query - we often do this when dealing with data from the wild by testing for has_tag first.
>> 
>> my %strands;
>> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
>> if( $cds->has_tag('gene') ) {
>> 	my ($gene) = $cds->get_tag_values('gene'); # get the 1st one, this returns a list
>> 	$strands{$gene} = $cds->strand; 
>> } else { # look in alternative places for a name, e.g. locus, 
>> ...
>> }
>> }
>> 
>> An alternative is to loop through your list of tags in order of preference
>> 
>> my %strands;
>> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
>> for my $tag ( qw(gene locus name product accession note) ) {  
>>  if( $cds->has_tag($tag) ) {
>> 	my ($name) = $cds->get_tag_values($tag); # get the 1st one, this returns a list
>> 	$strands{$name} = $cds->strand;
>>       $seen = 1;
>>       last;
>> }
>> if( ! $seen ) { 
>> 	warn("not tag found for feature at ", $cds->location->to_FTstring, "\n");
>> }
>> }
>> 
>> On Feb 24, 2012, at 12:43 PM, Adlai Burman wrote:
>> 
>>> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
>>> 
>>> #!/usr/bin/perl                                                                                                     
>>> use strict;
>>> use warnings;
>>> use IO::String;
>>> use Bio::Perl;
>>> use Bio::SeqIO;
>>> use IO::String;
>>> 
>>> my @files = </Users/adlai/Dropbox/atrsh/*>;
>>> foreach my $file(@files){
>>> 
>>> 
>>> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
>>> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
>>> .
>>> .
>>> .
>>> #do nifty stuff
>>> }
>>> 
>>> For some files this approach works just fine.
>>> For others the script dies immediately with the error message:
>>> 
>>> ------------- EXCEPTION -------------
>>> MSG: asking for tag value that does not exist gene
>>> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>>> STACK toplevel tosend.pl:16
>>> -------------------------------------
>>> 
>>> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
>>> Does anyone know why this is a problem and what can be done to circumvent it?
>>> 
>>> Thanks,
>>> Adlai
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>> 
>> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From adlai at refenestration.com  Fri Feb 24 16:55:57 2012
From: adlai at refenestration.com (Adlai Burman)
Date: Fri, 24 Feb 2012 22:55:57 +0100
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
	<D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>
Message-ID: <20C8CE5C-FBA5-4333-8A85-86804595DB3C@refenestration.com>

Jason,
Your first solution, indeed, did the trick (though I'm not sure why). There was no need to for checking "else." I'm not sure why some records with a full set of "gene" tags would not parse without the check, but everything parsed with it.

Brian, you were right.

Thanks again,

Adlai
On Feb 24, 2012, at 10:21 PM, Jason Stajich wrote:

> not all CDS will be annotated with a 'gene' tag, this is due to variation in how annotation is done and that there is not a requirement that there be a gene tag for all CDS features.
> 
> You can protect your query - we often do this when dealing with data from the wild by testing for has_tag first.
> 
> my %strands;
> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
> if( $cds->has_tag('gene') ) {
> 	my ($gene) = $cds->get_tag_values('gene'); # get the 1st one, this returns a list
> 	$strands{$gene} = $cds->strand; 
> } else { # look in alternative places for a name, e.g. locus, 
>  ...
> }
> }
> 
> An alternative is to loop through your list of tags in order of preference
> 
> my %strands;
> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
> for my $tag ( qw(gene locus name product accession note) ) {  
>   if( $cds->has_tag($tag) ) {
> 	my ($name) = $cds->get_tag_values($tag); # get the 1st one, this returns a list
> 	$strands{$name} = $cds->strand;
>        $seen = 1;
>        last;
> }
> if( ! $seen ) { 
> 	warn("not tag found for feature at ", $cds->location->to_FTstring, "\n");
> }
> }
> 
> On Feb 24, 2012, at 12:43 PM, Adlai Burman wrote:
> 
>> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
>> 
>> #!/usr/bin/perl                                                                                                     
>> use strict;
>> use warnings;
>> use IO::String;
>> use Bio::Perl;
>> use Bio::SeqIO;
>> use IO::String;
>> 
>> my @files = </Users/adlai/Dropbox/atrsh/*>;
>> foreach my $file(@files){
>> 
>> 
>> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
>> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
>> .
>> .
>> .
>> #do nifty stuff
>> }
>> 
>> For some files this approach works just fine.
>> For others the script dies immediately with the error message:
>> 
>> ------------- EXCEPTION -------------
>> MSG: asking for tag value that does not exist gene
>> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>> STACK toplevel tosend.pl:16
>> -------------------------------------
>> 
>> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
>> Does anyone know why this is a problem and what can be done to circumvent it?
>> 
>> Thanks,
>> Adlai
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
> 



From adlai at refenestration.com  Fri Feb 24 16:57:24 2012
From: adlai at refenestration.com (Adlai Burman)
Date: Fri, 24 Feb 2012 22:57:24 +0100
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <A97AF018-3476-4E42-8190-A2E8AD7B782A@illinois.edu>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
	<D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>
	<C1EE8D29-1480-4DF0-BCBE-400F202A6210@refenestration.com>
	<A97AF018-3476-4E42-8190-A2E8AD7B782A@illinois.edu>
Message-ID: <1230FA01-6821-4C33-9C15-14669E5DCEFA@refenestration.com>


On Feb 24, 2012, at 10:46 PM, Fields, Christopher J wrote:

> Using has_tag('gene') as a pre-screen works for me for both example seqs.
> 

Me too :-)

Dobrou noc and cheers,

Adlai
> chris
> 
> On Feb 24, 2012, at 3:33 PM, Adlai Burman wrote:
> 
>> Thanks so much, Jason.
>> I will give that a try in after I get a few hours of much needed sleep :-)
>> 
>> 
>> On Feb 24, 2012, at 10:21 PM, Jason Stajich wrote:
>> 
>>> not all CDS will be annotated with a 'gene' tag, this is due to variation in how annotation is done and that there is not a requirement that there be a gene tag for all CDS features.
>>> 
>>> You can protect your query - we often do this when dealing with data from the wild by testing for has_tag first.
>>> 
>>> my %strands;
>>> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
>>> if( $cds->has_tag('gene') ) {
>>> 	my ($gene) = $cds->get_tag_values('gene'); # get the 1st one, this returns a list
>>> 	$strands{$gene} = $cds->strand; 
>>> } else { # look in alternative places for a name, e.g. locus, 
>>> ...
>>> }
>>> }
>>> 
>>> An alternative is to loop through your list of tags in order of preference
>>> 
>>> my %strands;
>>> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
>>> for my $tag ( qw(gene locus name product accession note) ) {  
>>> if( $cds->has_tag($tag) ) {
>>> 	my ($name) = $cds->get_tag_values($tag); # get the 1st one, this returns a list
>>> 	$strands{$name} = $cds->strand;
>>>      $seen = 1;
>>>      last;
>>> }
>>> if( ! $seen ) { 
>>> 	warn("not tag found for feature at ", $cds->location->to_FTstring, "\n");
>>> }
>>> }
>>> 
>>> On Feb 24, 2012, at 12:43 PM, Adlai Burman wrote:
>>> 
>>>> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
>>>> 
>>>> #!/usr/bin/perl                                                                                                     
>>>> use strict;
>>>> use warnings;
>>>> use IO::String;
>>>> use Bio::Perl;
>>>> use Bio::SeqIO;
>>>> use IO::String;
>>>> 
>>>> my @files = </Users/adlai/Dropbox/atrsh/*>;
>>>> foreach my $file(@files){
>>>> 
>>>> 
>>>> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
>>>> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
>>>> .
>>>> .
>>>> .
>>>> #do nifty stuff
>>>> }
>>>> 
>>>> For some files this approach works just fine.
>>>> For others the script dies immediately with the error message:
>>>> 
>>>> ------------- EXCEPTION -------------
>>>> MSG: asking for tag value that does not exist gene
>>>> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>>>> STACK toplevel tosend.pl:16
>>>> -------------------------------------
>>>> 
>>>> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
>>>> Does anyone know why this is a problem and what can be done to circumvent it?
>>>> 
>>>> Thanks,
>>>> Adlai
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> Jason Stajich
>>> jason.stajich at gmail.com
>>> jason at bioperl.org
>>> 
>>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 



From bosborne11 at verizon.net  Fri Feb 24 16:03:49 2012
From: bosborne11 at verizon.net (Brian Osborne)
Date: Fri, 24 Feb 2012 16:03:49 -0500
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
Message-ID: <1840B7A6-D949-44CA-8CDE-1313F06CD0CD@verizon.net>

Adlai,

You are absolutely sure that every single CDS feature has a "gene" tag inside it?

If this is not the case then you have to use the "if ($cds_feature->has_tag("gene")) ?" type of logic.

Brian O.

On Feb 24, 2012, at 3:43 PM, Adlai Burman wrote:

> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
> 
> #!/usr/bin/perl                                                                                                     
> use strict;
> use warnings;
> use IO::String;
> use Bio::Perl;
> use Bio::SeqIO;
> use IO::String;
> 
> my @files = </Users/adlai/Dropbox/atrsh/*>;
> foreach my $file(@files){
> 
> 
> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
> .
> .
> .
> #do nifty stuff
> }
> 
> For some files this approach works just fine.
> For others the script dies immediately with the error message:
> 
> ------------- EXCEPTION -------------
> MSG: asking for tag value that does not exist gene
> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
> STACK toplevel tosend.pl:16
> -------------------------------------
> 
> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
> Does anyone know why this is a problem and what can be done to circumvent it?
> 
> Thanks,
> Adlai
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Fri Feb 24 17:38:07 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 24 Feb 2012 22:38:07 +0000
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <20C8CE5C-FBA5-4333-8A85-86804595DB3C@refenestration.com>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
	<D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>
	<20C8CE5C-FBA5-4333-8A85-86804595DB3C@refenestration.com>
Message-ID: <665C4737-93DA-4466-986B-380D8F266A58@illinois.edu>

There is possibly a slight disconnect here.  The primary tag you are looking for is 'CDS'.  Here is an example of both the primary tag for 'CDS' and 'gene' from NC_012927:

     gene            complement(join(91716..92516,69640..69753))
                     /locus_tag="BaolC_p001"
                     /trans_splicing
                     /db_xref="GeneID:8223103"
     CDS             complement(join(91716..91744,92285..92516,69640..69753))
                     /locus_tag="BaolC_p001"
                     /trans_splicing
                     /codon_start=1
                     /transl_table=11
                     /product="ribosomal protein S12"
                     /protein_id="YP_003029720.1"
                     /db_xref="GI:253729537"
                     /db_xref="GeneID:8223103"
                     /translation="MPTVKQLIRNARQPIRNARKSAALKGCPQRRGTCARVYTINPKK
                     PNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYRIIRGTL
                     DAVAVKNRQQGRSKYGVKKPKK"

This 'CDS' example has no 'gene' regular tag, in fact none that I looked at did.  But there is another feature (above it) that does have the *primary* tag 'gene' and same locus_tag and dbxref GeneID (it does have tags such as 'locus_tag', 'trans_splicing', etc).  Is that what you mean?

The way that BioPerl deals with this is to return two different independent features, one with the 'CDS' primary tag and one with the 'gene' primary tag.  Past attempts to somehow combine these (and then disambiguate them again later if needed for output) can be problematic, or at least they once were.

chris


On Feb 24, 2012, at 3:55 PM, Adlai Burman wrote:

> Jason,
> Your first solution, indeed, did the trick (though I'm not sure why). There was no need to for checking "else." I'm not sure why some records with a full set of "gene" tags would not parse without the check, but everything parsed with it.
> 
> Brian, you were right.
> 
> Thanks again,
> 
> Adlai
> On Feb 24, 2012, at 10:21 PM, Jason Stajich wrote:
> 
>> not all CDS will be annotated with a 'gene' tag, this is due to variation in how annotation is done and that there is not a requirement that there be a gene tag for all CDS features.
>> 
>> You can protect your query - we often do this when dealing with data from the wild by testing for has_tag first.
>> 
>> my %strands;
>> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
>> if( $cds->has_tag('gene') ) {
>> 	my ($gene) = $cds->get_tag_values('gene'); # get the 1st one, this returns a list
>> 	$strands{$gene} = $cds->strand; 
>> } else { # look in alternative places for a name, e.g. locus, 
>> ...
>> }
>> }
>> 
>> An alternative is to loop through your list of tags in order of preference
>> 
>> my %strands;
>> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
>> for my $tag ( qw(gene locus name product accession note) ) {  
>>  if( $cds->has_tag($tag) ) {
>> 	my ($name) = $cds->get_tag_values($tag); # get the 1st one, this returns a list
>> 	$strands{$name} = $cds->strand;
>>       $seen = 1;
>>       last;
>> }
>> if( ! $seen ) { 
>> 	warn("not tag found for feature at ", $cds->location->to_FTstring, "\n");
>> }
>> }
>> 
>> On Feb 24, 2012, at 12:43 PM, Adlai Burman wrote:
>> 
>>> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
>>> 
>>> #!/usr/bin/perl                                                                                                     
>>> use strict;
>>> use warnings;
>>> use IO::String;
>>> use Bio::Perl;
>>> use Bio::SeqIO;
>>> use IO::String;
>>> 
>>> my @files = </Users/adlai/Dropbox/atrsh/*>;
>>> foreach my $file(@files){
>>> 
>>> 
>>> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
>>> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
>>> .
>>> .
>>> .
>>> #do nifty stuff
>>> }
>>> 
>>> For some files this approach works just fine.
>>> For others the script dies immediately with the error message:
>>> 
>>> ------------- EXCEPTION -------------
>>> MSG: asking for tag value that does not exist gene
>>> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>>> STACK toplevel tosend.pl:16
>>> -------------------------------------
>>> 
>>> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
>>> Does anyone know why this is a problem and what can be done to circumvent it?
>>> 
>>> Thanks,
>>> Adlai
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>> 
>> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From adlai at refenestration.com  Fri Feb 24 18:07:37 2012
From: adlai at refenestration.com (Adlai Burman)
Date: Sat, 25 Feb 2012 00:07:37 +0100
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <665C4737-93DA-4466-986B-380D8F266A58@illinois.edu>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
	<D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>
	<20C8CE5C-FBA5-4333-8A85-86804595DB3C@refenestration.com>
	<665C4737-93DA-4466-986B-380D8F266A58@illinois.edu>
Message-ID: <758BCF25-5C17-449E-B8F0-3E3DFDF8784D@refenestration.com>

I apologize, Chris. That was a terrible example I sent. I accidentally sent the only record for which there actually are no regular 'gene' tags. Other gb records that failed before Jason's tag check include NC_005086 and they all have regular 'gene' tags. I should have referenced that one.
I appreciate your checking into that and sorry about the red herring. Boy is my face blushed.

A.


On Feb 24, 2012, at 11:38 PM, Fields, Christopher J wrote:

> There is possibly a slight disconnect here.  The primary tag you are looking for is 'CDS'.  Here is an example of both the primary tag for 'CDS' and 'gene' from NC_012927:
> 
>     gene            complement(join(91716..92516,69640..69753))
>                     /locus_tag="BaolC_p001"
>                     /trans_splicing
>                     /db_xref="GeneID:8223103"
>     CDS             complement(join(91716..91744,92285..92516,69640..69753))
>                     /locus_tag="BaolC_p001"
>                     /trans_splicing
>                     /codon_start=1
>                     /transl_table=11
>                     /product="ribosomal protein S12"
>                     /protein_id="YP_003029720.1"
>                     /db_xref="GI:253729537"
>                     /db_xref="GeneID:8223103"
>                     /translation="MPTVKQLIRNARQPIRNARKSAALKGCPQRRGTCARVYTINPKK
>                     PNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYRIIRGTL
>                     DAVAVKNRQQGRSKYGVKKPKK"
> 
> This 'CDS' example has no 'gene' regular tag, in fact none that I looked at did.  But there is another feature (above it) that does have the *primary* tag 'gene' and same locus_tag and dbxref GeneID (it does have tags such as 'locus_tag', 'trans_splicing', etc).  Is that what you mean?
> 
> The way that BioPerl deals with this is to return two different independent features, one with the 'CDS' primary tag and one with the 'gene' primary tag.  Past attempts to somehow combine these (and then disambiguate them again later if needed for output) can be problematic, or at least they once were.
> 
> chris
> 
> 
> On Feb 24, 2012, at 3:55 PM, Adlai Burman wrote:
> 
>> Jason,
>> Your first solution, indeed, did the trick (though I'm not sure why). There was no need to for checking "else." I'm not sure why some records with a full set of "gene" tags would not parse without the check, but everything parsed with it.
>> 
>> Brian, you were right.
>> 
>> Thanks again,
>> 
>> Adlai
>> On Feb 24, 2012, at 10:21 PM, Jason Stajich wrote:
>> 
>>> not all CDS will be annotated with a 'gene' tag, this is due to variation in how annotation is done and that there is not a requirement that there be a gene tag for all CDS features.
>>> 
>>> You can protect your query - we often do this when dealing with data from the wild by testing for has_tag first.
>>> 
>>> my %strands;
>>> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
>>> if( $cds->has_tag('gene') ) {
>>> 	my ($gene) = $cds->get_tag_values('gene'); # get the 1st one, this returns a list
>>> 	$strands{$gene} = $cds->strand; 
>>> } else { # look in alternative places for a name, e.g. locus, 
>>> ...
>>> }
>>> }
>>> 
>>> An alternative is to loop through your list of tags in order of preference
>>> 
>>> my %strands;
>>> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
>>> for my $tag ( qw(gene locus name product accession note) ) {  
>>> if( $cds->has_tag($tag) ) {
>>> 	my ($name) = $cds->get_tag_values($tag); # get the 1st one, this returns a list
>>> 	$strands{$name} = $cds->strand;
>>>      $seen = 1;
>>>      last;
>>> }
>>> if( ! $seen ) { 
>>> 	warn("not tag found for feature at ", $cds->location->to_FTstring, "\n");
>>> }
>>> }
>>> 
>>> On Feb 24, 2012, at 12:43 PM, Adlai Burman wrote:
>>> 
>>>> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
>>>> 
>>>> #!/usr/bin/perl                                                                                                     
>>>> use strict;
>>>> use warnings;
>>>> use IO::String;
>>>> use Bio::Perl;
>>>> use Bio::SeqIO;
>>>> use IO::String;
>>>> 
>>>> my @files = </Users/adlai/Dropbox/atrsh/*>;
>>>> foreach my $file(@files){
>>>> 
>>>> 
>>>> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
>>>> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
>>>> .
>>>> .
>>>> .
>>>> #do nifty stuff
>>>> }
>>>> 
>>>> For some files this approach works just fine.
>>>> For others the script dies immediately with the error message:
>>>> 
>>>> ------------- EXCEPTION -------------
>>>> MSG: asking for tag value that does not exist gene
>>>> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>>>> STACK toplevel tosend.pl:16
>>>> -------------------------------------
>>>> 
>>>> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
>>>> Does anyone know why this is a problem and what can be done to circumvent it?
>>>> 
>>>> Thanks,
>>>> Adlai
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> Jason Stajich
>>> jason.stajich at gmail.com
>>> jason at bioperl.org
>>> 
>>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 



From cjfields at illinois.edu  Fri Feb 24 18:28:39 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 24 Feb 2012 23:28:39 +0000
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <758BCF25-5C17-449E-B8F0-3E3DFDF8784D@refenestration.com>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
	<D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>
	<20C8CE5C-FBA5-4333-8A85-86804595DB3C@refenestration.com>
	<665C4737-93DA-4466-986B-380D8F266A58@illinois.edu>,
	<758BCF25-5C17-449E-B8F0-3E3DFDF8784D@refenestration.com>
Message-ID: <0F3F54D9-84BF-4136-8D23-52A979351038@illinois.edu>

No problem. This highlights the #1 problem with genbank files (and the reasons we keep things as simple as possible), namely lack of consistency.  Not a problem with NCBI per se, but a problem nonetheless. 

Chris

On Feb 24, 2012, at 5:07 PM, "Adlai Burman" <adlai at refenestration.com> wrote:

> I apologize, Chris. That was a terrible example I sent. I accidentally sent the only record for which there actually are no regular 'gene' tags. Other gb records that failed before Jason's tag check include NC_005086 and they all have regular 'gene' tags. I should have referenced that one.
> I appreciate your checking into that and sorry about the red herring. Boy is my face blushed.
> 
> A.
> 
> 
> On Feb 24, 2012, at 11:38 PM, Fields, Christopher J wrote:
> 
>> There is possibly a slight disconnect here.  The primary tag you are looking for is 'CDS'.  Here is an example of both the primary tag for 'CDS' and 'gene' from NC_012927:
>> 
>>    gene            complement(join(91716..92516,69640..69753))
>>                    /locus_tag="BaolC_p001"
>>                    /trans_splicing
>>                    /db_xref="GeneID:8223103"
>>    CDS             complement(join(91716..91744,92285..92516,69640..69753))
>>                    /locus_tag="BaolC_p001"
>>                    /trans_splicing
>>                    /codon_start=1
>>                    /transl_table=11
>>                    /product="ribosomal protein S12"
>>                    /protein_id="YP_003029720.1"
>>                    /db_xref="GI:253729537"
>>                    /db_xref="GeneID:8223103"
>>                    /translation="MPTVKQLIRNARQPIRNARKSAALKGCPQRRGTCARVYTINPKK
>>                    PNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYRIIRGTL
>>                    DAVAVKNRQQGRSKYGVKKPKK"
>> 
>> This 'CDS' example has no 'gene' regular tag, in fact none that I looked at did.  But there is another feature (above it) that does have the *primary* tag 'gene' and same locus_tag and dbxref GeneID (it does have tags such as 'locus_tag', 'trans_splicing', etc).  Is that what you mean?
>> 
>> The way that BioPerl deals with this is to return two different independent features, one with the 'CDS' primary tag and one with the 'gene' primary tag.  Past attempts to somehow combine these (and then disambiguate them again later if needed for output) can be problematic, or at least they once were.
>> 
>> chris
>> 
>> 
>> On Feb 24, 2012, at 3:55 PM, Adlai Burman wrote:
>> 
>>> Jason,
>>> Your first solution, indeed, did the trick (though I'm not sure why). There was no need to for checking "else." I'm not sure why some records with a full set of "gene" tags would not parse without the check, but everything parsed with it.
>>> 
>>> Brian, you were right.
>>> 
>>> Thanks again,
>>> 
>>> Adlai
>>> On Feb 24, 2012, at 10:21 PM, Jason Stajich wrote:
>>> 
>>>> not all CDS will be annotated with a 'gene' tag, this is due to variation in how annotation is done and that there is not a requirement that there be a gene tag for all CDS features.
>>>> 
>>>> You can protect your query - we often do this when dealing with data from the wild by testing for has_tag first.
>>>> 
>>>> my %strands;
>>>> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
>>>> if( $cds->has_tag('gene') ) {
>>>>    my ($gene) = $cds->get_tag_values('gene'); # get the 1st one, this returns a list
>>>>    $strands{$gene} = $cds->strand; 
>>>> } else { # look in alternative places for a name, e.g. locus, 
>>>> ...
>>>> }
>>>> }
>>>> 
>>>> An alternative is to loop through your list of tags in order of preference
>>>> 
>>>> my %strands;
>>>> for my $cds ( grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) {
>>>> for my $tag ( qw(gene locus name product accession note) ) {  
>>>> if( $cds->has_tag($tag) ) {
>>>>    my ($name) = $cds->get_tag_values($tag); # get the 1st one, this returns a list
>>>>    $strands{$name} = $cds->strand;
>>>>     $seen = 1;
>>>>     last;
>>>> }
>>>> if( ! $seen ) { 
>>>>    warn("not tag found for feature at ", $cds->location->to_FTstring, "\n");
>>>> }
>>>> }
>>>> 
>>>> On Feb 24, 2012, at 12:43 PM, Adlai Burman wrote:
>>>> 
>>>>> I have come across a perplexing problem with trying to parse sequence features into hashes from gb records. This is the minimal code which shows my problem:
>>>>> 
>>>>> #!/usr/bin/perl                                                                                                     
>>>>> use strict;
>>>>> use warnings;
>>>>> use IO::String;
>>>>> use Bio::Perl;
>>>>> use Bio::SeqIO;
>>>>> use IO::String;
>>>>> 
>>>>> my @files = </Users/adlai/Dropbox/atrsh/*>;
>>>>> foreach my $file(@files){
>>>>> 
>>>>> 
>>>>> my @cds_features = grep {$_->primary_tag eq 'CDS' } Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
>>>>> my %strands = map {$_->get_tag_values('gene'), $_->strand} @cds_features; ##This Is The Culprit. 
>>>>> .
>>>>> .
>>>>> .
>>>>> #do nifty stuff
>>>>> }
>>>>> 
>>>>> For some files this approach works just fine.
>>>>> For others the script dies immediately with the error message:
>>>>> 
>>>>> ------------- EXCEPTION -------------
>>>>> MSG: asking for tag value that does not exist gene
>>>>> STACK Bio::SeqFeature::Generic::get_tag_values /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>>>>> STACK toplevel tosend.pl:16
>>>>> -------------------------------------
>>>>> 
>>>>> The difference in the files that parse and those that don't seems to be that the files that crash have "intron" and "exon" tags. They ALL have "gene" tags.
>>>>> Does anyone know why this is a problem and what can be done to circumvent it?
>>>>> 
>>>>> Thanks,
>>>>> Adlai
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> Jason Stajich
>>>> jason.stajich at gmail.com
>>>> jason at bioperl.org
>>>> 
>>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 


From yang.liu0508 at gmail.com  Sat Feb 25 01:52:05 2012
From: yang.liu0508 at gmail.com (yang liu)
Date: Sat, 25 Feb 2012 01:52:05 -0500
Subject: [Bioperl-l] extract sequences and save into files by genes
Message-ID: <CA+BmzaLxVneYsRXk73nbdhd2D-j-XExF7tLD7MYZ6fD2MU1v+Q@mail.gmail.com>

Dear colleagues,

I have multiple files named by species name. Each file has ca. 100
different genes. I want to extract the sequences and save them by gene.
In the output file, the gene name would be the species name. How should I
do?

The input file would be like this (with the file name, Acidosasa.txt,
Acorus.txt....)

>rps12
ATGCCAACGGTTAAACAACTTATTAGAAACGCAAGACAGCCAATACGAAATGCTAGAAAATCGCCCGCGC
TTAAGGGATGTCCTCAGCGTCGAGGAACATGTGCTAGGGTGTATACTATCAACCCCAAAAAACCCAACTC
>psbA
TTATCCATTAAGAGATGGAACTTCAAGAACAGCTAGGTCTAGAGGGAAGTTGTGAGCATTACGTTCGTGC
ATTACCTCCATACCAAGATTAGCACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGGCTAT
.....

I hope the output file to be like this, file name = rps12.txt, psbA.txt....

within rps12.txt, the sequence is like,

>Acidosasa

ATGCCAACGGTTAAACAACTTATTAGAAACGCAAGACAGCCAATACGAAATGCTAGAAAATCGCCCGCGC
TTAAGGGATGTCCTCAGCGTCGAGGAACATGTGCTAGGGTGTATACTATCAACCCCAAAAAACCCAACTC





>Acorus
ATGCCAACTATTAAACAACTTATTAGAAACACAAGACAGCCAATCCGAAATGTC

I do not know if I expressed clearly.

Thanks.

From abhishek.vit at gmail.com  Sun Feb 26 01:24:14 2012
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Sat, 25 Feb 2012 22:24:14 -0800
Subject: [Bioperl-l] fetching all alignments from a sam/bam by read
 header in perl
In-Reply-To: <CAJbA1KBifpnFJS_fu5T5quODvK3gs5TsP9Z=9xXJLn85Wm_2Tg@mail.gmail.com>
References: <CAJbA1KCpjhWALG1KYJTNKexnt8ba7vfGpPm0q8kUr0SBvRe73w@mail.gmail.com>
	<CAKVJ-_4vLDHcUmhAFn2Mw0oy=sjdgn1TQrj47AhO25kcwy=oaQ@mail.gmail.com>
	<CAJbA1KBifpnFJS_fu5T5quODvK3gs5TsP9Z=9xXJLn85Wm_2Tg@mail.gmail.com>
Message-ID: <CAJbA1KA0mhK8=RaT7JGsNSa5odYkQ4pZ=oe-dgmM1NHX_swZmA@mail.gmail.com>

Hi Guys

Reading the doc page for Bio::DB::SAM I see there is a way to fetch reads
by name (read id) but the documentation also says this is slow.(copied
below).  I need to do about 300-500 million look ups and if each one is
costly I wanted to know if there is another slick low level way.  For my
application I would not have feature location just the read name.

-name          Filter on reads with the designated name. Note that
                 this can be a slow operation unless accompanied by
                 the feature location as well.


-Abhi



On Fri, Feb 24, 2012 at 6:58 AM, Abhishek Pratap <abhishek.vit at gmail.com>wrote:

> Hi Peter
>
> You got it right.
>
> Here is the link :
>
> http://biostar.stackexchange.com/questions/17787/fetching-all-alignments-from-a-sam-bam-by-read-header-in-perl
>
>
>
> -A
>
> On Fri, Feb 24, 2012 at 1:24 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > On Fri, Feb 24, 2012 at 12:55 AM, Abhishek Pratap
> > <abhishek.vit at gmail.com> wrote:
> >> I am wondering if there is a slick way access all the possible
> >> alignments for a read present in sam or bam file given the read
> >> header. Since the existing codebase is in perl I would prefer
> >> something which can be done in/via perl.
> >>
> >> By default BAM's are indexed by location so the inbuilt samtools
> >> indexing wont work I guess.
> >>
> >> I should also say the input bam file will have in the order of 500
> >> million total alignments and many reads are expected to be aligned to
> >> more than one place in the genome. Given the size of the data loading
> >> it all in one big hash is not turning out to be memory friendly.
> >
> > Are you asking for SAM/BAM read lookup by read name?
> >
> >> PS:  I also posted this earlier on Biostar.
> >
> > Link?
> >
> > Peter
>

From florent.angly at gmail.com  Sun Feb 26 01:44:06 2012
From: florent.angly at gmail.com (Florent Angly)
Date: Sun, 26 Feb 2012 16:44:06 +1000
Subject: [Bioperl-l] Fate of Bio::Tools::PCRSimulation
Message-ID: <4F49D4B6.5050301@gmail.com>

Hi all,

I am interested in the Bio::Tools::PCRSimulation module. Supposedly it 
was added to Bioperl 0.3 and is also mentionned in the Bio::PrimedSeq 
module. However, I cannot find in the current Bioperl codebase. Any idea 
where it went?

The reason I am asking is because I have some code to do silico PCR 
using regular expressions. I wanted to modularize my code more and make 
it into a module for Bioperl. Of course, if there is something similar 
in Bioperl already, I need to have a look at it. If there is nothing 
similar, what namespace do you suggest to use? 
Bio::Tools::AmpliconExtractor? Bio::Tools::AmpliconSearch? 
Bio::Tools::InSilicoPCR?

Thanks,

Florent

From j_martin at lbl.gov  Sun Feb 26 11:39:16 2012
From: j_martin at lbl.gov (Joel Martin)
Date: Sun, 26 Feb 2012 08:39:16 -0800
Subject: [Bioperl-l] fetching all alignments from a sam/bam by read
 header in perl
In-Reply-To: <CAJbA1KA0mhK8=RaT7JGsNSa5odYkQ4pZ=oe-dgmM1NHX_swZmA@mail.gmail.com>
References: <CAJbA1KCpjhWALG1KYJTNKexnt8ba7vfGpPm0q8kUr0SBvRe73w@mail.gmail.com>
	<CAKVJ-_4vLDHcUmhAFn2Mw0oy=sjdgn1TQrj47AhO25kcwy=oaQ@mail.gmail.com>
	<CAJbA1KBifpnFJS_fu5T5quODvK3gs5TsP9Z=9xXJLn85Wm_2Tg@mail.gmail.com>
	<CAJbA1KA0mhK8=RaT7JGsNSa5odYkQ4pZ=oe-dgmM1NHX_swZmA@mail.gmail.com>
Message-ID: <CA+9Kz75S23fbCmre9dPSvS1CaJRwTrcj_4EZgp_Aao=hybpmWw@mail.gmail.com>

Sort the bam by name so all hits are adjacent.  If you need to subsequently
do random lookups then you could add / alter tags for each read with
multiple hits indicating where those hits are and resort the bam by
coordinate.

Joel

On Sat, Feb 25, 2012 at 10:24 PM, Abhishek Pratap <abhishek.vit at gmail.com>wrote:

> Hi Guys
>
> Reading the doc page for Bio::DB::SAM I see there is a way to fetch reads
> by name (read id) but the documentation also says this is slow.(copied
> below).  I need to do about 300-500 million look ups and if each one is
> costly I wanted to know if there is another slick low level way.  For my
> application I would not have feature location just the read name.
>
> -name          Filter on reads with the designated name. Note that
>                 this can be a slow operation unless accompanied by
>                 the feature location as well.
>
>
> -Abhi
>
>
>
> On Fri, Feb 24, 2012 at 6:58 AM, Abhishek Pratap <abhishek.vit at gmail.com
> >wrote:
>
> > Hi Peter
> >
> > You got it right.
> >
> > Here is the link :
> >
> >
> http://biostar.stackexchange.com/questions/17787/fetching-all-alignments-from-a-sam-bam-by-read-header-in-perl
> >
> >
> >
> > -A
> >
> > On Fri, Feb 24, 2012 at 1:24 AM, Peter Cock <p.j.a.cock at googlemail.com>
> > wrote:
> > > On Fri, Feb 24, 2012 at 12:55 AM, Abhishek Pratap
> > > <abhishek.vit at gmail.com> wrote:
> > >> I am wondering if there is a slick way access all the possible
> > >> alignments for a read present in sam or bam file given the read
> > >> header. Since the existing codebase is in perl I would prefer
> > >> something which can be done in/via perl.
> > >>
> > >> By default BAM's are indexed by location so the inbuilt samtools
> > >> indexing wont work I guess.
> > >>
> > >> I should also say the input bam file will have in the order of 500
> > >> million total alignments and many reads are expected to be aligned to
> > >> more than one place in the genome. Given the size of the data loading
> > >> it all in one big hash is not turning out to be memory friendly.
> > >
> > > Are you asking for SAM/BAM read lookup by read name?
> > >
> > >> PS:  I also posted this earlier on Biostar.
> > >
> > > Link?
> > >
> > > Peter
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From fossandonc at hotmail.com  Sun Feb 26 14:08:55 2012
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Sun, 26 Feb 2012 16:08:55 -0300
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <0F3F54D9-84BF-4136-8D23-52A979351038@illinois.edu>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>	<D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>	<20C8CE5C-FBA5-4333-8A85-86804595DB3C@refenestration.com>	<665C4737-93DA-4466-986B-380D8F266A58@illinois.edu>,
	<758BCF25-5C17-449E-B8F0-3E3DFDF8784D@refenestration.com>
	<0F3F54D9-84BF-4136-8D23-52A979351038@illinois.edu>
Message-ID: <BLU0-SMTP44094D9FFBFC9D3E0E644F3CF680@phx.gbl>

I have been parsing Genbank files with Bioperl for a long time now, so for
many types of data I wrote a code that always checks  if the data exists
before asking for it, to avoid scripts crashes/warnings (I remember I made
customs GBKs deleting specific lines to manually check for crashes). I use
that in all my programs and they work fine. I use Perl ternaries for most
one-liners:

my $version    = $seq_obj->version || '';
my $definition = $seq_obj->desc    || '';
my $dna_shape  = $seq_obj->is_circular ? 'circular' : 'linear';

my $prot_id = $feat->has_tag('protein_id') ?
($feat->get_tag_values('protein_id'))[0] : '';
my $product = $feat->has_tag('product')    ?
($feat->get_tag_values('product'))[0]    : '';

I usually try to code defensively when parsing Genbanks, expecting every
step to go wrong. For example, try to parse ?Escherichia coli str. K-12
substr. MG1655 chromosome? (NC_000913.gbk), and you will see many things go
wrong (like CDS without /protein_id or /product tags). ;)

Francisco J. Ossandon


-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: viernes, 24 de febrero de 2012 20:29
Para: Adlai Burman
CC: <bioperl-l at lists.open-bio.org>; Jason Stajich
Asunto: Re: [Bioperl-l] Odd problem with get_tag_values

No problem. This highlights the #1 problem with genbank files (and the
reasons we keep things as simple as possible), namely lack of consistency.
Not a problem with NCBI per se, but a problem nonetheless. 

Chris

On Feb 24, 2012, at 5:07 PM, "Adlai Burman" <adlai at refenestration.com>
wrote:

> I apologize, Chris. That was a terrible example I sent. I accidentally
sent the only record for which there actually are no regular 'gene' tags.
Other gb records that failed before Jason's tag check include NC_005086 and
they all have regular 'gene' tags. I should have referenced that one.
> I appreciate your checking into that and sorry about the red herring. Boy
is my face blushed.
> 
> A.
> 
> 
> On Feb 24, 2012, at 11:38 PM, Fields, Christopher J wrote:
> 
>> There is possibly a slight disconnect here.  The primary tag you are
looking for is 'CDS'.  Here is an example of both the primary tag for 'CDS'
and 'gene' from NC_012927:
>> 
>>    gene            complement(join(91716..92516,69640..69753))
>>                    /locus_tag="BaolC_p001"
>>                    /trans_splicing
>>                    /db_xref="GeneID:8223103"
>>    CDS
complement(join(91716..91744,92285..92516,69640..69753))
>>                    /locus_tag="BaolC_p001"
>>                    /trans_splicing
>>                    /codon_start=1
>>                    /transl_table=11
>>                    /product="ribosomal protein S12"
>>                    /protein_id="YP_003029720.1"
>>                    /db_xref="GI:253729537"
>>                    /db_xref="GeneID:8223103"
>>
/translation="MPTVKQLIRNARQPIRNARKSAALKGCPQRRGTCARVYTINPKK
>>
PNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYRIIRGTL
>>                    DAVAVKNRQQGRSKYGVKKPKK"
>> 
>> This 'CDS' example has no 'gene' regular tag, in fact none that I looked
at did.  But there is another feature (above it) that does have the
*primary* tag 'gene' and same locus_tag and dbxref GeneID (it does have tags
such as 'locus_tag', 'trans_splicing', etc).  Is that what you mean?
>> 
>> The way that BioPerl deals with this is to return two different
independent features, one with the 'CDS' primary tag and one with the 'gene'
primary tag.  Past attempts to somehow combine these (and then disambiguate
them again later if needed for output) can be problematic, or at least they
once were.
>> 
>> chris
>> 
>> 
>> On Feb 24, 2012, at 3:55 PM, Adlai Burman wrote:
>> 
>>> Jason,
>>> Your first solution, indeed, did the trick (though I'm not sure why).
There was no need to for checking "else." I'm not sure why some records with
a full set of "gene" tags would not parse without the check, but everything
parsed with it.
>>> 
>>> Brian, you were right.
>>> 
>>> Thanks again,
>>> 
>>> Adlai
>>> On Feb 24, 2012, at 10:21 PM, Jason Stajich wrote:
>>> 
>>>> not all CDS will be annotated with a 'gene' tag, this is due to
variation in how annotation is done and that there is not a requirement that
there be a gene tag for all CDS features.
>>>> 
>>>> You can protect your query - we often do this when dealing with data
from the wild by testing for has_tag first.
>>>> 
>>>> my %strands;
>>>> for my $cds ( grep {$_->primary_tag eq 'CDS' } 
>>>> Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) { if(
$cds->has_tag('gene') ) {
>>>>    my ($gene) = $cds->get_tag_values('gene'); # get the 1st one, this
returns a list
>>>>    $strands{$gene} = $cds->strand; } else { # look in alternative 
>>>> places for a name, e.g. locus, ...
>>>> }
>>>> }
>>>> 
>>>> An alternative is to loop through your list of tags in order of 
>>>> preference
>>>> 
>>>> my %strands;
>>>> for my $cds ( grep {$_->primary_tag eq 'CDS' } 
>>>> Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures ) { for 
>>>> my $tag ( qw(gene locus name product accession note) ) { if(
$cds->has_tag($tag) ) {
>>>>    my ($name) = $cds->get_tag_values($tag); # get the 1st one, this
returns a list
>>>>    $strands{$name} = $cds->strand;
>>>>     $seen = 1;
>>>>     last;
>>>> }
>>>> if( ! $seen ) { 
>>>>    warn("not tag found for feature at ", 
>>>> $cds->location->to_FTstring, "\n"); } }
>>>> 
>>>> On Feb 24, 2012, at 12:43 PM, Adlai Burman wrote:
>>>> 
>>>>> I have come across a perplexing problem with trying to parse sequence
features into hashes from gb records. This is the minimal code which shows
my problem:
>>>>> 
>>>>> #!/usr/bin/perl

>>>>> use strict;
>>>>> use warnings;
>>>>> use IO::String;
>>>>> use Bio::Perl;
>>>>> use Bio::SeqIO;
>>>>> use IO::String;
>>>>> 
>>>>> my @files = </Users/adlai/Dropbox/atrsh/*>; foreach my 
>>>>> $file(@files){
>>>>> 
>>>>> 
>>>>> my @cds_features = grep {$_->primary_tag eq 'CDS' } 
>>>>> Bio::SeqIO->new(-file => $file)->next_seq->get_SeqFeatures;
>>>>> my %strands = map {$_->get_tag_values('gene'), $_->strand}
@cds_features; ##This Is The Culprit. 
>>>>> .
>>>>> .
>>>>> .
>>>>> #do nifty stuff
>>>>> }
>>>>> 
>>>>> For some files this approach works just fine.
>>>>> For others the script dies immediately with the error message:
>>>>> 
>>>>> ------------- EXCEPTION -------------
>>>>> MSG: asking for tag value that does not exist gene STACK 
>>>>> Bio::SeqFeature::Generic::get_tag_values 
>>>>> /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>>>>> STACK toplevel tosend.pl:16
>>>>> -------------------------------------
>>>>> 
>>>>> The difference in the files that parse and those that don't seems to
be that the files that crash have "intron" and "exon" tags. They ALL have
"gene" tags.
>>>>> Does anyone know why this is a problem and what can be done to
circumvent it?
>>>>> 
>>>>> Thanks,
>>>>> Adlai
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> Jason Stajich
>>>> jason.stajich at gmail.com
>>>> jason at bioperl.org
>>>> 
>>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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 roy.chaudhuri at gmail.com  Mon Feb 27 05:33:48 2012
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Mon, 27 Feb 2012 10:33:48 +0000
Subject: [Bioperl-l] Odd problem with get_tag_values
In-Reply-To: <1230FA01-6821-4C33-9C15-14669E5DCEFA@refenestration.com>
References: <1C2950DB-455A-4B80-8D23-4A241FB857BE@refenestration.com>
	<D17CA1B8-36E8-471A-B483-18419DABD364@gmail.com>
	<C1EE8D29-1480-4DF0-BCBE-400F202A6210@refenestration.com>
	<A97AF018-3476-4E42-8190-A2E8AD7B782A@illinois.edu>
	<1230FA01-6821-4C33-9C15-14669E5DCEFA@refenestration.com>
Message-ID: <4F4B5C0C.8080102@gmail.com>

Just to chip in on this, you can use get_tagset_values instead of 
get_tag_values - the former has (to me) the more Perl-ish behaviour of 
returning an empty list if there are none of the requested tags present, 
meaning that you can skip the has_tag step.

Cheers,
Roy.

On 24/02/2012 21:57, Adlai Burman wrote:
>
> On Feb 24, 2012, at 10:46 PM, Fields, Christopher J wrote:
>
>> Using has_tag('gene') as a pre-screen works for me for both example
>> seqs.
>>
>
> Me too :-)
>
> Dobrou noc and cheers,
>
> Adlai
>> chris
>>
>> On Feb 24, 2012, at 3:33 PM, Adlai Burman wrote:
>>
>>> Thanks so much, Jason. I will give that a try in after I get a
>>> few hours of much needed sleep :-)
>>>
>>>
>>> On Feb 24, 2012, at 10:21 PM, Jason Stajich wrote:
>>>
>>>> not all CDS will be annotated with a 'gene' tag, this is due to
>>>> variation in how annotation is done and that there is not a
>>>> requirement that there be a gene tag for all CDS features.
>>>>
>>>> You can protect your query - we often do this when dealing with
>>>> data from the wild by testing for has_tag first.
>>>>
>>>> my %strands; for my $cds ( grep {$_->primary_tag eq 'CDS' }
>>>> Bio::SeqIO->new(-file =>  $file)->next_seq->get_SeqFeatures )
>>>> { if( $cds->has_tag('gene') ) { my ($gene) =
>>>> $cds->get_tag_values('gene'); # get the 1st one, this returns a
>>>> list $strands{$gene} = $cds->strand; } else { # look in
>>>> alternative places for a name, e.g. locus, ... } }
>>>>
>>>> An alternative is to loop through your list of tags in order of
>>>> preference
>>>>
>>>> my %strands; for my $cds ( grep {$_->primary_tag eq 'CDS' }
>>>> Bio::SeqIO->new(-file =>  $file)->next_seq->get_SeqFeatures )
>>>> { for my $tag ( qw(gene locus name product accession note) ) {
>>>> if( $cds->has_tag($tag) ) { my ($name) =
>>>> $cds->get_tag_values($tag); # get the 1st one, this returns a
>>>> list $strands{$name} = $cds->strand; $seen = 1; last; } if( !
>>>> $seen ) { warn("not tag found for feature at ",
>>>> $cds->location->to_FTstring, "\n"); } }
>>>>
>>>> On Feb 24, 2012, at 12:43 PM, Adlai Burman wrote:
>>>>
>>>>> I have come across a perplexing problem with trying to parse
>>>>> sequence features into hashes from gb records. This is the
>>>>> minimal code which shows my problem:
>>>>>
>>>>> #!/usr/bin/perl use strict; use warnings; use IO::String; use
>>>>> Bio::Perl; use Bio::SeqIO; use IO::String;
>>>>>
>>>>> my @files =</Users/adlai/Dropbox/atrsh/*>; foreach my
>>>>> $file(@files){
>>>>>
>>>>>
>>>>> my @cds_features = grep {$_->primary_tag eq 'CDS' }
>>>>> Bio::SeqIO->new(-file =>  $file)->next_seq->get_SeqFeatures;
>>>>> my %strands = map {$_->get_tag_values('gene'), $_->strand}
>>>>> @cds_features; ##This Is The Culprit. . . . #do nifty stuff
>>>>> }
>>>>>
>>>>> For some files this approach works just fine. For others the
>>>>> script dies immediately with the error message:
>>>>>
>>>>> ------------- EXCEPTION ------------- MSG: asking for tag
>>>>> value that does not exist gene STACK
>>>>> Bio::SeqFeature::Generic::get_tag_values
>>>>> /Users/adlai/Downloads/BioPerl-1.6.1/Bio/SeqFeature/Generic.pm:517
>>>>>
>>>>>
STACK toplevel tosend.pl:16
>>>>> -------------------------------------
>>>>>
>>>>> The difference in the files that parse and those that don't
>>>>> seems to be that the files that crash have "intron" and
>>>>> "exon" tags. They ALL have "gene" tags. Does anyone know why
>>>>> this is a problem and what can be done to circumvent it?
>>>>>
>>>>> Thanks, Adlai
>>>>>
>>>>>
>>>>> _______________________________________________ Bioperl-l
>>>>> mailing list Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Jason Stajich jason.stajich at gmail.com jason at bioperl.org
>>>>
>>>>
>>>
>>>
>>> _______________________________________________ Bioperl-l mailing
>>> list Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
>
> _______________________________________________ Bioperl-l mailing
> list Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From MEC at stowers.org  Mon Feb 27 10:47:51 2012
From: MEC at stowers.org (Cook, Malcolm)
Date: Mon, 27 Feb 2012 09:47:51 -0600
Subject: [Bioperl-l] extract sequences and save into files by genes
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF997D77D30@EXCHMB-02.stowers-institute.org>

You don't need bioperl for this one.....

The following perl one liner will do it for you.

perl -p -e 'if (1==$.) {($species = $ARGV) =~ s|\.txt||}; if (s/^>(.*)/">${species}"/e) {$gene=$1; open($O{$gene},qq{>> ${gene}.txt}); select($O{$gene})} ; close ARGV  if eof' *.txt


~Malcolm

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of yang liu
> Sent: Saturday, February 25, 2012 12:52 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] extract sequences and save into files by genes
> 
> Dear colleagues,
> 
> I have multiple files named by species name. Each file has ca. 100
> different genes. I want to extract the sequences and save them by gene.
> In the output file, the gene name would be the species name. How should I
> do?
> 
> The input file would be like this (with the file name, Acidosasa.txt,
> Acorus.txt....)
> 
> >rps12
> ATGCCAACGGTTAAACAACTTATTAGAAACGCAAGACAGCCAATACGAAATGCT
> AGAAAATCGCCCGCGC
> TTAAGGGATGTCCTCAGCGTCGAGGAACATGTGCTAGGGTGTATACTATCAACCC
> CAAAAAACCCAACTC
> >psbA
> TTATCCATTAAGAGATGGAACTTCAAGAACAGCTAGGTCTAGAGGGAAGTTGTG
> AGCATTACGTTCGTGC
> ATTACCTCCATACCAAGATTAGCACGGTTGATGATATCAGCCCAAGTATTAATAAC
> GCGACCTTGGCTAT
> .....
> 
> I hope the output file to be like this, file name = rps12.txt, psbA.txt....
> 
> within rps12.txt, the sequence is like,
> 
> >Acidosasa
> 
> ATGCCAACGGTTAAACAACTTATTAGAAACGCAAGACAGCCAATACGAAATGCT
> AGAAAATCGCCCGCGC
> TTAAGGGATGTCCTCAGCGTCGAGGAACATGTGCTAGGGTGTATACTATCAACCC
> CAAAAAACCCAACTC
> 
> 
> 
> 
> 
> >Acorus
> ATGCCAACTATTAAACAACTTATTAGAAACACAAGACAGCCAATCCGAAATGTC
> 
> I do not know if I expressed clearly.
> 
> Thanks.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From rbuels at gmail.com  Mon Feb 27 11:24:59 2012
From: rbuels at gmail.com (Robert Buels)
Date: Mon, 27 Feb 2012 11:24:59 -0500
Subject: [Bioperl-l] Update: call for Google Summer of Code project ideas
Message-ID: <4F4BAE5B.40309@gmail.com>

Hi all,

As kindly pointed out by Reece Hart, the previous email I sent out 
calling for Google Summer of Code project ideas, had the wrong due date 
for project ideas in it.

I actually want them to all be in place by Friday, March 2, which is 
this coming Friday.

== Instructions for Wiki Editing ==

For each of the OBF projects that wants to do GSoC again this year, please:

a.) Update the list of project ideas on your project's GSoC page 
(BioPython, BioPerl, BioRuby, etc).  Add new ones, remove ones that have 
already been done or no longer relevant, etc.

b.) Update the list of project ideas on the main OBF GSoC page 
(http://www.open-bio.org/wiki/Google_Summer_of_Code) to match.

c.) Let me know via email that you have done so and it's ready for 
Google to peruse.

== end instructions ==

Again, please have the updates done by this Friday (March 2). The number 
and quality of the project ideas are part of the evaluation process for 
whether OBF is accepted as a Summer of Code organization again this 
year, so let's come up with some good ones.  :-)

Rob

----
Robert Buels
(prospective) 2012 OBF GSoC Organization Admin

From rondonbio at yahoo.com.br  Mon Feb 27 12:53:12 2012
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Mon, 27 Feb 2012 09:53:12 -0800 (PST)
Subject: [Bioperl-l] unninstall Bioperl
In-Reply-To: <3F5F0A6E-C51E-4DF9-A293-924A5AA5245B@illinois.edu>
References: <1329332355.18626.YahooMailNeo@web130206.mail.mud.yahoo.com>
	<1329335001.11066.YahooMailNeo@web130202.mail.mud.yahoo.com>
	<1329335028.66134.YahooMailNeo@web130206.mail.mud.yahoo.com>
	<3F5F0A6E-C51E-4DF9-A293-924A5AA5245B@illinois.edu>
Message-ID: <1330365192.12597.YahooMailNeo@web130205.mail.mud.yahoo.com>

Hi guys! thanks for all helps.
I want to unninstall Bioperl and than, install it again. do you know how to unninstall?

thank you

Rondon

From l.m.timmermans at students.uu.nl  Mon Feb 27 14:34:25 2012
From: l.m.timmermans at students.uu.nl (Leon Timmermans)
Date: Mon, 27 Feb 2012 20:34:25 +0100
Subject: [Bioperl-l] unninstall Bioperl
In-Reply-To: <1330365192.12597.YahooMailNeo@web130205.mail.mud.yahoo.com>
References: <1329332355.18626.YahooMailNeo@web130206.mail.mud.yahoo.com>
	<1329335001.11066.YahooMailNeo@web130202.mail.mud.yahoo.com>
	<1329335028.66134.YahooMailNeo@web130206.mail.mud.yahoo.com>
	<3F5F0A6E-C51E-4DF9-A293-924A5AA5245B@illinois.edu>
	<1330365192.12597.YahooMailNeo@web130205.mail.mud.yahoo.com>
Message-ID: <CAC1jpXBq=S2Hta+6HoUez9shXCEjs=PQSes5dK_S0aMXeQ78Bw@mail.gmail.com>

For uninstalling, you may want to try pm-uninstall (**App-pmuninstall on
CPAN).

Leon

On Mon, Feb 27, 2012 at 6:53 PM, Rondon Neto <rondonbio at yahoo.com.br> wrote:

> Hi guys! thanks for all helps.
> I want to unninstall Bioperl and than, install it again. do you know how
> to unninstall?
>
> thank you
>
> Rondon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From cjfields at illinois.edu  Mon Feb 27 14:38:51 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 27 Feb 2012 19:38:51 +0000
Subject: [Bioperl-l] unninstall Bioperl
In-Reply-To: <CAC1jpXBq=S2Hta+6HoUez9shXCEjs=PQSes5dK_S0aMXeQ78Bw@mail.gmail.com>
References: <1329332355.18626.YahooMailNeo@web130206.mail.mud.yahoo.com>
	<1329335001.11066.YahooMailNeo@web130202.mail.mud.yahoo.com>
	<1329335028.66134.YahooMailNeo@web130206.mail.mud.yahoo.com>
	<3F5F0A6E-C51E-4DF9-A293-924A5AA5245B@illinois.edu>
	<1330365192.12597.YahooMailNeo@web130205.mail.mud.yahoo.com>
	<CAC1jpXBq=S2Hta+6HoUez9shXCEjs=PQSes5dK_S0aMXeQ78Bw@mail.gmail.com>
Message-ID: <4781354A-7B22-4ECA-9532-84198B1B7338@illinois.edu>

There is also './Build install uninst=1'.

chris

On Feb 27, 2012, at 1:34 PM, Leon Timmermans wrote:

> For uninstalling, you may want to try pm-uninstall (**App-pmuninstall on
> CPAN).
> 
> Leon
> 
> On Mon, Feb 27, 2012 at 6:53 PM, Rondon Neto <rondonbio at yahoo.com.br> wrote:
> 
>> Hi guys! thanks for all helps.
>> I want to unninstall Bioperl and than, install it again. do you know how
>> to unninstall?
>> 
>> thank you
>> 
>> Rondon
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Mon Feb 27 16:18:54 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 27 Feb 2012 21:18:54 +0000
Subject: [Bioperl-l] Fate of Bio::Tools::PCRSimulation
In-Reply-To: <4F49D4B6.5050301@gmail.com>
References: <4F49D4B6.5050301@gmail.com>
Message-ID: <D60FDDB5-5EC6-4A91-954B-3A3EB27921CF@illinois.edu>

On Feb 26, 2012, at 12:44 AM, Florent Angly wrote:

> Hi all,
> 
> I am interested in the Bio::Tools::PCRSimulation module. Supposedly it was added to Bioperl 0.3 and is also mentionned in the Bio::PrimedSeq module. However, I cannot find in the current Bioperl codebase. Any idea where it went?

No idea; I can't find it anywhere in the code base either, and the github repo contains history going back to the original CVS repo.  You can try contacting the author, possibly.

> The reason I am asking is because I have some code to do silico PCR using regular expressions. I wanted to modularize my code more and make it into a module for Bioperl. Of course, if there is something similar in Bioperl already, I need to have a look at it. If there is nothing similar, what namespace do you suggest to use? Bio::Tools::AmpliconExtractor? Bio::Tools::AmpliconSearch? Bio::Tools::InSilicoPCR?
> 
> Thanks,
> 
> Florent


Maybe the last (InSilicoPCR).  

chris



From MEC at stowers.org  Tue Feb 28 11:55:13 2012
From: MEC at stowers.org (Cook, Malcolm)
Date: Tue, 28 Feb 2012 10:55:13 -0600
Subject: [Bioperl-l] extract sequences and save into files by genes
In-Reply-To: <CA+BmzaJU31d2xitzqnr0MAXYHGLGmDdifteLSSdF3NhvE7TxPw@mail.gmail.com>
References: <2C40E43D1F7A56408C4463FD245DDDF997D77D30@EXCHMB-02.stowers-institute.org>
	<CA+BmzaJU31d2xitzqnr0MAXYHGLGmDdifteLSSdF3NhvE7TxPw@mail.gmail.com>
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF997D77EDD@EXCHMB-02.stowers-institute.org>

Yang,

I'm replying back on-list.

You wrote in your other email that my one-liner worked once you learned to run perl from the command line under cygwin.

Great.  Glad to help.  Good luck.  Welcome to the fray!

~Malcolm

From: yang liu [mailto:yang.liu0508 at gmail.com]
Sent: Monday, February 27, 2012 10:04 PM
To: Cook, Malcolm
Subject: Re: [Bioperl-l] extract sequences and save into files by genes

Hello Malcolm,

Thanks for your help. But when I run it, it returned the following line.
'\.txt' is not recognized as an internal or external command, operable program or batch file.

I am using windows 7, is that the problem? I have perl installed.
In windows command, I firstly changed to the folder the target files exist, and then paste your script line.
I am a beginner of perl.

Thanks again for your help.

Yang.


On Mon, Feb 27, 2012 at 10:47 AM, Cook, Malcolm <MEC at stowers.org<mailto:MEC at stowers.org>> wrote:
You don't need bioperl for this one.....

The following perl one liner will do it for you.

perl -p -e 'if (1==$.) {($species = $ARGV) =~ s|\.txt||}; if (s/^>(.*)/">${species}"/e) {$gene=$1; open($O{$gene},qq{>> ${gene}.txt}); select($O{$gene})} ; close ARGV  if eof' *.txt


~Malcolm

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-bounces at lists.open-bio.org> [mailto:bioperl-l-<mailto:bioperl-l->
> bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>] On Behalf Of yang liu
> Sent: Saturday, February 25, 2012 12:52 AM
> To: bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>
> Subject: [Bioperl-l] extract sequences and save into files by genes
>
> Dear colleagues,
>
> I have multiple files named by species name. Each file has ca. 100
> different genes. I want to extract the sequences and save them by gene.
> In the output file, the gene name would be the species name. How should I
> do?
>
> The input file would be like this (with the file name, Acidosasa.txt,
> Acorus.txt....)
>
> >rps12
> ATGCCAACGGTTAAACAACTTATTAGAAACGCAAGACAGCCAATACGAAATGCT
> AGAAAATCGCCCGCGC
> TTAAGGGATGTCCTCAGCGTCGAGGAACATGTGCTAGGGTGTATACTATCAACCC
> CAAAAAACCCAACTC
> >psbA
> TTATCCATTAAGAGATGGAACTTCAAGAACAGCTAGGTCTAGAGGGAAGTTGTG
> AGCATTACGTTCGTGC
> ATTACCTCCATACCAAGATTAGCACGGTTGATGATATCAGCCCAAGTATTAATAAC
> GCGACCTTGGCTAT
> .....
>
> I hope the output file to be like this, file name = rps12.txt, psbA.txt....
>
> within rps12.txt, the sequence is like,
>
> >Acidosasa
>
> ATGCCAACGGTTAAACAACTTATTAGAAACGCAAGACAGCCAATACGAAATGCT
> AGAAAATCGCCCGCGC
> TTAAGGGATGTCCTCAGCGTCGAGGAACATGTGCTAGGGTGTATACTATCAACCC
> CAAAAAACCCAACTC
>
>
>
>
>
> >Acorus
> ATGCCAACTATTAAACAACTTATTAGAAACACAAGACAGCCAATCCGAAATGTC
>
> I do not know if I expressed clearly.
>
> Thanks.
> _______________________________________________
> 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



From crrcri at ibmb.csic.es  Fri Feb 24 10:40:48 2012
From: crrcri at ibmb.csic.es (Casandra)
Date: Fri, 24 Feb 2012 16:40:48 +0100
Subject: [Bioperl-l] BLAST in Bioperl - Can't call method "next_result"
References: <43344F4C-9FDE-4A28-A3D0-BE05E68A32EA@gmail.com>
Message-ID: <3BFA0762-0494-4733-9217-341455C81C77@ibmb.csic.es>

Hi, I am installing BLAST to use it into BioPerl but I'm having some  
problems and I can't find how to fix them:

  I follow the steps in here: http://www.ncbi.nlm.nih.gov/books/NBK52640/ 
  (at least I think I did it right) for mac.

and I downloaded swissprot.gz db to try with the following script:

#!/bin/perl -w

use Bio::Seq;
use Bio::SearchIO;
use Bio::Tools::Run::StandAloneBlast;

$blast_obj = Bio::Tools::Run::StandAloneBlast->new(-program  =>  
'blastp', -database => '~/scripts/ncbi-blast-2.2.25+/db/swissprot.fa');
$seq_obj = Bio::Seq->new(-id  =>"test query", -seq =>"MMSMLGGL");
$report_obj = $blast_obj->blastall($seq_obj);
$result_obj = $report_obj->next_result;
print $result_obj->num_hits;

That I wrote based on http://www.bioperl.org/wiki/HOWTO:Beginners   
BLAST section.

But I'm not sure if this step that they say " The example code assumes  
that you used the formatdb program to index the database sequence file  
"db.fa"" I did it properly. I just downloaded the swissprot db, keep  
it into /db directory and adapt the script to this. I haven't used  
this "formatdb" so I don't know if this script is not updated or if it  
should run anyway.

This is what I get:

Mercuri:BioPerl Casandra$ perl bp_blast.pl

--------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [test query]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [test query]
---------------------------------------------------
Use of uninitialized value in join or string at /Library/Perl/Updates/ 
5.8.8/darwin-thread-multi-2level/File/Spec/Unix.pm line 86.

--------------------- WARNING ---------------------
MSG: cannot find path to blastall
---------------------------------------------------
Can't call method "next_result" on an undefined value at bp_blast.pl  
line 13.


Just for curiosity, when I change
$report_obj = $blast_obj->blastall($seq_obj);

to
$report_obj = $blast_obj->blast($seq_obj);

I get this message instead:

Mercuri:BioPerl Casandra$ perl bp_blast.pl
Can't locate object method "next_result" via package "Bio::Seq" at  
bp_blast.pl line 13.

Thanks a lot




From limericksean at gmail.com  Tue Feb 28 16:11:13 2012
From: limericksean at gmail.com (Sean O'Keeffe)
Date: Tue, 28 Feb 2012 16:11:13 -0500
Subject: [Bioperl-l] fastq splitter
Message-ID: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>

Hi,
I'm trying to write a quick script to separate one large PE fastq file into
2 separate files, one for each mate pair

The file is of the format (mate1)
@HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
+
BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA

&& (mate2)

@HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
+
##################################################


My idea is to separate using a regex such that / 1:/ would be the first
mate pair and / 2:/ would go in the second mate file.
I implemented the code below but each output file is empty. Can someone
spot my error?

Thanks,
Sean.

my $infile   = shift;
my $outfile1 = $infile."_1";
my $outfile2 = $infile."_2";

my $seqin = Bio::SeqIO->new(
                             -file   => "<$infile",
                             -format => "fastq",
                             );
my $seqout1 = Bio::SeqIO->new(
                              -file   => ">$outfile1",
                              -format => "fastq",
                              );

my $seqout2 = Bio::SeqIO->new(
                              -file   => ">$outfile2",
                              -format => "fastq",
                              );
while (my $inseq = $seqin->next_seq) {
    if ($seqin->desc =~ / 1:/){
      $seqout1->write_seq($inseq);
    } else {
      $seqout2->write_seq($inseq);
    }
}

From kajendiran56 at googlemail.com  Tue Feb 28 05:57:03 2012
From: kajendiran56 at googlemail.com (kajendiran mahendiran)
Date: Tue, 28 Feb 2012 02:57:03 -0800 (PST)
Subject: [Bioperl-l] gerp++
Message-ID: <01356797-31c0-4aae-a7ed-4365d361d8fd@w19g2000vbe.googlegroups.com>

Dear All,
         thank you for taking the time to look at my post. I am trying
to use the Bioperl module to analyse gerpelem output. I have used the
following code:

use Bio::Tools::Run::Phylo::Gerp;

my$parser = Bio::Tools::Phylo::Gerp->new(-file => "test.rates.elems");

while (my $feat = $parser->next_result()) {
    my ($start) = $feat->start();
    my ($end) = $feat->end();
    my ($rs_score) = $feat->score();
    my ($p_value) = ($feat->annotation->get_Annotations('p-value'))[0]-
>value();
    print $start, "\t", $end, "\t", $rs_score, "\t", $p_value, "\n";
}

The file I am trying to read is:
region	4850138	4850158	19.72	5.48888e-09	223119	0	0
region	221586	221606	19.72	5.48888e-09	223139	0	0
region	865234	865254	19.72	5.48888e-09	223159	0	0
region	4108337	4108490	42.8171	5.57134e-09	223312	0	0
region	2780908	2781050	42.5108	5.67614e-09	223454	0.1	4.3
region	3603457	3603637	42.9148	5.68931e-09	223634	0.1	4.3
region	995791	995961	42.9233	5.72716e-09	223804	0.1	4.3
region	1250933	1251094	42.8291	5.83297e-09	223965	0.1	4.3
region	4219830	4219941	40.856	5.97931e-09	224076	0.1	4.3
region	712708	712796	38.8442	6.04126e-09	224164	0.1	4.3
region	3170105	3170125	19.482	6.0786e-09	224184	0.1	4.3
region	3297610	3297802	42.563	6.08115e-09	224376	0.1	4.3
region	5296586	5296776	42.5578	6.14513e-09	224566	0.1	4.3
region	1400348	1400508	42.6387	6.30399e-09	224726	0.1	4.3
region	4103587	4103685	39.7477	6.48804e-09	224824	0.1	4.3
region	278040	278082	29.8649	6.50312e-09	224866	0.1	4.3
region	5449691	5449882	42.4149	6.58323e-09	225057	0.1	4.3
region	4435258	4435437	42.384	6.90672e-09	225236	0.1	4.3

The program runs without any errors but there is no print out. It
appears that the parser is undefined and I cannot seem to figure out
why. I am new to bioinformatics and I would appreciate any help. I am
trying to figure out what the columns correspond to in the gerpelems
output, the format does not correspond to the format given in the
manual for gerp++. There are additional numbers also in the .elems
file and I am not sure what they mean.

Thank you once again for your help.
Kajendiran

From mmuratet at hudsonalpha.org  Tue Feb 28 16:26:25 2012
From: mmuratet at hudsonalpha.org (Michael Muratet)
Date: Tue, 28 Feb 2012 15:26:25 -0600
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
Message-ID: <2E3E60E8-370A-4495-8A59-1B62C59B2AF8@hudsonalpha.org>


On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:

> Hi,
> I'm trying to write a quick script to separate one large PE fastq  
> file into
> 2 separate files, one for each mate pair
>
> The file is of the format (mate1)
> @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> +
> BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
>
> && (mate2)
>
> @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> +
> ##################################################
>
>
> My idea is to separate using a regex such that / 1:/ would be the  
> first
> mate pair and / 2:/ would go in the second mate file.
> I implemented the code below but each output file is empty. Can  
> someone
> spot my error?
>
> Thanks,
> Sean.
>
> my $infile   = shift;
> my $outfile1 = $infile."_1";
> my $outfile2 = $infile."_2";
>
> my $seqin = Bio::SeqIO->new(
>                             -file   => "<$infile",
>                             -format => "fastq",
>                             );
> my $seqout1 = Bio::SeqIO->new(
>                              -file   => ">$outfile1",
>                              -format => "fastq",
>                              );
>
> my $seqout2 = Bio::SeqIO->new(
>                              -file   => ">$outfile2",
>                              -format => "fastq",
>                              );
> while (my $inseq = $seqin->next_seq) {
>    if ($seqin->desc =~ / 1:/){
Hi Sean

You're using the desc operator on the stream, not the seq object.

Cheers

Mike

>      $seqout1->write_seq($inseq);
>    } else {
>      $seqout2->write_seq($inseq);
>    }
> }
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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

Room 4005
601 Genome Way
Huntsville, Alabama 35806






From cjfields at illinois.edu  Tue Feb 28 16:50:30 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 28 Feb 2012 21:50:30 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
Message-ID: <2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>

Sean,

If you trust the data enough, in that:

1) each record is 4 lines, 
2) mate pairs are consecutive in the file, and
3) that read 1 always preceeds read 2 in the pair, 

then I would simply iterate through 4 lines at a time and dump to the two separate files, maybe using a flip-flop or simple record count and modulus switch.  You can always run a check on the header with a regex if you don't trust it completely.

Just from the sanity point-of-view, unless you're doing a lot of validation I wouldn't use Bio::SeqIO::fastq, unless you have some time on your hands and a relatively low number of seqs (it's notoriously slow at the moment).

chris

On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:

> Hi,
> I'm trying to write a quick script to separate one large PE fastq file into
> 2 separate files, one for each mate pair
> 
> The file is of the format (mate1)
> @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> +
> BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> 
> && (mate2)
> 
> @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> +
> ##################################################
> 
> 
> My idea is to separate using a regex such that / 1:/ would be the first
> mate pair and / 2:/ would go in the second mate file.
> I implemented the code below but each output file is empty. Can someone
> spot my error?
> 
> Thanks,
> Sean.
> 
> my $infile   = shift;
> my $outfile1 = $infile."_1";
> my $outfile2 = $infile."_2";
> 
> my $seqin = Bio::SeqIO->new(
>                             -file   => "<$infile",
>                             -format => "fastq",
>                             );
> my $seqout1 = Bio::SeqIO->new(
>                              -file   => ">$outfile1",
>                              -format => "fastq",
>                              );
> 
> my $seqout2 = Bio::SeqIO->new(
>                              -file   => ">$outfile2",
>                              -format => "fastq",
>                              );
> while (my $inseq = $seqin->next_seq) {
>    if ($seqin->desc =~ / 1:/){
>      $seqout1->write_seq($inseq);
>    } else {
>      $seqout2->write_seq($inseq);
>    }
> }
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Tue Feb 28 17:17:47 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 28 Feb 2012 22:17:47 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
Message-ID: <A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>

That's a bit odd.  Are you using an old version of the FASTQ parser?  It was revised a while ago, prior to the v1.6.1 release (the error matches one in the older parser)

chris

On Feb 28, 2012, at 4:01 PM, Sean O'Keeffe wrote:

> Hi Chris,
> Unfortunately the read pairs are not consecutive. It seems they are cat'd together. 
> I could use split -l on the line number that they're glued together I guess.
> If this is an overnight job for a bunch of files, I can wait so don't mind using the module if it worked.
> 
> Someone pointed out I need to switch $seqin->desc to $inseq->desc.
> However, now it spits out fasta output instead of fastq and returns a bunch of warnings: Seq/Qual descriptions don't match; using sequence description
> 
> Hmm.
> 
> On 28 February 2012 16:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
> Sean,
> 
> If you trust the data enough, in that:
> 
> 1) each record is 4 lines,
> 2) mate pairs are consecutive in the file, and
> 3) that read 1 always preceeds read 2 in the pair,
> 
> then I would simply iterate through 4 lines at a time and dump to the two separate files, maybe using a flip-flop or simple record count and modulus switch.  You can always run a check on the header with a regex if you don't trust it completely.
> 
> Just from the sanity point-of-view, unless you're doing a lot of validation I wouldn't use Bio::SeqIO::fastq, unless you have some time on your hands and a relatively low number of seqs (it's notoriously slow at the moment).
> 
> chris
> 
> On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
> 
> > Hi,
> > I'm trying to write a quick script to separate one large PE fastq file into
> > 2 separate files, one for each mate pair
> >
> > The file is of the format (mate1)
> > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > +
> > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> >
> > && (mate2)
> >
> > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > +
> > ##################################################
> >
> >
> > My idea is to separate using a regex such that / 1:/ would be the first
> > mate pair and / 2:/ would go in the second mate file.
> > I implemented the code below but each output file is empty. Can someone
> > spot my error?
> >
> > Thanks,
> > Sean.
> >
> > my $infile   = shift;
> > my $outfile1 = $infile."_1";
> > my $outfile2 = $infile."_2";
> >
> > my $seqin = Bio::SeqIO->new(
> >                             -file   => "<$infile",
> >                             -format => "fastq",
> >                             );
> > my $seqout1 = Bio::SeqIO->new(
> >                              -file   => ">$outfile1",
> >                              -format => "fastq",
> >                              );
> >
> > my $seqout2 = Bio::SeqIO->new(
> >                              -file   => ">$outfile2",
> >                              -format => "fastq",
> >                              );
> > while (my $inseq = $seqin->next_seq) {
> >    if ($seqin->desc =~ / 1:/){
> >      $seqout1->write_seq($inseq);
> >    } else {
> >      $seqout2->write_seq($inseq);
> >    }
> > }
> > _______________________________________________
> > 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  Wed Feb 29 17:33:04 2012
From: florent.angly at gmail.com (Florent Angly)
Date: Thu, 01 Mar 2012 08:33:04 +1000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <2E3E60E8-370A-4495-8A59-1B62C59B2AF8@hudsonalpha.org>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E3E60E8-370A-4495-8A59-1B62C59B2AF8@hudsonalpha.org>
Message-ID: <4F4EA7A0.9050002@gmail.com>

Also, the desc() method returns the part after the whitespace in the 
FASTA header.
Hence, instead of / 1:/, your regular expression should not have the 
space and should be written /1:/. In fact, it would be even better 
(faster) it it were written as an anchored regular expression that 
matches only the beginning of the description, /^1:/

Note that you are apparently using the latest Illumina format, that does 
not follow previous convention on paired-end read headers. Hence your 
script will not work properly with non-latest-Illumina paired-end files.

Florent



On 29/02/12 07:26, Michael Muratet wrote:
>
> On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
>
>> Hi,
>> I'm trying to write a quick script to separate one large PE fastq 
>> file into
>> 2 separate files, one for each mate pair
>>
>> The file is of the format (mate1)
>> @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
>> CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
>> +
>> BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
>>
>> && (mate2)
>>
>> @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
>> TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
>> +
>> ##################################################
>>
>>
>> My idea is to separate using a regex such that / 1:/ would be the first
>> mate pair and / 2:/ would go in the second mate file.
>> I implemented the code below but each output file is empty. Can someone
>> spot my error?
>>
>> Thanks,
>> Sean.
>>
>> my $infile   = shift;
>> my $outfile1 = $infile."_1";
>> my $outfile2 = $infile."_2";
>>
>> my $seqin = Bio::SeqIO->new(
>>                             -file   => "<$infile",
>>                             -format => "fastq",
>>                             );
>> my $seqout1 = Bio::SeqIO->new(
>>                              -file   => ">$outfile1",
>>                              -format => "fastq",
>>                              );
>>
>> my $seqout2 = Bio::SeqIO->new(
>>                              -file   => ">$outfile2",
>>                              -format => "fastq",
>>                              );
>> while (my $inseq = $seqin->next_seq) {
>>    if ($seqin->desc =~ / 1:/){
> Hi Sean
>
> You're using the desc operator on the stream, not the seq object.
>
> Cheers
>
> Mike
>
>>      $seqout1->write_seq($inseq);
>>    } else {
>>      $seqout2->write_seq($inseq);
>>    }
>> }
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet at hudsonalpha.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From limericksean at gmail.com  Tue Feb 28 17:01:18 2012
From: limericksean at gmail.com (Sean O'Keeffe)
Date: Tue, 28 Feb 2012 17:01:18 -0500
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
Message-ID: <CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>

Hi Chris,
Unfortunately the read pairs are not consecutive. It seems they are cat'd
together.
I could use split -l on the line number that they're glued together I guess.
If this is an overnight job for a bunch of files, I can wait so don't mind
using the module if it worked.

Someone pointed out I need to switch $seqin->desc to $inseq->desc.
However, now it spits out fasta output instead of fastq and returns a bunch
of warnings: Seq/Qual descriptions don't match; using sequence description

Hmm.

On 28 February 2012 16:50, Fields, Christopher J <cjfields at illinois.edu>wrote:

> Sean,
>
> If you trust the data enough, in that:
>
> 1) each record is 4 lines,
> 2) mate pairs are consecutive in the file, and
> 3) that read 1 always preceeds read 2 in the pair,
>
> then I would simply iterate through 4 lines at a time and dump to the two
> separate files, maybe using a flip-flop or simple record count and modulus
> switch.  You can always run a check on the header with a regex if you don't
> trust it completely.
>
> Just from the sanity point-of-view, unless you're doing a lot of
> validation I wouldn't use Bio::SeqIO::fastq, unless you have some time on
> your hands and a relatively low number of seqs (it's notoriously slow at
> the moment).
>
> chris
>
> On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
>
> > Hi,
> > I'm trying to write a quick script to separate one large PE fastq file
> into
> > 2 separate files, one for each mate pair
> >
> > The file is of the format (mate1)
> > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > +
> > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> >
> > && (mate2)
> >
> > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > +
> > ##################################################
> >
> >
> > My idea is to separate using a regex such that / 1:/ would be the first
> > mate pair and / 2:/ would go in the second mate file.
> > I implemented the code below but each output file is empty. Can someone
> > spot my error?
> >
> > Thanks,
> > Sean.
> >
> > my $infile   = shift;
> > my $outfile1 = $infile."_1";
> > my $outfile2 = $infile."_2";
> >
> > my $seqin = Bio::SeqIO->new(
> >                             -file   => "<$infile",
> >                             -format => "fastq",
> >                             );
> > my $seqout1 = Bio::SeqIO->new(
> >                              -file   => ">$outfile1",
> >                              -format => "fastq",
> >                              );
> >
> > my $seqout2 = Bio::SeqIO->new(
> >                              -file   => ">$outfile2",
> >                              -format => "fastq",
> >                              );
> > while (my $inseq = $seqin->next_seq) {
> >    if ($seqin->desc =~ / 1:/){
> >      $seqout1->write_seq($inseq);
> >    } else {
> >      $seqout2->write_seq($inseq);
> >    }
> > }
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

From cjfields at illinois.edu  Tue Feb 28 21:40:26 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 29 Feb 2012 02:40:26 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROwMidXRobpPcqmNfYs9LYJ7uVvVnb4CV5jiowOHHLBQMA@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
	<CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>
	<CALTeROwMidXRobpPcqmNfYs9LYJ7uVvVnb4CV5jiowOHHLBQMA@mail.gmail.com>
Message-ID: <5AFAB73B-7284-4B42-9810-646B89C83B20@illinois.edu>

That should work.  Can you send the output of 'perldoc Bio::SeqIO::fastq'?  That should indicate what is being called.

chris

On Feb 28, 2012, at 5:50 PM, Sean O'Keeffe wrote:

> $ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
> 1.006001
> 
> Isn't that 1.6.1 - does it need upgrading ?
> 
> On 28 February 2012 18:36, Sean O'Keeffe <limericksean at gmail.com> wrote:
> Could be. I'll check. 
> 
> On 28 February 2012 17:17, Fields, Christopher J <cjfields at illinois.edu> wrote:
> That's a bit odd.  Are you using an old version of the FASTQ parser?  It was revised a while ago, prior to the v1.6.1 release (the error matches one in the older parser)
> 
> chris
> 
> On Feb 28, 2012, at 4:01 PM, Sean O'Keeffe wrote:
> 
> > Hi Chris,
> > Unfortunately the read pairs are not consecutive. It seems they are cat'd together.
> > I could use split -l on the line number that they're glued together I guess.
> > If this is an overnight job for a bunch of files, I can wait so don't mind using the module if it worked.
> >
> > Someone pointed out I need to switch $seqin->desc to $inseq->desc.
> > However, now it spits out fasta output instead of fastq and returns a bunch of warnings: Seq/Qual descriptions don't match; using sequence description
> >
> > Hmm.
> >
> > On 28 February 2012 16:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
> > Sean,
> >
> > If you trust the data enough, in that:
> >
> > 1) each record is 4 lines,
> > 2) mate pairs are consecutive in the file, and
> > 3) that read 1 always preceeds read 2 in the pair,
> >
> > then I would simply iterate through 4 lines at a time and dump to the two separate files, maybe using a flip-flop or simple record count and modulus switch.  You can always run a check on the header with a regex if you don't trust it completely.
> >
> > Just from the sanity point-of-view, unless you're doing a lot of validation I wouldn't use Bio::SeqIO::fastq, unless you have some time on your hands and a relatively low number of seqs (it's notoriously slow at the moment).
> >
> > chris
> >
> > On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
> >
> > > Hi,
> > > I'm trying to write a quick script to separate one large PE fastq file into
> > > 2 separate files, one for each mate pair
> > >
> > > The file is of the format (mate1)
> > > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > > +
> > > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> > >
> > > && (mate2)
> > >
> > > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > > +
> > > ##################################################
> > >
> > >
> > > My idea is to separate using a regex such that / 1:/ would be the first
> > > mate pair and / 2:/ would go in the second mate file.
> > > I implemented the code below but each output file is empty. Can someone
> > > spot my error?
> > >
> > > Thanks,
> > > Sean.
> > >
> > > my $infile   = shift;
> > > my $outfile1 = $infile."_1";
> > > my $outfile2 = $infile."_2";
> > >
> > > my $seqin = Bio::SeqIO->new(
> > >                             -file   => "<$infile",
> > >                             -format => "fastq",
> > >                             );
> > > my $seqout1 = Bio::SeqIO->new(
> > >                              -file   => ">$outfile1",
> > >                              -format => "fastq",
> > >                              );
> > >
> > > my $seqout2 = Bio::SeqIO->new(
> > >                              -file   => ">$outfile2",
> > >                              -format => "fastq",
> > >                              );
> > > while (my $inseq = $seqin->next_seq) {
> > >    if ($seqin->desc =~ / 1:/){
> > >      $seqout1->write_seq($inseq);
> > >    } else {
> > >      $seqout2->write_seq($inseq);
> > >    }
> > > }
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> 
> 
> 



From cjfields at illinois.edu  Tue Feb 28 21:42:27 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 29 Feb 2012 02:42:27 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <4F4EA7A0.9050002@gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E3E60E8-370A-4495-8A59-1B62C59B2AF8@hudsonalpha.org>
	<4F4EA7A0.9050002@gmail.com>
Message-ID: <F8B9BFED-83D8-45BC-A37C-30704111D05A@illinois.edu>

Frankly, there never seemed to be a real fixed standard in the way that FASTQ headers were written (and just when it seems there is some consensus, Illumina pulls the rug out from under you), hence the reason I leave it alone.  We could add some ID munging in there if needed, would just need a qr// with a standard fallback.

chris

On Feb 29, 2012, at 4:33 PM, Florent Angly wrote:

> Also, the desc() method returns the part after the whitespace in the FASTA header.
> Hence, instead of / 1:/, your regular expression should not have the space and should be written /1:/. In fact, it would be even better (faster) it it were written as an anchored regular expression that matches only the beginning of the description, /^1:/
> 
> Note that you are apparently using the latest Illumina format, that does not follow previous convention on paired-end read headers. Hence your script will not work properly with non-latest-Illumina paired-end files.
> 
> Florent
> 
> 
> 
> On 29/02/12 07:26, Michael Muratet wrote:
>> 
>> On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
>> 
>>> Hi,
>>> I'm trying to write a quick script to separate one large PE fastq file into
>>> 2 separate files, one for each mate pair
>>> 
>>> The file is of the format (mate1)
>>> @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
>>> CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
>>> +
>>> BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
>>> 
>>> && (mate2)
>>> 
>>> @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
>>> TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
>>> +
>>> ##################################################
>>> 
>>> 
>>> My idea is to separate using a regex such that / 1:/ would be the first
>>> mate pair and / 2:/ would go in the second mate file.
>>> I implemented the code below but each output file is empty. Can someone
>>> spot my error?
>>> 
>>> Thanks,
>>> Sean.
>>> 
>>> my $infile   = shift;
>>> my $outfile1 = $infile."_1";
>>> my $outfile2 = $infile."_2";
>>> 
>>> my $seqin = Bio::SeqIO->new(
>>>                            -file   => "<$infile",
>>>                            -format => "fastq",
>>>                            );
>>> my $seqout1 = Bio::SeqIO->new(
>>>                             -file   => ">$outfile1",
>>>                             -format => "fastq",
>>>                             );
>>> 
>>> my $seqout2 = Bio::SeqIO->new(
>>>                             -file   => ">$outfile2",
>>>                             -format => "fastq",
>>>                             );
>>> while (my $inseq = $seqin->next_seq) {
>>>   if ($seqin->desc =~ / 1:/){
>> Hi Sean
>> 
>> You're using the desc operator on the stream, not the seq object.
>> 
>> Cheers
>> 
>> Mike
>> 
>>>     $seqout1->write_seq($inseq);
>>>   } else {
>>>     $seqout2->write_seq($inseq);
>>>   }
>>> }
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> Michael Muratet, Ph.D.
>> Senior Scientist
>> HudsonAlpha Institute for Biotechnology
>> mmuratet at hudsonalpha.org
>> (256) 327-0473 (p)
>> (256) 327-0966 (f)
>> 
>> Room 4005
>> 601 Genome Way
>> Huntsville, Alabama 35806
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
>> 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 limericksean at gmail.com  Tue Feb 28 18:36:43 2012
From: limericksean at gmail.com (Sean O'Keeffe)
Date: Tue, 28 Feb 2012 18:36:43 -0500
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
Message-ID: <CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>

Could be. I'll check.

On 28 February 2012 17:17, Fields, Christopher J <cjfields at illinois.edu>wrote:

> That's a bit odd.  Are you using an old version of the FASTQ parser?  It
> was revised a while ago, prior to the v1.6.1 release (the error matches one
> in the older parser)
>
> chris
>
> On Feb 28, 2012, at 4:01 PM, Sean O'Keeffe wrote:
>
> > Hi Chris,
> > Unfortunately the read pairs are not consecutive. It seems they are
> cat'd together.
> > I could use split -l on the line number that they're glued together I
> guess.
> > If this is an overnight job for a bunch of files, I can wait so don't
> mind using the module if it worked.
> >
> > Someone pointed out I need to switch $seqin->desc to $inseq->desc.
> > However, now it spits out fasta output instead of fastq and returns a
> bunch of warnings: Seq/Qual descriptions don't match; using sequence
> description
> >
> > Hmm.
> >
> > On 28 February 2012 16:50, Fields, Christopher J <cjfields at illinois.edu>
> wrote:
> > Sean,
> >
> > If you trust the data enough, in that:
> >
> > 1) each record is 4 lines,
> > 2) mate pairs are consecutive in the file, and
> > 3) that read 1 always preceeds read 2 in the pair,
> >
> > then I would simply iterate through 4 lines at a time and dump to the
> two separate files, maybe using a flip-flop or simple record count and
> modulus switch.  You can always run a check on the header with a regex if
> you don't trust it completely.
> >
> > Just from the sanity point-of-view, unless you're doing a lot of
> validation I wouldn't use Bio::SeqIO::fastq, unless you have some time on
> your hands and a relatively low number of seqs (it's notoriously slow at
> the moment).
> >
> > chris
> >
> > On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
> >
> > > Hi,
> > > I'm trying to write a quick script to separate one large PE fastq file
> into
> > > 2 separate files, one for each mate pair
> > >
> > > The file is of the format (mate1)
> > > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > > +
> > > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> > >
> > > && (mate2)
> > >
> > > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > > +
> > > ##################################################
> > >
> > >
> > > My idea is to separate using a regex such that / 1:/ would be the first
> > > mate pair and / 2:/ would go in the second mate file.
> > > I implemented the code below but each output file is empty. Can someone
> > > spot my error?
> > >
> > > Thanks,
> > > Sean.
> > >
> > > my $infile   = shift;
> > > my $outfile1 = $infile."_1";
> > > my $outfile2 = $infile."_2";
> > >
> > > my $seqin = Bio::SeqIO->new(
> > >                             -file   => "<$infile",
> > >                             -format => "fastq",
> > >                             );
> > > my $seqout1 = Bio::SeqIO->new(
> > >                              -file   => ">$outfile1",
> > >                              -format => "fastq",
> > >                              );
> > >
> > > my $seqout2 = Bio::SeqIO->new(
> > >                              -file   => ">$outfile2",
> > >                              -format => "fastq",
> > >                              );
> > > while (my $inseq = $seqin->next_seq) {
> > >    if ($seqin->desc =~ / 1:/){
> > >      $seqout1->write_seq($inseq);
> > >    } else {
> > >      $seqout2->write_seq($inseq);
> > >    }
> > > }
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>

From limericksean at gmail.com  Tue Feb 28 18:50:25 2012
From: limericksean at gmail.com (Sean O'Keeffe)
Date: Tue, 28 Feb 2012 18:50:25 -0500
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
	<CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>
Message-ID: <CALTeROwMidXRobpPcqmNfYs9LYJ7uVvVnb4CV5jiowOHHLBQMA@mail.gmail.com>

$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
1.006001

Isn't that 1.6.1 - does it need upgrading ?

On 28 February 2012 18:36, Sean O'Keeffe <limericksean at gmail.com> wrote:

> Could be. I'll check.
>
> On 28 February 2012 17:17, Fields, Christopher J <cjfields at illinois.edu>wrote:
>
>> That's a bit odd.  Are you using an old version of the FASTQ parser?  It
>> was revised a while ago, prior to the v1.6.1 release (the error matches one
>> in the older parser)
>>
>> chris
>>
>> On Feb 28, 2012, at 4:01 PM, Sean O'Keeffe wrote:
>>
>> > Hi Chris,
>> > Unfortunately the read pairs are not consecutive. It seems they are
>> cat'd together.
>> > I could use split -l on the line number that they're glued together I
>> guess.
>> > If this is an overnight job for a bunch of files, I can wait so don't
>> mind using the module if it worked.
>> >
>> > Someone pointed out I need to switch $seqin->desc to $inseq->desc.
>> > However, now it spits out fasta output instead of fastq and returns a
>> bunch of warnings: Seq/Qual descriptions don't match; using sequence
>> description
>> >
>> > Hmm.
>> >
>> > On 28 February 2012 16:50, Fields, Christopher J <cjfields at illinois.edu>
>> wrote:
>> > Sean,
>> >
>> > If you trust the data enough, in that:
>> >
>> > 1) each record is 4 lines,
>> > 2) mate pairs are consecutive in the file, and
>> > 3) that read 1 always preceeds read 2 in the pair,
>> >
>> > then I would simply iterate through 4 lines at a time and dump to the
>> two separate files, maybe using a flip-flop or simple record count and
>> modulus switch.  You can always run a check on the header with a regex if
>> you don't trust it completely.
>> >
>> > Just from the sanity point-of-view, unless you're doing a lot of
>> validation I wouldn't use Bio::SeqIO::fastq, unless you have some time on
>> your hands and a relatively low number of seqs (it's notoriously slow at
>> the moment).
>> >
>> > chris
>> >
>> > On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
>> >
>> > > Hi,
>> > > I'm trying to write a quick script to separate one large PE fastq
>> file into
>> > > 2 separate files, one for each mate pair
>> > >
>> > > The file is of the format (mate1)
>> > > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
>> > > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
>> > > +
>> > > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
>> > >
>> > > && (mate2)
>> > >
>> > > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
>> > > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
>> > > +
>> > > ##################################################
>> > >
>> > >
>> > > My idea is to separate using a regex such that / 1:/ would be the
>> first
>> > > mate pair and / 2:/ would go in the second mate file.
>> > > I implemented the code below but each output file is empty. Can
>> someone
>> > > spot my error?
>> > >
>> > > Thanks,
>> > > Sean.
>> > >
>> > > my $infile   = shift;
>> > > my $outfile1 = $infile."_1";
>> > > my $outfile2 = $infile."_2";
>> > >
>> > > my $seqin = Bio::SeqIO->new(
>> > >                             -file   => "<$infile",
>> > >                             -format => "fastq",
>> > >                             );
>> > > my $seqout1 = Bio::SeqIO->new(
>> > >                              -file   => ">$outfile1",
>> > >                              -format => "fastq",
>> > >                              );
>> > >
>> > > my $seqout2 = Bio::SeqIO->new(
>> > >                              -file   => ">$outfile2",
>> > >                              -format => "fastq",
>> > >                              );
>> > > while (my $inseq = $seqin->next_seq) {
>> > >    if ($seqin->desc =~ / 1:/){
>> > >      $seqout1->write_seq($inseq);
>> > >    } else {
>> > >      $seqout2->write_seq($inseq);
>> > >    }
>> > > }
>> > > _______________________________________________
>> > > Bioperl-l mailing list
>> > > Bioperl-l at lists.open-bio.org
>> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>> >
>>
>>
>

From p.j.a.cock at googlemail.com  Wed Feb 29 05:32:20 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Feb 2012 10:32:20 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <F8B9BFED-83D8-45BC-A37C-30704111D05A@illinois.edu>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E3E60E8-370A-4495-8A59-1B62C59B2AF8@hudsonalpha.org>
	<4F4EA7A0.9050002@gmail.com>
	<F8B9BFED-83D8-45BC-A37C-30704111D05A@illinois.edu>
Message-ID: <CAKVJ-_5S0DoRh-NzEtjvJue7Oso6fjefhRRaBDLUK7V+rHQSLQ@mail.gmail.com>

On Wed, Feb 29, 2012 at 2:42 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Frankly, there never seemed to be a real fixed standard in the way that FASTQ
> headers were written (and just when it seems there is some consensus, Illumina
> pulls the rug out from under you), hence the reason I leave it alone. ?We could
> add some ID munging in there if needed, would just need a qr// with a standard
> fallback.
>
> chris

Indeed - just like FASTA, it seems every company/tool/database has its own
conventions about the FASTQ ID line and how to stuff as much meta-data
into it as possible. This is a major reason why I hope unaligned reads in
SAM/BAM takes off - places like the Sanger and Broad use this in their
pipelines.

http://blastedbio.blogspot.com/2011/10/fastq-must-die-long-live-sambam.html

Peter


From mmuratet at hudsonalpha.org  Wed Feb 29 08:07:48 2012
From: mmuratet at hudsonalpha.org (Michael Muratet)
Date: Wed, 29 Feb 2012 07:07:48 -0600
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
Message-ID: <C2CD1913-98AF-4AD9-A1CB-E79115886A89@hudsonalpha.org>


On Feb 28, 2012, at 4:01 PM, Sean O'Keeffe wrote:

> Hi Chris,
> Unfortunately the read pairs are not consecutive. It seems they are  
> cat'd
> together.
> I could use split -l on the line number that they're glued together  
> I guess.
> If this is an overnight job for a bunch of files, I can wait so  
> don't mind
> using the module if it worked.
>
> Someone pointed out I need to switch $seqin->desc to $inseq->desc.
> However, now it spits out fasta output instead of fastq and returns  
> a bunch
> of warnings: Seq/Qual descriptions don't match; using sequence  
> description
Hi Sean
Apparently the bioperl parser expects the the 'second' header line,  
i.e.,

@first_header
sequence
+second_header
quality_scores

to have the same (redundant) identifier. When it encounters a blank  
line, which is the way the Illumina pipeline writes it out, it warns  
you.

I think you have to explicitly write out the quality scores in fastq  
format.

Cheers

Mike

>
> Hmm.
>
> On 28 February 2012 16:50, Fields, Christopher J <cjfields at illinois.edu 
> >wrote:
>
>> Sean,
>>
>> If you trust the data enough, in that:
>>
>> 1) each record is 4 lines,
>> 2) mate pairs are consecutive in the file, and
>> 3) that read 1 always preceeds read 2 in the pair,
>>
>> then I would simply iterate through 4 lines at a time and dump to  
>> the two
>> separate files, maybe using a flip-flop or simple record count and  
>> modulus
>> switch.  You can always run a check on the header with a regex if  
>> you don't
>> trust it completely.
>>
>> Just from the sanity point-of-view, unless you're doing a lot of
>> validation I wouldn't use Bio::SeqIO::fastq, unless you have some  
>> time on
>> your hands and a relatively low number of seqs (it's notoriously  
>> slow at
>> the moment).
>>
>> chris
>>
>> On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
>>
>>> Hi,
>>> I'm trying to write a quick script to separate one large PE fastq  
>>> file
>> into
>>> 2 separate files, one for each mate pair
>>>
>>> The file is of the format (mate1)
>>> @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
>>> CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
>>> +
>>> BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
>>>
>>> && (mate2)
>>>
>>> @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
>>> TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
>>> +
>>> ##################################################
>>>
>>>
>>> My idea is to separate using a regex such that / 1:/ would be the  
>>> first
>>> mate pair and / 2:/ would go in the second mate file.
>>> I implemented the code below but each output file is empty. Can  
>>> someone
>>> spot my error?
>>>
>>> Thanks,
>>> Sean.
>>>
>>> my $infile   = shift;
>>> my $outfile1 = $infile."_1";
>>> my $outfile2 = $infile."_2";
>>>
>>> my $seqin = Bio::SeqIO->new(
>>>                            -file   => "<$infile",
>>>                            -format => "fastq",
>>>                            );
>>> my $seqout1 = Bio::SeqIO->new(
>>>                             -file   => ">$outfile1",
>>>                             -format => "fastq",
>>>                             );
>>>
>>> my $seqout2 = Bio::SeqIO->new(
>>>                             -file   => ">$outfile2",
>>>                             -format => "fastq",
>>>                             );
>>> while (my $inseq = $seqin->next_seq) {
>>>   if ($seqin->desc =~ / 1:/){
>>>     $seqout1->write_seq($inseq);
>>>   } else {
>>>     $seqout2->write_seq($inseq);
>>>   }
>>> }
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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

Room 4005
601 Genome Way
Huntsville, Alabama 35806






From fs5 at sanger.ac.uk  Fri Feb 24 12:28:56 2012
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 24 Feb 2012 17:28:56 +0000
Subject: [Bioperl-l] BLAST example doesn't work
In-Reply-To: <33362540.post@talk.nabble.com>
References: <33362540.post@talk.nabble.com>
Message-ID: <4F47C8D8.9080302@sanger.ac.uk>

it seems that the command line is incorrectly constructed as "blastall 
run ..." and I guess that's because the StandAloneBlast module didn't 
see your "program" parameter.

try:

my $factory = Bio::Tools::Run::StandAloneBlast->new(

   -program =>  'blastn',

   -database =>  'nr',

   -e =>  '1e-5'

);


(parameter keys should start with "-")


Hope that helps

Frank




On 21/02/12 09:16, Enzyme wrote:
> use Bio::Tools::Run::StandAloneBlast;
> my $factory = Bio::Tools::Run::StandAloneBlast->new(p =>  'blastn',
>                                                      d =>  'nr',
>                                                      e =>  '1e-5');
> my $seq = Bio::PrimarySeq->new(-id =>  'test1',
>                                 -seq =>  'AGATCAGTAGATGATAGGGGTAGA');
> my $report = $factory->blastall($seq); # get back a {{PM|Bio::SearchIO}}
> report


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From cjfields at illinois.edu  Wed Feb 29 09:38:50 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 29 Feb 2012 14:38:50 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <C2CD1913-98AF-4AD9-A1CB-E79115886A89@hudsonalpha.org>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<C2CD1913-98AF-4AD9-A1CB-E79115886A89@hudsonalpha.org>
Message-ID: <2DC85C62-F086-41D9-A812-B8BFBBF95517@illinois.edu>

On Feb 29, 2012, at 7:07 AM, Michael Muratet wrote:

> On Feb 28, 2012, at 4:01 PM, Sean O'Keeffe wrote:
> 
>> Hi Chris,
>> Unfortunately the read pairs are not consecutive. It seems they are cat'd
>> together.
>> I could use split -l on the line number that they're glued together I guess.
>> If this is an overnight job for a bunch of files, I can wait so don't mind
>> using the module if it worked.
>> 
>> Someone pointed out I need to switch $seqin->desc to $inseq->desc.
>> However, now it spits out fasta output instead of fastq and returns a bunch
>> of warnings: Seq/Qual descriptions don't match; using sequence description
> Hi Sean
> Apparently the bioperl parser expects the the 'second' header line, i.e.,
> 
> @first_header
> sequence
> +second_header
> quality_scores
> 
> to have the same (redundant) identifier. When it encounters a blank line, which is the way the Illumina pipeline writes it out, it warns you.
> 
> I think you have to explicitly write out the quality scores in fastq format.
> 
> Cheers
> 
> Mike

Actually no, that's not true for the latest versions.  It was completely refactored in coordination with Peter Cock (Biopython) and the other Bio* toolkits along with EMBOSS to parse a wide range of FASTQ data (including the solexa/illumina variants), and also attempt to catch bad formatting issues.  See this pub:

http://www.ncbi.nlm.nih.gov/pubmed/20015970

This is one of the primary test examples that passes:

@EAS54_6_R1_2_1_413_324
CCCTTCTTGTCTTCAGCGTTTCTCC
+
;;3;;;;;;;;;;;;7;;;;;;;88
@EAS54_6_R1_2_1_540_792
TTGGCAGGCCAAGGCCGATGGATCA
+
;;;;;;;;;;;7;;;;;-;;;3;83
@EAS54_6_R1_2_1_443_348
GTTGCTTCTGGCGTGGGTGGGGGGG
+
;;;;;;;;;;;9;7;;.7;393333


chris



From fs5 at sanger.ac.uk  Mon Feb 27 04:48:30 2012
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Mon, 27 Feb 2012 09:48:30 +0000
Subject: [Bioperl-l] Fate of Bio::Tools::PCRSimulation
In-Reply-To: <4F49D4B6.5050301@gmail.com>
References: <4F49D4B6.5050301@gmail.com>
Message-ID: <4F4B516E.9090407@sanger.ac.uk>

Hi Florent,

I was recently thiking about something similar when adding 
delete/insert/ligate methods to Bio:;SeqUtils (now in bioperl-live). I 
was about to add a PCR method as well and I think it would fit in with 
that module. Similar to other methods in this module, the PCR method 
should be able to handle sequence features and annotations, so that the 
amplicons are fully annotated. I'd be willing to discuss this further 
and work with yuo on that if you like.

Cheers,

Frank


On 26/02/12 06:44, Florent Angly wrote:
> Hi all,
>
> I am interested in the Bio::Tools::PCRSimulation module. Supposedly it
> was added to Bioperl 0.3 and is also mentionned in the Bio::PrimedSeq
> module. However, I cannot find in the current Bioperl codebase. Any idea
> where it went?
>
> The reason I am asking is because I have some code to do silico PCR
> using regular expressions. I wanted to modularize my code more and make
> it into a module for Bioperl. Of course, if there is something similar
> in Bioperl already, I need to have a look at it. If there is nothing
> similar, what namespace do you suggest to use?
> Bio::Tools::AmpliconExtractor? Bio::Tools::AmpliconSearch?
> Bio::Tools::InSilicoPCR?
>
> Thanks,
>
> Florent
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From cjfields at illinois.edu  Wed Feb 29 10:23:54 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 29 Feb 2012 15:23:54 +0000
Subject: [Bioperl-l] Fate of Bio::Tools::PCRSimulation
In-Reply-To: <4F4E3EEF.5050506@cam.ac.uk>
References: <4F49D4B6.5050301@gmail.com>
	<D60FDDB5-5EC6-4A91-954B-3A3EB27921CF@illinois.edu>
	<4F4E3EEF.5050506@cam.ac.uk>
Message-ID: <4325EF60-919F-46EF-91BB-D31160F0B587@illinois.edu>

Seems like it was meant to be added at some point but was never committed.  Definitely not in the github history for 1.3.x, this commit corresponds to the v1.3.4 tag:

   https://github.com/bioperl/bioperl-live/tree/0a67fa444eb19a70876017607f70ab72be38755a

and it's not there.  

I agree with Roy, it would be nice to somehow make this a little more generic or pluggable on how it maps primers (maybe with a default pure perl method).  I also think this shouldn't be bound to bioperl-live considering our current plans, it would best happen in a separate repo.

chris

On Feb 29, 2012, at 9:06 AM, Roy Chaudhuri wrote:

> The code for Bio::Tools::PCRSimulation can be downloaded as part of this archive:
> http://www.salmonella.org/bioperl/primer3_v0.3.tgz
> 
> (There's supposedly a more recent version here:
> http://www.salmonella.org/bioperl/nucleotide_analyses.tgz
> but that file seems to be truncated).
> 
> I have no idea how much would be salvagable. It seems to just use index to map the primers to the sequence, I guess it would make more sense to at least give the option of something more sophisticated like Primer3, BLAST or even a short read mapper.
> 
> Cheers,
> Roy.
> 
> 
> On 27/02/2012 21:18, Fields, Christopher J wrote:
>> On Feb 26, 2012, at 12:44 AM, Florent Angly wrote:
>> 
>>> Hi all,
>>> 
>>> I am interested in the Bio::Tools::PCRSimulation module. Supposedly
>>> it was added to Bioperl 0.3 and is also mentionned in the
>>> Bio::PrimedSeq module. However, I cannot find in the current
>>> Bioperl codebase. Any idea where it went?
>> 
>> No idea; I can't find it anywhere in the code base either, and the
>> github repo contains history going back to the original CVS repo.
>> You can try contacting the author, possibly.
>> 
>>> The reason I am asking is because I have some code to do silico PCR
>>> using regular expressions. I wanted to modularize my code more and
>>> make it into a module for Bioperl. Of course, if there is something
>>> similar in Bioperl already, I need to have a look at it. If there
>>> is nothing similar, what namespace do you suggest to use?
>>> Bio::Tools::AmpliconExtractor? Bio::Tools::AmpliconSearch?
>>> Bio::Tools::InSilicoPCR?
>>> 
>>> Thanks,
>>> 
>>> Florent
>> 
>> 
>> Maybe the last (InSilicoPCR).
>> 
>> chris
>> 
>> 
>> _______________________________________________ Bioperl-l mailing
>> list Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From cjfields at illinois.edu  Wed Feb 29 10:27:38 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 29 Feb 2012 15:27:38 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CAKVJ-_5S0DoRh-NzEtjvJue7Oso6fjefhRRaBDLUK7V+rHQSLQ@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E3E60E8-370A-4495-8A59-1B62C59B2AF8@hudsonalpha.org>
	<4F4EA7A0.9050002@gmail.com>
	<F8B9BFED-83D8-45BC-A37C-30704111D05A@illinois.edu>
	<CAKVJ-_5S0DoRh-NzEtjvJue7Oso6fjefhRRaBDLUK7V+rHQSLQ@mail.gmail.com>
Message-ID: <3E9B001D-89E5-42B6-835D-96D8CE362AE3@illinois.edu>

On Feb 29, 2012, at 4:32 AM, Peter Cock wrote:

> On Wed, Feb 29, 2012 at 2:42 AM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> Frankly, there never seemed to be a real fixed standard in the way that FASTQ
>> headers were written (and just when it seems there is some consensus, Illumina
>> pulls the rug out from under you), hence the reason I leave it alone.  We could
>> add some ID munging in there if needed, would just need a qr// with a standard
>> fallback.
>> 
>> chris
> 
> Indeed - just like FASTA, it seems every company/tool/database has its own
> conventions about the FASTQ ID line and how to stuff as much meta-data
> into it as possible. This is a major reason why I hope unaligned reads in
> SAM/BAM takes off - places like the Sanger and Broad use this in their
> pipelines.
> 
> http://blastedbio.blogspot.com/2011/10/fastq-must-die-long-live-sambam.html
> 
> Peter

Unaligned BAM makes the most sense.  I've also been talking with the HDF5 folks here sporadically, they're still keen on promoting BioHDF (it is pretty fast), though that has cooled considerably.

Anyone working directly with CRAM in their pipelines?

chris

From p.j.a.cock at googlemail.com  Wed Feb 29 10:32:55 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Feb 2012 15:32:55 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <3E9B001D-89E5-42B6-835D-96D8CE362AE3@illinois.edu>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E3E60E8-370A-4495-8A59-1B62C59B2AF8@hudsonalpha.org>
	<4F4EA7A0.9050002@gmail.com>
	<F8B9BFED-83D8-45BC-A37C-30704111D05A@illinois.edu>
	<CAKVJ-_5S0DoRh-NzEtjvJue7Oso6fjefhRRaBDLUK7V+rHQSLQ@mail.gmail.com>
	<3E9B001D-89E5-42B6-835D-96D8CE362AE3@illinois.edu>
Message-ID: <CAKVJ-_5dhy7Js6Y67fPmS-_f+=UKF=NFY40CQuD=SnoFFHLUhw@mail.gmail.com>

On Wed, Feb 29, 2012 at 3:27 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> On Feb 29, 2012, at 4:32 AM, Peter Cock wrote:
>
>> On Wed, Feb 29, 2012 at 2:42 AM, Fields, Christopher J
>> <cjfields at illinois.edu> wrote:
>>> Frankly, there never seemed to be a real fixed standard in the way that FASTQ
>>> headers were written (and just when it seems there is some consensus, Illumina
>>> pulls the rug out from under you), hence the reason I leave it alone. ?We could
>>> add some ID munging in there if needed, would just need a qr// with a standard
>>> fallback.
>>>
>>> chris
>>
>> Indeed - just like FASTA, it seems every company/tool/database has its own
>> conventions about the FASTQ ID line and how to stuff as much meta-data
>> into it as possible. This is a major reason why I hope unaligned reads in
>> SAM/BAM takes off - places like the Sanger and Broad use this in their
>> pipelines.
>>
>> http://blastedbio.blogspot.com/2011/10/fastq-must-die-long-live-sambam.html
>>
>> Peter
>
> Unaligned BAM makes the most sense. ?I've also been talking with the
> HDF5 folks here sporadically, they're still keen on promoting BioHDF
> (it is pretty fast), though that has cooled considerably.
>
> Anyone working directly with CRAM in their pipelines?
>
> chris

I understand that Sanger are looking at moving their pipelines from BAM to
CRAM later this year, but CRAM is still quite new and in flux.

Peter


From cjfields at illinois.edu  Wed Feb 29 10:56:11 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 29 Feb 2012 15:56:11 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CAKVJ-_5dhy7Js6Y67fPmS-_f+=UKF=NFY40CQuD=SnoFFHLUhw@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E3E60E8-370A-4495-8A59-1B62C59B2AF8@hudsonalpha.org>
	<4F4EA7A0.9050002@gmail.com>
	<F8B9BFED-83D8-45BC-A37C-30704111D05A@illinois.edu>
	<CAKVJ-_5S0DoRh-NzEtjvJue7Oso6fjefhRRaBDLUK7V+rHQSLQ@mail.gmail.com>
	<3E9B001D-89E5-42B6-835D-96D8CE362AE3@illinois.edu>
	<CAKVJ-_5dhy7Js6Y67fPmS-_f+=UKF=NFY40CQuD=SnoFFHLUhw@mail.gmail.com>
Message-ID: <A59198B4-56CE-406B-994E-86118DDCCE0F@illinois.edu>


On Feb 29, 2012, at 9:32 AM, Peter Cock wrote:

> On Wed, Feb 29, 2012 at 3:27 PM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> On Feb 29, 2012, at 4:32 AM, Peter Cock wrote:
>> 
>>> On Wed, Feb 29, 2012 at 2:42 AM, Fields, Christopher J
>>> <cjfields at illinois.edu> wrote:
>>>> Frankly, there never seemed to be a real fixed standard in the way that FASTQ
>>>> headers were written (and just when it seems there is some consensus, Illumina
>>>> pulls the rug out from under you), hence the reason I leave it alone.  We could
>>>> add some ID munging in there if needed, would just need a qr// with a standard
>>>> fallback.
>>>> 
>>>> chris
>>> 
>>> Indeed - just like FASTA, it seems every company/tool/database has its own
>>> conventions about the FASTQ ID line and how to stuff as much meta-data
>>> into it as possible. This is a major reason why I hope unaligned reads in
>>> SAM/BAM takes off - places like the Sanger and Broad use this in their
>>> pipelines.
>>> 
>>> http://blastedbio.blogspot.com/2011/10/fastq-must-die-long-live-sambam.html
>>> 
>>> Peter
>> 
>> Unaligned BAM makes the most sense.  I've also been talking with the
>> HDF5 folks here sporadically, they're still keen on promoting BioHDF
>> (it is pretty fast), though that has cooled considerably.
>> 
>> Anyone working directly with CRAM in their pipelines?
>> 
>> chris
> 
> I understand that Sanger are looking at moving their pipelines from BAM to
> CRAM later this year, but CRAM is still quite new and in flux.
> 
> Peter

Yeah, I wasn't sure how the community outside of Sanger is approaching this.  

chris

From rrc22 at cam.ac.uk  Wed Feb 29 10:06:23 2012
From: rrc22 at cam.ac.uk (Roy Chaudhuri)
Date: Wed, 29 Feb 2012 15:06:23 +0000
Subject: [Bioperl-l] Fate of Bio::Tools::PCRSimulation
In-Reply-To: <D60FDDB5-5EC6-4A91-954B-3A3EB27921CF@illinois.edu>
References: <4F49D4B6.5050301@gmail.com>
	<D60FDDB5-5EC6-4A91-954B-3A3EB27921CF@illinois.edu>
Message-ID: <4F4E3EEF.5050506@cam.ac.uk>

The code for Bio::Tools::PCRSimulation can be downloaded as part of this 
archive:
http://www.salmonella.org/bioperl/primer3_v0.3.tgz

(There's supposedly a more recent version here:
http://www.salmonella.org/bioperl/nucleotide_analyses.tgz
but that file seems to be truncated).

I have no idea how much would be salvagable. It seems to just use index 
to map the primers to the sequence, I guess it would make more sense to 
at least give the option of something more sophisticated like Primer3, 
BLAST or even a short read mapper.

Cheers,
Roy.


On 27/02/2012 21:18, Fields, Christopher J wrote:
> On Feb 26, 2012, at 12:44 AM, Florent Angly wrote:
>
>> Hi all,
>>
>> I am interested in the Bio::Tools::PCRSimulation module. Supposedly
>> it was added to Bioperl 0.3 and is also mentionned in the
>> Bio::PrimedSeq module. However, I cannot find in the current
>> Bioperl codebase. Any idea where it went?
>
> No idea; I can't find it anywhere in the code base either, and the
> github repo contains history going back to the original CVS repo.
> You can try contacting the author, possibly.
>
>> The reason I am asking is because I have some code to do silico PCR
>> using regular expressions. I wanted to modularize my code more and
>> make it into a module for Bioperl. Of course, if there is something
>> similar in Bioperl already, I need to have a look at it. If there
>> is nothing similar, what namespace do you suggest to use?
>> Bio::Tools::AmpliconExtractor? Bio::Tools::AmpliconSearch?
>> Bio::Tools::InSilicoPCR?
>>
>> Thanks,
>>
>> Florent
>
>
> Maybe the last (InSilicoPCR).
>
> chris
>
>
> _______________________________________________ Bioperl-l mailing
> list Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From limericksean at gmail.com  Wed Feb 29 11:30:05 2012
From: limericksean at gmail.com (Sean O'Keeffe)
Date: Wed, 29 Feb 2012 11:30:05 -0500
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <5AFAB73B-7284-4B42-9810-646B89C83B20@illinois.edu>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
	<CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>
	<CALTeROwMidXRobpPcqmNfYs9LYJ7uVvVnb4CV5jiowOHHLBQMA@mail.gmail.com>
	<5AFAB73B-7284-4B42-9810-646B89C83B20@illinois.edu>
Message-ID: <CALTeROyvXQX1cRM6BxYcGUf0RR9KOxCwde53cQq0KNN6GErFOA@mail.gmail.com>

Hi Chris,
Here's the perldoc for fastq - it does seem to indicate that the optional
descriptor (+) must match the first header. (See DESCRIPTION).
Maybe this version doesn't include the updated code you mention which Peter
Cock has worked on.

Sean.

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

Bio::SeqIO::fastq(3)  User Contributed Perl Documentation
Bio::SeqIO::fastq(3)

NAME
       Bio::SeqIO::fastq - fastq sequence input/output stream

SYNOPSIS
         ################## pertains to FASTQ parsing only
##################

         # grabs the FASTQ parser, specifies the Illumina variant
         my $in = Bio::SeqIO->new(-format    => ?fastq-illumina?,
                                  -file      => ?mydata.fq?);

         # simple ?fastq? format defaults to ?sanger? variant
         my $out = Bio::SeqIO->new(-format    => ?fastq?,
                                  -file      => ?>mydata.fq?);

         # $seq is a Bio::Seq::Quality object
         while (my $seq = $in->next_seq) {
             $out->write_seq($seq);  # convert Illumina 1.3 to Sanger format
         }

         # for 4x faster parsing, one can do something like this for raw
data
         use Bio::Seq::Quality;

         # $data is a hash reference containing all arguments to be passed
to
         # the Bio::Seq::Quality constructor
         while (my $data = $in->next_dataset) {
             # process $data, such as trim, etc
             my $seq = Bio::Seq::Quality->new(%$data);

             # for now, write_seq only accepts Bio::Seq::Quality, but may
be modified
             # to allow raw hash references for speed
             $out->write_seq($data);
         }

DESCRIPTION
       This object can transform Bio::Seq and Bio::Seq::Quality objects to
and from FASTQ flat file databases.

       FASTQ is a file format used frequently at the Sanger Centre and in
next-gen sequencing to bundle a FASTA sequence and its quality data. A
typical FASTQ entry takes the from:

         @HCDPQ1D0501
         GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT.....
         +HCDPQ1D0501
         !??*((((***+))%%%++)(%%%%).1***-+*??))**55CCF>>>>>>CCCCCCC65.....

       where:

         @ = descriptor, followed by one or more sequence lines
         + = optional descriptor (if present, must match first one),
followed by one or
             more qual lines

       FASTQ and Bio::Seq::Quality mapping

       FASTQ files have sequence and quality data on single line or
multiple lines, and the quality values are single-byte encoded. Data are
mapped very simply to Bio::Seq::Quality instances:

           Data                                        Bio::Seq::Quality
method

------------------------------------------------------------------------
           first non-whitespace chars in descriptor    id^
           descriptor line                             desc^
           sequence lines                              seq
           quality                                     qual*
           FASTQ variant                               namespace

           ^ first nonwhitespace chars are id(), everything else after (to
end of line)
             is in desc()
           * Converted to PHRED quality scores where applicable (?solexa?)

       FASTQ variants

       This parser supports all variants of FASTQ, including Illumina v 1.0
and 1.3:

           variant                note
           -----------------------------------------------------------
           sanger                 original
           solexa                 Solexa, Inc. (2004), aka Illumina 1.0
           illumina               Illumina 1.3

       The variant can be specified by passing by either passing the
additional -variant parameter to the constructor:

         my $in = Bio::SeqIO->new(-format    => ?fastq?,
                                  -variant   => ?solexa?,
                                  -file      => ?mysol.fq?);

       or by passing the format and variant together (Bio::SeqIO will now
handle this and convert it accordingly to the proper argument):

         my $in = Bio::SeqIO->new(-format    => ?fastq-solexa?,
                                  -file      => ?mysol.fq?);

       Variants can be converted back and forth from one another; however,
due to the difference in scaling for solexa quality reads, converting from
?illumina? or ?sanger? FASTQ to solexa is not recommended.
....

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

On 28 February 2012 21:40, Fields, Christopher J <cjfields at illinois.edu>wrote:

> That should work.  Can you send the output of 'perldoc Bio::SeqIO::fastq'?
>  That should indicate what is being called.
>
> chris
>
> On Feb 28, 2012, at 5:50 PM, Sean O'Keeffe wrote:
>
> > $ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
> > 1.006001
> >
> > Isn't that 1.6.1 - does it need upgrading ?
> >
> > On 28 February 2012 18:36, Sean O'Keeffe <limericksean at gmail.com> wrote:
> > Could be. I'll check.
> >
> > On 28 February 2012 17:17, Fields, Christopher J <cjfields at illinois.edu>
> wrote:
> > That's a bit odd.  Are you using an old version of the FASTQ parser?  It
> was revised a while ago, prior to the v1.6.1 release (the error matches one
> in the older parser)
> >
> > chris
> >
> > On Feb 28, 2012, at 4:01 PM, Sean O'Keeffe wrote:
> >
> > > Hi Chris,
> > > Unfortunately the read pairs are not consecutive. It seems they are
> cat'd together.
> > > I could use split -l on the line number that they're glued together I
> guess.
> > > If this is an overnight job for a bunch of files, I can wait so don't
> mind using the module if it worked.
> > >
> > > Someone pointed out I need to switch $seqin->desc to $inseq->desc.
> > > However, now it spits out fasta output instead of fastq and returns a
> bunch of warnings: Seq/Qual descriptions don't match; using sequence
> description
> > >
> > > Hmm.
> > >
> > > On 28 February 2012 16:50, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
> > > Sean,
> > >
> > > If you trust the data enough, in that:
> > >
> > > 1) each record is 4 lines,
> > > 2) mate pairs are consecutive in the file, and
> > > 3) that read 1 always preceeds read 2 in the pair,
> > >
> > > then I would simply iterate through 4 lines at a time and dump to the
> two separate files, maybe using a flip-flop or simple record count and
> modulus switch.  You can always run a check on the header with a regex if
> you don't trust it completely.
> > >
> > > Just from the sanity point-of-view, unless you're doing a lot of
> validation I wouldn't use Bio::SeqIO::fastq, unless you have some time on
> your hands and a relatively low number of seqs (it's notoriously slow at
> the moment).
> > >
> > > chris
> > >
> > > On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
> > >
> > > > Hi,
> > > > I'm trying to write a quick script to separate one large PE fastq
> file into
> > > > 2 separate files, one for each mate pair
> > > >
> > > > The file is of the format (mate1)
> > > > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > > > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > > > +
> > > > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> > > >
> > > > && (mate2)
> > > >
> > > > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > > > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > > > +
> > > > ##################################################
> > > >
> > > >
> > > > My idea is to separate using a regex such that / 1:/ would be the
> first
> > > > mate pair and / 2:/ would go in the second mate file.
> > > > I implemented the code below but each output file is empty. Can
> someone
> > > > spot my error?
> > > >
> > > > Thanks,
> > > > Sean.
> > > >
> > > > my $infile   = shift;
> > > > my $outfile1 = $infile."_1";
> > > > my $outfile2 = $infile."_2";
> > > >
> > > > my $seqin = Bio::SeqIO->new(
> > > >                             -file   => "<$infile",
> > > >                             -format => "fastq",
> > > >                             );
> > > > my $seqout1 = Bio::SeqIO->new(
> > > >                              -file   => ">$outfile1",
> > > >                              -format => "fastq",
> > > >                              );
> > > >
> > > > my $seqout2 = Bio::SeqIO->new(
> > > >                              -file   => ">$outfile2",
> > > >                              -format => "fastq",
> > > >                              );
> > > > while (my $inseq = $seqin->next_seq) {
> > > >    if ($seqin->desc =~ / 1:/){
> > > >      $seqout1->write_seq($inseq);
> > > >    } else {
> > > >      $seqout2->write_seq($inseq);
> > > >    }
> > > > }
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >
> > >
> >
> >
> >
>
>


From p.j.a.cock at googlemail.com  Wed Feb 29 11:39:13 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Feb 2012 16:39:13 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROyvXQX1cRM6BxYcGUf0RR9KOxCwde53cQq0KNN6GErFOA@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
	<CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>
	<CALTeROwMidXRobpPcqmNfYs9LYJ7uVvVnb4CV5jiowOHHLBQMA@mail.gmail.com>
	<5AFAB73B-7284-4B42-9810-646B89C83B20@illinois.edu>
	<CALTeROyvXQX1cRM6BxYcGUf0RR9KOxCwde53cQq0KNN6GErFOA@mail.gmail.com>
Message-ID: <CAKVJ-_4RRE2kQ=tbD3SKsY+R1BLVzonSVz8q_pVajYPsPJCw8Q@mail.gmail.com>

On Wed, Feb 29, 2012 at 4:30 PM, Sean O'Keeffe <limericksean at gmail.com> wrote:
> Hi Chris,
> Here's the perldoc for fastq - it does seem to indicate that the optional
> descriptor (+) must match the first header. (See DESCRIPTION).

i.e. If present, it must match. But the repeated descriptor can
(and for space efficiency should) be omitted.

As Chris mentioned earlier, there are sample files in the test suite
which omit the repeated descriptor so this should be working OK.

Peter

From cjfields at illinois.edu  Wed Feb 29 12:00:39 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 29 Feb 2012 17:00:39 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROyvXQX1cRM6BxYcGUf0RR9KOxCwde53cQq0KNN6GErFOA@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
	<CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>
	<CALTeROwMidXRobpPcqmNfYs9LYJ7uVvVnb4CV5jiowOHHLBQMA@mail.gmail.com>
	<5AFAB73B-7284-4B42-9810-646B89C83B20@illinois.edu>
	<CALTeROyvXQX1cRM6BxYcGUf0RR9KOxCwde53cQq0KNN6GErFOA@mail.gmail.com>
Message-ID: <17CE7C71-FBCD-43D0-99F6-0C5305B0F354@illinois.edu>

Key part of that is the second descriptor (e.g. the one for the qual line) is *optional*, otherwise if there is anything present it must match the descriptor for the sequence.

My concern is the error you mentioned doesn't exist in that version.  The only explanation is the wrong fastq parser version is being used.  Is it possible you have two versions of bioperl installed (maybe a system one and a local one)?  Or is the script you have invoked directly as an executable, maybe calling a specific version of perl with it's own @INC?

chris

On Feb 29, 2012, at 10:30 AM, Sean O'Keeffe wrote:

> Hi Chris,
> Here's the perldoc for fastq - it does seem to indicate that the optional descriptor (+) must match the first header. (See DESCRIPTION). 
> Maybe this version doesn't include the updated code you mention which Peter Cock has worked on.
> 
> Sean.
> 
> ======================================
>  
> Bio::SeqIO::fastq(3)  User Contributed Perl Documentation Bio::SeqIO::fastq(3)
> 
> NAME
>        Bio::SeqIO::fastq - fastq sequence input/output stream
> 
> SYNOPSIS
>          ################## pertains to FASTQ parsing only ##################
> 
>          # grabs the FASTQ parser, specifies the Illumina variant
>          my $in = Bio::SeqIO->new(-format    => ?fastq-illumina?,
>                                   -file      => ?mydata.fq?);
> 
>          # simple ?fastq? format defaults to ?sanger? variant
>          my $out = Bio::SeqIO->new(-format    => ?fastq?,
>                                   -file      => ?>mydata.fq?);
> 
>          # $seq is a Bio::Seq::Quality object
>          while (my $seq = $in->next_seq) {
>              $out->write_seq($seq);  # convert Illumina 1.3 to Sanger format
>          }
> 
>          # for 4x faster parsing, one can do something like this for raw data
>          use Bio::Seq::Quality;
> 
>          # $data is a hash reference containing all arguments to be passed to
>          # the Bio::Seq::Quality constructor
>          while (my $data = $in->next_dataset) {
>              # process $data, such as trim, etc
>              my $seq = Bio::Seq::Quality->new(%$data);
> 
>              # for now, write_seq only accepts Bio::Seq::Quality, but may be modified
>              # to allow raw hash references for speed
>              $out->write_seq($data);
>          }
> 
> DESCRIPTION
>        This object can transform Bio::Seq and Bio::Seq::Quality objects to and from FASTQ flat file databases.
> 
>        FASTQ is a file format used frequently at the Sanger Centre and in next-gen sequencing to bundle a FASTA sequence and its quality data. A typical FASTQ entry takes the from:
> 
>          @HCDPQ1D0501
>          GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT.....
>          +HCDPQ1D0501
>          !??*((((***+))%%%++)(%%%%).1***-+*??))**55CCF>>>>>>CCCCCCC65.....
> 
>        where:
> 
>          @ = descriptor, followed by one or more sequence lines
>          + = optional descriptor (if present, must match first one), followed by one or
>              more qual lines
> 
>        FASTQ and Bio::Seq::Quality mapping
> 
>        FASTQ files have sequence and quality data on single line or multiple lines, and the quality values are single-byte encoded. Data are mapped very simply to Bio::Seq::Quality instances:
> 
>            Data                                        Bio::Seq::Quality method
>            ------------------------------------------------------------------------
>            first non-whitespace chars in descriptor    id^
>            descriptor line                             desc^
>            sequence lines                              seq
>            quality                                     qual*
>            FASTQ variant                               namespace
> 
>            ^ first nonwhitespace chars are id(), everything else after (to end of line)
>              is in desc()
>            * Converted to PHRED quality scores where applicable (?solexa?)
> 
>        FASTQ variants
> 
>        This parser supports all variants of FASTQ, including Illumina v 1.0 and 1.3:
> 
>            variant                note
>            -----------------------------------------------------------
>            sanger                 original
>            solexa                 Solexa, Inc. (2004), aka Illumina 1.0
>            illumina               Illumina 1.3
> 
>        The variant can be specified by passing by either passing the additional -variant parameter to the constructor:
> 
>          my $in = Bio::SeqIO->new(-format    => ?fastq?,
>                                   -variant   => ?solexa?,
>                                   -file      => ?mysol.fq?);
> 
>        or by passing the format and variant together (Bio::SeqIO will now handle this and convert it accordingly to the proper argument):
> 
>          my $in = Bio::SeqIO->new(-format    => ?fastq-solexa?,
>                                   -file      => ?mysol.fq?);
> 
>        Variants can be converted back and forth from one another; however, due to the difference in scaling for solexa quality reads, converting from ?illumina? or ?sanger? FASTQ to solexa is not recommended.
> ....
> 
> ============================================
> 
> On 28 February 2012 21:40, Fields, Christopher J <cjfields at illinois.edu> wrote:
> That should work.  Can you send the output of 'perldoc Bio::SeqIO::fastq'?  That should indicate what is being called.
> 
> chris
> 
> On Feb 28, 2012, at 5:50 PM, Sean O'Keeffe wrote:
> 
> > $ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
> > 1.006001
> >
> > Isn't that 1.6.1 - does it need upgrading ?
> >
> > On 28 February 2012 18:36, Sean O'Keeffe <limericksean at gmail.com> wrote:
> > Could be. I'll check.
> >
> > On 28 February 2012 17:17, Fields, Christopher J <cjfields at illinois.edu> wrote:
> > That's a bit odd.  Are you using an old version of the FASTQ parser?  It was revised a while ago, prior to the v1.6.1 release (the error matches one in the older parser)
> >
> > chris
> >
> > On Feb 28, 2012, at 4:01 PM, Sean O'Keeffe wrote:
> >
> > > Hi Chris,
> > > Unfortunately the read pairs are not consecutive. It seems they are cat'd together.
> > > I could use split -l on the line number that they're glued together I guess.
> > > If this is an overnight job for a bunch of files, I can wait so don't mind using the module if it worked.
> > >
> > > Someone pointed out I need to switch $seqin->desc to $inseq->desc.
> > > However, now it spits out fasta output instead of fastq and returns a bunch of warnings: Seq/Qual descriptions don't match; using sequence description
> > >
> > > Hmm.
> > >
> > > On 28 February 2012 16:50, Fields, Christopher J <cjfields at illinois.edu> wrote:
> > > Sean,
> > >
> > > If you trust the data enough, in that:
> > >
> > > 1) each record is 4 lines,
> > > 2) mate pairs are consecutive in the file, and
> > > 3) that read 1 always preceeds read 2 in the pair,
> > >
> > > then I would simply iterate through 4 lines at a time and dump to the two separate files, maybe using a flip-flop or simple record count and modulus switch.  You can always run a check on the header with a regex if you don't trust it completely.
> > >
> > > Just from the sanity point-of-view, unless you're doing a lot of validation I wouldn't use Bio::SeqIO::fastq, unless you have some time on your hands and a relatively low number of seqs (it's notoriously slow at the moment).
> > >
> > > chris
> > >
> > > On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
> > >
> > > > Hi,
> > > > I'm trying to write a quick script to separate one large PE fastq file into
> > > > 2 separate files, one for each mate pair
> > > >
> > > > The file is of the format (mate1)
> > > > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > > > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > > > +
> > > > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> > > >
> > > > && (mate2)
> > > >
> > > > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > > > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > > > +
> > > > ##################################################
> > > >
> > > >
> > > > My idea is to separate using a regex such that / 1:/ would be the first
> > > > mate pair and / 2:/ would go in the second mate file.
> > > > I implemented the code below but each output file is empty. Can someone
> > > > spot my error?
> > > >
> > > > Thanks,
> > > > Sean.
> > > >
> > > > my $infile   = shift;
> > > > my $outfile1 = $infile."_1";
> > > > my $outfile2 = $infile."_2";
> > > >
> > > > my $seqin = Bio::SeqIO->new(
> > > >                             -file   => "<$infile",
> > > >                             -format => "fastq",
> > > >                             );
> > > > my $seqout1 = Bio::SeqIO->new(
> > > >                              -file   => ">$outfile1",
> > > >                              -format => "fastq",
> > > >                              );
> > > >
> > > > my $seqout2 = Bio::SeqIO->new(
> > > >                              -file   => ">$outfile2",
> > > >                              -format => "fastq",
> > > >                              );
> > > > while (my $inseq = $seqin->next_seq) {
> > > >    if ($seqin->desc =~ / 1:/){
> > > >      $seqout1->write_seq($inseq);
> > > >    } else {
> > > >      $seqout2->write_seq($inseq);
> > > >    }
> > > > }
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >
> > >
> >
> >
> >
> 
> 



From p.j.a.cock at googlemail.com  Wed Feb 29 12:03:03 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Feb 2012 17:03:03 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROx+H=gkKnnZWZy1LW7h4va0N2UK+KwTXgMdMDvi-G3REg@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
	<CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>
	<CALTeROwMidXRobpPcqmNfYs9LYJ7uVvVnb4CV5jiowOHHLBQMA@mail.gmail.com>
	<5AFAB73B-7284-4B42-9810-646B89C83B20@illinois.edu>
	<CALTeROyvXQX1cRM6BxYcGUf0RR9KOxCwde53cQq0KNN6GErFOA@mail.gmail.com>
	<CAKVJ-_4RRE2kQ=tbD3SKsY+R1BLVzonSVz8q_pVajYPsPJCw8Q@mail.gmail.com>
	<CALTeROx+H=gkKnnZWZy1LW7h4va0N2UK+KwTXgMdMDvi-G3REg@mail.gmail.com>
Message-ID: <CAKVJ-_7ySM-V5Gg5Xi8tZdg-uH_fz5R=bgpDMnAO9XrFWem+tA@mail.gmail.com>

On Wed, Feb 29, 2012 at 4:56 PM, Sean O'Keeffe <limericksean at gmail.com> wrote:
> But wouldn't that result in a 3 line fastq output line which would screw up
> other programs expecting 4 fastq lines? - e.g. bowtie.

No, I mean the third line is just the plus character and the new line.

Again, I refer you to the example Chris quoted earlier:

http://lists.open-bio.org/pipermail/bioperl-l/2012-February/036271.html

Peter

From cjfields at illinois.edu  Wed Feb 29 12:05:57 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 29 Feb 2012 17:05:57 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROx+H=gkKnnZWZy1LW7h4va0N2UK+KwTXgMdMDvi-G3REg@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
	<CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>
	<CALTeROwMidXRobpPcqmNfYs9LYJ7uVvVnb4CV5jiowOHHLBQMA@mail.gmail.com>
	<5AFAB73B-7284-4B42-9810-646B89C83B20@illinois.edu>
	<CALTeROyvXQX1cRM6BxYcGUf0RR9KOxCwde53cQq0KNN6GErFOA@mail.gmail.com>
	<CAKVJ-_4RRE2kQ=tbD3SKsY+R1BLVzonSVz8q_pVajYPsPJCw8Q@mail.gmail.com>
	<CALTeROx+H=gkKnnZWZy1LW7h4va0N2UK+KwTXgMdMDvi-G3REg@mail.gmail.com>
Message-ID: <CABE93E1-4365-4CEB-A4B2-C411AA048B19@illinois.edu>

No, the output by default leaves off the optional descriptor:

[cjfields at pyrimidine]$ cat test.pl 
#!/usr/bin/env perl
use strict;
use warnings;
use Bio::SeqIO;

my $in = Bio::SeqIO->new(-fh => \*STDIN, -format => 'fastq');
my $out = Bio::SeqIO->new(-fh => \*STDOUT, -format => 'fastq');
while (my $seq = $in->next_seq) {$out->write_seq($seq)};
[cjfields at pyrimidine]$ perl test.pl < example.fastq 
@EAS54_6_R1_2_1_413_324
CCCTTCTTGTCTTCAGCGTTTCTCC
+
;;3;;;;;;;;;;;;7;;;;;;;88
@EAS54_6_R1_2_1_540_792
TTGGCAGGCCAAGGCCGATGGATCA
+
;;;;;;;;;;;7;;;;;-;;;3;83
@EAS54_6_R1_2_1_443_348
GTTGCTTCTGGCGTGGGTGGGGGGG
+
;;;;;;;;;;;9;7;;.7;393333


chris

On Feb 29, 2012, at 10:56 AM, Sean O'Keeffe wrote:

> But wouldn't that result in a 3 line fastq output line which would screw up other programs expecting 4 fastq lines? - e.g. bowtie.
> 
> On 29 February 2012 11:39, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Wed, Feb 29, 2012 at 4:30 PM, Sean O'Keeffe <limericksean at gmail.com> wrote:
> > Hi Chris,
> > Here's the perldoc for fastq - it does seem to indicate that the optional
> > descriptor (+) must match the first header. (See DESCRIPTION).
> 
> i.e. If present, it must match. But the repeated descriptor can
> (and for space efficiency should) be omitted.
> 
> As Chris mentioned earlier, there are sample files in the test suite
> which omit the repeated descriptor so this should be working OK.
> 
> Peter
> 



From cjfields at illinois.edu  Wed Feb 29 12:13:03 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 29 Feb 2012 17:13:03 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
Message-ID: <D8578EF2-3FB5-48AC-A55D-B6127A9C4706@illinois.edu>

Sean,

To follow up just in case it was a bug, tested with your seq examples and they also work, so my guess is something else is wrong locally.

[cjfields at pyrimidine-laptop sean]$ perl test.pl < example2.fastq 
@HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
+
BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
@HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
+
##################################################

chris

On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:

> Hi,
> I'm trying to write a quick script to separate one large PE fastq file into
> 2 separate files, one for each mate pair
> 
> The file is of the format (mate1)
> @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> +
> BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> 
> && (mate2)
> 
> @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> +
> ##################################################
> 
> 
> My idea is to separate using a regex such that / 1:/ would be the first
> mate pair and / 2:/ would go in the second mate file.
> I implemented the code below but each output file is empty. Can someone
> spot my error?
> 
> Thanks,
> Sean.
> 
> my $infile   = shift;
> my $outfile1 = $infile."_1";
> my $outfile2 = $infile."_2";
> 
> my $seqin = Bio::SeqIO->new(
>                             -file   => "<$infile",
>                             -format => "fastq",
>                             );
> my $seqout1 = Bio::SeqIO->new(
>                              -file   => ">$outfile1",
>                              -format => "fastq",
>                              );
> 
> my $seqout2 = Bio::SeqIO->new(
>                              -file   => ">$outfile2",
>                              -format => "fastq",
>                              );
> while (my $inseq = $seqin->next_seq) {
>    if ($seqin->desc =~ / 1:/){
>      $seqout1->write_seq($inseq);
>    } else {
>      $seqout2->write_seq($inseq);
>    }
> }
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From limericksean at gmail.com  Wed Feb 29 11:56:44 2012
From: limericksean at gmail.com (Sean O'Keeffe)
Date: Wed, 29 Feb 2012 11:56:44 -0500
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CAKVJ-_4RRE2kQ=tbD3SKsY+R1BLVzonSVz8q_pVajYPsPJCw8Q@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
	<CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>
	<CALTeROwMidXRobpPcqmNfYs9LYJ7uVvVnb4CV5jiowOHHLBQMA@mail.gmail.com>
	<5AFAB73B-7284-4B42-9810-646B89C83B20@illinois.edu>
	<CALTeROyvXQX1cRM6BxYcGUf0RR9KOxCwde53cQq0KNN6GErFOA@mail.gmail.com>
	<CAKVJ-_4RRE2kQ=tbD3SKsY+R1BLVzonSVz8q_pVajYPsPJCw8Q@mail.gmail.com>
Message-ID: <CALTeROx+H=gkKnnZWZy1LW7h4va0N2UK+KwTXgMdMDvi-G3REg@mail.gmail.com>

But wouldn't that result in a 3 line fastq output line which would screw up
other programs expecting 4 fastq lines? - e.g. bowtie.

On 29 February 2012 11:39, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, Feb 29, 2012 at 4:30 PM, Sean O'Keeffe <limericksean at gmail.com>
> wrote:
> > Hi Chris,
> > Here's the perldoc for fastq - it does seem to indicate that the optional
> > descriptor (+) must match the first header. (See DESCRIPTION).
>
> i.e. If present, it must match. But the repeated descriptor can
> (and for space efficiency should) be omitted.
>
> As Chris mentioned earlier, there are sample files in the test suite
> which omit the repeated descriptor so this should be working OK.
>
> Peter
>

From limericksean at gmail.com  Wed Feb 29 12:33:01 2012
From: limericksean at gmail.com (Sean O'Keeffe)
Date: Wed, 29 Feb 2012 12:33:01 -0500
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <D8578EF2-3FB5-48AC-A55D-B6127A9C4706@illinois.edu>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<D8578EF2-3FB5-48AC-A55D-B6127A9C4706@illinois.edu>
Message-ID: <CALTeROwpauXp8EG8A__Oi-nRFOdsY3Tcr5wSymNx9OacP7-A5Q@mail.gmail.com>

Yes. I ran my script on a cluster which may have had bioperl installed, not
sure.
Running it locally = success.

Thanks all!



On 29 February 2012 12:13, Fields, Christopher J <cjfields at illinois.edu>wrote:

> Sean,
>
> To follow up just in case it was a bug, tested with your seq examples and
> they also work, so my guess is something else is wrong locally.
>
> [cjfields at pyrimidine-laptop sean]$ perl test.pl < example2.fastq
> @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> +
> BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> +
> ##################################################
>
> chris
>
> On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
>
> > Hi,
> > I'm trying to write a quick script to separate one large PE fastq file
> into
> > 2 separate files, one for each mate pair
> >
> > The file is of the format (mate1)
> > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > +
> > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> >
> > && (mate2)
> >
> > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > +
> > ##################################################
> >
> >
> > My idea is to separate using a regex such that / 1:/ would be the first
> > mate pair and / 2:/ would go in the second mate file.
> > I implemented the code below but each output file is empty. Can someone
> > spot my error?
> >
> > Thanks,
> > Sean.
> >
> > my $infile   = shift;
> > my $outfile1 = $infile."_1";
> > my $outfile2 = $infile."_2";
> >
> > my $seqin = Bio::SeqIO->new(
> >                             -file   => "<$infile",
> >                             -format => "fastq",
> >                             );
> > my $seqout1 = Bio::SeqIO->new(
> >                              -file   => ">$outfile1",
> >                              -format => "fastq",
> >                              );
> >
> > my $seqout2 = Bio::SeqIO->new(
> >                              -file   => ">$outfile2",
> >                              -format => "fastq",
> >                              );
> > while (my $inseq = $seqin->next_seq) {
> >    if ($seqin->desc =~ / 1:/){
> >      $seqout1->write_seq($inseq);
> >    } else {
> >      $seqout2->write_seq($inseq);
> >    }
> > }
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

From thomas.sharpton at gmail.com  Wed Feb 29 13:11:39 2012
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Wed, 29 Feb 2012 10:11:39 -0800
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROwpauXp8EG8A__Oi-nRFOdsY3Tcr5wSymNx9OacP7-A5Q@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<D8578EF2-3FB5-48AC-A55D-B6127A9C4706@illinois.edu>
	<CALTeROwpauXp8EG8A__Oi-nRFOdsY3Tcr5wSymNx9OacP7-A5Q@mail.gmail.com>
Message-ID: <CAHxmPd+Qdfjq5Nc55FgK=riTYGnOiFX9q9RBfy_9QAjPCSt8RA@mail.gmail.com>

This was an interesting thread to follow (I'm about to dive into Illimina
data). Glad you found the cause of the problem, Sean.

FYI - you may already know this trick, but when I work on a cluster, my
first command in my submission script is to always source my bash profile
(.profile, .bashrc, etc. depending on your setup).

This way you can control the structure of the PERL5LIB variable (among
others) on the slave nodes and ensure your local perl modules are
preferentially called.

Of course there are other solutions to this problem too.

Best,
Tom
On Feb 29, 2012 9:38 AM, "Sean O&apos;Keeffe" <limericksean at gmail.com>
wrote:

> Yes. I ran my script on a cluster which may have had bioperl installed, not
> sure.
> Running it locally = success.
>
> Thanks all!
>
>
>
> On 29 February 2012 12:13, Fields, Christopher J <cjfields at illinois.edu
> >wrote:
>
> > Sean,
> >
> > To follow up just in case it was a bug, tested with your seq examples and
> > they also work, so my guess is something else is wrong locally.
> >
> > [cjfields at pyrimidine-laptop sean]$ perl test.pl < example2.fastq
> > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > +
> > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > +
> > ##################################################
> >
> > chris
> >
> > On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
> >
> > > Hi,
> > > I'm trying to write a quick script to separate one large PE fastq file
> > into
> > > 2 separate files, one for each mate pair
> > >
> > > The file is of the format (mate1)
> > > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > > +
> > > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> > >
> > > && (mate2)
> > >
> > > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > > +
> > > ##################################################
> > >
> > >
> > > My idea is to separate using a regex such that / 1:/ would be the first
> > > mate pair and / 2:/ would go in the second mate file.
> > > I implemented the code below but each output file is empty. Can someone
> > > spot my error?
> > >
> > > Thanks,
> > > Sean.
> > >
> > > my $infile   = shift;
> > > my $outfile1 = $infile."_1";
> > > my $outfile2 = $infile."_2";
> > >
> > > my $seqin = Bio::SeqIO->new(
> > >                             -file   => "<$infile",
> > >                             -format => "fastq",
> > >                             );
> > > my $seqout1 = Bio::SeqIO->new(
> > >                              -file   => ">$outfile1",
> > >                              -format => "fastq",
> > >                              );
> > >
> > > my $seqout2 = Bio::SeqIO->new(
> > >                              -file   => ">$outfile2",
> > >                              -format => "fastq",
> > >                              );
> > > while (my $inseq = $seqin->next_seq) {
> > >    if ($seqin->desc =~ / 1:/){
> > >      $seqout1->write_seq($inseq);
> > >    } else {
> > >      $seqout2->write_seq($inseq);
> > >    }
> > > }
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From cjfields at illinois.edu  Wed Feb 29 13:23:27 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 29 Feb 2012 18:23:27 +0000
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CAHxmPd+Qdfjq5Nc55FgK=riTYGnOiFX9q9RBfy_9QAjPCSt8RA@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<D8578EF2-3FB5-48AC-A55D-B6127A9C4706@illinois.edu>
	<CALTeROwpauXp8EG8A__Oi-nRFOdsY3Tcr5wSymNx9OacP7-A5Q@mail.gmail.com>
	<CAHxmPd+Qdfjq5Nc55FgK=riTYGnOiFX9q9RBfy_9QAjPCSt8RA@mail.gmail.com>
Message-ID: <D8725A2E-3BA8-4AF5-BE90-CF9D73F5A867@illinois.edu>

Just want to say, if you can set up a local perl and local::lib it makes your life a LOT easier.  Particularly if you are running jobs on older versions of RHEL, which notoriously stuck with outdated/broken versions of perl (as well as other tools).

chris

On Feb 29, 2012, at 12:11 PM, Thomas Sharpton wrote:

> This was an interesting thread to follow (I'm about to dive into Illimina data). Glad you found the cause of the problem, Sean.
> 
> FYI - you may already know this trick, but when I work on a cluster, my first command in my submission script is to always source my bash profile (.profile, .bashrc, etc. depending on your setup).
> 
> This way you can control the structure of the PERL5LIB variable (among others) on the slave nodes and ensure your local perl modules are preferentially called.
> 
> Of course there are other solutions to this problem too.
> 
> Best,
> Tom
> 
> On Feb 29, 2012 9:38 AM, "Sean O&apos;Keeffe" <limericksean at gmail.com> wrote:
> Yes. I ran my script on a cluster which may have had bioperl installed, not
> sure.
> Running it locally = success.
> 
> Thanks all!
> 
> 
> 
> On 29 February 2012 12:13, Fields, Christopher J <cjfields at illinois.edu>wrote:
> 
> > Sean,
> >
> > To follow up just in case it was a bug, tested with your seq examples and
> > they also work, so my guess is something else is wrong locally.
> >
> > [cjfields at pyrimidine-laptop sean]$ perl test.pl < example2.fastq
> > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > +
> > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > +
> > ##################################################
> >
> > chris
> >
> > On Feb 28, 2012, at 3:11 PM, Sean O'Keeffe wrote:
> >
> > > Hi,
> > > I'm trying to write a quick script to separate one large PE fastq file
> > into
> > > 2 separate files, one for each mate pair
> > >
> > > The file is of the format (mate1)
> > > @HWI-ST156:445:C0EDLACXX:4:1101:1496:1039 1:N:0:ATCACG
> > > CTGCTGGTAGTGCCCAAAGACCTCGAATACAATGGGCTTGGTTTTGATGT
> > > +
> > > BCCFFFFEHHHHHJJJJJHIIJIJJIIGIJJJJJJJIJJJI?FHJJIIJA
> > >
> > > && (mate2)
> > >
> > > @HWI-ST156:445:C0EDLACXX:4:2308:20877:199811 2:Y:0:ATCACG
> > > TCATAAAAATAACAAAACCACCACCCCATACAAACTCTACTCATCTCCAC
> > > +
> > > ##################################################
> > >
> > >
> > > My idea is to separate using a regex such that / 1:/ would be the first
> > > mate pair and / 2:/ would go in the second mate file.
> > > I implemented the code below but each output file is empty. Can someone
> > > spot my error?
> > >
> > > Thanks,
> > > Sean.
> > >
> > > my $infile   = shift;
> > > my $outfile1 = $infile."_1";
> > > my $outfile2 = $infile."_2";
> > >
> > > my $seqin = Bio::SeqIO->new(
> > >                             -file   => "<$infile",
> > >                             -format => "fastq",
> > >                             );
> > > my $seqout1 = Bio::SeqIO->new(
> > >                              -file   => ">$outfile1",
> > >                              -format => "fastq",
> > >                              );
> > >
> > > my $seqout2 = Bio::SeqIO->new(
> > >                              -file   => ">$outfile2",
> > >                              -format => "fastq",
> > >                              );
> > > while (my $inseq = $seqin->next_seq) {
> > >    if ($seqin->desc =~ / 1:/){
> > >      $seqout1->write_seq($inseq);
> > >    } else {
> > >      $seqout2->write_seq($inseq);
> > >    }
> > > }
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From Scott.Markel at accelrys.com  Wed Feb 29 13:25:05 2012
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Wed, 29 Feb 2012 10:25:05 -0800
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <CALTeROx+H=gkKnnZWZy1LW7h4va0N2UK+KwTXgMdMDvi-G3REg@mail.gmail.com>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<2E9A9DC1-DE74-4EFD-84D1-53FCF44CB0E4@illinois.edu>
	<CALTeROxtTP9_ws2417RkWL97Dq7sgsG5jGeEbAXXpKm51qha=A@mail.gmail.com>
	<A83845AF-1CB0-4511-AB72-A6E8FB559709@illinois.edu>
	<CALTeROyJ0Jzepuf73Y9wPW1Hg-JL7hDmT2OUXLJ6rYj=gt7rDw@mail.gmail.com>
	<CALTeROwMidXRobpPcqmNfYs9LYJ7uVvVnb4CV5jiowOHHLBQMA@mail.gmail.com>
	<5AFAB73B-7284-4B42-9810-646B89C83B20@illinois.edu>
	<CALTeROyvXQX1cRM6BxYcGUf0RR9KOxCwde53cQq0KNN6GErFOA@mail.gmail.com>
	<CAKVJ-_4RRE2kQ=tbD3SKsY+R1BLVzonSVz8q_pVajYPsPJCw8Q@mail.gmail.com>
	<CALTeROx+H=gkKnnZWZy1LW7h4va0N2UK+KwTXgMdMDvi-G3REg@mail.gmail.com>
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97704652DE6F5@EXCH1-COLO.accelrys.net>

The leading character ('+') of the optional descriptor line is still written, just not the rest of the line.  The line count shouldn't change.

Scott


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Sean O'Keeffe
Sent: Wednesday, 29 February 29 2012 8:57 AM
To: Peter Cock
Cc: Chris Fields; <Bioperl-l at lists.open-bio.org>
Subject: Re: [Bioperl-l] fastq splitter

But wouldn't that result in a 3 line fastq output line which would screw up
other programs expecting 4 fastq lines? - e.g. bowtie.

On 29 February 2012 11:39, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, Feb 29, 2012 at 4:30 PM, Sean O'Keeffe <limericksean at gmail.com>
> wrote:
> > Hi Chris,
> > Here's the perldoc for fastq - it does seem to indicate that the optional
> > descriptor (+) must match the first header. (See DESCRIPTION).
>
> i.e. If present, it must match. But the repeated descriptor can
> (and for space efficiency should) be omitted.
>
> As Chris mentioned earlier, there are sample files in the test suite
> which omit the repeated descriptor so this should be working OK.
>
> Peter
>
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hartzell at alerce.com  Wed Feb 29 14:52:39 2012
From: hartzell at alerce.com (George Hartzell)
Date: Wed, 29 Feb 2012 11:52:39 -0800
Subject: [Bioperl-l] fastq splitter
In-Reply-To: <D8725A2E-3BA8-4AF5-BE90-CF9D73F5A867@illinois.edu>
References: <CALTeROy56_GAh-G3i=StW8r+4jsy_3X_4ekdOdaRQ203=bQ4mA@mail.gmail.com>
	<D8578EF2-3FB5-48AC-A55D-B6127A9C4706@illinois.edu>
	<CALTeROwpauXp8EG8A__Oi-nRFOdsY3Tcr5wSymNx9OacP7-A5Q@mail.gmail.com>
	<CAHxmPd+Qdfjq5Nc55FgK=riTYGnOiFX9q9RBfy_9QAjPCSt8RA@mail.gmail.com>
	<D8725A2E-3BA8-4AF5-BE90-CF9D73F5A867@illinois.edu>
Message-ID: <20302.33287.509248.407270@gargle.gargle.HOWL>

Fields, Christopher J writes:
 > Just want to say, if you can set up a local perl and local::lib it
 > makes your life a LOT easier.  Particularly if you are running jobs
 > on older versions of RHEL, which notoriously stuck with
 > outdated/broken versions of perl (as well as other tools). 
 > [...]

And Perlbrew takes away your last excuse for not building perls and
setting up local::lib's.

  http://perlbrew.pl/

g.

From cjfields at illinois.edu  Wed Feb 29 21:30:38 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 1 Mar 2012 02:30:38 +0000
Subject: [Bioperl-l] Fate of Bio::Tools::PCRSimulation
In-Reply-To: <4F501063.4010109@gmail.com>
References: <4F49D4B6.5050301@gmail.com>
	<D60FDDB5-5EC6-4A91-954B-3A3EB27921CF@illinois.edu>
	<4F4E3EEF.5050506@cam.ac.uk>
	<4325EF60-919F-46EF-91BB-D31160F0B587@illinois.edu>
	<4F501063.4010109@gmail.com>
Message-ID: <BBB440B8-9FD7-4B5B-A87C-73F0B99DDB9E@illinois.edu>

There are a number of very good reasons to separate out common code and create new repos for new code.  The problem about adding new code into core is it ties your code development to bioperl-live's release cycle and versioning.  Also, what I (and others) would not like to see is any additional dependencies introduced, but a separate release allows you to (1) both add a dependency w/o affecting core, and (2) make it required, so no fiddling with checking for the module prior to running tests on it.  

As an example, I can easily see something like Bio::SearchIO::blastxml living on it's own since it has a set of outside dependencies.

BTW, separation of modules into separate distributions (even single modules) based on functionality above and beyond that defined in a core is very common in the perl world.  Beyond the obvious example of anything non-core in perl (all installable via CPAN), Moose, Dist::Zilla, Catalyst, Dancer, etc all have separately installable dists that layer additional functionality and have a separate maintenance path.  

chris

On Mar 1, 2012, at 6:12 PM, Florent Angly wrote:

> Thanks for everybody's feedback.
> 
> I am looking at existing modules to hold template sequence, amplicon sequence and primer information. There is the Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq. At the moment the PrimedSeq object places Primer objects on the target sequence. I have been looking at refreshing these modules (they are quite old), add some sanity to them and make sure they are suitable for a generic implementation of PCR (or amplicon search, which I find a more suitable name since it is a far cry from simulating PCR cycles, etc).
> 
> I will make a remote branch today to make it easier for interested parties to experiment and contribute.
> 
> As you can see Chris, the amplicon search feature would use two existing bioperl-live modules and only add one, tentatively in the Bio::Tools::AmpliconSearch namespace. I am not convinced that this warrants a separate distro.
> 
> Florent
> 
> On 01/03/12 01:23, Fields, Christopher J wrote:
>> Seems like it was meant to be added at some point but was never committed.  Definitely not in the github history for 1.3.x, this commit corresponds to the v1.3.4 tag:
>> 
>>    https://github.com/bioperl/bioperl-live/tree/0a67fa444eb19a70876017607f70ab72be38755a
>> 
>> and it's not there.
>> 
>> I agree with Roy, it would be nice to somehow make this a little more generic or pluggable on how it maps primers (maybe with a default pure perl method).  I also think this shouldn't be bound to bioperl-live considering our current plans, it would best happen in a separate repo.
>> 
>> chris
>> 
>> On Feb 29, 2012, at 9:06 AM, Roy Chaudhuri wrote:
>> 
>>> The code for Bio::Tools::PCRSimulation can be downloaded as part of this archive:
>>> http://www.salmonella.org/bioperl/primer3_v0.3.tgz
>>> 
>>> (There's supposedly a more recent version here:
>>> http://www.salmonella.org/bioperl/nucleotide_analyses.tgz
>>> but that file seems to be truncated).
>>> 
>>> I have no idea how much would be salvagable. It seems to just use index to map the primers to the sequence, I guess it would make more sense to at least give the option of something more sophisticated like Primer3, BLAST or even a short read mapper.
>>> 
>>> Cheers,
>>> Roy.
>>> 
>>> 
>>> On 27/02/2012 21:18, Fields, Christopher J wrote:
>>>> On Feb 26, 2012, at 12:44 AM, Florent Angly wrote:
>>>> 
>>>>> Hi all,
>>>>> 
>>>>> I am interested in the Bio::Tools::PCRSimulation module. Supposedly
>>>>> it was added to Bioperl 0.3 and is also mentionned in the
>>>>> Bio::PrimedSeq module. However, I cannot find in the current
>>>>> Bioperl codebase. Any idea where it went?
>>>> No idea; I can't find it anywhere in the code base either, and the
>>>> github repo contains history going back to the original CVS repo.
>>>> You can try contacting the author, possibly.
>>>> 
>>>>> The reason I am asking is because I have some code to do silico PCR
>>>>> using regular expressions. I wanted to modularize my code more and
>>>>> make it into a module for Bioperl. Of course, if there is something
>>>>> similar in Bioperl already, I need to have a look at it. If there
>>>>> is nothing similar, what namespace do you suggest to use?
>>>>> Bio::Tools::AmpliconExtractor? Bio::Tools::AmpliconSearch?
>>>>> Bio::Tools::InSilicoPCR?
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Florent
>>>> 
>>>> Maybe the last (InSilicoPCR).
>>>> 
>>>> chris
>>>> 
>>>> 
>>>> _______________________________________________ Bioperl-l mailing
>>>> list Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From cjfields at illinois.edu  Wed Feb 29 21:42:06 2012
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 1 Mar 2012 02:42:06 +0000
Subject: [Bioperl-l] Fate of Bio::Tools::PCRSimulation
In-Reply-To: <BBB440B8-9FD7-4B5B-A87C-73F0B99DDB9E@illinois.edu>
References: <4F49D4B6.5050301@gmail.com>
	<D60FDDB5-5EC6-4A91-954B-3A3EB27921CF@illinois.edu>
	<4F4E3EEF.5050506@cam.ac.uk>
	<4325EF60-919F-46EF-91BB-D31160F0B587@illinois.edu>
	<4F501063.4010109@gmail.com>
	<BBB440B8-9FD7-4B5B-A87C-73F0B99DDB9E@illinois.edu>
Message-ID: <96E7CE58-0657-4194-A906-83022348F84A@illinois.edu>

Florent, 

Just want to add, my previous response isn't meant as an admonishment, hope it didn't come across that way, but sometimes email makes it hard to discern the difference.  I simply meant to demonstrate my opinion that I find releasing one's code is much simpler (e.g. you can decide the rules and dictate when the code is ready for release), and if we can make getting good code into user's hands easier, more flexible, and more consistent I think that is always a better path.  

chris

On Feb 29, 2012, at 8:30 PM, Fields, Christopher J wrote:

> There are a number of very good reasons to separate out common code and create new repos for new code.  The problem about adding new code into core is it ties your code development to bioperl-live's release cycle and versioning.  Also, what I (and others) would not like to see is any additional dependencies introduced, but a separate release allows you to (1) both add a dependency w/o affecting core, and (2) make it required, so no fiddling with checking for the module prior to running tests on it.  
> 
> As an example, I can easily see something like Bio::SearchIO::blastxml living on it's own since it has a set of outside dependencies.
> 
> BTW, separation of modules into separate distributions (even single modules) based on functionality above and beyond that defined in a core is very common in the perl world.  Beyond the obvious example of anything non-core in perl (all installable via CPAN), Moose, Dist::Zilla, Catalyst, Dancer, etc all have separately installable dists that layer additional functionality and have a separate maintenance path.  
> 
> chris
> 
> On Mar 1, 2012, at 6:12 PM, Florent Angly wrote:
> 
>> Thanks for everybody's feedback.
>> 
>> I am looking at existing modules to hold template sequence, amplicon sequence and primer information. There is the Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq. At the moment the PrimedSeq object places Primer objects on the target sequence. I have been looking at refreshing these modules (they are quite old), add some sanity to them and make sure they are suitable for a generic implementation of PCR (or amplicon search, which I find a more suitable name since it is a far cry from simulating PCR cycles, etc).
>> 
>> I will make a remote branch today to make it easier for interested parties to experiment and contribute.
>> 
>> As you can see Chris, the amplicon search feature would use two existing bioperl-live modules and only add one, tentatively in the Bio::Tools::AmpliconSearch namespace. I am not convinced that this warrants a separate distro.
>> 
>> Florent
>> 
>> On 01/03/12 01:23, Fields, Christopher J wrote:
>>> Seems like it was meant to be added at some point but was never committed.  Definitely not in the github history for 1.3.x, this commit corresponds to the v1.3.4 tag:
>>> 
>>>   https://github.com/bioperl/bioperl-live/tree/0a67fa444eb19a70876017607f70ab72be38755a
>>> 
>>> and it's not there.
>>> 
>>> I agree with Roy, it would be nice to somehow make this a little more generic or pluggable on how it maps primers (maybe with a default pure perl method).  I also think this shouldn't be bound to bioperl-live considering our current plans, it would best happen in a separate repo.
>>> 
>>> chris
>>> 
>>> On Feb 29, 2012, at 9:06 AM, Roy Chaudhuri wrote:
>>> 
>>>> The code for Bio::Tools::PCRSimulation can be downloaded as part of this archive:
>>>> http://www.salmonella.org/bioperl/primer3_v0.3.tgz
>>>> 
>>>> (There's supposedly a more recent version here:
>>>> http://www.salmonella.org/bioperl/nucleotide_analyses.tgz
>>>> but that file seems to be truncated).
>>>> 
>>>> I have no idea how much would be salvagable. It seems to just use index to map the primers to the sequence, I guess it would make more sense to at least give the option of something more sophisticated like Primer3, BLAST or even a short read mapper.
>>>> 
>>>> Cheers,
>>>> Roy.
>>>> 
>>>> 
>>>> On 27/02/2012 21:18, Fields, Christopher J wrote:
>>>>> On Feb 26, 2012, at 12:44 AM, Florent Angly wrote:
>>>>> 
>>>>>> Hi all,
>>>>>> 
>>>>>> I am interested in the Bio::Tools::PCRSimulation module. Supposedly
>>>>>> it was added to Bioperl 0.3 and is also mentionned in the
>>>>>> Bio::PrimedSeq module. However, I cannot find in the current
>>>>>> Bioperl codebase. Any idea where it went?
>>>>> No idea; I can't find it anywhere in the code base either, and the
>>>>> github repo contains history going back to the original CVS repo.
>>>>> You can try contacting the author, possibly.
>>>>> 
>>>>>> The reason I am asking is because I have some code to do silico PCR
>>>>>> using regular expressions. I wanted to modularize my code more and
>>>>>> make it into a module for Bioperl. Of course, if there is something
>>>>>> similar in Bioperl already, I need to have a look at it. If there
>>>>>> is nothing similar, what namespace do you suggest to use?
>>>>>> Bio::Tools::AmpliconExtractor? Bio::Tools::AmpliconSearch?
>>>>>> Bio::Tools::InSilicoPCR?
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Florent
>>>>> 
>>>>> Maybe the last (InSilicoPCR).
>>>>> 
>>>>> chris
>>>>> 
>>>>> 
>>>>> _______________________________________________ Bioperl-l mailing
>>>>> list Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l