Fields, Christopher J | 19 Dec 19:17 2013

Re: BioPerl release 1.6.923

Glad to hear!  We may have another point release out sometime in the next few days to deal with errors we’re
seeing related to I/O, but if this is working for you then you aren’t affected.

chris

On Dec 19, 2013, at 11:24 AM, Govind Chandra <govind.chandra <at> jic.ac.uk> wrote:

> 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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>> 
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Gmane