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

[Roy Chaudhuri]

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