[Bioperl-l] [BioSQL-l] How is is_circular recorded in BioSQL (by BioPerl)?

Chris Fields cjfields at illinois.edu
Mon Jul 25 16:33:01 UTC 2011

On Jul 25, 2011, at 11:29 AM, Peter Cock wrote:

> On Mon, Jul 25, 2011 at 5:25 PM, Roy Chaudhuri <roy.chaudhuri at gmail.com> wrote:
>>>> Actually, when round-tripping a GenBank file through BioSQL, the LOCUS
>>>> line molecule type ends up in lower case, which makes me wonder if it is
>>>> coming from alphabet in the biosequence table.
>>> If so, that may break for viral GenBank files where the LOCUS line may say
>>> RNA, but the sequence is given using acgt (i.e. the DNA alphabet).
>> Just tried it and that does seem to be the case. It's not the only thing
>> that breaks on round tripping, for example circular genomes become linear.
> Sounds like one or two bug reports are needed,
> http://redmine.open-bio.org/projects/bioperl
> We already have one open on Biopython for this:
> https://redmine.open-bio.org/issues/2578
> Peter

If these reports have examples we can work on a fix.


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