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

[Peter Cock]

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