Fields, Christopher J | 5 Oct 16:33 2013

Re: can't get seq with bioperl

On Oct 5, 2013, at 4:50 AM, Peter Cock <p.j.a.cock <at> googlemail.com> wrote:

> On Wed, Sep 25, 2013 at 11:07 PM, Danyu Wu <danyuwu <at> hotmail.com> wrote:
>> 
>> Hello,
>> 
>> I can not get the seq from a genbank format entry using
>> bioperl when both CONTIG and ORIGIN are present.  Any
>> help is greatly appreciated!
>> 
> 
> See point [2] in this NCBI RefSeq announcement:
> http://www.ncbi.nlm.nih.gov/mailman/pipermail/refseq-announce/2013q3/000110.html
> 
> Scott Markel raised this potential issue in July,
> 
> http://lists.open-bio.org/pipermail/bioperl-l/2013-July/037427.html
> http://lists.open-bio.org/pipermail/bioperl-l/2013-July/037428.html
> 
> I'd fixed this in Biopython but it sounds like BioPerl may
> still need updating.
> 
> Regards,
> 
> Peter

It was never submitted as a bug, now corrected.  I'll try to follow up on it this weekend.

chris

Gmane