Govind Chandra | 19 Dec 18:24 2013
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Re: BioPerl release 1.6.923

Thanks Chris and others for release 1.6.923.

The issue with Genbank files having CONTIG lines in them seems
sorted. Output of the test script is pasted below.

Best wishes

Govind

### Output begins ###

withContigLine.gbk

Bioperl reports length as 19314.
Length of the sequence string is 19314.

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

withoutContigLine.gbk

Bioperl reports length as 19314.
Length of the sequence string is 19314.

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

Perl version is: 5.018000
Bioperl version is: 1.006923
Bioperl version again: 49.46.48.48.54.57.50.51

### Output ends ###

Govind Chandra
Molecular Microbiology
John Innes Centre
Norwich
UK.

On Wed, Dec 18, 2013 at 12:00:04PM -0500, bioperl-l-request <at> lists.open-bio.org wrote:
> 
> Message: 1
> Date: Wed, 18 Dec 2013 10:26:19 +0000
> From: Govind Chandra <govind.chandra <at> jic.ac.uk>
> Subject: Re: [Bioperl-l] Genbank files with CONTIG lines in them.
> To: <bioperl-l <at> lists.open-bio.org>
> Message-ID: <20131218102619.GA10116 <at> n61347.nbi.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
> 
> Thanks Chris and Peter.
> 
> Best wishes
> 
> Govind
> 
> On Tue, Dec 17, 2013 at 12:00:03PM -0500, bioperl-l-request <at> lists.open-bio.org wrote:
> > Message: 3
> > Date: Tue, 17 Dec 2013 13:46:29 +0000
> > From: "Fields, Christopher J" <cjfields <at> illinois.edu>
> > Subject: Re: [Bioperl-l] Genbank files with CONTIG lines in them.
> > To: Peter Cock <p.j.a.cock <at> googlemail.com>
> > Cc: Govind Chandra <govind.chandra <at> jic.ac.uk>,	BioPerl List
> > 	<bioperl-l <at> lists.open-bio.org>
> > Message-ID: <7BCB02AA-454A-4DC6-BE13-6DA56BC01BEF <at> illinois.edu>
> > Content-Type: text/plain; charset="Windows-1252"
> > 
> > On Dec 17, 2013, at 7:32 AM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote:
> > 
> > > On Tue, Dec 17, 2013 at 11:52 AM, Govind Chandra
> > > <govind.chandra <at> jic.ac.uk> wrote:
> > >> Hi Chris,
> > >> 
> > >> As you suggested, I upgraded to Bioperl version 1.6.922 but the
> > >> problem remains. Below is the output of my test script again.
> > >> 
> > >> withContigLine.gbk
> > >> 
> > >> Bioperl reports length as 19314.
> > >> Length of the sequence string is .
> > >> 
> > >> =========================================
> > >> 
> > >> withoutContigLine.gbk
> > >> 
> > >> Bioperl reports length as 19314.
> > >> Length of the sequence string is 19314.
> > >> 
> > >> =========================================
> > >> 
> > >> Perl version is: 5.018000
> > >> Bioperl version is: 1.006922
> > >> Bioperl version again: 49.46.48.48.54.57.50.50
> > >> 
> > >> Thanks
> > >> 
> > >> Govind
> > > 
> > > This sounds like the issue raised in July and again in October,
> > > where Chris thought it had been fixed:
> > > http://lists.open-bio.org/pipermail/bioperl-l/2013-October/071235.html
> > > 
> > > See also point [2] in this NCBI RefSeq announcement:
> > > http://www.ncbi.nlm.nih.gov/mailman/pipermail/refseq-announce/2013q3/000110.html
> > > 
> > > Peter
> > 
> > Yep, it should be addressed:
> > 
> > https://github.com/bioperl/bioperl-live/commit/dd2cd5f1c46fa97bff21524a3e1c6a14f57d2b02
> > 
> > Looks like it didn?t make the last release.  I?ll have a look at trying to get a 1.6 point release out to fix it.
> > 
> > chris
> > 
> > 
> > 
> > 
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Gmane