[Bioperl-l] BioPerl release 1.6.923

[Govind Chandra]

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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