Peter Cock | 17 Dec 14:32 2013

Re: Genbank files with CONTIG lines in them.

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

Gmane