From florent.angly at gmail.com  Wed May  1 22:16:02 2013
From: florent.angly at gmail.com (Florent Angly)
Date: Thu, 02 May 2013 12:16:02 +1000
Subject: [Bioperl-l] Downloading sequences in batch from Trace Archive
In-Reply-To: <CAA7rn9dtgtkdPLU9v=b3Jq0CWPvph59BYp2r5-jJRRt94dB1RA@mail.gmail.com>
References: <CAA7rn9dtgtkdPLU9v=b3Jq0CWPvph59BYp2r5-jJRRt94dB1RA@mail.gmail.com>
Message-ID: <5181CC62.9000609@gmail.com>

Maybe using EUtilities?
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service

Florent


On 30/04/13 06:25, shalabh sharma wrote:
> Hi All,
>            Is there any module in Bioperl that can download sequences from
> NCBI's trace archive?
>
> Thanks
> Shalabh
>


From jason.stajich at gmail.com  Thu May  2 01:42:55 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 1 May 2013 22:42:55 -0700
Subject: [Bioperl-l] Fwd: doubt
References: <CACPwBoTqbeNuY6hGW9gpQagL2ZXdknwcM_0Q7QMMCyqEz9FXcg@mail.gmail.com>
Message-ID: <B094273D-B6AB-4DE8-8B65-FFAA3FB30D8A@gmail.com>



Begin forwarded message:

> From: ARYA DAS <aryaanildas at gmail.com>
> Subject: doubt
> Date: May 1, 2013 10:42:21 PM PDT
> To: jason at bioperl.org
> 
> sir,
> 
>     Am using windows7 n was trying to install bio perl in it..i have
> already installed active perl.5.16.3.1603 . n was followeing the
> installation procedure mentioned .when i tried GUI installation .. i cant
> find bioperl package when i try to search them for installation.
> while using command line..
> 
> ppm> install PPM-Repositories
> 
> shows error like cant find package that provides PPM repositories,
> 
> and when i try manually ,on reaching the
> perl Build test
> 
> it says build is recognised as an internal or external file.
> 
> please help if time permits
> 
> regards,
> arya

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


From voldrani at gmail.com  Sun May  5 00:03:38 2013
From: voldrani at gmail.com (Chris Maloney)
Date: Sun, 5 May 2013 00:03:38 -0400
Subject: [Bioperl-l] Wiki work, Template:Doclink
Message-ID: <CABE9g5Ps+NDmziDZNro8UZ5_RMOP1ru1fmKOpFh+DFh=equRfQ@mail.gmail.com>

The module pages on the wiki could look a little better, like this one
for example:  http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast.
 There used to be a bunch of extra whitespace at the top of the page,
which was caused by extra line breaks in Template:Doclink, which I
just removed.

But, I think there are other improvements that could be made.  I would
like to turn this into an infobox -- which are the helpful informative
tables of info on Wikipedia that appear on many articles on the upper
right.  That would allow us to add more links -- like to metacpan, for
example.

It is not completely trivial to import infoboxes into a wiki though, I
just discovered.  I just went through the exercise on my home wiki,
and it involves importing a lot of templates from Wikipedia, and
fixing up the common.css.  You can see the full list of imported
templates here:
http://chrismaloney.org/wiki/index.php?title=Special:RecentChanges&limit=100.
 I don't *think* this should cause any problems, but I'm not 100%
sure.  On the other hand, if it does, it should be easy to roll back
-- it's a wiki, after all.

Does anybody have a problem if I do this?  I'll wait a day for
responses, and tackle this tomorrow, if no one objects.

-- Chris M.

From armendarez77 at hotmail.com  Tue May  7 20:32:22 2013
From: armendarez77 at hotmail.com (Veronica A.)
Date: Tue, 7 May 2013 17:32:22 -0700
Subject: [Bioperl-l] Bio::SeqIO doesn't write all gbk sequences from
	Bio::DB::GenBank
Message-ID: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>

Hello,
I'm currently running Bio::Perl 1.6.1 on Ubuntu 12.04.2 LTS and have noticed a problem with Bio::SeqIO when writing genbank files using the write_seq() function;  some of the files do not include an 'ORIGIN' tag or the sequence.

I am using GI#s (50 at a time every 2 minutes) to retrieve genbank files via Bio::DB::GenBank.

----------------------------------------START CODE----------------------------------
my $gb = Bio::DB::GenBank->new(-verbose=>-1);my $seqout = Bio::SeqIO->new(-file=>">$fileName", '-format'=>'Genbank', -alphabet=>'dna', -flush=>0, -verbose=>-1);while(@ids){     my @batchArray = splice(@ids, 0, 50);     my $batchArrayRef = \@batchArray;
     my $streamObj;     my $pid = fork();     if($pid == 0){          eval{               $streamObj = $gb->get_Stream_by_id($batchArrayRef);          };          if($@){               print "Error: ".$@."\n";          }          else{               while(my $seqObj = $streamObj->next_seq()){                    unless($seqObj->accession_number() =~ /N[A-Z]\_/){                        #print "ID: ".$seqObj->id()."\n";                        #print "Seq:\n".$seqObj->seq()."\n";                         $seqout->write_seq($seqObj);                    }                }          }          exit 0;     }}waitpid($pid,0);sleep(120);
----------------------------------------END CODE----------------------------------
Most of the Genbank files written to the output file have sequences, but there is a small portion that do not, even though they should.  For example, JX287367, in NCBI includes an 'ORIGIN' tag and sequence and when I use the print function before writing to file, the sequence is printed to STDOUT, but the 'ORIGIN' tag and sequence are not written to the output gbk file.  The following is found in the final output file:
----------------------------------START GBK-----------------------------------------
LOCUS       JX287367                 588 bp    DNA     linear   BCT 19-DEC-2012DEFINITION  Chlamydia trachomatis strain UW-5/CX pyruvoyl-dependent arginine            decarboxylase (aaxB) gene, complete cds.ACCESSION   JX287367VERSION     JX287367.1  GI:404351720KEYWORDS    .SOURCE      Chlamydia trachomatis  ORGANISM  Chlamydia trachomatis            Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;            Chlamydia/Chlamydophila group; Chlamydia.REFERENCE   1  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Characterization of the activity and expression of arginine            decarboxylase in human and animal Chlamydia pathogens  JOURNAL   FEMS Microbiol. Lett. 337 (2), 140-146 (2012)   PUBMED   23043454REFERENCE   2  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Direct Submission  JOURNAL   Submitted (06-JUL-2012) Department of Microbiology and Immunology,            F. Edward Hebert School of Medicine, Uniformed Services University            of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD            20814, USAFEATURES             Location/Qualifiers     source          1..588                     /mol_type="genomic DNA"                     /db_xref="taxon:813"                     /strain="UW-5/CX"                     /organism="Chlamydia trachomatis"                     /serovar="E"     gene            1..588                     /gene="aaxB"     CDS             1..588                     /protein_id="AFR60849.1"                     /gene="aaxB"                     /transl_table=11                     /note="AaxB"                     /db_xref="GI:404351721"                     /codon_start=1                     /product="pyruvoyl-dependent arginine decarboxylase"                     /translation="MPYGTRYPTLAFHTGGVGESDDGMPPQPFETFCYDSALLQAKIE                     NFNIVPYTSVLPKELFGNILPVDQCTKFFKHGAVLEVIMAGRGATVTDGTQAIATGVG                     ICWGKDKNGELIGGWAAEYVEFFPTWIDDEIAESHAKMWLKKSLQHELDLRSVSKHSE                     FQYFHNYINIRKKFGFCLTALGFLNFENVAPAVIQ"
//
----------------------------------END GBK-----------------------------------------
Can anyone tell what I am missing or why this is happening?  I don't know if this has happened in earlier BioPerl versions as up until now, I usually downloaded sequences straight from NCBI, but that became too time consuming....but this seems to be as well :S
Thank you in advance for any help,
Veronica
 		 	   		  

From cjfields at illinois.edu  Tue May  7 22:17:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 8 May 2013 02:17:43 +0000
Subject: [Bioperl-l] Bio::SeqIO doesn't write all gbk sequences
	from	Bio::DB::GenBank
In-Reply-To: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>
References: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E166A0@CHIMBX5.ad.uillinois.edu>

Veronica,

Your mail may have garbled the script and example file.  Can you paste these in a gist?

https://gist.github.com/

chris

On May 7, 2013, at 7:32 PM, Veronica A. <armendarez77 at hotmail.com> wrote:

> Hello,
> I'm currently running Bio::Perl 1.6.1 on Ubuntu 12.04.2 LTS and have noticed a problem with Bio::SeqIO when writing genbank files using the write_seq() function;  some of the files do not include an 'ORIGIN' tag or the sequence.
> 
> I am using GI#s (50 at a time every 2 minutes) to retrieve genbank files via Bio::DB::GenBank.
> 
> ----------------------------------------START CODE----------------------------------
> my $gb = Bio::DB::GenBank->new(-verbose=>-1);my $seqout = Bio::SeqIO->new(-file=>">$fileName", '-format'=>'Genbank', -alphabet=>'dna', -flush=>0, -verbose=>-1);while(@ids){     my @batchArray = splice(@ids, 0, 50);     my $batchArrayRef = \@batchArray;
>     my $streamObj;     my $pid = fork();     if($pid == 0){          eval{               $streamObj = $gb->get_Stream_by_id($batchArrayRef);          };          if($@){               print "Error: ".$@."\n";          }          else{               while(my $seqObj = $streamObj->next_seq()){                    unless($seqObj->accession_number() =~ /N[A-Z]\_/){                        #print "ID: ".$seqObj->id()."\n";                        #print "Seq:\n".$seqObj->seq()."\n";                         $seqout->write_seq($seqObj);                    }                }          }          exit 0;     }}waitpid($pid,0);sleep(120);
> ----------------------------------------END CODE----------------------------------
> Most of the Genbank files written to the output file have sequences, but there is a small portion that do not, even though they should.  For example, JX287367, in NCBI includes an 'ORIGIN' tag and sequence and when I use the print function before writing to file, the sequence is printed to STDOUT, but the 'ORIGIN' tag and sequence are not written to the output gbk file.  The following is found in the final output file:
> ----------------------------------START GBK-----------------------------------------
> LOCUS       JX287367                 588 bp    DNA     linear   BCT 19-DEC-2012DEFINITION  Chlamydia trachomatis strain UW-5/CX pyruvoyl-dependent arginine            decarboxylase (aaxB) gene, complete cds.ACCESSION   JX287367VERSION     JX287367.1  GI:404351720KEYWORDS    .SOURCE      Chlamydia trachomatis  ORGANISM  Chlamydia trachomatis            Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;            Chlamydia/Chlamydophila group; Chlamydia.REFERENCE   1  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Characterization of the activity and expression of arginine            decarboxylase in human and animal Chlamydia pathogens  JOURNAL   FEMS Microbiol. Lett. 337 (2), 140-146 (2012)   PUBMED   23043454REFERENCE   2  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Direct Submission  JOURNAL   Submitted (06-JUL-2012) Department of Microbiology and Immunology,            F. Edward Hebert School of Med!
> icine, Uniformed Services University            of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD            20814, USAFEATURES             Location/Qualifiers     source          1..588                     /mol_type="genomic DNA"                     /db_xref="taxon:813"                     /strain="UW-5/CX"                     /organism="Chlamydia trachomatis"                     /serovar="E"     gene            1..588                     /gene="aaxB"     CDS             1..588                     /protein_id="AFR60849.1"                     /gene="aaxB"                     /transl_table=11                     /note="AaxB"                     /db_xref="GI:404351721"                     /codon_start=1                     /product="pyruvoyl-dependent arginine decarboxylase"                     /translation="MPYGTRYPTLAFHTGGVGESDDGMPPQPFETFCYDSALLQAKIE                     NFNIVPYTSVLPKELFGNILPVDQCTKFFKHGAVLEVIMAGRGATVTDGTQAIATGVG                     ICWGKDKNGELIGGW!
> AAEYVEFFPTWIDDEIAESHAKMWLKKSLQHELDLRSVSKHSE                     FQYFHN
> YINIRKKFGFCLTALGFLNFENVAPAVIQ"
> //
> ----------------------------------END GBK-----------------------------------------
> Can anyone tell what I am missing or why this is happening?  I don't know if this has happened in earlier BioPerl versions as up until now, I usually downloaded sequences straight from NCBI, but that became too time consuming....but this seems to be as well :S
> Thank you in advance for any help,
> Veronica
> 		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From witch.of.agnessi at gmail.com  Wed May  8 15:24:53 2013
From: witch.of.agnessi at gmail.com (WoA)
Date: Wed, 8 May 2013 12:24:53 -0700 (PDT)
Subject: [Bioperl-l] Extracting matching subsequence from pairwise alignment
Message-ID: <1368041092972-16935.post@n3.nabble.com>

Hello All,

I've a pairwise global alignemnet of two DNA sequences generated by the
program NEEDLE of EMBOSS package. I wish to extract the sub-sequence that
matches/aligns to a given region of the other sequence. In  this alignment
<http://pastebin.com/wrhEDzJU>   (Pastebin Link) the given region (actually
the CDS) falls between base number 24:485 in the original sequence with ID
'XM_001005073.' I wish to extract the sub-sequence in the sequence ID
'Homolog' that aligns with that 24:485 region of the other sequence.

I'm using Bioperl to parse the alignment. I find out the the alignment
column numbers corresponding to 24:485 region in the particular sequence,
using 'column_from_residue_number'. Then I extract the sub-sequence from the
'aligned' other sequence(containing gaps) using the corresponding column
numbers. Finally I remove the gap characters.

Am I doing this thing correctly and are there any pitfalls ? Is there any
better way to do it by (Bio)Perl/Python? The code goes here:
use strict;
use warnings;
use Bio::AlignIO;

# read in an alignment generated by the EMBOSS program Needle
my $in = new Bio::AlignIO(-format => 'emboss',
                  -file   => 'test_needle.aln');

while( my $aln = $in->next_aln ) {
          #Seqnames: 'XM_001005073.'(CDS:24-485),'Homolog'
          my ($cds_start,$cds_end)=(24,485);#
          my $col_cdsstart = $aln->column_from_residue_number(
'XM_001005073.', $cds_start);
          my $col_cdsend= $aln->column_from_residue_number( 'XM_001005073.',
$cds_end);

          foreach my $seq ($aln->each_seq) {
                    if($seq->id() eq 'Homolog'){
                        my
$homolog_cds=$seq->subseq($col_cdsstart,$col_cdsend);
                         $homolog_cds=~s/\-//g;
                        print $homolog_cds,"\n";
                    }

        }
}





--
View this message in context: http://bioperl.996286.n3.nabble.com/Extracting-matching-subsequence-from-pairwise-alignment-tp16935.html
Sent from the Bioperl-L mailing list archive at Nabble.com.

From hlapp at drycafe.net  Wed May 15 16:44:07 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 15 May 2013 16:44:07 -0400
Subject: [Bioperl-l] Workshop on Sustainable Software for Science: Practice
	and Experiences
Message-ID: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>

FYI, if you haven't seen this yet:

http://wssspe.researchcomputing.org.uk/

It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?

Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)

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




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From carandraug+dev at gmail.com  Wed May 15 21:53:55 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 16 May 2013 02:53:55 +0100
Subject: [Bioperl-l] sets of sequences - how to read?
Message-ID: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>

Hi

when accessing entrez gene using eutils to get multiple genes, NCBI
now returns an Entrezgene-Set[1] rather than a list of EntrezGene.
This change must have happened sometime on the last 2 months. Compare:

use Bio::DB::EUtilities;

my %sets = (
  eutil   => 'efetch',
  db      => 'gene',
  retmode => 'text',
  rettype => 'asn1',
  email   => 'bioperl-l at lists.open-bio.org',
);

## this mimics the previous behaviour of the NCBI server but the
multiple requests will annoy their servers
my @ids = (3014, 85235);
my $response;
foreach (@ids) {
  my $fetcher = Bio::DB::EUtilities->new(%sets, id => $_);
  $response .= $fetcher->get_Response->content;
}
print $fetcher->get_Response->content;

## this used to be the right way to do it, but now returns an Entrezgene-Set
my $fetcher = Bio::DB::EUtilities->new(%sets, id => \@ids);
$response .= $fetcher->get_Response->content;
print $fetcher->get_Response->content;

There is no module to read these Entrezgene-Set in Perl at the moment,
since Bio::ASN1::EntrezGene; is not able to handle them. I have
contacted the module author and set him a fix[2] and he said he'll try
to look into it next week.

However, even with the fix there is another problem. How would one
access a set of sequences using the Bio::SeqIO API? There is no method
to do that. One could say, to ignore them, and make next_seq return
the next sequence of the set. But then we are losing data. After all,
it's perfectly viable to have multiple Entrezgene-Set in one file.
What would be the right way to do this?

Carn?

[1] http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/IEB/ToolBox/CPP_DOC/asn_spec/Entrezgene-Set.html
[2] https://github.com/carandraug/bio-asn1-entrezgene/commit/69d505056d8b7897df6271ffb7a5f39d58873c6b


From cjfields at illinois.edu  Thu May 16 00:43:22 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 04:43:22 +0000
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice	and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>

Jason and I have discussed looking into opportunity's like this, I think it makes sense to try a joint submission.  

chris

On May 15, 2013, at 3:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
> 
> http://wssspe.researchcomputing.org.uk/
> 
> It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?
> 
> Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)
> 
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> 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  Thu May 16 05:10:25 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 May 2013 10:10:25 +0100
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice and Experiences
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>

On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Jason and I have discussed looking into opportunity's like this, I think it makes
> sense to try a joint submission.
>
> chris

This sounds like a good idea, although given the time and place I am
unlikely to be able to attend in person:

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

Rather than trying to discuss this over four mailing lists should we switch
to the cross project list open-bio-l, or continue off-list?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thanks,

Peter

From miquel.ramia at uab.cat  Thu May 16 06:42:29 2013
From: miquel.ramia at uab.cat (=?ISO-8859-1?Q?Miquel_R=E0mia?=)
Date: Thu, 16 May 2013 12:42:29 +0200
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
Message-ID: <5194B815.2010401@uab.cat>

Hi all,

I get this message when compiling Bio::DB::Sam:

Building Bio-SamTools

gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'

collect2: ld returned 1 exit status

make: *** [bam2bedgraph] Error 1


Is this error related to the module or some dependencies? or maybe a 
problem with my system?

Any help appreciated, thanks!


-- 
Miquel R?mia Jes?s
PhD. candidate (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Aut?noma de Barcelona (UAB)
08193, Cerdanyola del Vall?s
Barcelona (Spain)


From cjfields at illinois.edu  Thu May 16 09:12:40 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 13:12:40 +0000
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <5194B815.2010401@uab.cat>
References: <5194B815.2010401@uab.cat>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>

It may be due to the new samtools release (v 0.1.19).  I know Heng Li has been working on the code over the last year for threading support (notice the undefined functions).  Have you tried v 0.1.18?

chris

On May 16, 2013, at 5:42 AM, Miquel R?mia <miquel.ramia at uab.cat> wrote:

> Hi all,
> 
> I get this message when compiling Bio::DB::Sam:
> 
> Building Bio-SamTools
> 
> gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
> 
> collect2: ld returned 1 exit status
> 
> make: *** [bam2bedgraph] Error 1
> 
> 
> Is this error related to the module or some dependencies? or maybe a problem with my system?
> 
> Any help appreciated, thanks!
> 
> 
> -- 
> Miquel R?mia Jes?s
> PhD. candidate (PIF)
> Evolutionary Bioinformatics Group
> (Genomics, Bioinformatics and Evolution Group)
> Lab MRB/014 - 93 586 89 58
> MRB - Institut de Biologia i Biomedicina (IBB)
> Universitat Aut?noma de Barcelona (UAB)
> 08193, Cerdanyola del Vall?s
> Barcelona (Spain)
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Thu May 16 09:09:45 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 13:09:45 +0000
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice and Experiences
In-Reply-To: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
	<CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1FBCF@CHIMBX5.ad.uillinois.edu>

Yes, though we need to make sure others (e.g. those not subscribed to open-bio-l) are in the loop.

November is a possibility for me.

chris

On May 16, 2013, at 4:10 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> Jason and I have discussed looking into opportunity's like this, I think it makes
>> sense to try a joint submission.
>> 
>> chris
> 
> This sounds like a good idea, although given the time and place I am
> unlikely to be able to attend in person:
> 
> First Workshop on Sustainable Software for Science: Practice and
> Experiences (WSSSPE)
> (to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
> http://wssspe.researchcomputing.org.uk/
> 
> Rather than trying to discuss this over four mailing lists should we switch
> to the cross project list open-bio-l, or continue off-list?
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> Thanks,
> 
> Peter



From andreas at sdsc.edu  Thu May 16 00:31:34 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 15 May 2013 21:31:34 -0700
Subject: [Bioperl-l] [Biojava-l] Workshop on Sustainable Software for
 Science: Practice and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <CALthepxHNLm4eHJcCQ4dLnhJr5OhGJJEKTAjH+x7Ppq0oFFnDA@mail.gmail.com>

Thanks Hilmar, you were faster than me in sending this out..

You are right, it would be very interesting to hear what some of the long
running open-bio projects have to say on the topic of sustainability. Let
me know if anybody is interested in a submission!

Andreas




On Wed, May 15, 2013 at 1:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
>
> http://wssspe.researchcomputing.org.uk/
>
> It seems to me that the Bio* projects, perhaps led by BioPerl as the
> oldest and thus longest running (nowadays more fancily called "sustained")
> of them would have a lot to say about the subject. Anyone interested in a
> joint submission?
>
> Also, I notice that Biojava's Andreas is on the organizing committee, so
> maybe he's been conspiring on something already :-)
>
>         -hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>

From cjfields at illinois.edu  Fri May 17 00:08:04 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 04:08:04 +0000
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>

This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.

My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.

chris

On May 15, 2013, at 8:53 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> when accessing entrez gene using eutils to get multiple genes, NCBI
> now returns an Entrezgene-Set[1] rather than a list of EntrezGene.
> This change must have happened sometime on the last 2 months. Compare:
> 
> use Bio::DB::EUtilities;
> 
> my %sets = (
>  eutil   => 'efetch',
>  db      => 'gene',
>  retmode => 'text',
>  rettype => 'asn1',
>  email   => 'bioperl-l at lists.open-bio.org',
> );
> 
> ## this mimics the previous behaviour of the NCBI server but the
> multiple requests will annoy their servers
> my @ids = (3014, 85235);
> my $response;
> foreach (@ids) {
>  my $fetcher = Bio::DB::EUtilities->new(%sets, id => $_);
>  $response .= $fetcher->get_Response->content;
> }
> print $fetcher->get_Response->content;
> 
> ## this used to be the right way to do it, but now returns an Entrezgene-Set
> my $fetcher = Bio::DB::EUtilities->new(%sets, id => \@ids);
> $response .= $fetcher->get_Response->content;
> print $fetcher->get_Response->content;
> 
> There is no module to read these Entrezgene-Set in Perl at the moment,
> since Bio::ASN1::EntrezGene; is not able to handle them. I have
> contacted the module author and set him a fix[2] and he said he'll try
> to look into it next week.
> 
> However, even with the fix there is another problem. How would one
> access a set of sequences using the Bio::SeqIO API? There is no method
> to do that. One could say, to ignore them, and make next_seq return
> the next sequence of the set. But then we are losing data. After all,
> it's perfectly viable to have multiple Entrezgene-Set in one file.
> What would be the right way to do this?
> 
> Carn?
> 
> [1] http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/IEB/ToolBox/CPP_DOC/asn_spec/Entrezgene-Set.html
> [2] https://github.com/carandraug/bio-asn1-entrezgene/commit/69d505056d8b7897df6271ffb7a5f39d58873c6b
> 
> _______________________________________________
> 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 May 17 00:16:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 04:16:12 +0000
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>
References: <5194B815.2010401@uab.cat>
	<118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>

For the record, this is now fixed in the latest Bio::Samtools (via Lincoln).

chris

On May 16, 2013, at 8:12 AM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> It may be due to the new samtools release (v 0.1.19).  I know Heng Li has been working on the code over the last year for threading support (notice the undefined functions).  Have you tried v 0.1.18?
> 
> chris
> 
> On May 16, 2013, at 5:42 AM, Miquel R?mia <miquel.ramia at uab.cat> wrote:
> 
>> Hi all,
>> 
>> I get this message when compiling Bio::DB::Sam:
>> 
>> Building Bio-SamTools
>> 
>> gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
>> 
>> collect2: ld returned 1 exit status
>> 
>> make: *** [bam2bedgraph] Error 1
>> 
>> 
>> Is this error related to the module or some dependencies? or maybe a problem with my system?
>> 
>> Any help appreciated, thanks!
>> 
>> 
>> -- 
>> Miquel R?mia Jes?s
>> PhD. candidate (PIF)
>> Evolutionary Bioinformatics Group
>> (Genomics, Bioinformatics and Evolution Group)
>> Lab MRB/014 - 93 586 89 58
>> MRB - Institut de Biologia i Biomedicina (IBB)
>> Universitat Aut?noma de Barcelona (UAB)
>> 08193, Cerdanyola del Vall?s
>> Barcelona (Spain)
>> 
>> _______________________________________________
>> 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  Fri May 17 01:12:24 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 17 May 2013 06:12:24 +0100
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>

On 17 May 2013 05:08, Fields, Christopher J <cjfields at illinois.edu> wrote:
> This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.
>
> My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.

:s I'm not sure I understood your suggestion. I think the problem is
just the introduction of a new concept, a "set" of stuff (genes in
this case), and how should SeqIO handle multiple sets.

Carn?


From shalabh.sharma7 at gmail.com  Fri May 17 10:54:55 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 17 May 2013 10:54:55 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
Message-ID: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>

HI,
                 First of all i am really sorry for sending this mail here,
i am not sure if this is the right forum. I know lot of people work on
similar stuff.
I wrote to NCBI but nobody replied.

Actually i am looking for all bacterial/microbial gene annotation
nucleotide fasta files.
Does anyone knows where to download these kind of files.
I tried *ffn files but they are not annotated.
Or is there any module in bioperl that i can use ?
I would really appreciate your help.

Thanks
Shalabh

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

From fossandonc at hotmail.com  Fri May 17 11:59:04 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 17 May 2013 11:59:04 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
Message-ID: <SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>

Hi,
You can get the annotations from here:
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/

The ".ffn" are the genes nucleotide fasta files but it does not show the
product name, on the other hand the ".faa" are the genes aminoacid fasta
files and shows the product name, but if you want both product and
nucleotide is much better to use the Genbank ".gbk" files that contains the
complete data and you can parse it easily using BioPerl to obtain all genes,
and then print the /protein_id, /product, and the nucleotide sequences in a
new fasta file. Check these to see how to do it:
http://www.bioperl.org/wiki/HOWTO:SeqIO
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

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 shalabh sharma
Enviado el: viernes, 17 de mayo de 2013 10:55
Para: bioperl-l
Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files

HI,
                 First of all i am really sorry for sending this mail here,
i am not sure if this is the right forum. I know lot of people work on
similar stuff.
I wrote to NCBI but nobody replied.

Actually i am looking for all bacterial/microbial gene annotation nucleotide
fasta files.
Does anyone knows where to download these kind of files.
I tried *ffn files but they are not annotated.
Or is there any module in bioperl that i can use ?
I would really appreciate your help.

Thanks
Shalabh

--
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences University of Georgia Athens, GA 30602-3636
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l


From shalabh.sharma7 at gmail.com  Fri May 17 12:26:26 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 17 May 2013 12:26:26 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
Message-ID: <CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>

Hey Francisco,
           Thanks a lot. Basically i just wanted gene nucleotide fasta
files with GI numbers.
I think i will have to parse it from gbk files.

-Shalabh


On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n <
fossandonc at hotmail.com> wrote:

> Hi,
> You can get the annotations from here:
> ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
>
> The ".ffn" are the genes nucleotide fasta files but it does not show the
> product name, on the other hand the ".faa" are the genes aminoacid fasta
> files and shows the product name, but if you want both product and
> nucleotide is much better to use the Genbank ".gbk" files that contains the
> complete data and you can parse it easily using BioPerl to obtain all
> genes,
> and then print the /protein_id, /product, and the nucleotide sequences in a
> new fasta file. Check these to see how to do it:
> http://www.bioperl.org/wiki/HOWTO:SeqIO
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>
> 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 shalabh sharma
> Enviado el: viernes, 17 de mayo de 2013 10:55
> Para: bioperl-l
> Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> HI,
>                  First of all i am really sorry for sending this mail here,
> i am not sure if this is the right forum. I know lot of people work on
> similar stuff.
> I wrote to NCBI but nobody replied.
>
> Actually i am looking for all bacterial/microbial gene annotation
> nucleotide
> fasta files.
> Does anyone knows where to download these kind of files.
> I tried *ffn files but they are not annotated.
> Or is there any module in bioperl that i can use ?
> I would really appreciate your help.
>
> Thanks
> Shalabh
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences University of Georgia Athens, GA 30602-3636
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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


From cjfields at illinois.edu  Fri May 17 13:37:53 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 17:37:53 +0000
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E22218@CHIMBX5.ad.uillinois.edu>

On May 17, 2013, at 12:12 AM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 17 May 2013 05:08, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.
>> 
>> My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.
> 
> :s I'm not sure I understood your suggestion. I think the problem is
> just the introduction of a new concept, a "set" of stuff (genes in
> this case), and how should SeqIO handle multiple sets.
> 
> Carn?


(note: critical point in this is Bio::ASN1::Entrezgene would allow this, I'm not sure it would.  Otherwise this is all really hand-wavy)

To me a 'set of stuff', particularly when the 'stuff' is stored sequentially in a flat file, is a simple 'database' or 'store' of similar items, where the class allows one the ability to look up particular members in the set, but also could store higher level information about the set as a whole if needed.  If it were me, I would implement a method particular to Bio::SeqIO::entrezgene that specifically creates and returns this ( next_geneset(), for instance ); next_seq() could then be implemented to iterate through the items in that database/store.  

Two useful things come out of this.  First, if the data for the Entrez Gene file/chunk are parsed to store offsets per ID, one would only need to parse out the chunks needed (offset of ID to next offset), then pass that into the parser and create objects on the fly.  This would probably be as fast or faster than (for instance) the greedy method of parsing the entire file and storing everything in objects up-front, then iterating through those objects one at a time, which I think is current behavior.

Second: if an index is created, the upfront cost is already paid (you could reuse the same index when parsing the same data).

An analogous example might be storing all FASTQ data in a sequencing run; I don't want to expend the effort to parse all the FASTQ data, but I may want to run operations on individual items in the set as well as store additional information about the data (barcodes per run, lanes, overall quality stats, etc).  

Does that make sense?  The pieces for this are lying around (Bio::Index::* for instance has methods for indexing flat files, and classes like Bio::DB::Fasta).

chris

From shalabh.sharma7 at gmail.com  Sun May 19 15:33:16 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Sun, 19 May 2013 15:33:16 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
	<CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>
Message-ID: <CAA7rn9ehQ1t1AizSLC15PFFh4mV8njfaTSY2ZVDqtzb2bEGBaA@mail.gmail.com>

Thanks Russell,
                            Actually i wanted all the Bacterial gene
nucleotide files, so i parsed it from *gbk. But yes these files might help
me for my other parts of my work.

Thanks
Shalabh


On Sun, May 19, 2013 at 3:26 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:

> Another option that I've used before is to download the gene2accession,
> gene2refseq,  and gene_info files from here
> ftp://ftp.ncbi.nih.gov/gene/DATA/ then parse out the data you require.
> It might work for you?
>
> --Russell
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:
> bioperl-l-bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> Sent: Saturday, 18 May 2013 4:26 a.m.
> To: Francisco J. Ossand?n
> Cc: bioperl-l
> Subject: Re: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> Hey Francisco,
>            Thanks a lot. Basically i just wanted gene nucleotide fasta
> files with GI numbers.
> I think i will have to parse it from gbk files.
>
> -Shalabh
>
>
> On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n <
> fossandonc at hotmail.com> wrote:
>
> > Hi,
> > You can get the annotations from here:
> > ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
> >
> > The ".ffn" are the genes nucleotide fasta files but it does not show
> > the product name, on the other hand the ".faa" are the genes aminoacid
> > fasta files and shows the product name, but if you want both product
> > and nucleotide is much better to use the Genbank ".gbk" files that
> > contains the complete data and you can parse it easily using BioPerl
> > to obtain all genes, and then print the /protein_id, /product, and the
> > nucleotide sequences in a new fasta file. Check these to see how to do
> > it:
> > http://www.bioperl.org/wiki/HOWTO:SeqIO
> > http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> >
> > 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 shalabh
> > sharma Enviado el: viernes, 17 de mayo de 2013 10:55
> > Para: bioperl-l
> > Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
> >
> > HI,
> >                  First of all i am really sorry for sending this mail
> > here, i am not sure if this is the right forum. I know lot of people
> > work on similar stuff.
> > I wrote to NCBI but nobody replied.
> >
> > Actually i am looking for all bacterial/microbial gene annotation
> > nucleotide fasta files.
> > Does anyone knows where to download these kind of files.
> > I tried *ffn files but they are not annotated.
> > Or is there any module in bioperl that i can use ?
> > I would really appreciate your help.
> >
> > Thanks
> > Shalabh
> >
> > --
> > Shalabh Sharma
> > Scientific Computing Professional Associate (Bioinformatics
> > Specialist) Department of Marine Sciences University of Georgia
> > Athens, GA 30602-3636 _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences University of Georgia Athens, GA 30602-3636
>
> _______________________________________________
> 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.
> =======================================================================
>



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


From Russell.Smithies at agresearch.co.nz  Sun May 19 15:26:35 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 20 May 2013 07:26:35 +1200
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
	<CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>

Another option that I've used before is to download the gene2accession, gene2refseq,  and gene_info files from here ftp://ftp.ncbi.nih.gov/gene/DATA/ then parse out the data you require.
It might work for you?

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of shalabh sharma
Sent: Saturday, 18 May 2013 4:26 a.m.
To: Francisco J. Ossand?n
Cc: bioperl-l
Subject: Re: [Bioperl-l] Downloading annotated Gene nucleotide fasta files

Hey Francisco,
           Thanks a lot. Basically i just wanted gene nucleotide fasta files with GI numbers.
I think i will have to parse it from gbk files.

-Shalabh


On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n < fossandonc at hotmail.com> wrote:

> Hi,
> You can get the annotations from here:
> ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
>
> The ".ffn" are the genes nucleotide fasta files but it does not show 
> the product name, on the other hand the ".faa" are the genes aminoacid 
> fasta files and shows the product name, but if you want both product 
> and nucleotide is much better to use the Genbank ".gbk" files that 
> contains the complete data and you can parse it easily using BioPerl 
> to obtain all genes, and then print the /protein_id, /product, and the 
> nucleotide sequences in a new fasta file. Check these to see how to do 
> it:
> http://www.bioperl.org/wiki/HOWTO:SeqIO
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>
> 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 shalabh 
> sharma Enviado el: viernes, 17 de mayo de 2013 10:55
> Para: bioperl-l
> Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> HI,
>                  First of all i am really sorry for sending this mail 
> here, i am not sure if this is the right forum. I know lot of people 
> work on similar stuff.
> I wrote to NCBI but nobody replied.
>
> Actually i am looking for all bacterial/microbial gene annotation 
> nucleotide fasta files.
> Does anyone knows where to download these kind of files.
> I tried *ffn files but they are not annotated.
> Or is there any module in bioperl that i can use ?
> I would really appreciate your help.
>
> Thanks
> Shalabh
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics 
> Specialist) Department of Marine Sciences University of Georgia 
> Athens, GA 30602-3636 _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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

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

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From miquel.ramia at uab.cat  Tue May 21 11:08:18 2013
From: miquel.ramia at uab.cat (=?ISO-8859-1?Q?Miquel_R=E0mia?=)
Date: Tue, 21 May 2013 17:08:18 +0200
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>
References: <5194B815.2010401@uab.cat>
	<"118F034CF4C3EF48A96F86CE585B94BF74E1F C2C"@CHIMBX5.ad.uillinois.edu>
	<118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>
Message-ID: <519B8DE2.2070308@uab.cat>

On 17/05/13 06:16, Fields, Christopher J wrote:
> For the record, this is now fixed in the latest Bio::Samtools (via Lincoln).
>
> chris
>
>

Compiled correctly!

thank you



-- 
Miquel R?mia Jes?s
PhD. candidate (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Aut?noma de Barcelona (UAB)
08193, Cerdanyola del Vall?s
Barcelona (Spain)


From b.l.cohen_home at btinternet.com  Mon May 20 14:49:50 2013
From: b.l.cohen_home at btinternet.com (Bernard Cohen)
Date: Mon, 20 May 2013 19:49:50 +0100 (BST)
Subject: [Bioperl-l] Phylip format error
Message-ID: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>

Hello!

I happen to have checked to see what the PERL webpage says about Phylip format for DNA alignment files and see that it is erroneous.?

I am not a PERL user and do not want to be bothered to register or otherwise learn how to make an official comment, so forward this for someone to pick up.

Phylip format allows up to 10 spaces for taxon names; the data must start in the 11th space. This can be checked on Jo Felsenstein's site.

The PERL page accessed by searching for "Phylip format PERL" allows only 8 spaces for the name.?

B. L. Cohen

From senanu.pearson at gmail.com  Wed May 22 16:15:24 2013
From: senanu.pearson at gmail.com (Senanu)
Date: Wed, 22 May 2013 13:15:24 -0700
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from alignment
Message-ID: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>

Hi all,

I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 

I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 

Is this a known problem? Is there another way to generate such a consensus?


my $in = Bio::AlignIO->new(-file => $files[0],
                           -format => 'XMFA');
while  (my $aln = $in->next_aln()) {
    foreach  my $seq ($aln->each_seq) {
        $seq->alphabet('dna');
    }
    my $con = $aln->consensus_iupac();
}


Thanks in advance.
Ngwenyama

From cjfields at illinois.edu  Wed May 22 19:17:50 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 22 May 2013 23:17:50 +0000
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from
 alignment
In-Reply-To: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
References: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E2A01D@CHIMBX5.ad.uillinois.edu>

On May 22, 2013, at 3:15 PM, Senanu <senanu.pearson at gmail.com> wrote:

> Hi all,
> 
> I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 

Probably the former, but...

> I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 

It shouldn't take that long, 7 Mb isn't that large.  Or is that 7 Mb for one genome?

> Is this a known problem? Is there another way to generate such a consensus?

The code isn't really optimized for this, but again this isn't terribly large.  Is the bottleneck reading the alignment in, or is it the consensus_iupac() step?  Hard to say w/o seeing the alignment data itself.

> my $in = Bio::AlignIO->new(-file => $files[0],
>                           -format => 'XMFA');
> while  (my $aln = $in->next_aln()) {
>    foreach  my $seq ($aln->each_seq) {
>        $seq->alphabet('dna');
>    }
>    my $con = $aln->consensus_iupac();
> }
> 
> 
> Thanks in advance.
> Ngwenyama
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

chris

From alexeymorozov1991 at gmail.com  Thu May 23 03:22:13 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Thu, 23 May 2013 16:22:13 +0900
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
Message-ID: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>

Which is also worsened by the fact that there is relaxed phylip format,
which allows up to 250 chars for taxon name. They are separated from a
sequence by single space, which creates problems if names were extended to
10 chars in strict Felsenstein's format by whitespaces. On the whole,
phylip is as messily defined format as one can make from a plain textfile
with information content of fasta.
Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
phylip and how does it tell dialects from one another. Even if code support
is OK, it may be worthwile to explain it somewhere at bioperl.org


2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>

> Hello!
>
> I happen to have checked to see what the PERL webpage says about Phylip
> format for DNA alignment files and see that it is erroneous.
>
> I am not a PERL user and do not want to be bothered to register or
> otherwise learn how to make an official comment, so forward this for
> someone to pick up.
>
> Phylip format allows up to 10 spaces for taxon names; the data must start
> in the 11th space. This can be checked on Jo Felsenstein's site.
>
> The PERL page accessed by searching for "Phylip format PERL" allows only 8
> spaces for the name.
>
> B. L. Cohen
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

From p.j.a.cock at googlemail.com  Thu May 23 04:30:21 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 May 2013 09:30:21 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>

On Thu, May 23, 2013 at 8:22 AM, Alexey Morozov
<alexeymorozov1991 at gmail.com> wrote:
> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org

Biopython's AlignIO defines both a (strict) "phylip" and "relaxed-phylip"
as two separate formats (or variants, like the "fastq" variants). Doing
the same in BioPerl would seem sensible since auto-detection is not
easy.

http://biopython.org/wiki/AlignIO#File_Formats

Peter

P.S. Where does that 250 characters for the taxon name limit come from?
The trouble with relaxed phylip is that some tools are more relaxed than
others ;)

From awitney at sgul.ac.uk  Thu May 23 04:43:15 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 23 May 2013 09:43:15 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <519DD6A3.8090304@sgul.ac.uk>


Not sure if there is an actual question in these messages, but BioPerl
can be used to generate valid Phylip format and run, like this:

## Build Align object
my $aln = Bio::SimpleAlign->new(-seqs=>$seqs);

## swap the taxa names with 8 characters long unique IDs
my ($aln_safe, $ref_name) = $aln->set_displayname_safe(8);

## Write out phylip format infile
Bio::AlignIO->new(-file=>'>infile.out', -format=>'phylip', -interleaved
=> 0)->write_aln($aln);

## run PHYLIP's pars program
my @params = (idlength=>10);   #, jumble=>"17,10");
my $tree_factory = Bio::Tools::Run::Phylo::Phylip::Pars->new(@params);
$tree_factory->quiet(1);  # Suppress pars messages to terminal
my $tree = $tree_factory->create_tree($aln_safe);

## fix the node labels back
my @nodes = sort { defined $a->id && defined $b->id && $a->id cmp $b->id
} $tree->get_nodes();
foreach my $nd (@nodes) {
	if ( $nd->is_Leaf ) {
		$nd->id($ref_name->{$nd->id_output})
	}
}

HTH

Adam

On 23/05/2013 08:22, Alexey Morozov wrote:
> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> 
> 2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>
> 
>> Hello!
>>
>> I happen to have checked to see what the PERL webpage says about Phylip
>> format for DNA alignment files and see that it is erroneous.
>>
>> I am not a PERL user and do not want to be bothered to register or
>> otherwise learn how to make an official comment, so forward this for
>> someone to pick up.
>>
>> Phylip format allows up to 10 spaces for taxon names; the data must start
>> in the 11th space. This can be checked on Jo Felsenstein's site.
>>
>> The PERL page accessed by searching for "Phylip format PERL" allows only 8
>> spaces for the name.
>>
>> B. L. Cohen
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> 
> 
> 

From cjfields at illinois.edu  Thu May 23 09:48:31 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 13:48:31 +0000
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E323A4@CITESMBX5.ad.uillinois.edu>

Alexey,

Just want to point out that 'relaxed phylip' format was introduced long after this parser was created; in fact (as Adam points out) there was an alternative workaround to deal with the lossy names.  

The content of that page is on a wiki, which anyone is free to edit (just need an OpenID to set up an account).

chris

On May 23, 2013, at 2:22 AM, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:

> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> 
> 2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>
> 
>> Hello!
>> 
>> I happen to have checked to see what the PERL webpage says about Phylip
>> format for DNA alignment files and see that it is erroneous.
>> 
>> I am not a PERL user and do not want to be bothered to register or
>> otherwise learn how to make an official comment, so forward this for
>> someone to pick up.
>> 
>> Phylip format allows up to 10 spaces for taxon names; the data must start
>> in the 11th space. This can be checked on Jo Felsenstein's site.
>> 
>> The PERL page accessed by searching for "Phylip format PERL" allows only 8
>> spaces for the name.
>> 
>> B. L. Cohen
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Thu May 23 10:05:32 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 14:05:32 +0000
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
	<CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>

On May 23, 2013, at 3:30 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, May 23, 2013 at 8:22 AM, Alexey Morozov
> <alexeymorozov1991 at gmail.com> wrote:
>> Which is also worsened by the fact that there is relaxed phylip format,
>> which allows up to 250 chars for taxon name. They are separated from a
>> sequence by single space, which creates problems if names were extended to
>> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
>> phylip is as messily defined format as one can make from a plain textfile
>> with information content of fasta.
>> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
>> phylip and how does it tell dialects from one another. Even if code support
>> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> Biopython's AlignIO defines both a (strict) "phylip" and "relaxed-phylip"
> as two separate formats (or variants, like the "fastq" variants). Doing
> the same in BioPerl would seem sensible since auto-detection is not
> easy.
> 
> http://biopython.org/wiki/AlignIO#File_Formats
> 
> Peter
> 
> P.S. Where does that 250 characters for the taxon name limit come from?
> The trouble with relaxed phylip is that some tools are more relaxed than
> others ;)

As Adam pointed out, prior to the introduction of 'relaxed phylip' we had an alternative solution that didn't require a modified format but still allowed one to use PHYLIP and other tools requesting the format.  I think 'relaxed phylip' was introduced by CIPRES a few years back.  Frankly, this is the first time I have seen this mentioned on the list; yay, yet another format variation :)

The variant format parsing (as implemented for SeqIO::fastq, as you know) deals with variant names like 'fastq-sanger', where the main format name is first, the variant of the format second.  The order in this case is reversed (relaxed-phylip), which I'm pretty sure will not work.  Not impossible to allow, but we would probably allow support like this initially:

my $in = Bio::AlignIO->new(-format => 'phylip',
                           -variant => 'relaxed',
                             ?);

chris

From cjfields at illinois.edu  Thu May 23 09:56:32 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 13:56:32 +0000
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from
 alignment
In-Reply-To: <92CD2F9D-7C8E-4941-9354-4BD80D8C2CB6@gmail.com>
References: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E2A01D@CHIMBX5.ad.uillinois.edu>
	<92CD2F9D-7C8E-4941-9354-4BD80D8C2CB6@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E32489@CITESMBX5.ad.uillinois.edu>

(keep the list cc'd)

On May 22, 2013, at 6:31 PM, Senanu <senanu.junk at gmail.com> wrote:

> On May 22, 2013, at 4:17 PM, Fields, Christopher J wrote:
> 
>> Hi all,
>>> 
>>> I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 
>> 
>> Probably the former, but...
>> 
>>> I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 
>> 
>> It shouldn't take that long, 7 Mb isn't that large.  Or is that 7 Mb for one genome?
> 
> It is 7Mb per genome, but there are only 2 genomes in the alignment, and the sequences are very similar to one another. 
> 
>> 
>>> Is this a known problem? Is there another way to generate such a consensus?
>> 
>> The code isn't really optimized for this, but again this isn't terribly large.  Is the bottleneck reading the alignment in, or is it the consensus_iupac() step?  Hard to say w/o seeing the alignment data itself.
> 
> The bottleneck is definitely with the consensus_iupac step. Reading the alignment in takes a few seconds. 

That's interesting, but again not surprising.  One would have to look at the code, but I wouldn't be surprised if the method is terribly inefficient.

chris

From p.j.a.cock at googlemail.com  Thu May 23 10:53:09 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 May 2013 15:53:09 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
	<CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_66x-c+Frmb0LVjYEB39OgxS6mabLKPBzEv38BoiOFMWg@mail.gmail.com>

On Thu, May 23, 2013 at 3:05 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
>
> I think 'relaxed phylip' was introduced by CIPRES a few years back.
> Frankly, this is the first time I have seen this mentioned on the list; yay,
> yet another format variation :)

The relaxed phylip 'format' goes back further than that, e.g.
http://lists.open-bio.org/pipermail/biopython-dev/2008-June/003899.html

RAxML and PHYML support relaxed phylip - but with their own ID limits.

Peter

From Ben.Ward at sainsbury-laboratory.ac.uk  Fri May 24 15:14:17 2013
From: Ben.Ward at sainsbury-laboratory.ac.uk (Ben Ward (TSL))
Date: Fri, 24 May 2013 19:14:17 +0000
Subject: [Bioperl-l] Building Many trees with Bioperl
Message-ID: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>

Hi,

I'm new to Bioperl and plan to make a script to automate making trees with many alignment files (themselves generated by automating the process of multiple alignment for many datasets by using clustalw in a bioperl script).
But I need to get it right for one pice of test data before I can do it for all:

What I have produced so far is the below. It's supposed to load in the alignment file as as SimpleAlign. Then use that alignment in phyml. I looked at the documentation and tried to follow examples.

However it gives me many errors like:
--------------------- WARNING ---------------------
MSG: Replacing one sequence [FXCNDTJ02P/1-366]

And then gives me:
Phyml command = /Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Phyml call (/Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output [/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip_phyml_stat.txt]: 11
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::Phylo::Phyml::_run /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
-----------------------------------------------------------

Can someone let me know if I'm going about this correctly and what I need to do to get it to work. I've also tried to run phyml by giving the filename in the run() method like:
my $inputfilename = 'outputalignmentfile';
my $tree = $factory->run("$inputfilename");

But I get the same EXCEPTION: Bio::Root::Exception message.

Thanks,
Ben W.

SCRIPT ---

#!/usr/bin/perl
use warnings;
use strict;
BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
use Bio::TreeIO;
use Bio::AlignIO;
use Bio::Tools::Run::Phylo::Phyml;

my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
-format => 'phylip');

my $aln = $alnin->next_aln();


# Make a Phyml factory.
my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
 -data_type => 'dna');

# Pass the factory an alignment and run:
# my $inputfilename = 'outputalignmentfile';

my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.


# Setup tree output stream...
my $treeio = Bio::TreeIO->new(-format => 'newick',
 -file => 'tree.newick');

$treeio->write_tree($tree);

exit 0;


From bosborne11 at verizon.net  Fri May 24 17:25:38 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Fri, 24 May 2013 17:25:38 -0400
Subject: [Bioperl-l] Building Many trees with Bioperl
In-Reply-To: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>
References: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>
Message-ID: <93D0963E-8399-468C-A32B-875FAA5054D1@verizon.net>

Ben,

What happens when you take the Phyml command itself and run it from the command line?

Also, a minor point: the message "MSG: Replacing one sequence [FXCNDTJ02P/1-366]" is not an error, it is a warning. An error accompanies an exit, warnings are just informative.

Brian O.


On May 24, 2013, at 3:14 PM, Ben Ward (TSL) <Ben.Ward at sainsbury-laboratory.ac.uk> wrote:

> Hi,
> 
> I'm new to Bioperl and plan to make a script to automate making trees with many alignment files (themselves generated by automating the process of multiple alignment for many datasets by using clustalw in a bioperl script).
> But I need to get it right for one pice of test data before I can do it for all:
> 
> What I have produced so far is the below. It's supposed to load in the alignment file as as SimpleAlign. Then use that alignment in phyml. I looked at the documentation and tried to follow examples.
> 
> However it gives me many errors like:
> --------------------- WARNING ---------------------
> MSG: Replacing one sequence [FXCNDTJ02P/1-366]
> 
> And then gives me:
> Phyml command = /Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Phyml call (/Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output [/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip_phyml_stat.txt]: 11
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
> STACK: Bio::Tools::Run::Phylo::Phyml::_run /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
> STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
> -----------------------------------------------------------
> 
> Can someone let me know if I'm going about this correctly and what I need to do to get it to work. I've also tried to run phyml by giving the filename in the run() method like:
> my $inputfilename = 'outputalignmentfile';
> my $tree = $factory->run("$inputfilename");
> 
> But I get the same EXCEPTION: Bio::Root::Exception message.
> 
> Thanks,
> Ben W.
> 
> SCRIPT ---
> 
> #!/usr/bin/perl
> use warnings;
> use strict;
> BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
> use Bio::TreeIO;
> use Bio::AlignIO;
> use Bio::Tools::Run::Phylo::Phyml;
> 
> my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
> -format => 'phylip');
> 
> my $aln = $alnin->next_aln();
> 
> 
> # Make a Phyml factory.
> my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
> -data_type => 'dna');
> 
> # Pass the factory an alignment and run:
> # my $inputfilename = 'outputalignmentfile';
> 
> my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.
> 
> 
> # Setup tree output stream...
> my $treeio = Bio::TreeIO->new(-format => 'newick',
> -file => 'tree.newick');
> 
> $treeio->write_tree($tree);
> 
> exit 0;
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From Ben.Ward at sainsbury-laboratory.ac.uk  Fri May 24 17:46:40 2013
From: Ben.Ward at sainsbury-laboratory.ac.uk (Ben Ward (TSL))
Date: Fri, 24 May 2013 21:46:40 +0000
Subject: [Bioperl-l] Building Many trees with Bioperl
In-Reply-To: <93D0963E-8399-468C-A32B-875FAA5054D1@verizon.net>
Message-ID: <CDC59B58.13A3%ben.ward@sainsbury-laboratory.ac.uk>

Hi,

If I just run phyml on the command line it seems to run ok - it accept's
my file and appears to undergo the tree building process - I haven't
actually see it complete yet, but ML and Bayes always does take a while -
and I have many reads that need to be aligned. But PhyML gets to the point
it asks - are you sure you want to proceed - I say yes, then it keeps
quiet and is currently working along to itself:

. 766 patterns found (out of a total of 795 sites).

. 58 sites without polymorphism (7.30%).

. Computing pairwise distances...

. Building BioNJ tree...

. WARNING: this analysis requires at least 556 MB of memory space.

. Do you really want to proceed? [Y/n] Y


It appears to be working =/
 
Best,
Ben.



On 24/05/2013 22:25, "Brian Osborne" <bosborne11 at verizon.net> wrote:

>Ben,
>
>What happens when you take the Phyml command itself and run it from the
>command line?
>
>Also, a minor point: the message "MSG: Replacing one sequence
>[FXCNDTJ02P/1-366]" is not an error, it is a warning. An error
>accompanies an exit, warnings are just informative.
>
>Brian O.
>
>
>On May 24, 2013, at 3:14 PM, Ben Ward (TSL)
><Ben.Ward at sainsbury-laboratory.ac.uk> wrote:
>
>> Hi,
>> 
>> I'm new to Bioperl and plan to make a script to automate making trees
>>with many alignment files (themselves generated by automating the
>>process of multiple alignment for many datasets by using clustalw in a
>>bioperl script).
>> But I need to get it right for one pice of test data before I can do it
>>for all:
>> 
>> What I have produced so far is the below. It's supposed to load in the
>>alignment file as as SimpleAlign. Then use that alignment in phyml. I
>>looked at the documentation and tried to follow examples.
>> 
>> However it gives me many errors like:
>> --------------------- WARNING ---------------------
>> MSG: Replacing one sequence [FXCNDTJ02P/1-366]
>> 
>> And then gives me:
>> Phyml command = /Users/wardb/clustalw2/phyml
>>/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyli
>>p  0 i 1 0 HKY e e 1 e BIONJ y y
>> 
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Phyml call (/Users/wardb/clustalw2/phyml
>>/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyli
>>p  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output
>>[/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyl
>>ip_phyml_stat.txt]: 11
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
>> STACK: Bio::Tools::Run::Phylo::Phyml::_run
>>/Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
>> STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
>> -----------------------------------------------------------
>> 
>> Can someone let me know if I'm going about this correctly and what I
>>need to do to get it to work. I've also tried to run phyml by giving the
>>filename in the run() method like:
>> my $inputfilename = 'outputalignmentfile';
>> my $tree = $factory->run("$inputfilename");
>> 
>> But I get the same EXCEPTION: Bio::Root::Exception message.
>> 
>> Thanks,
>> Ben W.
>> 
>> SCRIPT ---
>> 
>> #!/usr/bin/perl
>> use warnings;
>> use strict;
>> BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
>> use Bio::TreeIO;
>> use Bio::AlignIO;
>> use Bio::Tools::Run::Phylo::Phyml;
>> 
>> my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
>> -format => 'phylip');
>> 
>> my $aln = $alnin->next_aln();
>> 
>> 
>> # Make a Phyml factory.
>> my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
>> -data_type => 'dna');
>> 
>> # Pass the factory an alignment and run:
>> # my $inputfilename = 'outputalignmentfile';
>> 
>> my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.
>> 
>> 
>> # Setup tree output stream...
>> my $treeio = Bio::TreeIO->new(-format => 'newick',
>> -file => 'tree.newick');
>> 
>> $treeio->write_tree($tree);
>> 
>> exit 0;
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



From himaghna.bhattacharjee at gmail.com  Tue May 28 11:59:02 2013
From: himaghna.bhattacharjee at gmail.com (Himaghna Bhattacharjee)
Date: Tue, 28 May 2013 21:29:02 +0530
Subject: [Bioperl-l] error in the link to install Kobe repository for windows
Message-ID: <CALd+KH1D8JVFJUNf+L7gM48B-iRsdcYkAZwuNOzi9bkVt7b49Q@mail.gmail.com>

Hey,
the link to install Kobe's repository for per 5.10 <"
http://cpan.uwinnipeg.ca/PPMPackages/10xx/
--">
seems to be broken as it shows Error 503 Service Temporarily Unavailable.
Could you please suggest an alternative ?

Thanks .
Himaghna Bhattacharjee
3rd year
B.E.(Hons.)Chemical Engineering
Birla Institute of Technology and Science,Pilani
Rajasthan 333 031

From wgallin at ualberta.ca  Tue May 28 13:49:02 2013
From: wgallin at ualberta.ca (Warren Gallin)
Date: Tue, 28 May 2013 11:49:02 -0600
Subject: [Bioperl-l] ReplacedBy value in esummary
Message-ID: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>

Hi,

	I just encountered a glitch when I was trying to update some entries in a database by finding updated GENBANK protein entries.

	The original record was gi 118091304 which has been replaced by gi 363734282

	I retrieved an ESummary of the record for gi 118091304 as a Bio::Tools::EUtilities::Summary::DocSum object (called $ds).

	When I then tried to retrieve the gi number for the replacement by using: 

my $replaced = $ds->get_contents_by_name('ReplacedBy');

 the returned value was 1, and when I dumped the ESummary record the relevant pair is ReplacedBy          :XP_421022.3.

The full Esummary dump is:

UID                 :118091304
Caption             :XP_421022
Title               :PREDICTED: similar to Potassium voltage-gated channel, subfamily Q, member
		    :1 [Gallus gallus]
Extra               :gi|118091304|ref|XP_421022.2|[118091304]
Gi                  :118091304
CreateDate          :2004/07/28
UpdateDate          :2006/11/16
Flags               :512
TaxId               :9031
Length              :643
Status              :replaced
ReplacedBy          :XP_421022.3
Comment             : This record was replaced or removed. 


	So two questions:

	1) Is the ReplacedBy value always supposed to be the new accession number version rather than the new gi number?
	2) Why would I be getting a returned value of 1 instead of the accession number that is in the summary record?

Any advice appreciated.

Warren Gallin

From cjfields at illinois.edu  Tue May 28 14:31:30 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 28 May 2013 18:31:30 +0000
Subject: [Bioperl-l] ReplacedBy value in esummary
In-Reply-To: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>
References: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E44377@CHIMBX5.ad.uillinois.edu>

On May 28, 2013, at 12:49 PM, Warren Gallin <wgallin at ualberta.ca> wrote:

> Hi,
> 
> 	I just encountered a glitch when I was trying to update some entries in a database by finding updated GENBANK protein entries.
> 
> 	The original record was gi 118091304 which has been replaced by gi 363734282
> 
> 	I retrieved an ESummary of the record for gi 118091304 as a Bio::Tools::EUtilities::Summary::DocSum object (called $ds).
> 
> 	When I then tried to retrieve the gi number for the replacement by using: 
> 
> my $replaced = $ds->get_contents_by_name('ReplacedBy');
> 
> the returned value was 1, and when I dumped the ESummary record the relevant pair is ReplacedBy          :XP_421022.3.
> 
> The full Esummary dump is:
> 
> UID                 :118091304
> Caption             :XP_421022
> Title               :PREDICTED: similar to Potassium voltage-gated channel, subfamily Q, member
> 		    :1 [Gallus gallus]
> Extra               :gi|118091304|ref|XP_421022.2|[118091304]
> Gi                  :118091304
> CreateDate          :2004/07/28
> UpdateDate          :2006/11/16
> Flags               :512
> TaxId               :9031
> Length              :643
> Status              :replaced
> ReplacedBy          :XP_421022.3
> Comment             : This record was replaced or removed. 
> 
> 
> 	So two questions:
> 
> 	1) Is the ReplacedBy value always supposed to be the new accession number version rather than the new gi number?

No idea, the best people to answer that would be NCBI (the idea of these modules was to simplify getting at that data instead of munging the XML, but whatever they report is mainly from NCBI, not bioperl).

> 	2) Why would I be getting a returned value of 1 instead of the accession number that is in the summary record?

The text dump above indicates the values do exist.  However, you are calling a method that returns a list (note the plural in the name) in scalar context, so you get the number of values.  If you always expect a single value, use:

    my ($replaced) = $ds->get_contents_by_name('ReplacedBy');

which forces array context.  That should fix it.

chris

> Any advice appreciated.
> 
> Warren Gallin
> _______________________________________________
> 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 May  1 22:16:02 2013
From: florent.angly at gmail.com (Florent Angly)
Date: Thu, 02 May 2013 12:16:02 +1000
Subject: [Bioperl-l] Downloading sequences in batch from Trace Archive
In-Reply-To: <CAA7rn9dtgtkdPLU9v=b3Jq0CWPvph59BYp2r5-jJRRt94dB1RA@mail.gmail.com>
References: <CAA7rn9dtgtkdPLU9v=b3Jq0CWPvph59BYp2r5-jJRRt94dB1RA@mail.gmail.com>
Message-ID: <5181CC62.9000609@gmail.com>

Maybe using EUtilities?
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service

Florent


On 30/04/13 06:25, shalabh sharma wrote:
> Hi All,
>            Is there any module in Bioperl that can download sequences from
> NCBI's trace archive?
>
> Thanks
> Shalabh
>



From jason.stajich at gmail.com  Thu May  2 01:42:55 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 1 May 2013 22:42:55 -0700
Subject: [Bioperl-l] Fwd: doubt
References: <CACPwBoTqbeNuY6hGW9gpQagL2ZXdknwcM_0Q7QMMCyqEz9FXcg@mail.gmail.com>
Message-ID: <B094273D-B6AB-4DE8-8B65-FFAA3FB30D8A@gmail.com>



Begin forwarded message:

> From: ARYA DAS <aryaanildas at gmail.com>
> Subject: doubt
> Date: May 1, 2013 10:42:21 PM PDT
> To: jason at bioperl.org
> 
> sir,
> 
>     Am using windows7 n was trying to install bio perl in it..i have
> already installed active perl.5.16.3.1603 . n was followeing the
> installation procedure mentioned .when i tried GUI installation .. i cant
> find bioperl package when i try to search them for installation.
> while using command line..
> 
> ppm> install PPM-Repositories
> 
> shows error like cant find package that provides PPM repositories,
> 
> and when i try manually ,on reaching the
> perl Build test
> 
> it says build is recognised as an internal or external file.
> 
> please help if time permits
> 
> regards,
> arya

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



From voldrani at gmail.com  Sun May  5 00:03:38 2013
From: voldrani at gmail.com (Chris Maloney)
Date: Sun, 5 May 2013 00:03:38 -0400
Subject: [Bioperl-l] Wiki work, Template:Doclink
Message-ID: <CABE9g5Ps+NDmziDZNro8UZ5_RMOP1ru1fmKOpFh+DFh=equRfQ@mail.gmail.com>

The module pages on the wiki could look a little better, like this one
for example:  http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast.
 There used to be a bunch of extra whitespace at the top of the page,
which was caused by extra line breaks in Template:Doclink, which I
just removed.

But, I think there are other improvements that could be made.  I would
like to turn this into an infobox -- which are the helpful informative
tables of info on Wikipedia that appear on many articles on the upper
right.  That would allow us to add more links -- like to metacpan, for
example.

It is not completely trivial to import infoboxes into a wiki though, I
just discovered.  I just went through the exercise on my home wiki,
and it involves importing a lot of templates from Wikipedia, and
fixing up the common.css.  You can see the full list of imported
templates here:
http://chrismaloney.org/wiki/index.php?title=Special:RecentChanges&limit=100.
 I don't *think* this should cause any problems, but I'm not 100%
sure.  On the other hand, if it does, it should be easy to roll back
-- it's a wiki, after all.

Does anybody have a problem if I do this?  I'll wait a day for
responses, and tackle this tomorrow, if no one objects.

-- Chris M.


From armendarez77 at hotmail.com  Tue May  7 20:32:22 2013
From: armendarez77 at hotmail.com (Veronica A.)
Date: Tue, 7 May 2013 17:32:22 -0700
Subject: [Bioperl-l] Bio::SeqIO doesn't write all gbk sequences from
	Bio::DB::GenBank
Message-ID: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>

Hello,
I'm currently running Bio::Perl 1.6.1 on Ubuntu 12.04.2 LTS and have noticed a problem with Bio::SeqIO when writing genbank files using the write_seq() function;  some of the files do not include an 'ORIGIN' tag or the sequence.

I am using GI#s (50 at a time every 2 minutes) to retrieve genbank files via Bio::DB::GenBank.

----------------------------------------START CODE----------------------------------
my $gb = Bio::DB::GenBank->new(-verbose=>-1);my $seqout = Bio::SeqIO->new(-file=>">$fileName", '-format'=>'Genbank', -alphabet=>'dna', -flush=>0, -verbose=>-1);while(@ids){     my @batchArray = splice(@ids, 0, 50);     my $batchArrayRef = \@batchArray;
     my $streamObj;     my $pid = fork();     if($pid == 0){          eval{               $streamObj = $gb->get_Stream_by_id($batchArrayRef);          };          if($@){               print "Error: ".$@."\n";          }          else{               while(my $seqObj = $streamObj->next_seq()){                    unless($seqObj->accession_number() =~ /N[A-Z]\_/){                        #print "ID: ".$seqObj->id()."\n";                        #print "Seq:\n".$seqObj->seq()."\n";                         $seqout->write_seq($seqObj);                    }                }          }          exit 0;     }}waitpid($pid,0);sleep(120);
----------------------------------------END CODE----------------------------------
Most of the Genbank files written to the output file have sequences, but there is a small portion that do not, even though they should.  For example, JX287367, in NCBI includes an 'ORIGIN' tag and sequence and when I use the print function before writing to file, the sequence is printed to STDOUT, but the 'ORIGIN' tag and sequence are not written to the output gbk file.  The following is found in the final output file:
----------------------------------START GBK-----------------------------------------
LOCUS       JX287367                 588 bp    DNA     linear   BCT 19-DEC-2012DEFINITION  Chlamydia trachomatis strain UW-5/CX pyruvoyl-dependent arginine            decarboxylase (aaxB) gene, complete cds.ACCESSION   JX287367VERSION     JX287367.1  GI:404351720KEYWORDS    .SOURCE      Chlamydia trachomatis  ORGANISM  Chlamydia trachomatis            Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;            Chlamydia/Chlamydophila group; Chlamydia.REFERENCE   1  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Characterization of the activity and expression of arginine            decarboxylase in human and animal Chlamydia pathogens  JOURNAL   FEMS Microbiol. Lett. 337 (2), 140-146 (2012)   PUBMED   23043454REFERENCE   2  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Direct Submission  JOURNAL   Submitted (06-JUL-2012) Department of Microbiology and Immunology,            F. Edward Hebert School of Medicine, Uniformed Services University            of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD            20814, USAFEATURES             Location/Qualifiers     source          1..588                     /mol_type="genomic DNA"                     /db_xref="taxon:813"                     /strain="UW-5/CX"                     /organism="Chlamydia trachomatis"                     /serovar="E"     gene            1..588                     /gene="aaxB"     CDS             1..588                     /protein_id="AFR60849.1"                     /gene="aaxB"                     /transl_table=11                     /note="AaxB"                     /db_xref="GI:404351721"                     /codon_start=1                     /product="pyruvoyl-dependent arginine decarboxylase"                     /translation="MPYGTRYPTLAFHTGGVGESDDGMPPQPFETFCYDSALLQAKIE                     NFNIVPYTSVLPKELFGNILPVDQCTKFFKHGAVLEVIMAGRGATVTDGTQAIATGVG                     ICWGKDKNGELIGGWAAEYVEFFPTWIDDEIAESHAKMWLKKSLQHELDLRSVSKHSE                     FQYFHNYINIRKKFGFCLTALGFLNFENVAPAVIQ"
//
----------------------------------END GBK-----------------------------------------
Can anyone tell what I am missing or why this is happening?  I don't know if this has happened in earlier BioPerl versions as up until now, I usually downloaded sequences straight from NCBI, but that became too time consuming....but this seems to be as well :S
Thank you in advance for any help,
Veronica
 		 	   		  


From cjfields at illinois.edu  Tue May  7 22:17:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 8 May 2013 02:17:43 +0000
Subject: [Bioperl-l] Bio::SeqIO doesn't write all gbk sequences
	from	Bio::DB::GenBank
In-Reply-To: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>
References: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E166A0@CHIMBX5.ad.uillinois.edu>

Veronica,

Your mail may have garbled the script and example file.  Can you paste these in a gist?

https://gist.github.com/

chris

On May 7, 2013, at 7:32 PM, Veronica A. <armendarez77 at hotmail.com> wrote:

> Hello,
> I'm currently running Bio::Perl 1.6.1 on Ubuntu 12.04.2 LTS and have noticed a problem with Bio::SeqIO when writing genbank files using the write_seq() function;  some of the files do not include an 'ORIGIN' tag or the sequence.
> 
> I am using GI#s (50 at a time every 2 minutes) to retrieve genbank files via Bio::DB::GenBank.
> 
> ----------------------------------------START CODE----------------------------------
> my $gb = Bio::DB::GenBank->new(-verbose=>-1);my $seqout = Bio::SeqIO->new(-file=>">$fileName", '-format'=>'Genbank', -alphabet=>'dna', -flush=>0, -verbose=>-1);while(@ids){     my @batchArray = splice(@ids, 0, 50);     my $batchArrayRef = \@batchArray;
>     my $streamObj;     my $pid = fork();     if($pid == 0){          eval{               $streamObj = $gb->get_Stream_by_id($batchArrayRef);          };          if($@){               print "Error: ".$@."\n";          }          else{               while(my $seqObj = $streamObj->next_seq()){                    unless($seqObj->accession_number() =~ /N[A-Z]\_/){                        #print "ID: ".$seqObj->id()."\n";                        #print "Seq:\n".$seqObj->seq()."\n";                         $seqout->write_seq($seqObj);                    }                }          }          exit 0;     }}waitpid($pid,0);sleep(120);
> ----------------------------------------END CODE----------------------------------
> Most of the Genbank files written to the output file have sequences, but there is a small portion that do not, even though they should.  For example, JX287367, in NCBI includes an 'ORIGIN' tag and sequence and when I use the print function before writing to file, the sequence is printed to STDOUT, but the 'ORIGIN' tag and sequence are not written to the output gbk file.  The following is found in the final output file:
> ----------------------------------START GBK-----------------------------------------
> LOCUS       JX287367                 588 bp    DNA     linear   BCT 19-DEC-2012DEFINITION  Chlamydia trachomatis strain UW-5/CX pyruvoyl-dependent arginine            decarboxylase (aaxB) gene, complete cds.ACCESSION   JX287367VERSION     JX287367.1  GI:404351720KEYWORDS    .SOURCE      Chlamydia trachomatis  ORGANISM  Chlamydia trachomatis            Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;            Chlamydia/Chlamydophila group; Chlamydia.REFERENCE   1  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Characterization of the activity and expression of arginine            decarboxylase in human and animal Chlamydia pathogens  JOURNAL   FEMS Microbiol. Lett. 337 (2), 140-146 (2012)   PUBMED   23043454REFERENCE   2  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Direct Submission  JOURNAL   Submitted (06-JUL-2012) Department of Microbiology and Immunology,            F. Edward Hebert School of Med!
> icine, Uniformed Services University            of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD            20814, USAFEATURES             Location/Qualifiers     source          1..588                     /mol_type="genomic DNA"                     /db_xref="taxon:813"                     /strain="UW-5/CX"                     /organism="Chlamydia trachomatis"                     /serovar="E"     gene            1..588                     /gene="aaxB"     CDS             1..588                     /protein_id="AFR60849.1"                     /gene="aaxB"                     /transl_table=11                     /note="AaxB"                     /db_xref="GI:404351721"                     /codon_start=1                     /product="pyruvoyl-dependent arginine decarboxylase"                     /translation="MPYGTRYPTLAFHTGGVGESDDGMPPQPFETFCYDSALLQAKIE                     NFNIVPYTSVLPKELFGNILPVDQCTKFFKHGAVLEVIMAGRGATVTDGTQAIATGVG                     ICWGKDKNGELIGGW!
> AAEYVEFFPTWIDDEIAESHAKMWLKKSLQHELDLRSVSKHSE                     FQYFHN
> YINIRKKFGFCLTALGFLNFENVAPAVIQ"
> //
> ----------------------------------END GBK-----------------------------------------
> Can anyone tell what I am missing or why this is happening?  I don't know if this has happened in earlier BioPerl versions as up until now, I usually downloaded sequences straight from NCBI, but that became too time consuming....but this seems to be as well :S
> Thank you in advance for any help,
> Veronica
> 		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From witch.of.agnessi at gmail.com  Wed May  8 15:24:53 2013
From: witch.of.agnessi at gmail.com (WoA)
Date: Wed, 8 May 2013 12:24:53 -0700 (PDT)
Subject: [Bioperl-l] Extracting matching subsequence from pairwise alignment
Message-ID: <1368041092972-16935.post@n3.nabble.com>

Hello All,

I've a pairwise global alignemnet of two DNA sequences generated by the
program NEEDLE of EMBOSS package. I wish to extract the sub-sequence that
matches/aligns to a given region of the other sequence. In  this alignment
<http://pastebin.com/wrhEDzJU>   (Pastebin Link) the given region (actually
the CDS) falls between base number 24:485 in the original sequence with ID
'XM_001005073.' I wish to extract the sub-sequence in the sequence ID
'Homolog' that aligns with that 24:485 region of the other sequence.

I'm using Bioperl to parse the alignment. I find out the the alignment
column numbers corresponding to 24:485 region in the particular sequence,
using 'column_from_residue_number'. Then I extract the sub-sequence from the
'aligned' other sequence(containing gaps) using the corresponding column
numbers. Finally I remove the gap characters.

Am I doing this thing correctly and are there any pitfalls ? Is there any
better way to do it by (Bio)Perl/Python? The code goes here:
use strict;
use warnings;
use Bio::AlignIO;

# read in an alignment generated by the EMBOSS program Needle
my $in = new Bio::AlignIO(-format => 'emboss',
                  -file   => 'test_needle.aln');

while( my $aln = $in->next_aln ) {
          #Seqnames: 'XM_001005073.'(CDS:24-485),'Homolog'
          my ($cds_start,$cds_end)=(24,485);#
          my $col_cdsstart = $aln->column_from_residue_number(
'XM_001005073.', $cds_start);
          my $col_cdsend= $aln->column_from_residue_number( 'XM_001005073.',
$cds_end);

          foreach my $seq ($aln->each_seq) {
                    if($seq->id() eq 'Homolog'){
                        my
$homolog_cds=$seq->subseq($col_cdsstart,$col_cdsend);
                         $homolog_cds=~s/\-//g;
                        print $homolog_cds,"\n";
                    }

        }
}





--
View this message in context: http://bioperl.996286.n3.nabble.com/Extracting-matching-subsequence-from-pairwise-alignment-tp16935.html
Sent from the Bioperl-L mailing list archive at Nabble.com.


From hlapp at drycafe.net  Wed May 15 16:44:07 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 15 May 2013 16:44:07 -0400
Subject: [Bioperl-l] Workshop on Sustainable Software for Science: Practice
	and Experiences
Message-ID: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>

FYI, if you haven't seen this yet:

http://wssspe.researchcomputing.org.uk/

It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?

Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)

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




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From carandraug+dev at gmail.com  Wed May 15 21:53:55 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 16 May 2013 02:53:55 +0100
Subject: [Bioperl-l] sets of sequences - how to read?
Message-ID: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>

Hi

when accessing entrez gene using eutils to get multiple genes, NCBI
now returns an Entrezgene-Set[1] rather than a list of EntrezGene.
This change must have happened sometime on the last 2 months. Compare:

use Bio::DB::EUtilities;

my %sets = (
  eutil   => 'efetch',
  db      => 'gene',
  retmode => 'text',
  rettype => 'asn1',
  email   => 'bioperl-l at lists.open-bio.org',
);

## this mimics the previous behaviour of the NCBI server but the
multiple requests will annoy their servers
my @ids = (3014, 85235);
my $response;
foreach (@ids) {
  my $fetcher = Bio::DB::EUtilities->new(%sets, id => $_);
  $response .= $fetcher->get_Response->content;
}
print $fetcher->get_Response->content;

## this used to be the right way to do it, but now returns an Entrezgene-Set
my $fetcher = Bio::DB::EUtilities->new(%sets, id => \@ids);
$response .= $fetcher->get_Response->content;
print $fetcher->get_Response->content;

There is no module to read these Entrezgene-Set in Perl at the moment,
since Bio::ASN1::EntrezGene; is not able to handle them. I have
contacted the module author and set him a fix[2] and he said he'll try
to look into it next week.

However, even with the fix there is another problem. How would one
access a set of sequences using the Bio::SeqIO API? There is no method
to do that. One could say, to ignore them, and make next_seq return
the next sequence of the set. But then we are losing data. After all,
it's perfectly viable to have multiple Entrezgene-Set in one file.
What would be the right way to do this?

Carn?

[1] http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/IEB/ToolBox/CPP_DOC/asn_spec/Entrezgene-Set.html
[2] https://github.com/carandraug/bio-asn1-entrezgene/commit/69d505056d8b7897df6271ffb7a5f39d58873c6b



From cjfields at illinois.edu  Thu May 16 00:43:22 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 04:43:22 +0000
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice	and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>

Jason and I have discussed looking into opportunity's like this, I think it makes sense to try a joint submission.  

chris

On May 15, 2013, at 3:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
> 
> http://wssspe.researchcomputing.org.uk/
> 
> It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?
> 
> Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)
> 
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> 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  Thu May 16 05:10:25 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 May 2013 10:10:25 +0100
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice and Experiences
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>

On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Jason and I have discussed looking into opportunity's like this, I think it makes
> sense to try a joint submission.
>
> chris

This sounds like a good idea, although given the time and place I am
unlikely to be able to attend in person:

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

Rather than trying to discuss this over four mailing lists should we switch
to the cross project list open-bio-l, or continue off-list?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thanks,

Peter


From miquel.ramia at uab.cat  Thu May 16 06:42:29 2013
From: miquel.ramia at uab.cat (=?ISO-8859-1?Q?Miquel_R=E0mia?=)
Date: Thu, 16 May 2013 12:42:29 +0200
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
Message-ID: <5194B815.2010401@uab.cat>

Hi all,

I get this message when compiling Bio::DB::Sam:

Building Bio-SamTools

gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'

collect2: ld returned 1 exit status

make: *** [bam2bedgraph] Error 1


Is this error related to the module or some dependencies? or maybe a 
problem with my system?

Any help appreciated, thanks!


-- 
Miquel R?mia Jes?s
PhD. candidate (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Aut?noma de Barcelona (UAB)
08193, Cerdanyola del Vall?s
Barcelona (Spain)



From cjfields at illinois.edu  Thu May 16 09:12:40 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 13:12:40 +0000
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <5194B815.2010401@uab.cat>
References: <5194B815.2010401@uab.cat>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>

It may be due to the new samtools release (v 0.1.19).  I know Heng Li has been working on the code over the last year for threading support (notice the undefined functions).  Have you tried v 0.1.18?

chris

On May 16, 2013, at 5:42 AM, Miquel R?mia <miquel.ramia at uab.cat> wrote:

> Hi all,
> 
> I get this message when compiling Bio::DB::Sam:
> 
> Building Bio-SamTools
> 
> gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
> 
> collect2: ld returned 1 exit status
> 
> make: *** [bam2bedgraph] Error 1
> 
> 
> Is this error related to the module or some dependencies? or maybe a problem with my system?
> 
> Any help appreciated, thanks!
> 
> 
> -- 
> Miquel R?mia Jes?s
> PhD. candidate (PIF)
> Evolutionary Bioinformatics Group
> (Genomics, Bioinformatics and Evolution Group)
> Lab MRB/014 - 93 586 89 58
> MRB - Institut de Biologia i Biomedicina (IBB)
> Universitat Aut?noma de Barcelona (UAB)
> 08193, Cerdanyola del Vall?s
> Barcelona (Spain)
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu May 16 09:09:45 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 13:09:45 +0000
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice and Experiences
In-Reply-To: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
	<CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1FBCF@CHIMBX5.ad.uillinois.edu>

Yes, though we need to make sure others (e.g. those not subscribed to open-bio-l) are in the loop.

November is a possibility for me.

chris

On May 16, 2013, at 4:10 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> Jason and I have discussed looking into opportunity's like this, I think it makes
>> sense to try a joint submission.
>> 
>> chris
> 
> This sounds like a good idea, although given the time and place I am
> unlikely to be able to attend in person:
> 
> First Workshop on Sustainable Software for Science: Practice and
> Experiences (WSSSPE)
> (to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
> http://wssspe.researchcomputing.org.uk/
> 
> Rather than trying to discuss this over four mailing lists should we switch
> to the cross project list open-bio-l, or continue off-list?
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> Thanks,
> 
> Peter




From andreas at sdsc.edu  Thu May 16 00:31:34 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 15 May 2013 21:31:34 -0700
Subject: [Bioperl-l] [Biojava-l] Workshop on Sustainable Software for
 Science: Practice and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <CALthepxHNLm4eHJcCQ4dLnhJr5OhGJJEKTAjH+x7Ppq0oFFnDA@mail.gmail.com>

Thanks Hilmar, you were faster than me in sending this out..

You are right, it would be very interesting to hear what some of the long
running open-bio projects have to say on the topic of sustainability. Let
me know if anybody is interested in a submission!

Andreas




On Wed, May 15, 2013 at 1:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
>
> http://wssspe.researchcomputing.org.uk/
>
> It seems to me that the Bio* projects, perhaps led by BioPerl as the
> oldest and thus longest running (nowadays more fancily called "sustained")
> of them would have a lot to say about the subject. Anyone interested in a
> joint submission?
>
> Also, I notice that Biojava's Andreas is on the organizing committee, so
> maybe he's been conspiring on something already :-)
>
>         -hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From cjfields at illinois.edu  Fri May 17 00:08:04 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 04:08:04 +0000
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>

This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.

My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.

chris

On May 15, 2013, at 8:53 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> when accessing entrez gene using eutils to get multiple genes, NCBI
> now returns an Entrezgene-Set[1] rather than a list of EntrezGene.
> This change must have happened sometime on the last 2 months. Compare:
> 
> use Bio::DB::EUtilities;
> 
> my %sets = (
>  eutil   => 'efetch',
>  db      => 'gene',
>  retmode => 'text',
>  rettype => 'asn1',
>  email   => 'bioperl-l at lists.open-bio.org',
> );
> 
> ## this mimics the previous behaviour of the NCBI server but the
> multiple requests will annoy their servers
> my @ids = (3014, 85235);
> my $response;
> foreach (@ids) {
>  my $fetcher = Bio::DB::EUtilities->new(%sets, id => $_);
>  $response .= $fetcher->get_Response->content;
> }
> print $fetcher->get_Response->content;
> 
> ## this used to be the right way to do it, but now returns an Entrezgene-Set
> my $fetcher = Bio::DB::EUtilities->new(%sets, id => \@ids);
> $response .= $fetcher->get_Response->content;
> print $fetcher->get_Response->content;
> 
> There is no module to read these Entrezgene-Set in Perl at the moment,
> since Bio::ASN1::EntrezGene; is not able to handle them. I have
> contacted the module author and set him a fix[2] and he said he'll try
> to look into it next week.
> 
> However, even with the fix there is another problem. How would one
> access a set of sequences using the Bio::SeqIO API? There is no method
> to do that. One could say, to ignore them, and make next_seq return
> the next sequence of the set. But then we are losing data. After all,
> it's perfectly viable to have multiple Entrezgene-Set in one file.
> What would be the right way to do this?
> 
> Carn?
> 
> [1] http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/IEB/ToolBox/CPP_DOC/asn_spec/Entrezgene-Set.html
> [2] https://github.com/carandraug/bio-asn1-entrezgene/commit/69d505056d8b7897df6271ffb7a5f39d58873c6b
> 
> _______________________________________________
> 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 May 17 00:16:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 04:16:12 +0000
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>
References: <5194B815.2010401@uab.cat>
	<118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>

For the record, this is now fixed in the latest Bio::Samtools (via Lincoln).

chris

On May 16, 2013, at 8:12 AM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> It may be due to the new samtools release (v 0.1.19).  I know Heng Li has been working on the code over the last year for threading support (notice the undefined functions).  Have you tried v 0.1.18?
> 
> chris
> 
> On May 16, 2013, at 5:42 AM, Miquel R?mia <miquel.ramia at uab.cat> wrote:
> 
>> Hi all,
>> 
>> I get this message when compiling Bio::DB::Sam:
>> 
>> Building Bio-SamTools
>> 
>> gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
>> 
>> collect2: ld returned 1 exit status
>> 
>> make: *** [bam2bedgraph] Error 1
>> 
>> 
>> Is this error related to the module or some dependencies? or maybe a problem with my system?
>> 
>> Any help appreciated, thanks!
>> 
>> 
>> -- 
>> Miquel R?mia Jes?s
>> PhD. candidate (PIF)
>> Evolutionary Bioinformatics Group
>> (Genomics, Bioinformatics and Evolution Group)
>> Lab MRB/014 - 93 586 89 58
>> MRB - Institut de Biologia i Biomedicina (IBB)
>> Universitat Aut?noma de Barcelona (UAB)
>> 08193, Cerdanyola del Vall?s
>> Barcelona (Spain)
>> 
>> _______________________________________________
>> 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  Fri May 17 01:12:24 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 17 May 2013 06:12:24 +0100
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>

On 17 May 2013 05:08, Fields, Christopher J <cjfields at illinois.edu> wrote:
> This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.
>
> My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.

:s I'm not sure I understood your suggestion. I think the problem is
just the introduction of a new concept, a "set" of stuff (genes in
this case), and how should SeqIO handle multiple sets.

Carn?



From shalabh.sharma7 at gmail.com  Fri May 17 10:54:55 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 17 May 2013 10:54:55 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
Message-ID: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>

HI,
                 First of all i am really sorry for sending this mail here,
i am not sure if this is the right forum. I know lot of people work on
similar stuff.
I wrote to NCBI but nobody replied.

Actually i am looking for all bacterial/microbial gene annotation
nucleotide fasta files.
Does anyone knows where to download these kind of files.
I tried *ffn files but they are not annotated.
Or is there any module in bioperl that i can use ?
I would really appreciate your help.

Thanks
Shalabh

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


From fossandonc at hotmail.com  Fri May 17 11:59:04 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 17 May 2013 11:59:04 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
Message-ID: <SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>

Hi,
You can get the annotations from here:
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/

The ".ffn" are the genes nucleotide fasta files but it does not show the
product name, on the other hand the ".faa" are the genes aminoacid fasta
files and shows the product name, but if you want both product and
nucleotide is much better to use the Genbank ".gbk" files that contains the
complete data and you can parse it easily using BioPerl to obtain all genes,
and then print the /protein_id, /product, and the nucleotide sequences in a
new fasta file. Check these to see how to do it:
http://www.bioperl.org/wiki/HOWTO:SeqIO
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

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 shalabh sharma
Enviado el: viernes, 17 de mayo de 2013 10:55
Para: bioperl-l
Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files

HI,
                 First of all i am really sorry for sending this mail here,
i am not sure if this is the right forum. I know lot of people work on
similar stuff.
I wrote to NCBI but nobody replied.

Actually i am looking for all bacterial/microbial gene annotation nucleotide
fasta files.
Does anyone knows where to download these kind of files.
I tried *ffn files but they are not annotated.
Or is there any module in bioperl that i can use ?
I would really appreciate your help.

Thanks
Shalabh

--
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences University of Georgia Athens, GA 30602-3636
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From shalabh.sharma7 at gmail.com  Fri May 17 12:26:26 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 17 May 2013 12:26:26 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
Message-ID: <CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>

Hey Francisco,
           Thanks a lot. Basically i just wanted gene nucleotide fasta
files with GI numbers.
I think i will have to parse it from gbk files.

-Shalabh


On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n <
fossandonc at hotmail.com> wrote:

> Hi,
> You can get the annotations from here:
> ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
>
> The ".ffn" are the genes nucleotide fasta files but it does not show the
> product name, on the other hand the ".faa" are the genes aminoacid fasta
> files and shows the product name, but if you want both product and
> nucleotide is much better to use the Genbank ".gbk" files that contains the
> complete data and you can parse it easily using BioPerl to obtain all
> genes,
> and then print the /protein_id, /product, and the nucleotide sequences in a
> new fasta file. Check these to see how to do it:
> http://www.bioperl.org/wiki/HOWTO:SeqIO
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>
> 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 shalabh sharma
> Enviado el: viernes, 17 de mayo de 2013 10:55
> Para: bioperl-l
> Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> HI,
>                  First of all i am really sorry for sending this mail here,
> i am not sure if this is the right forum. I know lot of people work on
> similar stuff.
> I wrote to NCBI but nobody replied.
>
> Actually i am looking for all bacterial/microbial gene annotation
> nucleotide
> fasta files.
> Does anyone knows where to download these kind of files.
> I tried *ffn files but they are not annotated.
> Or is there any module in bioperl that i can use ?
> I would really appreciate your help.
>
> Thanks
> Shalabh
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences University of Georgia Athens, GA 30602-3636
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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



From cjfields at illinois.edu  Fri May 17 13:37:53 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 17:37:53 +0000
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E22218@CHIMBX5.ad.uillinois.edu>

On May 17, 2013, at 12:12 AM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 17 May 2013 05:08, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.
>> 
>> My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.
> 
> :s I'm not sure I understood your suggestion. I think the problem is
> just the introduction of a new concept, a "set" of stuff (genes in
> this case), and how should SeqIO handle multiple sets.
> 
> Carn?


(note: critical point in this is Bio::ASN1::Entrezgene would allow this, I'm not sure it would.  Otherwise this is all really hand-wavy)

To me a 'set of stuff', particularly when the 'stuff' is stored sequentially in a flat file, is a simple 'database' or 'store' of similar items, where the class allows one the ability to look up particular members in the set, but also could store higher level information about the set as a whole if needed.  If it were me, I would implement a method particular to Bio::SeqIO::entrezgene that specifically creates and returns this ( next_geneset(), for instance ); next_seq() could then be implemented to iterate through the items in that database/store.  

Two useful things come out of this.  First, if the data for the Entrez Gene file/chunk are parsed to store offsets per ID, one would only need to parse out the chunks needed (offset of ID to next offset), then pass that into the parser and create objects on the fly.  This would probably be as fast or faster than (for instance) the greedy method of parsing the entire file and storing everything in objects up-front, then iterating through those objects one at a time, which I think is current behavior.

Second: if an index is created, the upfront cost is already paid (you could reuse the same index when parsing the same data).

An analogous example might be storing all FASTQ data in a sequencing run; I don't want to expend the effort to parse all the FASTQ data, but I may want to run operations on individual items in the set as well as store additional information about the data (barcodes per run, lanes, overall quality stats, etc).  

Does that make sense?  The pieces for this are lying around (Bio::Index::* for instance has methods for indexing flat files, and classes like Bio::DB::Fasta).

chris


From shalabh.sharma7 at gmail.com  Sun May 19 15:33:16 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Sun, 19 May 2013 15:33:16 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
	<CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>
Message-ID: <CAA7rn9ehQ1t1AizSLC15PFFh4mV8njfaTSY2ZVDqtzb2bEGBaA@mail.gmail.com>

Thanks Russell,
                            Actually i wanted all the Bacterial gene
nucleotide files, so i parsed it from *gbk. But yes these files might help
me for my other parts of my work.

Thanks
Shalabh


On Sun, May 19, 2013 at 3:26 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:

> Another option that I've used before is to download the gene2accession,
> gene2refseq,  and gene_info files from here
> ftp://ftp.ncbi.nih.gov/gene/DATA/ then parse out the data you require.
> It might work for you?
>
> --Russell
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:
> bioperl-l-bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> Sent: Saturday, 18 May 2013 4:26 a.m.
> To: Francisco J. Ossand?n
> Cc: bioperl-l
> Subject: Re: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> Hey Francisco,
>            Thanks a lot. Basically i just wanted gene nucleotide fasta
> files with GI numbers.
> I think i will have to parse it from gbk files.
>
> -Shalabh
>
>
> On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n <
> fossandonc at hotmail.com> wrote:
>
> > Hi,
> > You can get the annotations from here:
> > ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
> >
> > The ".ffn" are the genes nucleotide fasta files but it does not show
> > the product name, on the other hand the ".faa" are the genes aminoacid
> > fasta files and shows the product name, but if you want both product
> > and nucleotide is much better to use the Genbank ".gbk" files that
> > contains the complete data and you can parse it easily using BioPerl
> > to obtain all genes, and then print the /protein_id, /product, and the
> > nucleotide sequences in a new fasta file. Check these to see how to do
> > it:
> > http://www.bioperl.org/wiki/HOWTO:SeqIO
> > http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> >
> > 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 shalabh
> > sharma Enviado el: viernes, 17 de mayo de 2013 10:55
> > Para: bioperl-l
> > Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
> >
> > HI,
> >                  First of all i am really sorry for sending this mail
> > here, i am not sure if this is the right forum. I know lot of people
> > work on similar stuff.
> > I wrote to NCBI but nobody replied.
> >
> > Actually i am looking for all bacterial/microbial gene annotation
> > nucleotide fasta files.
> > Does anyone knows where to download these kind of files.
> > I tried *ffn files but they are not annotated.
> > Or is there any module in bioperl that i can use ?
> > I would really appreciate your help.
> >
> > Thanks
> > Shalabh
> >
> > --
> > Shalabh Sharma
> > Scientific Computing Professional Associate (Bioinformatics
> > Specialist) Department of Marine Sciences University of Georgia
> > Athens, GA 30602-3636 _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences University of Georgia Athens, GA 30602-3636
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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> to which it is addressed and may contain confidential and/or privileged
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>



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



From Russell.Smithies at agresearch.co.nz  Sun May 19 15:26:35 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 20 May 2013 07:26:35 +1200
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
	<CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>

Another option that I've used before is to download the gene2accession, gene2refseq,  and gene_info files from here ftp://ftp.ncbi.nih.gov/gene/DATA/ then parse out the data you require.
It might work for you?

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of shalabh sharma
Sent: Saturday, 18 May 2013 4:26 a.m.
To: Francisco J. Ossand?n
Cc: bioperl-l
Subject: Re: [Bioperl-l] Downloading annotated Gene nucleotide fasta files

Hey Francisco,
           Thanks a lot. Basically i just wanted gene nucleotide fasta files with GI numbers.
I think i will have to parse it from gbk files.

-Shalabh


On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n < fossandonc at hotmail.com> wrote:

> Hi,
> You can get the annotations from here:
> ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
>
> The ".ffn" are the genes nucleotide fasta files but it does not show 
> the product name, on the other hand the ".faa" are the genes aminoacid 
> fasta files and shows the product name, but if you want both product 
> and nucleotide is much better to use the Genbank ".gbk" files that 
> contains the complete data and you can parse it easily using BioPerl 
> to obtain all genes, and then print the /protein_id, /product, and the 
> nucleotide sequences in a new fasta file. Check these to see how to do 
> it:
> http://www.bioperl.org/wiki/HOWTO:SeqIO
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>
> 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 shalabh 
> sharma Enviado el: viernes, 17 de mayo de 2013 10:55
> Para: bioperl-l
> Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> HI,
>                  First of all i am really sorry for sending this mail 
> here, i am not sure if this is the right forum. I know lot of people 
> work on similar stuff.
> I wrote to NCBI but nobody replied.
>
> Actually i am looking for all bacterial/microbial gene annotation 
> nucleotide fasta files.
> Does anyone knows where to download these kind of files.
> I tried *ffn files but they are not annotated.
> Or is there any module in bioperl that i can use ?
> I would really appreciate your help.
>
> Thanks
> Shalabh
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics 
> Specialist) Department of Marine Sciences University of Georgia 
> Athens, GA 30602-3636 _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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

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

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From miquel.ramia at uab.cat  Tue May 21 11:08:18 2013
From: miquel.ramia at uab.cat (=?ISO-8859-1?Q?Miquel_R=E0mia?=)
Date: Tue, 21 May 2013 17:08:18 +0200
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>
References: <5194B815.2010401@uab.cat>
	<"118F034CF4C3EF48A96F86CE585B94BF74E1F C2C"@CHIMBX5.ad.uillinois.edu>
	<118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>
Message-ID: <519B8DE2.2070308@uab.cat>

On 17/05/13 06:16, Fields, Christopher J wrote:
> For the record, this is now fixed in the latest Bio::Samtools (via Lincoln).
>
> chris
>
>

Compiled correctly!

thank you



-- 
Miquel R?mia Jes?s
PhD. candidate (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Aut?noma de Barcelona (UAB)
08193, Cerdanyola del Vall?s
Barcelona (Spain)



From b.l.cohen_home at btinternet.com  Mon May 20 14:49:50 2013
From: b.l.cohen_home at btinternet.com (Bernard Cohen)
Date: Mon, 20 May 2013 19:49:50 +0100 (BST)
Subject: [Bioperl-l] Phylip format error
Message-ID: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>

Hello!

I happen to have checked to see what the PERL webpage says about Phylip format for DNA alignment files and see that it is erroneous.?

I am not a PERL user and do not want to be bothered to register or otherwise learn how to make an official comment, so forward this for someone to pick up.

Phylip format allows up to 10 spaces for taxon names; the data must start in the 11th space. This can be checked on Jo Felsenstein's site.

The PERL page accessed by searching for "Phylip format PERL" allows only 8 spaces for the name.?

B. L. Cohen


From senanu.pearson at gmail.com  Wed May 22 16:15:24 2013
From: senanu.pearson at gmail.com (Senanu)
Date: Wed, 22 May 2013 13:15:24 -0700
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from alignment
Message-ID: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>

Hi all,

I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 

I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 

Is this a known problem? Is there another way to generate such a consensus?


my $in = Bio::AlignIO->new(-file => $files[0],
                           -format => 'XMFA');
while  (my $aln = $in->next_aln()) {
    foreach  my $seq ($aln->each_seq) {
        $seq->alphabet('dna');
    }
    my $con = $aln->consensus_iupac();
}


Thanks in advance.
Ngwenyama


From cjfields at illinois.edu  Wed May 22 19:17:50 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 22 May 2013 23:17:50 +0000
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from
 alignment
In-Reply-To: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
References: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E2A01D@CHIMBX5.ad.uillinois.edu>

On May 22, 2013, at 3:15 PM, Senanu <senanu.pearson at gmail.com> wrote:

> Hi all,
> 
> I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 

Probably the former, but...

> I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 

It shouldn't take that long, 7 Mb isn't that large.  Or is that 7 Mb for one genome?

> Is this a known problem? Is there another way to generate such a consensus?

The code isn't really optimized for this, but again this isn't terribly large.  Is the bottleneck reading the alignment in, or is it the consensus_iupac() step?  Hard to say w/o seeing the alignment data itself.

> my $in = Bio::AlignIO->new(-file => $files[0],
>                           -format => 'XMFA');
> while  (my $aln = $in->next_aln()) {
>    foreach  my $seq ($aln->each_seq) {
>        $seq->alphabet('dna');
>    }
>    my $con = $aln->consensus_iupac();
> }
> 
> 
> Thanks in advance.
> Ngwenyama
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

chris


From alexeymorozov1991 at gmail.com  Thu May 23 03:22:13 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Thu, 23 May 2013 16:22:13 +0900
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
Message-ID: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>

Which is also worsened by the fact that there is relaxed phylip format,
which allows up to 250 chars for taxon name. They are separated from a
sequence by single space, which creates problems if names were extended to
10 chars in strict Felsenstein's format by whitespaces. On the whole,
phylip is as messily defined format as one can make from a plain textfile
with information content of fasta.
Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
phylip and how does it tell dialects from one another. Even if code support
is OK, it may be worthwile to explain it somewhere at bioperl.org


2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>

> Hello!
>
> I happen to have checked to see what the PERL webpage says about Phylip
> format for DNA alignment files and see that it is erroneous.
>
> I am not a PERL user and do not want to be bothered to register or
> otherwise learn how to make an official comment, so forward this for
> someone to pick up.
>
> Phylip format allows up to 10 spaces for taxon names; the data must start
> in the 11th space. This can be checked on Jo Felsenstein's site.
>
> The PERL page accessed by searching for "Phylip format PERL" allows only 8
> spaces for the name.
>
> B. L. Cohen
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.


From p.j.a.cock at googlemail.com  Thu May 23 04:30:21 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 May 2013 09:30:21 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>

On Thu, May 23, 2013 at 8:22 AM, Alexey Morozov
<alexeymorozov1991 at gmail.com> wrote:
> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org

Biopython's AlignIO defines both a (strict) "phylip" and "relaxed-phylip"
as two separate formats (or variants, like the "fastq" variants). Doing
the same in BioPerl would seem sensible since auto-detection is not
easy.

http://biopython.org/wiki/AlignIO#File_Formats

Peter

P.S. Where does that 250 characters for the taxon name limit come from?
The trouble with relaxed phylip is that some tools are more relaxed than
others ;)


From awitney at sgul.ac.uk  Thu May 23 04:43:15 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 23 May 2013 09:43:15 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <519DD6A3.8090304@sgul.ac.uk>


Not sure if there is an actual question in these messages, but BioPerl
can be used to generate valid Phylip format and run, like this:

## Build Align object
my $aln = Bio::SimpleAlign->new(-seqs=>$seqs);

## swap the taxa names with 8 characters long unique IDs
my ($aln_safe, $ref_name) = $aln->set_displayname_safe(8);

## Write out phylip format infile
Bio::AlignIO->new(-file=>'>infile.out', -format=>'phylip', -interleaved
=> 0)->write_aln($aln);

## run PHYLIP's pars program
my @params = (idlength=>10);   #, jumble=>"17,10");
my $tree_factory = Bio::Tools::Run::Phylo::Phylip::Pars->new(@params);
$tree_factory->quiet(1);  # Suppress pars messages to terminal
my $tree = $tree_factory->create_tree($aln_safe);

## fix the node labels back
my @nodes = sort { defined $a->id && defined $b->id && $a->id cmp $b->id
} $tree->get_nodes();
foreach my $nd (@nodes) {
	if ( $nd->is_Leaf ) {
		$nd->id($ref_name->{$nd->id_output})
	}
}

HTH

Adam

On 23/05/2013 08:22, Alexey Morozov wrote:
> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> 
> 2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>
> 
>> Hello!
>>
>> I happen to have checked to see what the PERL webpage says about Phylip
>> format for DNA alignment files and see that it is erroneous.
>>
>> I am not a PERL user and do not want to be bothered to register or
>> otherwise learn how to make an official comment, so forward this for
>> someone to pick up.
>>
>> Phylip format allows up to 10 spaces for taxon names; the data must start
>> in the 11th space. This can be checked on Jo Felsenstein's site.
>>
>> The PERL page accessed by searching for "Phylip format PERL" allows only 8
>> spaces for the name.
>>
>> B. L. Cohen
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> 
> 
> 


From cjfields at illinois.edu  Thu May 23 09:48:31 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 13:48:31 +0000
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E323A4@CITESMBX5.ad.uillinois.edu>

Alexey,

Just want to point out that 'relaxed phylip' format was introduced long after this parser was created; in fact (as Adam points out) there was an alternative workaround to deal with the lossy names.  

The content of that page is on a wiki, which anyone is free to edit (just need an OpenID to set up an account).

chris

On May 23, 2013, at 2:22 AM, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:

> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> 
> 2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>
> 
>> Hello!
>> 
>> I happen to have checked to see what the PERL webpage says about Phylip
>> format for DNA alignment files and see that it is erroneous.
>> 
>> I am not a PERL user and do not want to be bothered to register or
>> otherwise learn how to make an official comment, so forward this for
>> someone to pick up.
>> 
>> Phylip format allows up to 10 spaces for taxon names; the data must start
>> in the 11th space. This can be checked on Jo Felsenstein's site.
>> 
>> The PERL page accessed by searching for "Phylip format PERL" allows only 8
>> spaces for the name.
>> 
>> B. L. Cohen
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu May 23 10:05:32 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 14:05:32 +0000
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
	<CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>

On May 23, 2013, at 3:30 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, May 23, 2013 at 8:22 AM, Alexey Morozov
> <alexeymorozov1991 at gmail.com> wrote:
>> Which is also worsened by the fact that there is relaxed phylip format,
>> which allows up to 250 chars for taxon name. They are separated from a
>> sequence by single space, which creates problems if names were extended to
>> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
>> phylip is as messily defined format as one can make from a plain textfile
>> with information content of fasta.
>> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
>> phylip and how does it tell dialects from one another. Even if code support
>> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> Biopython's AlignIO defines both a (strict) "phylip" and "relaxed-phylip"
> as two separate formats (or variants, like the "fastq" variants). Doing
> the same in BioPerl would seem sensible since auto-detection is not
> easy.
> 
> http://biopython.org/wiki/AlignIO#File_Formats
> 
> Peter
> 
> P.S. Where does that 250 characters for the taxon name limit come from?
> The trouble with relaxed phylip is that some tools are more relaxed than
> others ;)

As Adam pointed out, prior to the introduction of 'relaxed phylip' we had an alternative solution that didn't require a modified format but still allowed one to use PHYLIP and other tools requesting the format.  I think 'relaxed phylip' was introduced by CIPRES a few years back.  Frankly, this is the first time I have seen this mentioned on the list; yay, yet another format variation :)

The variant format parsing (as implemented for SeqIO::fastq, as you know) deals with variant names like 'fastq-sanger', where the main format name is first, the variant of the format second.  The order in this case is reversed (relaxed-phylip), which I'm pretty sure will not work.  Not impossible to allow, but we would probably allow support like this initially:

my $in = Bio::AlignIO->new(-format => 'phylip',
                           -variant => 'relaxed',
                             ?);

chris


From cjfields at illinois.edu  Thu May 23 09:56:32 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 13:56:32 +0000
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from
 alignment
In-Reply-To: <92CD2F9D-7C8E-4941-9354-4BD80D8C2CB6@gmail.com>
References: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E2A01D@CHIMBX5.ad.uillinois.edu>
	<92CD2F9D-7C8E-4941-9354-4BD80D8C2CB6@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E32489@CITESMBX5.ad.uillinois.edu>

(keep the list cc'd)

On May 22, 2013, at 6:31 PM, Senanu <senanu.junk at gmail.com> wrote:

> On May 22, 2013, at 4:17 PM, Fields, Christopher J wrote:
> 
>> Hi all,
>>> 
>>> I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 
>> 
>> Probably the former, but...
>> 
>>> I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 
>> 
>> It shouldn't take that long, 7 Mb isn't that large.  Or is that 7 Mb for one genome?
> 
> It is 7Mb per genome, but there are only 2 genomes in the alignment, and the sequences are very similar to one another. 
> 
>> 
>>> Is this a known problem? Is there another way to generate such a consensus?
>> 
>> The code isn't really optimized for this, but again this isn't terribly large.  Is the bottleneck reading the alignment in, or is it the consensus_iupac() step?  Hard to say w/o seeing the alignment data itself.
> 
> The bottleneck is definitely with the consensus_iupac step. Reading the alignment in takes a few seconds. 

That's interesting, but again not surprising.  One would have to look at the code, but I wouldn't be surprised if the method is terribly inefficient.

chris


From p.j.a.cock at googlemail.com  Thu May 23 10:53:09 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 May 2013 15:53:09 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
	<CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_66x-c+Frmb0LVjYEB39OgxS6mabLKPBzEv38BoiOFMWg@mail.gmail.com>

On Thu, May 23, 2013 at 3:05 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
>
> I think 'relaxed phylip' was introduced by CIPRES a few years back.
> Frankly, this is the first time I have seen this mentioned on the list; yay,
> yet another format variation :)

The relaxed phylip 'format' goes back further than that, e.g.
http://lists.open-bio.org/pipermail/biopython-dev/2008-June/003899.html

RAxML and PHYML support relaxed phylip - but with their own ID limits.

Peter


From Ben.Ward at sainsbury-laboratory.ac.uk  Fri May 24 15:14:17 2013
From: Ben.Ward at sainsbury-laboratory.ac.uk (Ben Ward (TSL))
Date: Fri, 24 May 2013 19:14:17 +0000
Subject: [Bioperl-l] Building Many trees with Bioperl
Message-ID: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>

Hi,

I'm new to Bioperl and plan to make a script to automate making trees with many alignment files (themselves generated by automating the process of multiple alignment for many datasets by using clustalw in a bioperl script).
But I need to get it right for one pice of test data before I can do it for all:

What I have produced so far is the below. It's supposed to load in the alignment file as as SimpleAlign. Then use that alignment in phyml. I looked at the documentation and tried to follow examples.

However it gives me many errors like:
--------------------- WARNING ---------------------
MSG: Replacing one sequence [FXCNDTJ02P/1-366]

And then gives me:
Phyml command = /Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Phyml call (/Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output [/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip_phyml_stat.txt]: 11
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::Phylo::Phyml::_run /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
-----------------------------------------------------------

Can someone let me know if I'm going about this correctly and what I need to do to get it to work. I've also tried to run phyml by giving the filename in the run() method like:
my $inputfilename = 'outputalignmentfile';
my $tree = $factory->run("$inputfilename");

But I get the same EXCEPTION: Bio::Root::Exception message.

Thanks,
Ben W.

SCRIPT ---

#!/usr/bin/perl
use warnings;
use strict;
BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
use Bio::TreeIO;
use Bio::AlignIO;
use Bio::Tools::Run::Phylo::Phyml;

my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
-format => 'phylip');

my $aln = $alnin->next_aln();


# Make a Phyml factory.
my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
 -data_type => 'dna');

# Pass the factory an alignment and run:
# my $inputfilename = 'outputalignmentfile';

my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.


# Setup tree output stream...
my $treeio = Bio::TreeIO->new(-format => 'newick',
 -file => 'tree.newick');

$treeio->write_tree($tree);

exit 0;



From bosborne11 at verizon.net  Fri May 24 17:25:38 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Fri, 24 May 2013 17:25:38 -0400
Subject: [Bioperl-l] Building Many trees with Bioperl
In-Reply-To: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>
References: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>
Message-ID: <93D0963E-8399-468C-A32B-875FAA5054D1@verizon.net>

Ben,

What happens when you take the Phyml command itself and run it from the command line?

Also, a minor point: the message "MSG: Replacing one sequence [FXCNDTJ02P/1-366]" is not an error, it is a warning. An error accompanies an exit, warnings are just informative.

Brian O.


On May 24, 2013, at 3:14 PM, Ben Ward (TSL) <Ben.Ward at sainsbury-laboratory.ac.uk> wrote:

> Hi,
> 
> I'm new to Bioperl and plan to make a script to automate making trees with many alignment files (themselves generated by automating the process of multiple alignment for many datasets by using clustalw in a bioperl script).
> But I need to get it right for one pice of test data before I can do it for all:
> 
> What I have produced so far is the below. It's supposed to load in the alignment file as as SimpleAlign. Then use that alignment in phyml. I looked at the documentation and tried to follow examples.
> 
> However it gives me many errors like:
> --------------------- WARNING ---------------------
> MSG: Replacing one sequence [FXCNDTJ02P/1-366]
> 
> And then gives me:
> Phyml command = /Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Phyml call (/Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output [/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip_phyml_stat.txt]: 11
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
> STACK: Bio::Tools::Run::Phylo::Phyml::_run /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
> STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
> -----------------------------------------------------------
> 
> Can someone let me know if I'm going about this correctly and what I need to do to get it to work. I've also tried to run phyml by giving the filename in the run() method like:
> my $inputfilename = 'outputalignmentfile';
> my $tree = $factory->run("$inputfilename");
> 
> But I get the same EXCEPTION: Bio::Root::Exception message.
> 
> Thanks,
> Ben W.
> 
> SCRIPT ---
> 
> #!/usr/bin/perl
> use warnings;
> use strict;
> BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
> use Bio::TreeIO;
> use Bio::AlignIO;
> use Bio::Tools::Run::Phylo::Phyml;
> 
> my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
> -format => 'phylip');
> 
> my $aln = $alnin->next_aln();
> 
> 
> # Make a Phyml factory.
> my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
> -data_type => 'dna');
> 
> # Pass the factory an alignment and run:
> # my $inputfilename = 'outputalignmentfile';
> 
> my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.
> 
> 
> # Setup tree output stream...
> my $treeio = Bio::TreeIO->new(-format => 'newick',
> -file => 'tree.newick');
> 
> $treeio->write_tree($tree);
> 
> exit 0;
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From Ben.Ward at sainsbury-laboratory.ac.uk  Fri May 24 17:46:40 2013
From: Ben.Ward at sainsbury-laboratory.ac.uk (Ben Ward (TSL))
Date: Fri, 24 May 2013 21:46:40 +0000
Subject: [Bioperl-l] Building Many trees with Bioperl
In-Reply-To: <93D0963E-8399-468C-A32B-875FAA5054D1@verizon.net>
Message-ID: <CDC59B58.13A3%ben.ward@sainsbury-laboratory.ac.uk>

Hi,

If I just run phyml on the command line it seems to run ok - it accept's
my file and appears to undergo the tree building process - I haven't
actually see it complete yet, but ML and Bayes always does take a while -
and I have many reads that need to be aligned. But PhyML gets to the point
it asks - are you sure you want to proceed - I say yes, then it keeps
quiet and is currently working along to itself:

. 766 patterns found (out of a total of 795 sites).

. 58 sites without polymorphism (7.30%).

. Computing pairwise distances...

. Building BioNJ tree...

. WARNING: this analysis requires at least 556 MB of memory space.

. Do you really want to proceed? [Y/n] Y


It appears to be working =/
 
Best,
Ben.



On 24/05/2013 22:25, "Brian Osborne" <bosborne11 at verizon.net> wrote:

>Ben,
>
>What happens when you take the Phyml command itself and run it from the
>command line?
>
>Also, a minor point: the message "MSG: Replacing one sequence
>[FXCNDTJ02P/1-366]" is not an error, it is a warning. An error
>accompanies an exit, warnings are just informative.
>
>Brian O.
>
>
>On May 24, 2013, at 3:14 PM, Ben Ward (TSL)
><Ben.Ward at sainsbury-laboratory.ac.uk> wrote:
>
>> Hi,
>> 
>> I'm new to Bioperl and plan to make a script to automate making trees
>>with many alignment files (themselves generated by automating the
>>process of multiple alignment for many datasets by using clustalw in a
>>bioperl script).
>> But I need to get it right for one pice of test data before I can do it
>>for all:
>> 
>> What I have produced so far is the below. It's supposed to load in the
>>alignment file as as SimpleAlign. Then use that alignment in phyml. I
>>looked at the documentation and tried to follow examples.
>> 
>> However it gives me many errors like:
>> --------------------- WARNING ---------------------
>> MSG: Replacing one sequence [FXCNDTJ02P/1-366]
>> 
>> And then gives me:
>> Phyml command = /Users/wardb/clustalw2/phyml
>>/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyli
>>p  0 i 1 0 HKY e e 1 e BIONJ y y
>> 
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Phyml call (/Users/wardb/clustalw2/phyml
>>/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyli
>>p  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output
>>[/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyl
>>ip_phyml_stat.txt]: 11
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
>> STACK: Bio::Tools::Run::Phylo::Phyml::_run
>>/Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
>> STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
>> -----------------------------------------------------------
>> 
>> Can someone let me know if I'm going about this correctly and what I
>>need to do to get it to work. I've also tried to run phyml by giving the
>>filename in the run() method like:
>> my $inputfilename = 'outputalignmentfile';
>> my $tree = $factory->run("$inputfilename");
>> 
>> But I get the same EXCEPTION: Bio::Root::Exception message.
>> 
>> Thanks,
>> Ben W.
>> 
>> SCRIPT ---
>> 
>> #!/usr/bin/perl
>> use warnings;
>> use strict;
>> BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
>> use Bio::TreeIO;
>> use Bio::AlignIO;
>> use Bio::Tools::Run::Phylo::Phyml;
>> 
>> my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
>> -format => 'phylip');
>> 
>> my $aln = $alnin->next_aln();
>> 
>> 
>> # Make a Phyml factory.
>> my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
>> -data_type => 'dna');
>> 
>> # Pass the factory an alignment and run:
>> # my $inputfilename = 'outputalignmentfile';
>> 
>> my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.
>> 
>> 
>> # Setup tree output stream...
>> my $treeio = Bio::TreeIO->new(-format => 'newick',
>> -file => 'tree.newick');
>> 
>> $treeio->write_tree($tree);
>> 
>> exit 0;
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>




From himaghna.bhattacharjee at gmail.com  Tue May 28 11:59:02 2013
From: himaghna.bhattacharjee at gmail.com (Himaghna Bhattacharjee)
Date: Tue, 28 May 2013 21:29:02 +0530
Subject: [Bioperl-l] error in the link to install Kobe repository for windows
Message-ID: <CALd+KH1D8JVFJUNf+L7gM48B-iRsdcYkAZwuNOzi9bkVt7b49Q@mail.gmail.com>

Hey,
the link to install Kobe's repository for per 5.10 <"
http://cpan.uwinnipeg.ca/PPMPackages/10xx/
--">
seems to be broken as it shows Error 503 Service Temporarily Unavailable.
Could you please suggest an alternative ?

Thanks .
Himaghna Bhattacharjee
3rd year
B.E.(Hons.)Chemical Engineering
Birla Institute of Technology and Science,Pilani
Rajasthan 333 031


From wgallin at ualberta.ca  Tue May 28 13:49:02 2013
From: wgallin at ualberta.ca (Warren Gallin)
Date: Tue, 28 May 2013 11:49:02 -0600
Subject: [Bioperl-l] ReplacedBy value in esummary
Message-ID: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>

Hi,

	I just encountered a glitch when I was trying to update some entries in a database by finding updated GENBANK protein entries.

	The original record was gi 118091304 which has been replaced by gi 363734282

	I retrieved an ESummary of the record for gi 118091304 as a Bio::Tools::EUtilities::Summary::DocSum object (called $ds).

	When I then tried to retrieve the gi number for the replacement by using: 

my $replaced = $ds->get_contents_by_name('ReplacedBy');

 the returned value was 1, and when I dumped the ESummary record the relevant pair is ReplacedBy          :XP_421022.3.

The full Esummary dump is:

UID                 :118091304
Caption             :XP_421022
Title               :PREDICTED: similar to Potassium voltage-gated channel, subfamily Q, member
		    :1 [Gallus gallus]
Extra               :gi|118091304|ref|XP_421022.2|[118091304]
Gi                  :118091304
CreateDate          :2004/07/28
UpdateDate          :2006/11/16
Flags               :512
TaxId               :9031
Length              :643
Status              :replaced
ReplacedBy          :XP_421022.3
Comment             : This record was replaced or removed. 


	So two questions:

	1) Is the ReplacedBy value always supposed to be the new accession number version rather than the new gi number?
	2) Why would I be getting a returned value of 1 instead of the accession number that is in the summary record?

Any advice appreciated.

Warren Gallin


From cjfields at illinois.edu  Tue May 28 14:31:30 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 28 May 2013 18:31:30 +0000
Subject: [Bioperl-l] ReplacedBy value in esummary
In-Reply-To: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>
References: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E44377@CHIMBX5.ad.uillinois.edu>

On May 28, 2013, at 12:49 PM, Warren Gallin <wgallin at ualberta.ca> wrote:

> Hi,
> 
> 	I just encountered a glitch when I was trying to update some entries in a database by finding updated GENBANK protein entries.
> 
> 	The original record was gi 118091304 which has been replaced by gi 363734282
> 
> 	I retrieved an ESummary of the record for gi 118091304 as a Bio::Tools::EUtilities::Summary::DocSum object (called $ds).
> 
> 	When I then tried to retrieve the gi number for the replacement by using: 
> 
> my $replaced = $ds->get_contents_by_name('ReplacedBy');
> 
> the returned value was 1, and when I dumped the ESummary record the relevant pair is ReplacedBy          :XP_421022.3.
> 
> The full Esummary dump is:
> 
> UID                 :118091304
> Caption             :XP_421022
> Title               :PREDICTED: similar to Potassium voltage-gated channel, subfamily Q, member
> 		    :1 [Gallus gallus]
> Extra               :gi|118091304|ref|XP_421022.2|[118091304]
> Gi                  :118091304
> CreateDate          :2004/07/28
> UpdateDate          :2006/11/16
> Flags               :512
> TaxId               :9031
> Length              :643
> Status              :replaced
> ReplacedBy          :XP_421022.3
> Comment             : This record was replaced or removed. 
> 
> 
> 	So two questions:
> 
> 	1) Is the ReplacedBy value always supposed to be the new accession number version rather than the new gi number?

No idea, the best people to answer that would be NCBI (the idea of these modules was to simplify getting at that data instead of munging the XML, but whatever they report is mainly from NCBI, not bioperl).

> 	2) Why would I be getting a returned value of 1 instead of the accession number that is in the summary record?

The text dump above indicates the values do exist.  However, you are calling a method that returns a list (note the plural in the name) in scalar context, so you get the number of values.  If you always expect a single value, use:

    my ($replaced) = $ds->get_contents_by_name('ReplacedBy');

which forces array context.  That should fix it.

chris

> Any advice appreciated.
> 
> Warren Gallin
> _______________________________________________
> 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 May  1 22:16:02 2013
From: florent.angly at gmail.com (Florent Angly)
Date: Thu, 02 May 2013 12:16:02 +1000
Subject: [Bioperl-l] Downloading sequences in batch from Trace Archive
In-Reply-To: <CAA7rn9dtgtkdPLU9v=b3Jq0CWPvph59BYp2r5-jJRRt94dB1RA@mail.gmail.com>
References: <CAA7rn9dtgtkdPLU9v=b3Jq0CWPvph59BYp2r5-jJRRt94dB1RA@mail.gmail.com>
Message-ID: <5181CC62.9000609@gmail.com>

Maybe using EUtilities?
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service

Florent


On 30/04/13 06:25, shalabh sharma wrote:
> Hi All,
>            Is there any module in Bioperl that can download sequences from
> NCBI's trace archive?
>
> Thanks
> Shalabh
>



From jason.stajich at gmail.com  Thu May  2 01:42:55 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 1 May 2013 22:42:55 -0700
Subject: [Bioperl-l] Fwd: doubt
References: <CACPwBoTqbeNuY6hGW9gpQagL2ZXdknwcM_0Q7QMMCyqEz9FXcg@mail.gmail.com>
Message-ID: <B094273D-B6AB-4DE8-8B65-FFAA3FB30D8A@gmail.com>



Begin forwarded message:

> From: ARYA DAS <aryaanildas at gmail.com>
> Subject: doubt
> Date: May 1, 2013 10:42:21 PM PDT
> To: jason at bioperl.org
> 
> sir,
> 
>     Am using windows7 n was trying to install bio perl in it..i have
> already installed active perl.5.16.3.1603 . n was followeing the
> installation procedure mentioned .when i tried GUI installation .. i cant
> find bioperl package when i try to search them for installation.
> while using command line..
> 
> ppm> install PPM-Repositories
> 
> shows error like cant find package that provides PPM repositories,
> 
> and when i try manually ,on reaching the
> perl Build test
> 
> it says build is recognised as an internal or external file.
> 
> please help if time permits
> 
> regards,
> arya

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



From voldrani at gmail.com  Sun May  5 00:03:38 2013
From: voldrani at gmail.com (Chris Maloney)
Date: Sun, 5 May 2013 00:03:38 -0400
Subject: [Bioperl-l] Wiki work, Template:Doclink
Message-ID: <CABE9g5Ps+NDmziDZNro8UZ5_RMOP1ru1fmKOpFh+DFh=equRfQ@mail.gmail.com>

The module pages on the wiki could look a little better, like this one
for example:  http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast.
 There used to be a bunch of extra whitespace at the top of the page,
which was caused by extra line breaks in Template:Doclink, which I
just removed.

But, I think there are other improvements that could be made.  I would
like to turn this into an infobox -- which are the helpful informative
tables of info on Wikipedia that appear on many articles on the upper
right.  That would allow us to add more links -- like to metacpan, for
example.

It is not completely trivial to import infoboxes into a wiki though, I
just discovered.  I just went through the exercise on my home wiki,
and it involves importing a lot of templates from Wikipedia, and
fixing up the common.css.  You can see the full list of imported
templates here:
http://chrismaloney.org/wiki/index.php?title=Special:RecentChanges&limit=100.
 I don't *think* this should cause any problems, but I'm not 100%
sure.  On the other hand, if it does, it should be easy to roll back
-- it's a wiki, after all.

Does anybody have a problem if I do this?  I'll wait a day for
responses, and tackle this tomorrow, if no one objects.

-- Chris M.


From armendarez77 at hotmail.com  Tue May  7 20:32:22 2013
From: armendarez77 at hotmail.com (Veronica A.)
Date: Tue, 7 May 2013 17:32:22 -0700
Subject: [Bioperl-l] Bio::SeqIO doesn't write all gbk sequences from
	Bio::DB::GenBank
Message-ID: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>

Hello,
I'm currently running Bio::Perl 1.6.1 on Ubuntu 12.04.2 LTS and have noticed a problem with Bio::SeqIO when writing genbank files using the write_seq() function;  some of the files do not include an 'ORIGIN' tag or the sequence.

I am using GI#s (50 at a time every 2 minutes) to retrieve genbank files via Bio::DB::GenBank.

----------------------------------------START CODE----------------------------------
my $gb = Bio::DB::GenBank->new(-verbose=>-1);my $seqout = Bio::SeqIO->new(-file=>">$fileName", '-format'=>'Genbank', -alphabet=>'dna', -flush=>0, -verbose=>-1);while(@ids){     my @batchArray = splice(@ids, 0, 50);     my $batchArrayRef = \@batchArray;
     my $streamObj;     my $pid = fork();     if($pid == 0){          eval{               $streamObj = $gb->get_Stream_by_id($batchArrayRef);          };          if($@){               print "Error: ".$@."\n";          }          else{               while(my $seqObj = $streamObj->next_seq()){                    unless($seqObj->accession_number() =~ /N[A-Z]\_/){                        #print "ID: ".$seqObj->id()."\n";                        #print "Seq:\n".$seqObj->seq()."\n";                         $seqout->write_seq($seqObj);                    }                }          }          exit 0;     }}waitpid($pid,0);sleep(120);
----------------------------------------END CODE----------------------------------
Most of the Genbank files written to the output file have sequences, but there is a small portion that do not, even though they should.  For example, JX287367, in NCBI includes an 'ORIGIN' tag and sequence and when I use the print function before writing to file, the sequence is printed to STDOUT, but the 'ORIGIN' tag and sequence are not written to the output gbk file.  The following is found in the final output file:
----------------------------------START GBK-----------------------------------------
LOCUS       JX287367                 588 bp    DNA     linear   BCT 19-DEC-2012DEFINITION  Chlamydia trachomatis strain UW-5/CX pyruvoyl-dependent arginine            decarboxylase (aaxB) gene, complete cds.ACCESSION   JX287367VERSION     JX287367.1  GI:404351720KEYWORDS    .SOURCE      Chlamydia trachomatis  ORGANISM  Chlamydia trachomatis            Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;            Chlamydia/Chlamydophila group; Chlamydia.REFERENCE   1  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Characterization of the activity and expression of arginine            decarboxylase in human and animal Chlamydia pathogens  JOURNAL   FEMS Microbiol. Lett. 337 (2), 140-146 (2012)   PUBMED   23043454REFERENCE   2  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Direct Submission  JOURNAL   Submitted (06-JUL-2012) Department of Microbiology and Immunology,            F. Edward Hebert School of Medicine, Uniformed Services University            of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD            20814, USAFEATURES             Location/Qualifiers     source          1..588                     /mol_type="genomic DNA"                     /db_xref="taxon:813"                     /strain="UW-5/CX"                     /organism="Chlamydia trachomatis"                     /serovar="E"     gene            1..588                     /gene="aaxB"     CDS             1..588                     /protein_id="AFR60849.1"                     /gene="aaxB"                     /transl_table=11                     /note="AaxB"                     /db_xref="GI:404351721"                     /codon_start=1                     /product="pyruvoyl-dependent arginine decarboxylase"                     /translation="MPYGTRYPTLAFHTGGVGESDDGMPPQPFETFCYDSALLQAKIE                     NFNIVPYTSVLPKELFGNILPVDQCTKFFKHGAVLEVIMAGRGATVTDGTQAIATGVG                     ICWGKDKNGELIGGWAAEYVEFFPTWIDDEIAESHAKMWLKKSLQHELDLRSVSKHSE                     FQYFHNYINIRKKFGFCLTALGFLNFENVAPAVIQ"
//
----------------------------------END GBK-----------------------------------------
Can anyone tell what I am missing or why this is happening?  I don't know if this has happened in earlier BioPerl versions as up until now, I usually downloaded sequences straight from NCBI, but that became too time consuming....but this seems to be as well :S
Thank you in advance for any help,
Veronica
 		 	   		  


From cjfields at illinois.edu  Tue May  7 22:17:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 8 May 2013 02:17:43 +0000
Subject: [Bioperl-l] Bio::SeqIO doesn't write all gbk sequences
	from	Bio::DB::GenBank
In-Reply-To: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>
References: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E166A0@CHIMBX5.ad.uillinois.edu>

Veronica,

Your mail may have garbled the script and example file.  Can you paste these in a gist?

https://gist.github.com/

chris

On May 7, 2013, at 7:32 PM, Veronica A. <armendarez77 at hotmail.com> wrote:

> Hello,
> I'm currently running Bio::Perl 1.6.1 on Ubuntu 12.04.2 LTS and have noticed a problem with Bio::SeqIO when writing genbank files using the write_seq() function;  some of the files do not include an 'ORIGIN' tag or the sequence.
> 
> I am using GI#s (50 at a time every 2 minutes) to retrieve genbank files via Bio::DB::GenBank.
> 
> ----------------------------------------START CODE----------------------------------
> my $gb = Bio::DB::GenBank->new(-verbose=>-1);my $seqout = Bio::SeqIO->new(-file=>">$fileName", '-format'=>'Genbank', -alphabet=>'dna', -flush=>0, -verbose=>-1);while(@ids){     my @batchArray = splice(@ids, 0, 50);     my $batchArrayRef = \@batchArray;
>     my $streamObj;     my $pid = fork();     if($pid == 0){          eval{               $streamObj = $gb->get_Stream_by_id($batchArrayRef);          };          if($@){               print "Error: ".$@."\n";          }          else{               while(my $seqObj = $streamObj->next_seq()){                    unless($seqObj->accession_number() =~ /N[A-Z]\_/){                        #print "ID: ".$seqObj->id()."\n";                        #print "Seq:\n".$seqObj->seq()."\n";                         $seqout->write_seq($seqObj);                    }                }          }          exit 0;     }}waitpid($pid,0);sleep(120);
> ----------------------------------------END CODE----------------------------------
> Most of the Genbank files written to the output file have sequences, but there is a small portion that do not, even though they should.  For example, JX287367, in NCBI includes an 'ORIGIN' tag and sequence and when I use the print function before writing to file, the sequence is printed to STDOUT, but the 'ORIGIN' tag and sequence are not written to the output gbk file.  The following is found in the final output file:
> ----------------------------------START GBK-----------------------------------------
> LOCUS       JX287367                 588 bp    DNA     linear   BCT 19-DEC-2012DEFINITION  Chlamydia trachomatis strain UW-5/CX pyruvoyl-dependent arginine            decarboxylase (aaxB) gene, complete cds.ACCESSION   JX287367VERSION     JX287367.1  GI:404351720KEYWORDS    .SOURCE      Chlamydia trachomatis  ORGANISM  Chlamydia trachomatis            Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;            Chlamydia/Chlamydophila group; Chlamydia.REFERENCE   1  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Characterization of the activity and expression of arginine            decarboxylase in human and animal Chlamydia pathogens  JOURNAL   FEMS Microbiol. Lett. 337 (2), 140-146 (2012)   PUBMED   23043454REFERENCE   2  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Direct Submission  JOURNAL   Submitted (06-JUL-2012) Department of Microbiology and Immunology,            F. Edward Hebert School of Med!
> icine, Uniformed Services University            of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD            20814, USAFEATURES             Location/Qualifiers     source          1..588                     /mol_type="genomic DNA"                     /db_xref="taxon:813"                     /strain="UW-5/CX"                     /organism="Chlamydia trachomatis"                     /serovar="E"     gene            1..588                     /gene="aaxB"     CDS             1..588                     /protein_id="AFR60849.1"                     /gene="aaxB"                     /transl_table=11                     /note="AaxB"                     /db_xref="GI:404351721"                     /codon_start=1                     /product="pyruvoyl-dependent arginine decarboxylase"                     /translation="MPYGTRYPTLAFHTGGVGESDDGMPPQPFETFCYDSALLQAKIE                     NFNIVPYTSVLPKELFGNILPVDQCTKFFKHGAVLEVIMAGRGATVTDGTQAIATGVG                     ICWGKDKNGELIGGW!
> AAEYVEFFPTWIDDEIAESHAKMWLKKSLQHELDLRSVSKHSE                     FQYFHN
> YINIRKKFGFCLTALGFLNFENVAPAVIQ"
> //
> ----------------------------------END GBK-----------------------------------------
> Can anyone tell what I am missing or why this is happening?  I don't know if this has happened in earlier BioPerl versions as up until now, I usually downloaded sequences straight from NCBI, but that became too time consuming....but this seems to be as well :S
> Thank you in advance for any help,
> Veronica
> 		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From witch.of.agnessi at gmail.com  Wed May  8 15:24:53 2013
From: witch.of.agnessi at gmail.com (WoA)
Date: Wed, 8 May 2013 12:24:53 -0700 (PDT)
Subject: [Bioperl-l] Extracting matching subsequence from pairwise alignment
Message-ID: <1368041092972-16935.post@n3.nabble.com>

Hello All,

I've a pairwise global alignemnet of two DNA sequences generated by the
program NEEDLE of EMBOSS package. I wish to extract the sub-sequence that
matches/aligns to a given region of the other sequence. In  this alignment
<http://pastebin.com/wrhEDzJU>   (Pastebin Link) the given region (actually
the CDS) falls between base number 24:485 in the original sequence with ID
'XM_001005073.' I wish to extract the sub-sequence in the sequence ID
'Homolog' that aligns with that 24:485 region of the other sequence.

I'm using Bioperl to parse the alignment. I find out the the alignment
column numbers corresponding to 24:485 region in the particular sequence,
using 'column_from_residue_number'. Then I extract the sub-sequence from the
'aligned' other sequence(containing gaps) using the corresponding column
numbers. Finally I remove the gap characters.

Am I doing this thing correctly and are there any pitfalls ? Is there any
better way to do it by (Bio)Perl/Python? The code goes here:
use strict;
use warnings;
use Bio::AlignIO;

# read in an alignment generated by the EMBOSS program Needle
my $in = new Bio::AlignIO(-format => 'emboss',
                  -file   => 'test_needle.aln');

while( my $aln = $in->next_aln ) {
          #Seqnames: 'XM_001005073.'(CDS:24-485),'Homolog'
          my ($cds_start,$cds_end)=(24,485);#
          my $col_cdsstart = $aln->column_from_residue_number(
'XM_001005073.', $cds_start);
          my $col_cdsend= $aln->column_from_residue_number( 'XM_001005073.',
$cds_end);

          foreach my $seq ($aln->each_seq) {
                    if($seq->id() eq 'Homolog'){
                        my
$homolog_cds=$seq->subseq($col_cdsstart,$col_cdsend);
                         $homolog_cds=~s/\-//g;
                        print $homolog_cds,"\n";
                    }

        }
}





--
View this message in context: http://bioperl.996286.n3.nabble.com/Extracting-matching-subsequence-from-pairwise-alignment-tp16935.html
Sent from the Bioperl-L mailing list archive at Nabble.com.


From hlapp at drycafe.net  Wed May 15 16:44:07 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 15 May 2013 16:44:07 -0400
Subject: [Bioperl-l] Workshop on Sustainable Software for Science: Practice
	and Experiences
Message-ID: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>

FYI, if you haven't seen this yet:

http://wssspe.researchcomputing.org.uk/

It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?

Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)

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




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From carandraug+dev at gmail.com  Wed May 15 21:53:55 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 16 May 2013 02:53:55 +0100
Subject: [Bioperl-l] sets of sequences - how to read?
Message-ID: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>

Hi

when accessing entrez gene using eutils to get multiple genes, NCBI
now returns an Entrezgene-Set[1] rather than a list of EntrezGene.
This change must have happened sometime on the last 2 months. Compare:

use Bio::DB::EUtilities;

my %sets = (
  eutil   => 'efetch',
  db      => 'gene',
  retmode => 'text',
  rettype => 'asn1',
  email   => 'bioperl-l at lists.open-bio.org',
);

## this mimics the previous behaviour of the NCBI server but the
multiple requests will annoy their servers
my @ids = (3014, 85235);
my $response;
foreach (@ids) {
  my $fetcher = Bio::DB::EUtilities->new(%sets, id => $_);
  $response .= $fetcher->get_Response->content;
}
print $fetcher->get_Response->content;

## this used to be the right way to do it, but now returns an Entrezgene-Set
my $fetcher = Bio::DB::EUtilities->new(%sets, id => \@ids);
$response .= $fetcher->get_Response->content;
print $fetcher->get_Response->content;

There is no module to read these Entrezgene-Set in Perl at the moment,
since Bio::ASN1::EntrezGene; is not able to handle them. I have
contacted the module author and set him a fix[2] and he said he'll try
to look into it next week.

However, even with the fix there is another problem. How would one
access a set of sequences using the Bio::SeqIO API? There is no method
to do that. One could say, to ignore them, and make next_seq return
the next sequence of the set. But then we are losing data. After all,
it's perfectly viable to have multiple Entrezgene-Set in one file.
What would be the right way to do this?

Carn?

[1] http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/IEB/ToolBox/CPP_DOC/asn_spec/Entrezgene-Set.html
[2] https://github.com/carandraug/bio-asn1-entrezgene/commit/69d505056d8b7897df6271ffb7a5f39d58873c6b



From cjfields at illinois.edu  Thu May 16 00:43:22 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 04:43:22 +0000
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice	and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>

Jason and I have discussed looking into opportunity's like this, I think it makes sense to try a joint submission.  

chris

On May 15, 2013, at 3:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
> 
> http://wssspe.researchcomputing.org.uk/
> 
> It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?
> 
> Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)
> 
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> 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  Thu May 16 05:10:25 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 May 2013 10:10:25 +0100
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice and Experiences
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>

On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Jason and I have discussed looking into opportunity's like this, I think it makes
> sense to try a joint submission.
>
> chris

This sounds like a good idea, although given the time and place I am
unlikely to be able to attend in person:

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

Rather than trying to discuss this over four mailing lists should we switch
to the cross project list open-bio-l, or continue off-list?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thanks,

Peter


From miquel.ramia at uab.cat  Thu May 16 06:42:29 2013
From: miquel.ramia at uab.cat (=?ISO-8859-1?Q?Miquel_R=E0mia?=)
Date: Thu, 16 May 2013 12:42:29 +0200
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
Message-ID: <5194B815.2010401@uab.cat>

Hi all,

I get this message when compiling Bio::DB::Sam:

Building Bio-SamTools

gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'

collect2: ld returned 1 exit status

make: *** [bam2bedgraph] Error 1


Is this error related to the module or some dependencies? or maybe a 
problem with my system?

Any help appreciated, thanks!


-- 
Miquel R?mia Jes?s
PhD. candidate (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Aut?noma de Barcelona (UAB)
08193, Cerdanyola del Vall?s
Barcelona (Spain)



From cjfields at illinois.edu  Thu May 16 09:12:40 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 13:12:40 +0000
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <5194B815.2010401@uab.cat>
References: <5194B815.2010401@uab.cat>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>

It may be due to the new samtools release (v 0.1.19).  I know Heng Li has been working on the code over the last year for threading support (notice the undefined functions).  Have you tried v 0.1.18?

chris

On May 16, 2013, at 5:42 AM, Miquel R?mia <miquel.ramia at uab.cat> wrote:

> Hi all,
> 
> I get this message when compiling Bio::DB::Sam:
> 
> Building Bio-SamTools
> 
> gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
> 
> collect2: ld returned 1 exit status
> 
> make: *** [bam2bedgraph] Error 1
> 
> 
> Is this error related to the module or some dependencies? or maybe a problem with my system?
> 
> Any help appreciated, thanks!
> 
> 
> -- 
> Miquel R?mia Jes?s
> PhD. candidate (PIF)
> Evolutionary Bioinformatics Group
> (Genomics, Bioinformatics and Evolution Group)
> Lab MRB/014 - 93 586 89 58
> MRB - Institut de Biologia i Biomedicina (IBB)
> Universitat Aut?noma de Barcelona (UAB)
> 08193, Cerdanyola del Vall?s
> Barcelona (Spain)
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu May 16 09:09:45 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 13:09:45 +0000
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice and Experiences
In-Reply-To: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
	<CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1FBCF@CHIMBX5.ad.uillinois.edu>

Yes, though we need to make sure others (e.g. those not subscribed to open-bio-l) are in the loop.

November is a possibility for me.

chris

On May 16, 2013, at 4:10 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> Jason and I have discussed looking into opportunity's like this, I think it makes
>> sense to try a joint submission.
>> 
>> chris
> 
> This sounds like a good idea, although given the time and place I am
> unlikely to be able to attend in person:
> 
> First Workshop on Sustainable Software for Science: Practice and
> Experiences (WSSSPE)
> (to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
> http://wssspe.researchcomputing.org.uk/
> 
> Rather than trying to discuss this over four mailing lists should we switch
> to the cross project list open-bio-l, or continue off-list?
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> Thanks,
> 
> Peter




From andreas at sdsc.edu  Thu May 16 00:31:34 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 15 May 2013 21:31:34 -0700
Subject: [Bioperl-l] [Biojava-l] Workshop on Sustainable Software for
 Science: Practice and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <CALthepxHNLm4eHJcCQ4dLnhJr5OhGJJEKTAjH+x7Ppq0oFFnDA@mail.gmail.com>

Thanks Hilmar, you were faster than me in sending this out..

You are right, it would be very interesting to hear what some of the long
running open-bio projects have to say on the topic of sustainability. Let
me know if anybody is interested in a submission!

Andreas




On Wed, May 15, 2013 at 1:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
>
> http://wssspe.researchcomputing.org.uk/
>
> It seems to me that the Bio* projects, perhaps led by BioPerl as the
> oldest and thus longest running (nowadays more fancily called "sustained")
> of them would have a lot to say about the subject. Anyone interested in a
> joint submission?
>
> Also, I notice that Biojava's Andreas is on the organizing committee, so
> maybe he's been conspiring on something already :-)
>
>         -hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From cjfields at illinois.edu  Fri May 17 00:08:04 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 04:08:04 +0000
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>

This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.

My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.

chris

On May 15, 2013, at 8:53 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> when accessing entrez gene using eutils to get multiple genes, NCBI
> now returns an Entrezgene-Set[1] rather than a list of EntrezGene.
> This change must have happened sometime on the last 2 months. Compare:
> 
> use Bio::DB::EUtilities;
> 
> my %sets = (
>  eutil   => 'efetch',
>  db      => 'gene',
>  retmode => 'text',
>  rettype => 'asn1',
>  email   => 'bioperl-l at lists.open-bio.org',
> );
> 
> ## this mimics the previous behaviour of the NCBI server but the
> multiple requests will annoy their servers
> my @ids = (3014, 85235);
> my $response;
> foreach (@ids) {
>  my $fetcher = Bio::DB::EUtilities->new(%sets, id => $_);
>  $response .= $fetcher->get_Response->content;
> }
> print $fetcher->get_Response->content;
> 
> ## this used to be the right way to do it, but now returns an Entrezgene-Set
> my $fetcher = Bio::DB::EUtilities->new(%sets, id => \@ids);
> $response .= $fetcher->get_Response->content;
> print $fetcher->get_Response->content;
> 
> There is no module to read these Entrezgene-Set in Perl at the moment,
> since Bio::ASN1::EntrezGene; is not able to handle them. I have
> contacted the module author and set him a fix[2] and he said he'll try
> to look into it next week.
> 
> However, even with the fix there is another problem. How would one
> access a set of sequences using the Bio::SeqIO API? There is no method
> to do that. One could say, to ignore them, and make next_seq return
> the next sequence of the set. But then we are losing data. After all,
> it's perfectly viable to have multiple Entrezgene-Set in one file.
> What would be the right way to do this?
> 
> Carn?
> 
> [1] http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/IEB/ToolBox/CPP_DOC/asn_spec/Entrezgene-Set.html
> [2] https://github.com/carandraug/bio-asn1-entrezgene/commit/69d505056d8b7897df6271ffb7a5f39d58873c6b
> 
> _______________________________________________
> 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 May 17 00:16:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 04:16:12 +0000
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>
References: <5194B815.2010401@uab.cat>
	<118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>

For the record, this is now fixed in the latest Bio::Samtools (via Lincoln).

chris

On May 16, 2013, at 8:12 AM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> It may be due to the new samtools release (v 0.1.19).  I know Heng Li has been working on the code over the last year for threading support (notice the undefined functions).  Have you tried v 0.1.18?
> 
> chris
> 
> On May 16, 2013, at 5:42 AM, Miquel R?mia <miquel.ramia at uab.cat> wrote:
> 
>> Hi all,
>> 
>> I get this message when compiling Bio::DB::Sam:
>> 
>> Building Bio-SamTools
>> 
>> gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
>> 
>> collect2: ld returned 1 exit status
>> 
>> make: *** [bam2bedgraph] Error 1
>> 
>> 
>> Is this error related to the module or some dependencies? or maybe a problem with my system?
>> 
>> Any help appreciated, thanks!
>> 
>> 
>> -- 
>> Miquel R?mia Jes?s
>> PhD. candidate (PIF)
>> Evolutionary Bioinformatics Group
>> (Genomics, Bioinformatics and Evolution Group)
>> Lab MRB/014 - 93 586 89 58
>> MRB - Institut de Biologia i Biomedicina (IBB)
>> Universitat Aut?noma de Barcelona (UAB)
>> 08193, Cerdanyola del Vall?s
>> Barcelona (Spain)
>> 
>> _______________________________________________
>> 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  Fri May 17 01:12:24 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 17 May 2013 06:12:24 +0100
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>

On 17 May 2013 05:08, Fields, Christopher J <cjfields at illinois.edu> wrote:
> This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.
>
> My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.

:s I'm not sure I understood your suggestion. I think the problem is
just the introduction of a new concept, a "set" of stuff (genes in
this case), and how should SeqIO handle multiple sets.

Carn?



From shalabh.sharma7 at gmail.com  Fri May 17 10:54:55 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 17 May 2013 10:54:55 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
Message-ID: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>

HI,
                 First of all i am really sorry for sending this mail here,
i am not sure if this is the right forum. I know lot of people work on
similar stuff.
I wrote to NCBI but nobody replied.

Actually i am looking for all bacterial/microbial gene annotation
nucleotide fasta files.
Does anyone knows where to download these kind of files.
I tried *ffn files but they are not annotated.
Or is there any module in bioperl that i can use ?
I would really appreciate your help.

Thanks
Shalabh

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


From fossandonc at hotmail.com  Fri May 17 11:59:04 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 17 May 2013 11:59:04 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
Message-ID: <SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>

Hi,
You can get the annotations from here:
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/

The ".ffn" are the genes nucleotide fasta files but it does not show the
product name, on the other hand the ".faa" are the genes aminoacid fasta
files and shows the product name, but if you want both product and
nucleotide is much better to use the Genbank ".gbk" files that contains the
complete data and you can parse it easily using BioPerl to obtain all genes,
and then print the /protein_id, /product, and the nucleotide sequences in a
new fasta file. Check these to see how to do it:
http://www.bioperl.org/wiki/HOWTO:SeqIO
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

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 shalabh sharma
Enviado el: viernes, 17 de mayo de 2013 10:55
Para: bioperl-l
Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files

HI,
                 First of all i am really sorry for sending this mail here,
i am not sure if this is the right forum. I know lot of people work on
similar stuff.
I wrote to NCBI but nobody replied.

Actually i am looking for all bacterial/microbial gene annotation nucleotide
fasta files.
Does anyone knows where to download these kind of files.
I tried *ffn files but they are not annotated.
Or is there any module in bioperl that i can use ?
I would really appreciate your help.

Thanks
Shalabh

--
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences University of Georgia Athens, GA 30602-3636
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From shalabh.sharma7 at gmail.com  Fri May 17 12:26:26 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 17 May 2013 12:26:26 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
Message-ID: <CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>

Hey Francisco,
           Thanks a lot. Basically i just wanted gene nucleotide fasta
files with GI numbers.
I think i will have to parse it from gbk files.

-Shalabh


On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n <
fossandonc at hotmail.com> wrote:

> Hi,
> You can get the annotations from here:
> ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
>
> The ".ffn" are the genes nucleotide fasta files but it does not show the
> product name, on the other hand the ".faa" are the genes aminoacid fasta
> files and shows the product name, but if you want both product and
> nucleotide is much better to use the Genbank ".gbk" files that contains the
> complete data and you can parse it easily using BioPerl to obtain all
> genes,
> and then print the /protein_id, /product, and the nucleotide sequences in a
> new fasta file. Check these to see how to do it:
> http://www.bioperl.org/wiki/HOWTO:SeqIO
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>
> 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 shalabh sharma
> Enviado el: viernes, 17 de mayo de 2013 10:55
> Para: bioperl-l
> Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> HI,
>                  First of all i am really sorry for sending this mail here,
> i am not sure if this is the right forum. I know lot of people work on
> similar stuff.
> I wrote to NCBI but nobody replied.
>
> Actually i am looking for all bacterial/microbial gene annotation
> nucleotide
> fasta files.
> Does anyone knows where to download these kind of files.
> I tried *ffn files but they are not annotated.
> Or is there any module in bioperl that i can use ?
> I would really appreciate your help.
>
> Thanks
> Shalabh
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences University of Georgia Athens, GA 30602-3636
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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



From cjfields at illinois.edu  Fri May 17 13:37:53 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 17:37:53 +0000
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E22218@CHIMBX5.ad.uillinois.edu>

On May 17, 2013, at 12:12 AM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 17 May 2013 05:08, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.
>> 
>> My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.
> 
> :s I'm not sure I understood your suggestion. I think the problem is
> just the introduction of a new concept, a "set" of stuff (genes in
> this case), and how should SeqIO handle multiple sets.
> 
> Carn?


(note: critical point in this is Bio::ASN1::Entrezgene would allow this, I'm not sure it would.  Otherwise this is all really hand-wavy)

To me a 'set of stuff', particularly when the 'stuff' is stored sequentially in a flat file, is a simple 'database' or 'store' of similar items, where the class allows one the ability to look up particular members in the set, but also could store higher level information about the set as a whole if needed.  If it were me, I would implement a method particular to Bio::SeqIO::entrezgene that specifically creates and returns this ( next_geneset(), for instance ); next_seq() could then be implemented to iterate through the items in that database/store.  

Two useful things come out of this.  First, if the data for the Entrez Gene file/chunk are parsed to store offsets per ID, one would only need to parse out the chunks needed (offset of ID to next offset), then pass that into the parser and create objects on the fly.  This would probably be as fast or faster than (for instance) the greedy method of parsing the entire file and storing everything in objects up-front, then iterating through those objects one at a time, which I think is current behavior.

Second: if an index is created, the upfront cost is already paid (you could reuse the same index when parsing the same data).

An analogous example might be storing all FASTQ data in a sequencing run; I don't want to expend the effort to parse all the FASTQ data, but I may want to run operations on individual items in the set as well as store additional information about the data (barcodes per run, lanes, overall quality stats, etc).  

Does that make sense?  The pieces for this are lying around (Bio::Index::* for instance has methods for indexing flat files, and classes like Bio::DB::Fasta).

chris


From shalabh.sharma7 at gmail.com  Sun May 19 15:33:16 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Sun, 19 May 2013 15:33:16 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
	<CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>
Message-ID: <CAA7rn9ehQ1t1AizSLC15PFFh4mV8njfaTSY2ZVDqtzb2bEGBaA@mail.gmail.com>

Thanks Russell,
                            Actually i wanted all the Bacterial gene
nucleotide files, so i parsed it from *gbk. But yes these files might help
me for my other parts of my work.

Thanks
Shalabh


On Sun, May 19, 2013 at 3:26 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:

> Another option that I've used before is to download the gene2accession,
> gene2refseq,  and gene_info files from here
> ftp://ftp.ncbi.nih.gov/gene/DATA/ then parse out the data you require.
> It might work for you?
>
> --Russell
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:
> bioperl-l-bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> Sent: Saturday, 18 May 2013 4:26 a.m.
> To: Francisco J. Ossand?n
> Cc: bioperl-l
> Subject: Re: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> Hey Francisco,
>            Thanks a lot. Basically i just wanted gene nucleotide fasta
> files with GI numbers.
> I think i will have to parse it from gbk files.
>
> -Shalabh
>
>
> On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n <
> fossandonc at hotmail.com> wrote:
>
> > Hi,
> > You can get the annotations from here:
> > ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
> >
> > The ".ffn" are the genes nucleotide fasta files but it does not show
> > the product name, on the other hand the ".faa" are the genes aminoacid
> > fasta files and shows the product name, but if you want both product
> > and nucleotide is much better to use the Genbank ".gbk" files that
> > contains the complete data and you can parse it easily using BioPerl
> > to obtain all genes, and then print the /protein_id, /product, and the
> > nucleotide sequences in a new fasta file. Check these to see how to do
> > it:
> > http://www.bioperl.org/wiki/HOWTO:SeqIO
> > http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> >
> > 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 shalabh
> > sharma Enviado el: viernes, 17 de mayo de 2013 10:55
> > Para: bioperl-l
> > Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
> >
> > HI,
> >                  First of all i am really sorry for sending this mail
> > here, i am not sure if this is the right forum. I know lot of people
> > work on similar stuff.
> > I wrote to NCBI but nobody replied.
> >
> > Actually i am looking for all bacterial/microbial gene annotation
> > nucleotide fasta files.
> > Does anyone knows where to download these kind of files.
> > I tried *ffn files but they are not annotated.
> > Or is there any module in bioperl that i can use ?
> > I would really appreciate your help.
> >
> > Thanks
> > Shalabh
> >
> > --
> > Shalabh Sharma
> > Scientific Computing Professional Associate (Bioinformatics
> > Specialist) Department of Marine Sciences University of Georgia
> > Athens, GA 30602-3636 _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences University of Georgia Athens, GA 30602-3636
>
> _______________________________________________
> 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.
> =======================================================================
>



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



From Russell.Smithies at agresearch.co.nz  Sun May 19 15:26:35 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 20 May 2013 07:26:35 +1200
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
	<CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>

Another option that I've used before is to download the gene2accession, gene2refseq,  and gene_info files from here ftp://ftp.ncbi.nih.gov/gene/DATA/ then parse out the data you require.
It might work for you?

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of shalabh sharma
Sent: Saturday, 18 May 2013 4:26 a.m.
To: Francisco J. Ossand?n
Cc: bioperl-l
Subject: Re: [Bioperl-l] Downloading annotated Gene nucleotide fasta files

Hey Francisco,
           Thanks a lot. Basically i just wanted gene nucleotide fasta files with GI numbers.
I think i will have to parse it from gbk files.

-Shalabh


On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n < fossandonc at hotmail.com> wrote:

> Hi,
> You can get the annotations from here:
> ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
>
> The ".ffn" are the genes nucleotide fasta files but it does not show 
> the product name, on the other hand the ".faa" are the genes aminoacid 
> fasta files and shows the product name, but if you want both product 
> and nucleotide is much better to use the Genbank ".gbk" files that 
> contains the complete data and you can parse it easily using BioPerl 
> to obtain all genes, and then print the /protein_id, /product, and the 
> nucleotide sequences in a new fasta file. Check these to see how to do 
> it:
> http://www.bioperl.org/wiki/HOWTO:SeqIO
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>
> 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 shalabh 
> sharma Enviado el: viernes, 17 de mayo de 2013 10:55
> Para: bioperl-l
> Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> HI,
>                  First of all i am really sorry for sending this mail 
> here, i am not sure if this is the right forum. I know lot of people 
> work on similar stuff.
> I wrote to NCBI but nobody replied.
>
> Actually i am looking for all bacterial/microbial gene annotation 
> nucleotide fasta files.
> Does anyone knows where to download these kind of files.
> I tried *ffn files but they are not annotated.
> Or is there any module in bioperl that i can use ?
> I would really appreciate your help.
>
> Thanks
> Shalabh
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics 
> Specialist) Department of Marine Sciences University of Georgia 
> Athens, GA 30602-3636 _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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

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

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From miquel.ramia at uab.cat  Tue May 21 11:08:18 2013
From: miquel.ramia at uab.cat (=?ISO-8859-1?Q?Miquel_R=E0mia?=)
Date: Tue, 21 May 2013 17:08:18 +0200
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>
References: <5194B815.2010401@uab.cat>
	<"118F034CF4C3EF48A96F86CE585B94BF74E1F C2C"@CHIMBX5.ad.uillinois.edu>
	<118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>
Message-ID: <519B8DE2.2070308@uab.cat>

On 17/05/13 06:16, Fields, Christopher J wrote:
> For the record, this is now fixed in the latest Bio::Samtools (via Lincoln).
>
> chris
>
>

Compiled correctly!

thank you



-- 
Miquel R?mia Jes?s
PhD. candidate (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Aut?noma de Barcelona (UAB)
08193, Cerdanyola del Vall?s
Barcelona (Spain)



From b.l.cohen_home at btinternet.com  Mon May 20 14:49:50 2013
From: b.l.cohen_home at btinternet.com (Bernard Cohen)
Date: Mon, 20 May 2013 19:49:50 +0100 (BST)
Subject: [Bioperl-l] Phylip format error
Message-ID: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>

Hello!

I happen to have checked to see what the PERL webpage says about Phylip format for DNA alignment files and see that it is erroneous.?

I am not a PERL user and do not want to be bothered to register or otherwise learn how to make an official comment, so forward this for someone to pick up.

Phylip format allows up to 10 spaces for taxon names; the data must start in the 11th space. This can be checked on Jo Felsenstein's site.

The PERL page accessed by searching for "Phylip format PERL" allows only 8 spaces for the name.?

B. L. Cohen


From senanu.pearson at gmail.com  Wed May 22 16:15:24 2013
From: senanu.pearson at gmail.com (Senanu)
Date: Wed, 22 May 2013 13:15:24 -0700
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from alignment
Message-ID: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>

Hi all,

I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 

I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 

Is this a known problem? Is there another way to generate such a consensus?


my $in = Bio::AlignIO->new(-file => $files[0],
                           -format => 'XMFA');
while  (my $aln = $in->next_aln()) {
    foreach  my $seq ($aln->each_seq) {
        $seq->alphabet('dna');
    }
    my $con = $aln->consensus_iupac();
}


Thanks in advance.
Ngwenyama


From cjfields at illinois.edu  Wed May 22 19:17:50 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 22 May 2013 23:17:50 +0000
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from
 alignment
In-Reply-To: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
References: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E2A01D@CHIMBX5.ad.uillinois.edu>

On May 22, 2013, at 3:15 PM, Senanu <senanu.pearson at gmail.com> wrote:

> Hi all,
> 
> I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 

Probably the former, but...

> I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 

It shouldn't take that long, 7 Mb isn't that large.  Or is that 7 Mb for one genome?

> Is this a known problem? Is there another way to generate such a consensus?

The code isn't really optimized for this, but again this isn't terribly large.  Is the bottleneck reading the alignment in, or is it the consensus_iupac() step?  Hard to say w/o seeing the alignment data itself.

> my $in = Bio::AlignIO->new(-file => $files[0],
>                           -format => 'XMFA');
> while  (my $aln = $in->next_aln()) {
>    foreach  my $seq ($aln->each_seq) {
>        $seq->alphabet('dna');
>    }
>    my $con = $aln->consensus_iupac();
> }
> 
> 
> Thanks in advance.
> Ngwenyama
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

chris


From alexeymorozov1991 at gmail.com  Thu May 23 03:22:13 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Thu, 23 May 2013 16:22:13 +0900
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
Message-ID: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>

Which is also worsened by the fact that there is relaxed phylip format,
which allows up to 250 chars for taxon name. They are separated from a
sequence by single space, which creates problems if names were extended to
10 chars in strict Felsenstein's format by whitespaces. On the whole,
phylip is as messily defined format as one can make from a plain textfile
with information content of fasta.
Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
phylip and how does it tell dialects from one another. Even if code support
is OK, it may be worthwile to explain it somewhere at bioperl.org


2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>

> Hello!
>
> I happen to have checked to see what the PERL webpage says about Phylip
> format for DNA alignment files and see that it is erroneous.
>
> I am not a PERL user and do not want to be bothered to register or
> otherwise learn how to make an official comment, so forward this for
> someone to pick up.
>
> Phylip format allows up to 10 spaces for taxon names; the data must start
> in the 11th space. This can be checked on Jo Felsenstein's site.
>
> The PERL page accessed by searching for "Phylip format PERL" allows only 8
> spaces for the name.
>
> B. L. Cohen
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.


From p.j.a.cock at googlemail.com  Thu May 23 04:30:21 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 May 2013 09:30:21 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>

On Thu, May 23, 2013 at 8:22 AM, Alexey Morozov
<alexeymorozov1991 at gmail.com> wrote:
> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org

Biopython's AlignIO defines both a (strict) "phylip" and "relaxed-phylip"
as two separate formats (or variants, like the "fastq" variants). Doing
the same in BioPerl would seem sensible since auto-detection is not
easy.

http://biopython.org/wiki/AlignIO#File_Formats

Peter

P.S. Where does that 250 characters for the taxon name limit come from?
The trouble with relaxed phylip is that some tools are more relaxed than
others ;)


From awitney at sgul.ac.uk  Thu May 23 04:43:15 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 23 May 2013 09:43:15 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <519DD6A3.8090304@sgul.ac.uk>


Not sure if there is an actual question in these messages, but BioPerl
can be used to generate valid Phylip format and run, like this:

## Build Align object
my $aln = Bio::SimpleAlign->new(-seqs=>$seqs);

## swap the taxa names with 8 characters long unique IDs
my ($aln_safe, $ref_name) = $aln->set_displayname_safe(8);

## Write out phylip format infile
Bio::AlignIO->new(-file=>'>infile.out', -format=>'phylip', -interleaved
=> 0)->write_aln($aln);

## run PHYLIP's pars program
my @params = (idlength=>10);   #, jumble=>"17,10");
my $tree_factory = Bio::Tools::Run::Phylo::Phylip::Pars->new(@params);
$tree_factory->quiet(1);  # Suppress pars messages to terminal
my $tree = $tree_factory->create_tree($aln_safe);

## fix the node labels back
my @nodes = sort { defined $a->id && defined $b->id && $a->id cmp $b->id
} $tree->get_nodes();
foreach my $nd (@nodes) {
	if ( $nd->is_Leaf ) {
		$nd->id($ref_name->{$nd->id_output})
	}
}

HTH

Adam

On 23/05/2013 08:22, Alexey Morozov wrote:
> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> 
> 2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>
> 
>> Hello!
>>
>> I happen to have checked to see what the PERL webpage says about Phylip
>> format for DNA alignment files and see that it is erroneous.
>>
>> I am not a PERL user and do not want to be bothered to register or
>> otherwise learn how to make an official comment, so forward this for
>> someone to pick up.
>>
>> Phylip format allows up to 10 spaces for taxon names; the data must start
>> in the 11th space. This can be checked on Jo Felsenstein's site.
>>
>> The PERL page accessed by searching for "Phylip format PERL" allows only 8
>> spaces for the name.
>>
>> B. L. Cohen
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> 
> 
> 


From cjfields at illinois.edu  Thu May 23 09:48:31 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 13:48:31 +0000
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E323A4@CITESMBX5.ad.uillinois.edu>

Alexey,

Just want to point out that 'relaxed phylip' format was introduced long after this parser was created; in fact (as Adam points out) there was an alternative workaround to deal with the lossy names.  

The content of that page is on a wiki, which anyone is free to edit (just need an OpenID to set up an account).

chris

On May 23, 2013, at 2:22 AM, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:

> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> 
> 2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>
> 
>> Hello!
>> 
>> I happen to have checked to see what the PERL webpage says about Phylip
>> format for DNA alignment files and see that it is erroneous.
>> 
>> I am not a PERL user and do not want to be bothered to register or
>> otherwise learn how to make an official comment, so forward this for
>> someone to pick up.
>> 
>> Phylip format allows up to 10 spaces for taxon names; the data must start
>> in the 11th space. This can be checked on Jo Felsenstein's site.
>> 
>> The PERL page accessed by searching for "Phylip format PERL" allows only 8
>> spaces for the name.
>> 
>> B. L. Cohen
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu May 23 10:05:32 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 14:05:32 +0000
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
	<CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>

On May 23, 2013, at 3:30 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, May 23, 2013 at 8:22 AM, Alexey Morozov
> <alexeymorozov1991 at gmail.com> wrote:
>> Which is also worsened by the fact that there is relaxed phylip format,
>> which allows up to 250 chars for taxon name. They are separated from a
>> sequence by single space, which creates problems if names were extended to
>> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
>> phylip is as messily defined format as one can make from a plain textfile
>> with information content of fasta.
>> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
>> phylip and how does it tell dialects from one another. Even if code support
>> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> Biopython's AlignIO defines both a (strict) "phylip" and "relaxed-phylip"
> as two separate formats (or variants, like the "fastq" variants). Doing
> the same in BioPerl would seem sensible since auto-detection is not
> easy.
> 
> http://biopython.org/wiki/AlignIO#File_Formats
> 
> Peter
> 
> P.S. Where does that 250 characters for the taxon name limit come from?
> The trouble with relaxed phylip is that some tools are more relaxed than
> others ;)

As Adam pointed out, prior to the introduction of 'relaxed phylip' we had an alternative solution that didn't require a modified format but still allowed one to use PHYLIP and other tools requesting the format.  I think 'relaxed phylip' was introduced by CIPRES a few years back.  Frankly, this is the first time I have seen this mentioned on the list; yay, yet another format variation :)

The variant format parsing (as implemented for SeqIO::fastq, as you know) deals with variant names like 'fastq-sanger', where the main format name is first, the variant of the format second.  The order in this case is reversed (relaxed-phylip), which I'm pretty sure will not work.  Not impossible to allow, but we would probably allow support like this initially:

my $in = Bio::AlignIO->new(-format => 'phylip',
                           -variant => 'relaxed',
                             ?);

chris


From cjfields at illinois.edu  Thu May 23 09:56:32 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 13:56:32 +0000
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from
 alignment
In-Reply-To: <92CD2F9D-7C8E-4941-9354-4BD80D8C2CB6@gmail.com>
References: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E2A01D@CHIMBX5.ad.uillinois.edu>
	<92CD2F9D-7C8E-4941-9354-4BD80D8C2CB6@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E32489@CITESMBX5.ad.uillinois.edu>

(keep the list cc'd)

On May 22, 2013, at 6:31 PM, Senanu <senanu.junk at gmail.com> wrote:

> On May 22, 2013, at 4:17 PM, Fields, Christopher J wrote:
> 
>> Hi all,
>>> 
>>> I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 
>> 
>> Probably the former, but...
>> 
>>> I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 
>> 
>> It shouldn't take that long, 7 Mb isn't that large.  Or is that 7 Mb for one genome?
> 
> It is 7Mb per genome, but there are only 2 genomes in the alignment, and the sequences are very similar to one another. 
> 
>> 
>>> Is this a known problem? Is there another way to generate such a consensus?
>> 
>> The code isn't really optimized for this, but again this isn't terribly large.  Is the bottleneck reading the alignment in, or is it the consensus_iupac() step?  Hard to say w/o seeing the alignment data itself.
> 
> The bottleneck is definitely with the consensus_iupac step. Reading the alignment in takes a few seconds. 

That's interesting, but again not surprising.  One would have to look at the code, but I wouldn't be surprised if the method is terribly inefficient.

chris


From p.j.a.cock at googlemail.com  Thu May 23 10:53:09 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 May 2013 15:53:09 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
	<CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_66x-c+Frmb0LVjYEB39OgxS6mabLKPBzEv38BoiOFMWg@mail.gmail.com>

On Thu, May 23, 2013 at 3:05 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
>
> I think 'relaxed phylip' was introduced by CIPRES a few years back.
> Frankly, this is the first time I have seen this mentioned on the list; yay,
> yet another format variation :)

The relaxed phylip 'format' goes back further than that, e.g.
http://lists.open-bio.org/pipermail/biopython-dev/2008-June/003899.html

RAxML and PHYML support relaxed phylip - but with their own ID limits.

Peter


From Ben.Ward at sainsbury-laboratory.ac.uk  Fri May 24 15:14:17 2013
From: Ben.Ward at sainsbury-laboratory.ac.uk (Ben Ward (TSL))
Date: Fri, 24 May 2013 19:14:17 +0000
Subject: [Bioperl-l] Building Many trees with Bioperl
Message-ID: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>

Hi,

I'm new to Bioperl and plan to make a script to automate making trees with many alignment files (themselves generated by automating the process of multiple alignment for many datasets by using clustalw in a bioperl script).
But I need to get it right for one pice of test data before I can do it for all:

What I have produced so far is the below. It's supposed to load in the alignment file as as SimpleAlign. Then use that alignment in phyml. I looked at the documentation and tried to follow examples.

However it gives me many errors like:
--------------------- WARNING ---------------------
MSG: Replacing one sequence [FXCNDTJ02P/1-366]

And then gives me:
Phyml command = /Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Phyml call (/Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output [/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip_phyml_stat.txt]: 11
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::Phylo::Phyml::_run /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
-----------------------------------------------------------

Can someone let me know if I'm going about this correctly and what I need to do to get it to work. I've also tried to run phyml by giving the filename in the run() method like:
my $inputfilename = 'outputalignmentfile';
my $tree = $factory->run("$inputfilename");

But I get the same EXCEPTION: Bio::Root::Exception message.

Thanks,
Ben W.

SCRIPT ---

#!/usr/bin/perl
use warnings;
use strict;
BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
use Bio::TreeIO;
use Bio::AlignIO;
use Bio::Tools::Run::Phylo::Phyml;

my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
-format => 'phylip');

my $aln = $alnin->next_aln();


# Make a Phyml factory.
my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
 -data_type => 'dna');

# Pass the factory an alignment and run:
# my $inputfilename = 'outputalignmentfile';

my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.


# Setup tree output stream...
my $treeio = Bio::TreeIO->new(-format => 'newick',
 -file => 'tree.newick');

$treeio->write_tree($tree);

exit 0;



From bosborne11 at verizon.net  Fri May 24 17:25:38 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Fri, 24 May 2013 17:25:38 -0400
Subject: [Bioperl-l] Building Many trees with Bioperl
In-Reply-To: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>
References: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>
Message-ID: <93D0963E-8399-468C-A32B-875FAA5054D1@verizon.net>

Ben,

What happens when you take the Phyml command itself and run it from the command line?

Also, a minor point: the message "MSG: Replacing one sequence [FXCNDTJ02P/1-366]" is not an error, it is a warning. An error accompanies an exit, warnings are just informative.

Brian O.


On May 24, 2013, at 3:14 PM, Ben Ward (TSL) <Ben.Ward at sainsbury-laboratory.ac.uk> wrote:

> Hi,
> 
> I'm new to Bioperl and plan to make a script to automate making trees with many alignment files (themselves generated by automating the process of multiple alignment for many datasets by using clustalw in a bioperl script).
> But I need to get it right for one pice of test data before I can do it for all:
> 
> What I have produced so far is the below. It's supposed to load in the alignment file as as SimpleAlign. Then use that alignment in phyml. I looked at the documentation and tried to follow examples.
> 
> However it gives me many errors like:
> --------------------- WARNING ---------------------
> MSG: Replacing one sequence [FXCNDTJ02P/1-366]
> 
> And then gives me:
> Phyml command = /Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Phyml call (/Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output [/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip_phyml_stat.txt]: 11
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
> STACK: Bio::Tools::Run::Phylo::Phyml::_run /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
> STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
> -----------------------------------------------------------
> 
> Can someone let me know if I'm going about this correctly and what I need to do to get it to work. I've also tried to run phyml by giving the filename in the run() method like:
> my $inputfilename = 'outputalignmentfile';
> my $tree = $factory->run("$inputfilename");
> 
> But I get the same EXCEPTION: Bio::Root::Exception message.
> 
> Thanks,
> Ben W.
> 
> SCRIPT ---
> 
> #!/usr/bin/perl
> use warnings;
> use strict;
> BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
> use Bio::TreeIO;
> use Bio::AlignIO;
> use Bio::Tools::Run::Phylo::Phyml;
> 
> my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
> -format => 'phylip');
> 
> my $aln = $alnin->next_aln();
> 
> 
> # Make a Phyml factory.
> my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
> -data_type => 'dna');
> 
> # Pass the factory an alignment and run:
> # my $inputfilename = 'outputalignmentfile';
> 
> my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.
> 
> 
> # Setup tree output stream...
> my $treeio = Bio::TreeIO->new(-format => 'newick',
> -file => 'tree.newick');
> 
> $treeio->write_tree($tree);
> 
> exit 0;
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From Ben.Ward at sainsbury-laboratory.ac.uk  Fri May 24 17:46:40 2013
From: Ben.Ward at sainsbury-laboratory.ac.uk (Ben Ward (TSL))
Date: Fri, 24 May 2013 21:46:40 +0000
Subject: [Bioperl-l] Building Many trees with Bioperl
In-Reply-To: <93D0963E-8399-468C-A32B-875FAA5054D1@verizon.net>
Message-ID: <CDC59B58.13A3%ben.ward@sainsbury-laboratory.ac.uk>

Hi,

If I just run phyml on the command line it seems to run ok - it accept's
my file and appears to undergo the tree building process - I haven't
actually see it complete yet, but ML and Bayes always does take a while -
and I have many reads that need to be aligned. But PhyML gets to the point
it asks - are you sure you want to proceed - I say yes, then it keeps
quiet and is currently working along to itself:

. 766 patterns found (out of a total of 795 sites).

. 58 sites without polymorphism (7.30%).

. Computing pairwise distances...

. Building BioNJ tree...

. WARNING: this analysis requires at least 556 MB of memory space.

. Do you really want to proceed? [Y/n] Y


It appears to be working =/
 
Best,
Ben.



On 24/05/2013 22:25, "Brian Osborne" <bosborne11 at verizon.net> wrote:

>Ben,
>
>What happens when you take the Phyml command itself and run it from the
>command line?
>
>Also, a minor point: the message "MSG: Replacing one sequence
>[FXCNDTJ02P/1-366]" is not an error, it is a warning. An error
>accompanies an exit, warnings are just informative.
>
>Brian O.
>
>
>On May 24, 2013, at 3:14 PM, Ben Ward (TSL)
><Ben.Ward at sainsbury-laboratory.ac.uk> wrote:
>
>> Hi,
>> 
>> I'm new to Bioperl and plan to make a script to automate making trees
>>with many alignment files (themselves generated by automating the
>>process of multiple alignment for many datasets by using clustalw in a
>>bioperl script).
>> But I need to get it right for one pice of test data before I can do it
>>for all:
>> 
>> What I have produced so far is the below. It's supposed to load in the
>>alignment file as as SimpleAlign. Then use that alignment in phyml. I
>>looked at the documentation and tried to follow examples.
>> 
>> However it gives me many errors like:
>> --------------------- WARNING ---------------------
>> MSG: Replacing one sequence [FXCNDTJ02P/1-366]
>> 
>> And then gives me:
>> Phyml command = /Users/wardb/clustalw2/phyml
>>/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyli
>>p  0 i 1 0 HKY e e 1 e BIONJ y y
>> 
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Phyml call (/Users/wardb/clustalw2/phyml
>>/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyli
>>p  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output
>>[/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyl
>>ip_phyml_stat.txt]: 11
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
>> STACK: Bio::Tools::Run::Phylo::Phyml::_run
>>/Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
>> STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
>> -----------------------------------------------------------
>> 
>> Can someone let me know if I'm going about this correctly and what I
>>need to do to get it to work. I've also tried to run phyml by giving the
>>filename in the run() method like:
>> my $inputfilename = 'outputalignmentfile';
>> my $tree = $factory->run("$inputfilename");
>> 
>> But I get the same EXCEPTION: Bio::Root::Exception message.
>> 
>> Thanks,
>> Ben W.
>> 
>> SCRIPT ---
>> 
>> #!/usr/bin/perl
>> use warnings;
>> use strict;
>> BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
>> use Bio::TreeIO;
>> use Bio::AlignIO;
>> use Bio::Tools::Run::Phylo::Phyml;
>> 
>> my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
>> -format => 'phylip');
>> 
>> my $aln = $alnin->next_aln();
>> 
>> 
>> # Make a Phyml factory.
>> my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
>> -data_type => 'dna');
>> 
>> # Pass the factory an alignment and run:
>> # my $inputfilename = 'outputalignmentfile';
>> 
>> my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.
>> 
>> 
>> # Setup tree output stream...
>> my $treeio = Bio::TreeIO->new(-format => 'newick',
>> -file => 'tree.newick');
>> 
>> $treeio->write_tree($tree);
>> 
>> exit 0;
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>




From himaghna.bhattacharjee at gmail.com  Tue May 28 11:59:02 2013
From: himaghna.bhattacharjee at gmail.com (Himaghna Bhattacharjee)
Date: Tue, 28 May 2013 21:29:02 +0530
Subject: [Bioperl-l] error in the link to install Kobe repository for windows
Message-ID: <CALd+KH1D8JVFJUNf+L7gM48B-iRsdcYkAZwuNOzi9bkVt7b49Q@mail.gmail.com>

Hey,
the link to install Kobe's repository for per 5.10 <"
http://cpan.uwinnipeg.ca/PPMPackages/10xx/
--">
seems to be broken as it shows Error 503 Service Temporarily Unavailable.
Could you please suggest an alternative ?

Thanks .
Himaghna Bhattacharjee
3rd year
B.E.(Hons.)Chemical Engineering
Birla Institute of Technology and Science,Pilani
Rajasthan 333 031


From wgallin at ualberta.ca  Tue May 28 13:49:02 2013
From: wgallin at ualberta.ca (Warren Gallin)
Date: Tue, 28 May 2013 11:49:02 -0600
Subject: [Bioperl-l] ReplacedBy value in esummary
Message-ID: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>

Hi,

	I just encountered a glitch when I was trying to update some entries in a database by finding updated GENBANK protein entries.

	The original record was gi 118091304 which has been replaced by gi 363734282

	I retrieved an ESummary of the record for gi 118091304 as a Bio::Tools::EUtilities::Summary::DocSum object (called $ds).

	When I then tried to retrieve the gi number for the replacement by using: 

my $replaced = $ds->get_contents_by_name('ReplacedBy');

 the returned value was 1, and when I dumped the ESummary record the relevant pair is ReplacedBy          :XP_421022.3.

The full Esummary dump is:

UID                 :118091304
Caption             :XP_421022
Title               :PREDICTED: similar to Potassium voltage-gated channel, subfamily Q, member
		    :1 [Gallus gallus]
Extra               :gi|118091304|ref|XP_421022.2|[118091304]
Gi                  :118091304
CreateDate          :2004/07/28
UpdateDate          :2006/11/16
Flags               :512
TaxId               :9031
Length              :643
Status              :replaced
ReplacedBy          :XP_421022.3
Comment             : This record was replaced or removed. 


	So two questions:

	1) Is the ReplacedBy value always supposed to be the new accession number version rather than the new gi number?
	2) Why would I be getting a returned value of 1 instead of the accession number that is in the summary record?

Any advice appreciated.

Warren Gallin


From cjfields at illinois.edu  Tue May 28 14:31:30 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 28 May 2013 18:31:30 +0000
Subject: [Bioperl-l] ReplacedBy value in esummary
In-Reply-To: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>
References: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E44377@CHIMBX5.ad.uillinois.edu>

On May 28, 2013, at 12:49 PM, Warren Gallin <wgallin at ualberta.ca> wrote:

> Hi,
> 
> 	I just encountered a glitch when I was trying to update some entries in a database by finding updated GENBANK protein entries.
> 
> 	The original record was gi 118091304 which has been replaced by gi 363734282
> 
> 	I retrieved an ESummary of the record for gi 118091304 as a Bio::Tools::EUtilities::Summary::DocSum object (called $ds).
> 
> 	When I then tried to retrieve the gi number for the replacement by using: 
> 
> my $replaced = $ds->get_contents_by_name('ReplacedBy');
> 
> the returned value was 1, and when I dumped the ESummary record the relevant pair is ReplacedBy          :XP_421022.3.
> 
> The full Esummary dump is:
> 
> UID                 :118091304
> Caption             :XP_421022
> Title               :PREDICTED: similar to Potassium voltage-gated channel, subfamily Q, member
> 		    :1 [Gallus gallus]
> Extra               :gi|118091304|ref|XP_421022.2|[118091304]
> Gi                  :118091304
> CreateDate          :2004/07/28
> UpdateDate          :2006/11/16
> Flags               :512
> TaxId               :9031
> Length              :643
> Status              :replaced
> ReplacedBy          :XP_421022.3
> Comment             : This record was replaced or removed. 
> 
> 
> 	So two questions:
> 
> 	1) Is the ReplacedBy value always supposed to be the new accession number version rather than the new gi number?

No idea, the best people to answer that would be NCBI (the idea of these modules was to simplify getting at that data instead of munging the XML, but whatever they report is mainly from NCBI, not bioperl).

> 	2) Why would I be getting a returned value of 1 instead of the accession number that is in the summary record?

The text dump above indicates the values do exist.  However, you are calling a method that returns a list (note the plural in the name) in scalar context, so you get the number of values.  If you always expect a single value, use:

    my ($replaced) = $ds->get_contents_by_name('ReplacedBy');

which forces array context.  That should fix it.

chris

> Any advice appreciated.
> 
> Warren Gallin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From florent.angly at gmail.com  Thu May  2 02:16:02 2013
From: florent.angly at gmail.com (Florent Angly)
Date: Thu, 02 May 2013 12:16:02 +1000
Subject: [Bioperl-l] Downloading sequences in batch from Trace Archive
In-Reply-To: <CAA7rn9dtgtkdPLU9v=b3Jq0CWPvph59BYp2r5-jJRRt94dB1RA@mail.gmail.com>
References: <CAA7rn9dtgtkdPLU9v=b3Jq0CWPvph59BYp2r5-jJRRt94dB1RA@mail.gmail.com>
Message-ID: <5181CC62.9000609@gmail.com>

Maybe using EUtilities?
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
http://www.bioperl.org/wiki/HOWTO:EUtilities_Web_Service

Florent


On 30/04/13 06:25, shalabh sharma wrote:
> Hi All,
>            Is there any module in Bioperl that can download sequences from
> NCBI's trace archive?
>
> Thanks
> Shalabh
>



From jason.stajich at gmail.com  Thu May  2 05:42:55 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 1 May 2013 22:42:55 -0700
Subject: [Bioperl-l] Fwd: doubt
References: <CACPwBoTqbeNuY6hGW9gpQagL2ZXdknwcM_0Q7QMMCyqEz9FXcg@mail.gmail.com>
Message-ID: <B094273D-B6AB-4DE8-8B65-FFAA3FB30D8A@gmail.com>



Begin forwarded message:

> From: ARYA DAS <aryaanildas at gmail.com>
> Subject: doubt
> Date: May 1, 2013 10:42:21 PM PDT
> To: jason at bioperl.org
> 
> sir,
> 
>     Am using windows7 n was trying to install bio perl in it..i have
> already installed active perl.5.16.3.1603 . n was followeing the
> installation procedure mentioned .when i tried GUI installation .. i cant
> find bioperl package when i try to search them for installation.
> while using command line..
> 
> ppm> install PPM-Repositories
> 
> shows error like cant find package that provides PPM repositories,
> 
> and when i try manually ,on reaching the
> perl Build test
> 
> it says build is recognised as an internal or external file.
> 
> please help if time permits
> 
> regards,
> arya

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



From voldrani at gmail.com  Sun May  5 04:03:38 2013
From: voldrani at gmail.com (Chris Maloney)
Date: Sun, 5 May 2013 00:03:38 -0400
Subject: [Bioperl-l] Wiki work, Template:Doclink
Message-ID: <CABE9g5Ps+NDmziDZNro8UZ5_RMOP1ru1fmKOpFh+DFh=equRfQ@mail.gmail.com>

The module pages on the wiki could look a little better, like this one
for example:  http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast.
 There used to be a bunch of extra whitespace at the top of the page,
which was caused by extra line breaks in Template:Doclink, which I
just removed.

But, I think there are other improvements that could be made.  I would
like to turn this into an infobox -- which are the helpful informative
tables of info on Wikipedia that appear on many articles on the upper
right.  That would allow us to add more links -- like to metacpan, for
example.

It is not completely trivial to import infoboxes into a wiki though, I
just discovered.  I just went through the exercise on my home wiki,
and it involves importing a lot of templates from Wikipedia, and
fixing up the common.css.  You can see the full list of imported
templates here:
http://chrismaloney.org/wiki/index.php?title=Special:RecentChanges&limit=100.
 I don't *think* this should cause any problems, but I'm not 100%
sure.  On the other hand, if it does, it should be easy to roll back
-- it's a wiki, after all.

Does anybody have a problem if I do this?  I'll wait a day for
responses, and tackle this tomorrow, if no one objects.

-- Chris M.


From armendarez77 at hotmail.com  Wed May  8 00:32:22 2013
From: armendarez77 at hotmail.com (Veronica A.)
Date: Tue, 7 May 2013 17:32:22 -0700
Subject: [Bioperl-l] Bio::SeqIO doesn't write all gbk sequences from
	Bio::DB::GenBank
Message-ID: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>

Hello,
I'm currently running Bio::Perl 1.6.1 on Ubuntu 12.04.2 LTS and have noticed a problem with Bio::SeqIO when writing genbank files using the write_seq() function;  some of the files do not include an 'ORIGIN' tag or the sequence.

I am using GI#s (50 at a time every 2 minutes) to retrieve genbank files via Bio::DB::GenBank.

----------------------------------------START CODE----------------------------------
my $gb = Bio::DB::GenBank->new(-verbose=>-1);my $seqout = Bio::SeqIO->new(-file=>">$fileName", '-format'=>'Genbank', -alphabet=>'dna', -flush=>0, -verbose=>-1);while(@ids){     my @batchArray = splice(@ids, 0, 50);     my $batchArrayRef = \@batchArray;
     my $streamObj;     my $pid = fork();     if($pid == 0){          eval{               $streamObj = $gb->get_Stream_by_id($batchArrayRef);          };          if($@){               print "Error: ".$@."\n";          }          else{               while(my $seqObj = $streamObj->next_seq()){                    unless($seqObj->accession_number() =~ /N[A-Z]\_/){                        #print "ID: ".$seqObj->id()."\n";                        #print "Seq:\n".$seqObj->seq()."\n";                         $seqout->write_seq($seqObj);                    }                }          }          exit 0;     }}waitpid($pid,0);sleep(120);
----------------------------------------END CODE----------------------------------
Most of the Genbank files written to the output file have sequences, but there is a small portion that do not, even though they should.  For example, JX287367, in NCBI includes an 'ORIGIN' tag and sequence and when I use the print function before writing to file, the sequence is printed to STDOUT, but the 'ORIGIN' tag and sequence are not written to the output gbk file.  The following is found in the final output file:
----------------------------------START GBK-----------------------------------------
LOCUS       JX287367                 588 bp    DNA     linear   BCT 19-DEC-2012DEFINITION  Chlamydia trachomatis strain UW-5/CX pyruvoyl-dependent arginine            decarboxylase (aaxB) gene, complete cds.ACCESSION   JX287367VERSION     JX287367.1  GI:404351720KEYWORDS    .SOURCE      Chlamydia trachomatis  ORGANISM  Chlamydia trachomatis            Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;            Chlamydia/Chlamydophila group; Chlamydia.REFERENCE   1  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Characterization of the activity and expression of arginine            decarboxylase in human and animal Chlamydia pathogens  JOURNAL   FEMS Microbiol. Lett. 337 (2), 140-146 (2012)   PUBMED   23043454REFERENCE   2  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Direct Submission  JOURNAL   Submitted (06-JUL-2012) Department of Microbiology and Immunology,            F. Edward Hebert School of Medicine, Uniformed Services University            of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD            20814, USAFEATURES             Location/Qualifiers     source          1..588                     /mol_type="genomic DNA"                     /db_xref="taxon:813"                     /strain="UW-5/CX"                     /organism="Chlamydia trachomatis"                     /serovar="E"     gene            1..588                     /gene="aaxB"     CDS             1..588                     /protein_id="AFR60849.1"                     /gene="aaxB"                     /transl_table=11                     /note="AaxB"                     /db_xref="GI:404351721"                     /codon_start=1                     /product="pyruvoyl-dependent arginine decarboxylase"                     /translation="MPYGTRYPTLAFHTGGVGESDDGMPPQPFETFCYDSALLQAKIE                     NFNIVPYTSVLPKELFGNILPVDQCTKFFKHGAVLEVIMAGRGATVTDGTQAIATGVG                     ICWGKDKNGELIGGWAAEYVEFFPTWIDDEIAESHAKMWLKKSLQHELDLRSVSKHSE                     FQYFHNYINIRKKFGFCLTALGFLNFENVAPAVIQ"
//
----------------------------------END GBK-----------------------------------------
Can anyone tell what I am missing or why this is happening?  I don't know if this has happened in earlier BioPerl versions as up until now, I usually downloaded sequences straight from NCBI, but that became too time consuming....but this seems to be as well :S
Thank you in advance for any help,
Veronica
 		 	   		  


From cjfields at illinois.edu  Wed May  8 02:17:43 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 8 May 2013 02:17:43 +0000
Subject: [Bioperl-l] Bio::SeqIO doesn't write all gbk sequences
	from	Bio::DB::GenBank
In-Reply-To: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>
References: <BLU178-W45C90A9489B006C3A43EE2D2BB0@phx.gbl>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E166A0@CHIMBX5.ad.uillinois.edu>

Veronica,

Your mail may have garbled the script and example file.  Can you paste these in a gist?

https://gist.github.com/

chris

On May 7, 2013, at 7:32 PM, Veronica A. <armendarez77 at hotmail.com> wrote:

> Hello,
> I'm currently running Bio::Perl 1.6.1 on Ubuntu 12.04.2 LTS and have noticed a problem with Bio::SeqIO when writing genbank files using the write_seq() function;  some of the files do not include an 'ORIGIN' tag or the sequence.
> 
> I am using GI#s (50 at a time every 2 minutes) to retrieve genbank files via Bio::DB::GenBank.
> 
> ----------------------------------------START CODE----------------------------------
> my $gb = Bio::DB::GenBank->new(-verbose=>-1);my $seqout = Bio::SeqIO->new(-file=>">$fileName", '-format'=>'Genbank', -alphabet=>'dna', -flush=>0, -verbose=>-1);while(@ids){     my @batchArray = splice(@ids, 0, 50);     my $batchArrayRef = \@batchArray;
>     my $streamObj;     my $pid = fork();     if($pid == 0){          eval{               $streamObj = $gb->get_Stream_by_id($batchArrayRef);          };          if($@){               print "Error: ".$@."\n";          }          else{               while(my $seqObj = $streamObj->next_seq()){                    unless($seqObj->accession_number() =~ /N[A-Z]\_/){                        #print "ID: ".$seqObj->id()."\n";                        #print "Seq:\n".$seqObj->seq()."\n";                         $seqout->write_seq($seqObj);                    }                }          }          exit 0;     }}waitpid($pid,0);sleep(120);
> ----------------------------------------END CODE----------------------------------
> Most of the Genbank files written to the output file have sequences, but there is a small portion that do not, even though they should.  For example, JX287367, in NCBI includes an 'ORIGIN' tag and sequence and when I use the print function before writing to file, the sequence is printed to STDOUT, but the 'ORIGIN' tag and sequence are not written to the output gbk file.  The following is found in the final output file:
> ----------------------------------START GBK-----------------------------------------
> LOCUS       JX287367                 588 bp    DNA     linear   BCT 19-DEC-2012DEFINITION  Chlamydia trachomatis strain UW-5/CX pyruvoyl-dependent arginine            decarboxylase (aaxB) gene, complete cds.ACCESSION   JX287367VERSION     JX287367.1  GI:404351720KEYWORDS    .SOURCE      Chlamydia trachomatis  ORGANISM  Chlamydia trachomatis            Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;            Chlamydia/Chlamydophila group; Chlamydia.REFERENCE   1  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Characterization of the activity and expression of arginine            decarboxylase in human and animal Chlamydia pathogens  JOURNAL   FEMS Microbiol. Lett. 337 (2), 140-146 (2012)   PUBMED   23043454REFERENCE   2  (bases 1 to 588)  AUTHORS   Bliven,K.A., Fisher,D.J. and Maurelli,A.T.  TITLE     Direct Submission  JOURNAL   Submitted (06-JUL-2012) Department of Microbiology and Immunology,            F. Edward Hebert School of Med!
> icine, Uniformed Services University            of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD            20814, USAFEATURES             Location/Qualifiers     source          1..588                     /mol_type="genomic DNA"                     /db_xref="taxon:813"                     /strain="UW-5/CX"                     /organism="Chlamydia trachomatis"                     /serovar="E"     gene            1..588                     /gene="aaxB"     CDS             1..588                     /protein_id="AFR60849.1"                     /gene="aaxB"                     /transl_table=11                     /note="AaxB"                     /db_xref="GI:404351721"                     /codon_start=1                     /product="pyruvoyl-dependent arginine decarboxylase"                     /translation="MPYGTRYPTLAFHTGGVGESDDGMPPQPFETFCYDSALLQAKIE                     NFNIVPYTSVLPKELFGNILPVDQCTKFFKHGAVLEVIMAGRGATVTDGTQAIATGVG                     ICWGKDKNGELIGGW!
> AAEYVEFFPTWIDDEIAESHAKMWLKKSLQHELDLRSVSKHSE                     FQYFHN
> YINIRKKFGFCLTALGFLNFENVAPAVIQ"
> //
> ----------------------------------END GBK-----------------------------------------
> Can anyone tell what I am missing or why this is happening?  I don't know if this has happened in earlier BioPerl versions as up until now, I usually downloaded sequences straight from NCBI, but that became too time consuming....but this seems to be as well :S
> Thank you in advance for any help,
> Veronica
> 		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From witch.of.agnessi at gmail.com  Wed May  8 19:24:53 2013
From: witch.of.agnessi at gmail.com (WoA)
Date: Wed, 8 May 2013 12:24:53 -0700 (PDT)
Subject: [Bioperl-l] Extracting matching subsequence from pairwise alignment
Message-ID: <1368041092972-16935.post@n3.nabble.com>

Hello All,

I've a pairwise global alignemnet of two DNA sequences generated by the
program NEEDLE of EMBOSS package. I wish to extract the sub-sequence that
matches/aligns to a given region of the other sequence. In  this alignment
<http://pastebin.com/wrhEDzJU>   (Pastebin Link) the given region (actually
the CDS) falls between base number 24:485 in the original sequence with ID
'XM_001005073.' I wish to extract the sub-sequence in the sequence ID
'Homolog' that aligns with that 24:485 region of the other sequence.

I'm using Bioperl to parse the alignment. I find out the the alignment
column numbers corresponding to 24:485 region in the particular sequence,
using 'column_from_residue_number'. Then I extract the sub-sequence from the
'aligned' other sequence(containing gaps) using the corresponding column
numbers. Finally I remove the gap characters.

Am I doing this thing correctly and are there any pitfalls ? Is there any
better way to do it by (Bio)Perl/Python? The code goes here:
use strict;
use warnings;
use Bio::AlignIO;

# read in an alignment generated by the EMBOSS program Needle
my $in = new Bio::AlignIO(-format => 'emboss',
                  -file   => 'test_needle.aln');

while( my $aln = $in->next_aln ) {
          #Seqnames: 'XM_001005073.'(CDS:24-485),'Homolog'
          my ($cds_start,$cds_end)=(24,485);#
          my $col_cdsstart = $aln->column_from_residue_number(
'XM_001005073.', $cds_start);
          my $col_cdsend= $aln->column_from_residue_number( 'XM_001005073.',
$cds_end);

          foreach my $seq ($aln->each_seq) {
                    if($seq->id() eq 'Homolog'){
                        my
$homolog_cds=$seq->subseq($col_cdsstart,$col_cdsend);
                         $homolog_cds=~s/\-//g;
                        print $homolog_cds,"\n";
                    }

        }
}





--
View this message in context: http://bioperl.996286.n3.nabble.com/Extracting-matching-subsequence-from-pairwise-alignment-tp16935.html
Sent from the Bioperl-L mailing list archive at Nabble.com.


From hlapp at drycafe.net  Wed May 15 20:44:07 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 15 May 2013 16:44:07 -0400
Subject: [Bioperl-l] Workshop on Sustainable Software for Science: Practice
	and Experiences
Message-ID: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>

FYI, if you haven't seen this yet:

http://wssspe.researchcomputing.org.uk/

It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?

Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)

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




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From carandraug+dev at gmail.com  Thu May 16 01:53:55 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Thu, 16 May 2013 02:53:55 +0100
Subject: [Bioperl-l] sets of sequences - how to read?
Message-ID: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>

Hi

when accessing entrez gene using eutils to get multiple genes, NCBI
now returns an Entrezgene-Set[1] rather than a list of EntrezGene.
This change must have happened sometime on the last 2 months. Compare:

use Bio::DB::EUtilities;

my %sets = (
  eutil   => 'efetch',
  db      => 'gene',
  retmode => 'text',
  rettype => 'asn1',
  email   => 'bioperl-l at lists.open-bio.org',
);

## this mimics the previous behaviour of the NCBI server but the
multiple requests will annoy their servers
my @ids = (3014, 85235);
my $response;
foreach (@ids) {
  my $fetcher = Bio::DB::EUtilities->new(%sets, id => $_);
  $response .= $fetcher->get_Response->content;
}
print $fetcher->get_Response->content;

## this used to be the right way to do it, but now returns an Entrezgene-Set
my $fetcher = Bio::DB::EUtilities->new(%sets, id => \@ids);
$response .= $fetcher->get_Response->content;
print $fetcher->get_Response->content;

There is no module to read these Entrezgene-Set in Perl at the moment,
since Bio::ASN1::EntrezGene; is not able to handle them. I have
contacted the module author and set him a fix[2] and he said he'll try
to look into it next week.

However, even with the fix there is another problem. How would one
access a set of sequences using the Bio::SeqIO API? There is no method
to do that. One could say, to ignore them, and make next_seq return
the next sequence of the set. But then we are losing data. After all,
it's perfectly viable to have multiple Entrezgene-Set in one file.
What would be the right way to do this?

Carn?

[1] http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/IEB/ToolBox/CPP_DOC/asn_spec/Entrezgene-Set.html
[2] https://github.com/carandraug/bio-asn1-entrezgene/commit/69d505056d8b7897df6271ffb7a5f39d58873c6b



From cjfields at illinois.edu  Thu May 16 04:43:22 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 04:43:22 +0000
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice	and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>

Jason and I have discussed looking into opportunity's like this, I think it makes sense to try a joint submission.  

chris

On May 15, 2013, at 3:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
> 
> http://wssspe.researchcomputing.org.uk/
> 
> It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?
> 
> Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)
> 
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> _______________________________________________
> 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  Thu May 16 09:10:25 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 May 2013 10:10:25 +0100
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice and Experiences
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>

On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Jason and I have discussed looking into opportunity's like this, I think it makes
> sense to try a joint submission.
>
> chris

This sounds like a good idea, although given the time and place I am
unlikely to be able to attend in person:

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

Rather than trying to discuss this over four mailing lists should we switch
to the cross project list open-bio-l, or continue off-list?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thanks,

Peter


From miquel.ramia at uab.cat  Thu May 16 10:42:29 2013
From: miquel.ramia at uab.cat (=?ISO-8859-1?Q?Miquel_R=E0mia?=)
Date: Thu, 16 May 2013 12:42:29 +0200
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
Message-ID: <5194B815.2010401@uab.cat>

Hi all,

I get this message when compiling Bio::DB::Sam:

Building Bio-SamTools

gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'

collect2: ld returned 1 exit status

make: *** [bam2bedgraph] Error 1


Is this error related to the module or some dependencies? or maybe a 
problem with my system?

Any help appreciated, thanks!


-- 
Miquel R?mia Jes?s
PhD. candidate (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Aut?noma de Barcelona (UAB)
08193, Cerdanyola del Vall?s
Barcelona (Spain)



From cjfields at illinois.edu  Thu May 16 13:12:40 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 13:12:40 +0000
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <5194B815.2010401@uab.cat>
References: <5194B815.2010401@uab.cat>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>

It may be due to the new samtools release (v 0.1.19).  I know Heng Li has been working on the code over the last year for threading support (notice the undefined functions).  Have you tried v 0.1.18?

chris

On May 16, 2013, at 5:42 AM, Miquel R?mia <miquel.ramia at uab.cat> wrote:

> Hi all,
> 
> I get this message when compiling Bio::DB::Sam:
> 
> Building Bio-SamTools
> 
> gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':
> 
> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
> 
> collect2: ld returned 1 exit status
> 
> make: *** [bam2bedgraph] Error 1
> 
> 
> Is this error related to the module or some dependencies? or maybe a problem with my system?
> 
> Any help appreciated, thanks!
> 
> 
> -- 
> Miquel R?mia Jes?s
> PhD. candidate (PIF)
> Evolutionary Bioinformatics Group
> (Genomics, Bioinformatics and Evolution Group)
> Lab MRB/014 - 93 586 89 58
> MRB - Institut de Biologia i Biomedicina (IBB)
> Universitat Aut?noma de Barcelona (UAB)
> 08193, Cerdanyola del Vall?s
> Barcelona (Spain)
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu May 16 13:09:45 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 16 May 2013 13:09:45 +0000
Subject: [Bioperl-l] Workshop on Sustainable Software for Science:
 Practice and Experiences
In-Reply-To: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
	<CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E1FBCF@CHIMBX5.ad.uillinois.edu>

Yes, though we need to make sure others (e.g. those not subscribed to open-bio-l) are in the loop.

November is a possibility for me.

chris

On May 16, 2013, at 4:10 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> Jason and I have discussed looking into opportunity's like this, I think it makes
>> sense to try a joint submission.
>> 
>> chris
> 
> This sounds like a good idea, although given the time and place I am
> unlikely to be able to attend in person:
> 
> First Workshop on Sustainable Software for Science: Practice and
> Experiences (WSSSPE)
> (to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
> http://wssspe.researchcomputing.org.uk/
> 
> Rather than trying to discuss this over four mailing lists should we switch
> to the cross project list open-bio-l, or continue off-list?
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> Thanks,
> 
> Peter




From andreas at sdsc.edu  Thu May 16 04:31:34 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 15 May 2013 21:31:34 -0700
Subject: [Bioperl-l] [Biojava-l] Workshop on Sustainable Software for
 Science: Practice and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <CALthepxHNLm4eHJcCQ4dLnhJr5OhGJJEKTAjH+x7Ppq0oFFnDA@mail.gmail.com>

Thanks Hilmar, you were faster than me in sending this out..

You are right, it would be very interesting to hear what some of the long
running open-bio projects have to say on the topic of sustainability. Let
me know if anybody is interested in a submission!

Andreas




On Wed, May 15, 2013 at 1:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
>
> http://wssspe.researchcomputing.org.uk/
>
> It seems to me that the Bio* projects, perhaps led by BioPerl as the
> oldest and thus longest running (nowadays more fancily called "sustained")
> of them would have a lot to say about the subject. Anyone interested in a
> joint submission?
>
> Also, I notice that Biojava's Andreas is on the organizing committee, so
> maybe he's been conspiring on something already :-)
>
>         -hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From cjfields at illinois.edu  Fri May 17 04:08:04 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 04:08:04 +0000
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>

This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.

My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.

chris

On May 15, 2013, at 8:53 PM, Carn? Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> when accessing entrez gene using eutils to get multiple genes, NCBI
> now returns an Entrezgene-Set[1] rather than a list of EntrezGene.
> This change must have happened sometime on the last 2 months. Compare:
> 
> use Bio::DB::EUtilities;
> 
> my %sets = (
>  eutil   => 'efetch',
>  db      => 'gene',
>  retmode => 'text',
>  rettype => 'asn1',
>  email   => 'bioperl-l at lists.open-bio.org',
> );
> 
> ## this mimics the previous behaviour of the NCBI server but the
> multiple requests will annoy their servers
> my @ids = (3014, 85235);
> my $response;
> foreach (@ids) {
>  my $fetcher = Bio::DB::EUtilities->new(%sets, id => $_);
>  $response .= $fetcher->get_Response->content;
> }
> print $fetcher->get_Response->content;
> 
> ## this used to be the right way to do it, but now returns an Entrezgene-Set
> my $fetcher = Bio::DB::EUtilities->new(%sets, id => \@ids);
> $response .= $fetcher->get_Response->content;
> print $fetcher->get_Response->content;
> 
> There is no module to read these Entrezgene-Set in Perl at the moment,
> since Bio::ASN1::EntrezGene; is not able to handle them. I have
> contacted the module author and set him a fix[2] and he said he'll try
> to look into it next week.
> 
> However, even with the fix there is another problem. How would one
> access a set of sequences using the Bio::SeqIO API? There is no method
> to do that. One could say, to ignore them, and make next_seq return
> the next sequence of the set. But then we are losing data. After all,
> it's perfectly viable to have multiple Entrezgene-Set in one file.
> What would be the right way to do this?
> 
> Carn?
> 
> [1] http://0-www.ncbi.nlm.nih.gov.elis.tmu.edu.tw/IEB/ToolBox/CPP_DOC/asn_spec/Entrezgene-Set.html
> [2] https://github.com/carandraug/bio-asn1-entrezgene/commit/69d505056d8b7897df6271ffb7a5f39d58873c6b
> 
> _______________________________________________
> 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 May 17 04:16:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 04:16:12 +0000
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>
References: <5194B815.2010401@uab.cat>
	<118F034CF4C3EF48A96F86CE585B94BF74E1FC2C@CHIMBX5.ad.uillinois.edu>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>

For the record, this is now fixed in the latest Bio::Samtools (via Lincoln).

chris

On May 16, 2013, at 8:12 AM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> It may be due to the new samtools release (v 0.1.19).  I know Heng Li has been working on the code over the last year for threading support (notice the undefined functions).  Have you tried v 0.1.18?
> 
> chris
> 
> On May 16, 2013, at 5:42 AM, Miquel R?mia <miquel.ramia at uab.cat> wrote:
> 
>> Hi all,
>> 
>> I get this message when compiling Bio::DB::Sam:
>> 
>> Building Bio-SamTools
>> 
>> gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o  -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':
>> 
>> /var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
>> 
>> collect2: ld returned 1 exit status
>> 
>> make: *** [bam2bedgraph] Error 1
>> 
>> 
>> Is this error related to the module or some dependencies? or maybe a problem with my system?
>> 
>> Any help appreciated, thanks!
>> 
>> 
>> -- 
>> Miquel R?mia Jes?s
>> PhD. candidate (PIF)
>> Evolutionary Bioinformatics Group
>> (Genomics, Bioinformatics and Evolution Group)
>> Lab MRB/014 - 93 586 89 58
>> MRB - Institut de Biologia i Biomedicina (IBB)
>> Universitat Aut?noma de Barcelona (UAB)
>> 08193, Cerdanyola del Vall?s
>> Barcelona (Spain)
>> 
>> _______________________________________________
>> 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  Fri May 17 05:12:24 2013
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 17 May 2013 06:12:24 +0100
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>

On 17 May 2013 05:08, Fields, Christopher J <cjfields at illinois.edu> wrote:
> This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.
>
> My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.

:s I'm not sure I understood your suggestion. I think the problem is
just the introduction of a new concept, a "set" of stuff (genes in
this case), and how should SeqIO handle multiple sets.

Carn?



From shalabh.sharma7 at gmail.com  Fri May 17 14:54:55 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 17 May 2013 10:54:55 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
Message-ID: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>

HI,
                 First of all i am really sorry for sending this mail here,
i am not sure if this is the right forum. I know lot of people work on
similar stuff.
I wrote to NCBI but nobody replied.

Actually i am looking for all bacterial/microbial gene annotation
nucleotide fasta files.
Does anyone knows where to download these kind of files.
I tried *ffn files but they are not annotated.
Or is there any module in bioperl that i can use ?
I would really appreciate your help.

Thanks
Shalabh

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


From fossandonc at hotmail.com  Fri May 17 15:59:04 2013
From: fossandonc at hotmail.com (=?iso-8859-1?Q?Francisco_J._Ossand=F3n?=)
Date: Fri, 17 May 2013 11:59:04 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
Message-ID: <SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>

Hi,
You can get the annotations from here:
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/

The ".ffn" are the genes nucleotide fasta files but it does not show the
product name, on the other hand the ".faa" are the genes aminoacid fasta
files and shows the product name, but if you want both product and
nucleotide is much better to use the Genbank ".gbk" files that contains the
complete data and you can parse it easily using BioPerl to obtain all genes,
and then print the /protein_id, /product, and the nucleotide sequences in a
new fasta file. Check these to see how to do it:
http://www.bioperl.org/wiki/HOWTO:SeqIO
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

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 shalabh sharma
Enviado el: viernes, 17 de mayo de 2013 10:55
Para: bioperl-l
Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files

HI,
                 First of all i am really sorry for sending this mail here,
i am not sure if this is the right forum. I know lot of people work on
similar stuff.
I wrote to NCBI but nobody replied.

Actually i am looking for all bacterial/microbial gene annotation nucleotide
fasta files.
Does anyone knows where to download these kind of files.
I tried *ffn files but they are not annotated.
Or is there any module in bioperl that i can use ?
I would really appreciate your help.

Thanks
Shalabh

--
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences University of Georgia Athens, GA 30602-3636
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From shalabh.sharma7 at gmail.com  Fri May 17 16:26:26 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Fri, 17 May 2013 12:26:26 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
Message-ID: <CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>

Hey Francisco,
           Thanks a lot. Basically i just wanted gene nucleotide fasta
files with GI numbers.
I think i will have to parse it from gbk files.

-Shalabh


On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n <
fossandonc at hotmail.com> wrote:

> Hi,
> You can get the annotations from here:
> ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
>
> The ".ffn" are the genes nucleotide fasta files but it does not show the
> product name, on the other hand the ".faa" are the genes aminoacid fasta
> files and shows the product name, but if you want both product and
> nucleotide is much better to use the Genbank ".gbk" files that contains the
> complete data and you can parse it easily using BioPerl to obtain all
> genes,
> and then print the /protein_id, /product, and the nucleotide sequences in a
> new fasta file. Check these to see how to do it:
> http://www.bioperl.org/wiki/HOWTO:SeqIO
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>
> 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 shalabh sharma
> Enviado el: viernes, 17 de mayo de 2013 10:55
> Para: bioperl-l
> Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> HI,
>                  First of all i am really sorry for sending this mail here,
> i am not sure if this is the right forum. I know lot of people work on
> similar stuff.
> I wrote to NCBI but nobody replied.
>
> Actually i am looking for all bacterial/microbial gene annotation
> nucleotide
> fasta files.
> Does anyone knows where to download these kind of files.
> I tried *ffn files but they are not annotated.
> Or is there any module in bioperl that i can use ?
> I would really appreciate your help.
>
> Thanks
> Shalabh
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences University of Georgia Athens, GA 30602-3636
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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



From cjfields at illinois.edu  Fri May 17 17:37:53 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 17 May 2013 17:37:53 +0000
Subject: [Bioperl-l] sets of sequences - how to read?
In-Reply-To: <CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>
References: <CAPOrs_2hRfmuxN57FA5HkciuXxy2j5R6aVgdq97AmJ+tpqYh1Q@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E21252@CHIMBX5.ad.uillinois.edu>
	<CAPOrs_2-un6UQaeMCMU6Zwu_L3Vj03G0zBGSGm54bABhZYQ_AA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E22218@CHIMBX5.ad.uillinois.edu>

On May 17, 2013, at 12:12 AM, Carn? Draug <carandraug+dev at gmail.com>
 wrote:

> On 17 May 2013 05:08, Fields, Christopher J <cjfields at illinois.edu> wrote:
>> This doesn't surprise me too much; I know there have been some changes brewing, but didn't know when they would land.  I guess that would be... <looks at watch>... now.
>> 
>> My feeling is this will require writing some code for a higher-level layer of abstraction, say a Bio::DB::* (which would allow some internal indexing of the files maybe using a Bio::Index::*, look ups for specific gene IDs, etc).  How hard that would be to implement is another thing, have no idea w/o seeing what the data look like beyond they are in ASN1.
> 
> :s I'm not sure I understood your suggestion. I think the problem is
> just the introduction of a new concept, a "set" of stuff (genes in
> this case), and how should SeqIO handle multiple sets.
> 
> Carn?


(note: critical point in this is Bio::ASN1::Entrezgene would allow this, I'm not sure it would.  Otherwise this is all really hand-wavy)

To me a 'set of stuff', particularly when the 'stuff' is stored sequentially in a flat file, is a simple 'database' or 'store' of similar items, where the class allows one the ability to look up particular members in the set, but also could store higher level information about the set as a whole if needed.  If it were me, I would implement a method particular to Bio::SeqIO::entrezgene that specifically creates and returns this ( next_geneset(), for instance ); next_seq() could then be implemented to iterate through the items in that database/store.  

Two useful things come out of this.  First, if the data for the Entrez Gene file/chunk are parsed to store offsets per ID, one would only need to parse out the chunks needed (offset of ID to next offset), then pass that into the parser and create objects on the fly.  This would probably be as fast or faster than (for instance) the greedy method of parsing the entire file and storing everything in objects up-front, then iterating through those objects one at a time, which I think is current behavior.

Second: if an index is created, the upfront cost is already paid (you could reuse the same index when parsing the same data).

An analogous example might be storing all FASTQ data in a sequencing run; I don't want to expend the effort to parse all the FASTQ data, but I may want to run operations on individual items in the set as well as store additional information about the data (barcodes per run, lanes, overall quality stats, etc).  

Does that make sense?  The pieces for this are lying around (Bio::Index::* for instance has methods for indexing flat files, and classes like Bio::DB::Fasta).

chris


From shalabh.sharma7 at gmail.com  Sun May 19 19:33:16 2013
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Sun, 19 May 2013 15:33:16 -0400
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
	<CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
	<18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>
Message-ID: <CAA7rn9ehQ1t1AizSLC15PFFh4mV8njfaTSY2ZVDqtzb2bEGBaA@mail.gmail.com>

Thanks Russell,
                            Actually i wanted all the Bacterial gene
nucleotide files, so i parsed it from *gbk. But yes these files might help
me for my other parts of my work.

Thanks
Shalabh


On Sun, May 19, 2013 at 3:26 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:

> Another option that I've used before is to download the gene2accession,
> gene2refseq,  and gene_info files from here
> ftp://ftp.ncbi.nih.gov/gene/DATA/ then parse out the data you require.
> It might work for you?
>
> --Russell
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:
> bioperl-l-bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> Sent: Saturday, 18 May 2013 4:26 a.m.
> To: Francisco J. Ossand?n
> Cc: bioperl-l
> Subject: Re: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> Hey Francisco,
>            Thanks a lot. Basically i just wanted gene nucleotide fasta
> files with GI numbers.
> I think i will have to parse it from gbk files.
>
> -Shalabh
>
>
> On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n <
> fossandonc at hotmail.com> wrote:
>
> > Hi,
> > You can get the annotations from here:
> > ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
> >
> > The ".ffn" are the genes nucleotide fasta files but it does not show
> > the product name, on the other hand the ".faa" are the genes aminoacid
> > fasta files and shows the product name, but if you want both product
> > and nucleotide is much better to use the Genbank ".gbk" files that
> > contains the complete data and you can parse it easily using BioPerl
> > to obtain all genes, and then print the /protein_id, /product, and the
> > nucleotide sequences in a new fasta file. Check these to see how to do
> > it:
> > http://www.bioperl.org/wiki/HOWTO:SeqIO
> > http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> >
> > 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 shalabh
> > sharma Enviado el: viernes, 17 de mayo de 2013 10:55
> > Para: bioperl-l
> > Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
> >
> > HI,
> >                  First of all i am really sorry for sending this mail
> > here, i am not sure if this is the right forum. I know lot of people
> > work on similar stuff.
> > I wrote to NCBI but nobody replied.
> >
> > Actually i am looking for all bacterial/microbial gene annotation
> > nucleotide fasta files.
> > Does anyone knows where to download these kind of files.
> > I tried *ffn files but they are not annotated.
> > Or is there any module in bioperl that i can use ?
> > I would really appreciate your help.
> >
> > Thanks
> > Shalabh
> >
> > --
> > Shalabh Sharma
> > Scientific Computing Professional Associate (Bioinformatics
> > Specialist) Department of Marine Sciences University of Georgia
> > Athens, GA 30602-3636 _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences University of Georgia Athens, GA 30602-3636
>
> _______________________________________________
> 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.
> =======================================================================
>



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



From Russell.Smithies at agresearch.co.nz  Sun May 19 19:26:35 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 20 May 2013 07:26:35 +1200
Subject: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
In-Reply-To: <CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
References: <CAA7rn9cap32H_G6kHG=9NCh=5Mc74GfXUY_LTOovtSBDyH3TLA@mail.gmail.com>
	<SNT133-ds17315AB2B8EA2C33569EEFCFAC0@phx.gbl>
	<CAA7rn9dazBaK8U8W_JJaQiHq8t-QfX44N0Dyv4jMYm0KZHMTTg@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF37365BCAEC2@exchsth.agresearch.co.nz>

Another option that I've used before is to download the gene2accession, gene2refseq,  and gene_info files from here ftp://ftp.ncbi.nih.gov/gene/DATA/ then parse out the data you require.
It might work for you?

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of shalabh sharma
Sent: Saturday, 18 May 2013 4:26 a.m.
To: Francisco J. Ossand?n
Cc: bioperl-l
Subject: Re: [Bioperl-l] Downloading annotated Gene nucleotide fasta files

Hey Francisco,
           Thanks a lot. Basically i just wanted gene nucleotide fasta files with GI numbers.
I think i will have to parse it from gbk files.

-Shalabh


On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossand?n < fossandonc at hotmail.com> wrote:

> Hi,
> You can get the annotations from here:
> ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
>
> The ".ffn" are the genes nucleotide fasta files but it does not show 
> the product name, on the other hand the ".faa" are the genes aminoacid 
> fasta files and shows the product name, but if you want both product 
> and nucleotide is much better to use the Genbank ".gbk" files that 
> contains the complete data and you can parse it easily using BioPerl 
> to obtain all genes, and then print the /protein_id, /product, and the 
> nucleotide sequences in a new fasta file. Check these to see how to do 
> it:
> http://www.bioperl.org/wiki/HOWTO:SeqIO
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>
> 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 shalabh 
> sharma Enviado el: viernes, 17 de mayo de 2013 10:55
> Para: bioperl-l
> Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files
>
> HI,
>                  First of all i am really sorry for sending this mail 
> here, i am not sure if this is the right forum. I know lot of people 
> work on similar stuff.
> I wrote to NCBI but nobody replied.
>
> Actually i am looking for all bacterial/microbial gene annotation 
> nucleotide fasta files.
> Does anyone knows where to download these kind of files.
> I tried *ffn files but they are not annotated.
> Or is there any module in bioperl that i can use ?
> I would really appreciate your help.
>
> Thanks
> Shalabh
>
> --
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics 
> Specialist) Department of Marine Sciences University of Georgia 
> Athens, GA 30602-3636 _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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

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

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From miquel.ramia at uab.cat  Tue May 21 15:08:18 2013
From: miquel.ramia at uab.cat (=?ISO-8859-1?Q?Miquel_R=E0mia?=)
Date: Tue, 21 May 2013 17:08:18 +0200
Subject: [Bioperl-l] Problem compiling Bio::DB::Sam
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>
References: <5194B815.2010401@uab.cat>
	<"118F034CF4C3EF48A96F86CE585B94BF74E1F C2C"@CHIMBX5.ad.uillinois.edu>
	<118F034CF4C3EF48A96F86CE585B94BF74E212B0@CHIMBX5.ad.uillinois.edu>
Message-ID: <519B8DE2.2070308@uab.cat>

On 17/05/13 06:16, Fields, Christopher J wrote:
> For the record, this is now fixed in the latest Bio::Samtools (via Lincoln).
>
> chris
>
>

Compiled correctly!

thank you



-- 
Miquel R?mia Jes?s
PhD. candidate (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Aut?noma de Barcelona (UAB)
08193, Cerdanyola del Vall?s
Barcelona (Spain)



From b.l.cohen_home at btinternet.com  Mon May 20 18:49:50 2013
From: b.l.cohen_home at btinternet.com (Bernard Cohen)
Date: Mon, 20 May 2013 19:49:50 +0100 (BST)
Subject: [Bioperl-l] Phylip format error
Message-ID: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>

Hello!

I happen to have checked to see what the PERL webpage says about Phylip format for DNA alignment files and see that it is erroneous.?

I am not a PERL user and do not want to be bothered to register or otherwise learn how to make an official comment, so forward this for someone to pick up.

Phylip format allows up to 10 spaces for taxon names; the data must start in the 11th space. This can be checked on Jo Felsenstein's site.

The PERL page accessed by searching for "Phylip format PERL" allows only 8 spaces for the name.?

B. L. Cohen


From senanu.pearson at gmail.com  Wed May 22 20:15:24 2013
From: senanu.pearson at gmail.com (Senanu)
Date: Wed, 22 May 2013 13:15:24 -0700
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from alignment
Message-ID: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>

Hi all,

I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 

I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 

Is this a known problem? Is there another way to generate such a consensus?


my $in = Bio::AlignIO->new(-file => $files[0],
                           -format => 'XMFA');
while  (my $aln = $in->next_aln()) {
    foreach  my $seq ($aln->each_seq) {
        $seq->alphabet('dna');
    }
    my $con = $aln->consensus_iupac();
}


Thanks in advance.
Ngwenyama


From cjfields at illinois.edu  Wed May 22 23:17:50 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 22 May 2013 23:17:50 +0000
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from
 alignment
In-Reply-To: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
References: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E2A01D@CHIMBX5.ad.uillinois.edu>

On May 22, 2013, at 3:15 PM, Senanu <senanu.pearson at gmail.com> wrote:

> Hi all,
> 
> I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 

Probably the former, but...

> I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 

It shouldn't take that long, 7 Mb isn't that large.  Or is that 7 Mb for one genome?

> Is this a known problem? Is there another way to generate such a consensus?

The code isn't really optimized for this, but again this isn't terribly large.  Is the bottleneck reading the alignment in, or is it the consensus_iupac() step?  Hard to say w/o seeing the alignment data itself.

> my $in = Bio::AlignIO->new(-file => $files[0],
>                           -format => 'XMFA');
> while  (my $aln = $in->next_aln()) {
>    foreach  my $seq ($aln->each_seq) {
>        $seq->alphabet('dna');
>    }
>    my $con = $aln->consensus_iupac();
> }
> 
> 
> Thanks in advance.
> Ngwenyama
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

chris


From alexeymorozov1991 at gmail.com  Thu May 23 07:22:13 2013
From: alexeymorozov1991 at gmail.com (Alexey Morozov)
Date: Thu, 23 May 2013 16:22:13 +0900
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
Message-ID: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>

Which is also worsened by the fact that there is relaxed phylip format,
which allows up to 250 chars for taxon name. They are separated from a
sequence by single space, which creates problems if names were extended to
10 chars in strict Felsenstein's format by whitespaces. On the whole,
phylip is as messily defined format as one can make from a plain textfile
with information content of fasta.
Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
phylip and how does it tell dialects from one another. Even if code support
is OK, it may be worthwile to explain it somewhere at bioperl.org


2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>

> Hello!
>
> I happen to have checked to see what the PERL webpage says about Phylip
> format for DNA alignment files and see that it is erroneous.
>
> I am not a PERL user and do not want to be bothered to register or
> otherwise learn how to make an official comment, so forward this for
> someone to pick up.
>
> Phylip format allows up to 10 spaces for taxon names; the data must start
> in the 11th space. This can be checked on Jo Felsenstein's site.
>
> The PERL page accessed by searching for "Phylip format PERL" allows only 8
> spaces for the name.
>
> B. L. Cohen
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.


From p.j.a.cock at googlemail.com  Thu May 23 08:30:21 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 May 2013 09:30:21 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>

On Thu, May 23, 2013 at 8:22 AM, Alexey Morozov
<alexeymorozov1991 at gmail.com> wrote:
> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org

Biopython's AlignIO defines both a (strict) "phylip" and "relaxed-phylip"
as two separate formats (or variants, like the "fastq" variants). Doing
the same in BioPerl would seem sensible since auto-detection is not
easy.

http://biopython.org/wiki/AlignIO#File_Formats

Peter

P.S. Where does that 250 characters for the taxon name limit come from?
The trouble with relaxed phylip is that some tools are more relaxed than
others ;)


From awitney at sgul.ac.uk  Thu May 23 08:43:15 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 23 May 2013 09:43:15 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <519DD6A3.8090304@sgul.ac.uk>


Not sure if there is an actual question in these messages, but BioPerl
can be used to generate valid Phylip format and run, like this:

## Build Align object
my $aln = Bio::SimpleAlign->new(-seqs=>$seqs);

## swap the taxa names with 8 characters long unique IDs
my ($aln_safe, $ref_name) = $aln->set_displayname_safe(8);

## Write out phylip format infile
Bio::AlignIO->new(-file=>'>infile.out', -format=>'phylip', -interleaved
=> 0)->write_aln($aln);

## run PHYLIP's pars program
my @params = (idlength=>10);   #, jumble=>"17,10");
my $tree_factory = Bio::Tools::Run::Phylo::Phylip::Pars->new(@params);
$tree_factory->quiet(1);  # Suppress pars messages to terminal
my $tree = $tree_factory->create_tree($aln_safe);

## fix the node labels back
my @nodes = sort { defined $a->id && defined $b->id && $a->id cmp $b->id
} $tree->get_nodes();
foreach my $nd (@nodes) {
	if ( $nd->is_Leaf ) {
		$nd->id($ref_name->{$nd->id_output})
	}
}

HTH

Adam

On 23/05/2013 08:22, Alexey Morozov wrote:
> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> 
> 2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>
> 
>> Hello!
>>
>> I happen to have checked to see what the PERL webpage says about Phylip
>> format for DNA alignment files and see that it is erroneous.
>>
>> I am not a PERL user and do not want to be bothered to register or
>> otherwise learn how to make an official comment, so forward this for
>> someone to pick up.
>>
>> Phylip format allows up to 10 spaces for taxon names; the data must start
>> in the 11th space. This can be checked on Jo Felsenstein's site.
>>
>> The PERL page accessed by searching for "Phylip format PERL" allows only 8
>> spaces for the name.
>>
>> B. L. Cohen
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> 
> 
> 


From cjfields at illinois.edu  Thu May 23 13:48:31 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 13:48:31 +0000
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E323A4@CITESMBX5.ad.uillinois.edu>

Alexey,

Just want to point out that 'relaxed phylip' format was introduced long after this parser was created; in fact (as Adam points out) there was an alternative workaround to deal with the lossy names.  

The content of that page is on a wiki, which anyone is free to edit (just need an OpenID to set up an account).

chris

On May 23, 2013, at 2:22 AM, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:

> Which is also worsened by the fact that there is relaxed phylip format,
> which allows up to 250 chars for taxon name. They are separated from a
> sequence by single space, which creates problems if names were extended to
> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
> phylip is as messily defined format as one can make from a plain textfile
> with information content of fasta.
> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
> phylip and how does it tell dialects from one another. Even if code support
> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> 
> 2013/5/21 Bernard Cohen <b.l.cohen_home at btinternet.com>
> 
>> Hello!
>> 
>> I happen to have checked to see what the PERL webpage says about Phylip
>> format for DNA alignment files and see that it is erroneous.
>> 
>> I am not a PERL user and do not want to be bothered to register or
>> otherwise learn how to make an official comment, so forward this for
>> someone to pick up.
>> 
>> Phylip format allows up to 10 spaces for taxon names; the data must start
>> in the 11th space. This can be checked on Jo Felsenstein's site.
>> 
>> The PERL page accessed by searching for "Phylip format PERL" allows only 8
>> spaces for the name.
>> 
>> B. L. Cohen
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Thu May 23 14:05:32 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 14:05:32 +0000
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
	<CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>

On May 23, 2013, at 3:30 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, May 23, 2013 at 8:22 AM, Alexey Morozov
> <alexeymorozov1991 at gmail.com> wrote:
>> Which is also worsened by the fact that there is relaxed phylip format,
>> which allows up to 250 chars for taxon name. They are separated from a
>> sequence by single space, which creates problems if names were extended to
>> 10 chars in strict Felsenstein's format by whitespaces. On the whole,
>> phylip is as messily defined format as one can make from a plain textfile
>> with information content of fasta.
>> Bioperl documentation says nothing about whether Bio::SeqIO accepts relaxed
>> phylip and how does it tell dialects from one another. Even if code support
>> is OK, it may be worthwile to explain it somewhere at bioperl.org
> 
> Biopython's AlignIO defines both a (strict) "phylip" and "relaxed-phylip"
> as two separate formats (or variants, like the "fastq" variants). Doing
> the same in BioPerl would seem sensible since auto-detection is not
> easy.
> 
> http://biopython.org/wiki/AlignIO#File_Formats
> 
> Peter
> 
> P.S. Where does that 250 characters for the taxon name limit come from?
> The trouble with relaxed phylip is that some tools are more relaxed than
> others ;)

As Adam pointed out, prior to the introduction of 'relaxed phylip' we had an alternative solution that didn't require a modified format but still allowed one to use PHYLIP and other tools requesting the format.  I think 'relaxed phylip' was introduced by CIPRES a few years back.  Frankly, this is the first time I have seen this mentioned on the list; yay, yet another format variation :)

The variant format parsing (as implemented for SeqIO::fastq, as you know) deals with variant names like 'fastq-sanger', where the main format name is first, the variant of the format second.  The order in this case is reversed (relaxed-phylip), which I'm pretty sure will not work.  Not impossible to allow, but we would probably allow support like this initially:

my $in = Bio::AlignIO->new(-format => 'phylip',
                           -variant => 'relaxed',
                             ?);

chris


From cjfields at illinois.edu  Thu May 23 13:56:32 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 23 May 2013 13:56:32 +0000
Subject: [Bioperl-l] Speed issues with making IUPAC consensus from
 alignment
In-Reply-To: <92CD2F9D-7C8E-4941-9354-4BD80D8C2CB6@gmail.com>
References: <1DE07C6C-0DEA-43EB-8F1A-BACB8534400F@gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E2A01D@CHIMBX5.ad.uillinois.edu>
	<92CD2F9D-7C8E-4941-9354-4BD80D8C2CB6@gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E32489@CITESMBX5.ad.uillinois.edu>

(keep the list cc'd)

On May 22, 2013, at 6:31 PM, Senanu <senanu.junk at gmail.com> wrote:

> On May 22, 2013, at 4:17 PM, Fields, Christopher J wrote:
> 
>> Hi all,
>>> 
>>> I am wondering if the consensus_iupac method of Bio::Align is known to be extremely slow, or if I'm doing something wrong. 
>> 
>> Probably the former, but...
>> 
>>> I have bacterial whole-genome alignments (~7 Mbases) that I made in progressiveMauve and wish to get an IUPAC consensus. (I know that progressiveMauve uses a non-standard XMFA format, but Bio::AlignIO seems to read them just fine.) The code below takes more than all night to make a consensus. It works fine on tiny test alignments. 
>> 
>> It shouldn't take that long, 7 Mb isn't that large.  Or is that 7 Mb for one genome?
> 
> It is 7Mb per genome, but there are only 2 genomes in the alignment, and the sequences are very similar to one another. 
> 
>> 
>>> Is this a known problem? Is there another way to generate such a consensus?
>> 
>> The code isn't really optimized for this, but again this isn't terribly large.  Is the bottleneck reading the alignment in, or is it the consensus_iupac() step?  Hard to say w/o seeing the alignment data itself.
> 
> The bottleneck is definitely with the consensus_iupac step. Reading the alignment in takes a few seconds. 

That's interesting, but again not surprising.  One would have to look at the code, but I wouldn't be surprised if the method is terribly inefficient.

chris


From p.j.a.cock at googlemail.com  Thu May 23 14:53:09 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 May 2013 15:53:09 +0100
Subject: [Bioperl-l] Phylip format error
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>
References: <1369075790.65165.YahooMailNeo@web87404.mail.ir2.yahoo.com>
	<CAK=7cMMtmvGJx4UJG=LyQaULcq74KuHqWZ3gbTJ4BeqFkA4Vag@mail.gmail.com>
	<CAKVJ-_5ftAVfTfSH5DRvoQovyfkZ0-Oa+CNJjgdG6EM6eFZetA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF74E32551@CITESMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_66x-c+Frmb0LVjYEB39OgxS6mabLKPBzEv38BoiOFMWg@mail.gmail.com>

On Thu, May 23, 2013 at 3:05 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
>
> I think 'relaxed phylip' was introduced by CIPRES a few years back.
> Frankly, this is the first time I have seen this mentioned on the list; yay,
> yet another format variation :)

The relaxed phylip 'format' goes back further than that, e.g.
http://lists.open-bio.org/pipermail/biopython-dev/2008-June/003899.html

RAxML and PHYML support relaxed phylip - but with their own ID limits.

Peter


From Ben.Ward at sainsbury-laboratory.ac.uk  Fri May 24 19:14:17 2013
From: Ben.Ward at sainsbury-laboratory.ac.uk (Ben Ward (TSL))
Date: Fri, 24 May 2013 19:14:17 +0000
Subject: [Bioperl-l] Building Many trees with Bioperl
Message-ID: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>

Hi,

I'm new to Bioperl and plan to make a script to automate making trees with many alignment files (themselves generated by automating the process of multiple alignment for many datasets by using clustalw in a bioperl script).
But I need to get it right for one pice of test data before I can do it for all:

What I have produced so far is the below. It's supposed to load in the alignment file as as SimpleAlign. Then use that alignment in phyml. I looked at the documentation and tried to follow examples.

However it gives me many errors like:
--------------------- WARNING ---------------------
MSG: Replacing one sequence [FXCNDTJ02P/1-366]

And then gives me:
Phyml command = /Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Phyml call (/Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output [/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip_phyml_stat.txt]: 11
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::Phylo::Phyml::_run /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
-----------------------------------------------------------

Can someone let me know if I'm going about this correctly and what I need to do to get it to work. I've also tried to run phyml by giving the filename in the run() method like:
my $inputfilename = 'outputalignmentfile';
my $tree = $factory->run("$inputfilename");

But I get the same EXCEPTION: Bio::Root::Exception message.

Thanks,
Ben W.

SCRIPT ---

#!/usr/bin/perl
use warnings;
use strict;
BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
use Bio::TreeIO;
use Bio::AlignIO;
use Bio::Tools::Run::Phylo::Phyml;

my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
-format => 'phylip');

my $aln = $alnin->next_aln();


# Make a Phyml factory.
my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
 -data_type => 'dna');

# Pass the factory an alignment and run:
# my $inputfilename = 'outputalignmentfile';

my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.


# Setup tree output stream...
my $treeio = Bio::TreeIO->new(-format => 'newick',
 -file => 'tree.newick');

$treeio->write_tree($tree);

exit 0;



From bosborne11 at verizon.net  Fri May 24 21:25:38 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Fri, 24 May 2013 17:25:38 -0400
Subject: [Bioperl-l] Building Many trees with Bioperl
In-Reply-To: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>
References: <CDC57A99.137A%ben.ward@sainsbury-laboratory.ac.uk>
Message-ID: <93D0963E-8399-468C-A32B-875FAA5054D1@verizon.net>

Ben,

What happens when you take the Phyml command itself and run it from the command line?

Also, a minor point: the message "MSG: Replacing one sequence [FXCNDTJ02P/1-366]" is not an error, it is a warning. An error accompanies an exit, warnings are just informative.

Brian O.


On May 24, 2013, at 3:14 PM, Ben Ward (TSL) <Ben.Ward at sainsbury-laboratory.ac.uk> wrote:

> Hi,
> 
> I'm new to Bioperl and plan to make a script to automate making trees with many alignment files (themselves generated by automating the process of multiple alignment for many datasets by using clustalw in a bioperl script).
> But I need to get it right for one pice of test data before I can do it for all:
> 
> What I have produced so far is the below. It's supposed to load in the alignment file as as SimpleAlign. Then use that alignment in phyml. I looked at the documentation and tried to follow examples.
> 
> However it gives me many errors like:
> --------------------- WARNING ---------------------
> MSG: Replacing one sequence [FXCNDTJ02P/1-366]
> 
> And then gives me:
> Phyml command = /Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Phyml call (/Users/wardb/clustalw2/phyml /var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output [/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phylip_phyml_stat.txt]: 11
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
> STACK: Bio::Tools::Run::Phylo::Phyml::_run /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
> STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
> -----------------------------------------------------------
> 
> Can someone let me know if I'm going about this correctly and what I need to do to get it to work. I've also tried to run phyml by giving the filename in the run() method like:
> my $inputfilename = 'outputalignmentfile';
> my $tree = $factory->run("$inputfilename");
> 
> But I get the same EXCEPTION: Bio::Root::Exception message.
> 
> Thanks,
> Ben W.
> 
> SCRIPT ---
> 
> #!/usr/bin/perl
> use warnings;
> use strict;
> BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
> use Bio::TreeIO;
> use Bio::AlignIO;
> use Bio::Tools::Run::Phylo::Phyml;
> 
> my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
> -format => 'phylip');
> 
> my $aln = $alnin->next_aln();
> 
> 
> # Make a Phyml factory.
> my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
> -data_type => 'dna');
> 
> # Pass the factory an alignment and run:
> # my $inputfilename = 'outputalignmentfile';
> 
> my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.
> 
> 
> # Setup tree output stream...
> my $treeio = Bio::TreeIO->new(-format => 'newick',
> -file => 'tree.newick');
> 
> $treeio->write_tree($tree);
> 
> exit 0;
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From Ben.Ward at sainsbury-laboratory.ac.uk  Fri May 24 21:46:40 2013
From: Ben.Ward at sainsbury-laboratory.ac.uk (Ben Ward (TSL))
Date: Fri, 24 May 2013 21:46:40 +0000
Subject: [Bioperl-l] Building Many trees with Bioperl
In-Reply-To: <93D0963E-8399-468C-A32B-875FAA5054D1@verizon.net>
Message-ID: <CDC59B58.13A3%ben.ward@sainsbury-laboratory.ac.uk>

Hi,

If I just run phyml on the command line it seems to run ok - it accept's
my file and appears to undergo the tree building process - I haven't
actually see it complete yet, but ML and Bayes always does take a while -
and I have many reads that need to be aligned. But PhyML gets to the point
it asks - are you sure you want to proceed - I say yes, then it keeps
quiet and is currently working along to itself:

. 766 patterns found (out of a total of 795 sites).

. 58 sites without polymorphism (7.30%).

. Computing pairwise distances...

. Building BioNJ tree...

. WARNING: this analysis requires at least 556 MB of memory space.

. Do you really want to proceed? [Y/n] Y


It appears to be working =/
 
Best,
Ben.



On 24/05/2013 22:25, "Brian Osborne" <bosborne11 at verizon.net> wrote:

>Ben,
>
>What happens when you take the Phyml command itself and run it from the
>command line?
>
>Also, a minor point: the message "MSG: Replacing one sequence
>[FXCNDTJ02P/1-366]" is not an error, it is a warning. An error
>accompanies an exit, warnings are just informative.
>
>Brian O.
>
>
>On May 24, 2013, at 3:14 PM, Ben Ward (TSL)
><Ben.Ward at sainsbury-laboratory.ac.uk> wrote:
>
>> Hi,
>> 
>> I'm new to Bioperl and plan to make a script to automate making trees
>>with many alignment files (themselves generated by automating the
>>process of multiple alignment for many datasets by using clustalw in a
>>bioperl script).
>> But I need to get it right for one pice of test data before I can do it
>>for all:
>> 
>> What I have produced so far is the below. It's supposed to load in the
>>alignment file as as SimpleAlign. Then use that alignment in phyml. I
>>looked at the documentation and tried to follow examples.
>> 
>> However it gives me many errors like:
>> --------------------- WARNING ---------------------
>> MSG: Replacing one sequence [FXCNDTJ02P/1-366]
>> 
>> And then gives me:
>> Phyml command = /Users/wardb/clustalw2/phyml
>>/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyli
>>p  0 i 1 0 HKY e e 1 e BIONJ y y
>> 
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Phyml call (/Users/wardb/clustalw2/phyml
>>/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyli
>>p  0 i 1 0 HKY e e 1 e BIONJ y y) did not give an output
>>[/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T/MTFzfN4jED/aln8058.phyl
>>ip_phyml_stat.txt]: 11
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
>> STACK: Bio::Tools::Run::Phylo::Phyml::_run
>>/Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:851
>> STACK: /Library/Perl/5.12/Bio/Tools/Run/Phylo/Phyml.pm:338
>> -----------------------------------------------------------
>> 
>> Can someone let me know if I'm going about this correctly and what I
>>need to do to get it to work. I've also tried to run phyml by giving the
>>filename in the run() method like:
>> my $inputfilename = 'outputalignmentfile';
>> my $tree = $factory->run("$inputfilename");
>> 
>> But I get the same EXCEPTION: Bio::Root::Exception message.
>> 
>> Thanks,
>> Ben W.
>> 
>> SCRIPT ---
>> 
>> #!/usr/bin/perl
>> use warnings;
>> use strict;
>> BEGIN { $ENV{PHYMLDIR} = '/Users/wardb/clustalw2' }
>> use Bio::TreeIO;
>> use Bio::AlignIO;
>> use Bio::Tools::Run::Phylo::Phyml;
>> 
>> my $alnin = Bio::AlignIO->new(-file => "<outputalignmentfile",
>> -format => 'phylip');
>> 
>> my $aln = $alnin->next_aln();
>> 
>> 
>> # Make a Phyml factory.
>> my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2,
>> -data_type => 'dna');
>> 
>> # Pass the factory an alignment and run:
>> # my $inputfilename = 'outputalignmentfile';
>> 
>> my $tree = $factory->run($aln); # $tree is a Bio::Tree::Tree object.
>> 
>> 
>> # Setup tree output stream...
>> my $treeio = Bio::TreeIO->new(-format => 'newick',
>> -file => 'tree.newick');
>> 
>> $treeio->write_tree($tree);
>> 
>> exit 0;
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>




From himaghna.bhattacharjee at gmail.com  Tue May 28 15:59:02 2013
From: himaghna.bhattacharjee at gmail.com (Himaghna Bhattacharjee)
Date: Tue, 28 May 2013 21:29:02 +0530
Subject: [Bioperl-l] error in the link to install Kobe repository for windows
Message-ID: <CALd+KH1D8JVFJUNf+L7gM48B-iRsdcYkAZwuNOzi9bkVt7b49Q@mail.gmail.com>

Hey,
the link to install Kobe's repository for per 5.10 <"
http://cpan.uwinnipeg.ca/PPMPackages/10xx/
--">
seems to be broken as it shows Error 503 Service Temporarily Unavailable.
Could you please suggest an alternative ?

Thanks .
Himaghna Bhattacharjee
3rd year
B.E.(Hons.)Chemical Engineering
Birla Institute of Technology and Science,Pilani
Rajasthan 333 031


From wgallin at ualberta.ca  Tue May 28 17:49:02 2013
From: wgallin at ualberta.ca (Warren Gallin)
Date: Tue, 28 May 2013 11:49:02 -0600
Subject: [Bioperl-l] ReplacedBy value in esummary
Message-ID: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>

Hi,

	I just encountered a glitch when I was trying to update some entries in a database by finding updated GENBANK protein entries.

	The original record was gi 118091304 which has been replaced by gi 363734282

	I retrieved an ESummary of the record for gi 118091304 as a Bio::Tools::EUtilities::Summary::DocSum object (called $ds).

	When I then tried to retrieve the gi number for the replacement by using: 

my $replaced = $ds->get_contents_by_name('ReplacedBy');

 the returned value was 1, and when I dumped the ESummary record the relevant pair is ReplacedBy          :XP_421022.3.

The full Esummary dump is:

UID                 :118091304
Caption             :XP_421022
Title               :PREDICTED: similar to Potassium voltage-gated channel, subfamily Q, member
		    :1 [Gallus gallus]
Extra               :gi|118091304|ref|XP_421022.2|[118091304]
Gi                  :118091304
CreateDate          :2004/07/28
UpdateDate          :2006/11/16
Flags               :512
TaxId               :9031
Length              :643
Status              :replaced
ReplacedBy          :XP_421022.3
Comment             : This record was replaced or removed. 


	So two questions:

	1) Is the ReplacedBy value always supposed to be the new accession number version rather than the new gi number?
	2) Why would I be getting a returned value of 1 instead of the accession number that is in the summary record?

Any advice appreciated.

Warren Gallin


From cjfields at illinois.edu  Tue May 28 18:31:30 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 28 May 2013 18:31:30 +0000
Subject: [Bioperl-l] ReplacedBy value in esummary
In-Reply-To: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>
References: <81794641-2693-4476-B2FA-6B742190D141@ualberta.ca>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF74E44377@CHIMBX5.ad.uillinois.edu>

On May 28, 2013, at 12:49 PM, Warren Gallin <wgallin at ualberta.ca> wrote:

> Hi,
> 
> 	I just encountered a glitch when I was trying to update some entries in a database by finding updated GENBANK protein entries.
> 
> 	The original record was gi 118091304 which has been replaced by gi 363734282
> 
> 	I retrieved an ESummary of the record for gi 118091304 as a Bio::Tools::EUtilities::Summary::DocSum object (called $ds).
> 
> 	When I then tried to retrieve the gi number for the replacement by using: 
> 
> my $replaced = $ds->get_contents_by_name('ReplacedBy');
> 
> the returned value was 1, and when I dumped the ESummary record the relevant pair is ReplacedBy          :XP_421022.3.
> 
> The full Esummary dump is:
> 
> UID                 :118091304
> Caption             :XP_421022
> Title               :PREDICTED: similar to Potassium voltage-gated channel, subfamily Q, member
> 		    :1 [Gallus gallus]
> Extra               :gi|118091304|ref|XP_421022.2|[118091304]
> Gi                  :118091304
> CreateDate          :2004/07/28
> UpdateDate          :2006/11/16
> Flags               :512
> TaxId               :9031
> Length              :643
> Status              :replaced
> ReplacedBy          :XP_421022.3
> Comment             : This record was replaced or removed. 
> 
> 
> 	So two questions:
> 
> 	1) Is the ReplacedBy value always supposed to be the new accession number version rather than the new gi number?

No idea, the best people to answer that would be NCBI (the idea of these modules was to simplify getting at that data instead of munging the XML, but whatever they report is mainly from NCBI, not bioperl).

> 	2) Why would I be getting a returned value of 1 instead of the accession number that is in the summary record?

The text dump above indicates the values do exist.  However, you are calling a method that returns a list (note the plural in the name) in scalar context, so you get the number of values.  If you always expect a single value, use:

    my ($replaced) = $ds->get_contents_by_name('ReplacedBy');

which forces array context.  That should fix it.

chris

> Any advice appreciated.
> 
> Warren Gallin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l