[Bioperl-l] Writing and retrieving Genbank files from BioSQL

[Fields, Christopher J]

I do think Roy is correct in saying this could be set as annotation.  In my opinion I would like Seq-pertinent information (alphabet, circular, mol type) at the level of the sequence.  At least, to me that makes more sense, as it describes information directly relevant about the sequence itself, whereas to me annotation are more about the sequence record (pubs, taxonomy, etc).  But I’m probably splitting hairs.

BTW I agree re: SQLite support in bioperl-db.  However, bioperl-db uses a home-grown ORM, so this would entail creating a SQLite-specific DB loader.  The intent has been to move bioperl-db over to a consistent ORM (DBIx::Class) that would easily allow this, but that GSoC project didn’t have takers :P

chris

On Apr 23, 2014, at 11:58 AM, Roy Chaudhuri <roy.chaudhuri at gmail.com> wrote:

> Hi Peter,
> 
> Just found your message on the Google group.
> 
> I think the correct way to deal with this would be to modify the BioSQL schema to include columns for is_circular and molecule type in the bioentry table.
> 
> However, if the BioSQL schema is considered immutable, a workaround would be for BioPerl, BioPython etc. to agree on a standard way of storing the information in the existing BioSQL schema.
> 
> I'd suggest we do this with two annotation tags:
> "is_circular", with a value of BioPerl $seq->is_circular (1 or NULL)
> "molecule", with a value of BioPerl $seq->molecule (DNA, RNA etc.)
> 
> Once a sequence is removed from the database, these annotation tags could be removed and put in the correct place in the BioPerl/BioPython object model.
> 
> Cheers,
> Roy.
> 
> > Thank you for chasing this issue Rik :)
> >
> > From the Biopython point of view, all I really need to know
> > is where the linear/circular and molecule type information
> > from the GenBank LOCUS line end up in the BioSQL tables
> > (to make Biopython put it in the same place).
> >
> > https://redmine.open-bio.org/issues/2578
> >
> > Sadly I don't currently have a working BioSQL + BioPerl test
> > setup (it would be great if BioPerl could add SQLite support -
> > which would make it easy to do cross project testing).
> >
> > Thanks,
> >
> > Peter
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l