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

[Fields, Christopher J]

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