[Bioperl-l] Genbank files with CONTIG lines in them.

[Govind Chandra]

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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