[BioSQL-l] SQLite support

[Peter]

On Mon, Dec 15, 2008 at 11:43 AM, Peter<biopython at maubp.freeserve.co.uk> wrote:
> On Mon, Dec 15, 2008, vanaquisl vanaquisl wrote:
>>
>> Hi folks,
>>
>> I am a brand new BioSQL user and I'd like to know if there will be a SQLite
>> support in the near future?
>
> As far as I know, BioSQL does not currently include a schema for SQLite.

This was one of the things Brad Chapman and I discussed with Hilmar Lapp
last week at BOSC/ISMB 2009. I've just filed BioSQL enhancement Bug 2870
on this: http://bugzilla.open-bio.org/show_bug.cgi?id=2870

>> I am about to use SQLite for a standalone lightweight Biopython application
>> and it would be very helpful if I could use BioSQL directly.
>
> Biopython can talk to a BioSQL database run on MySQL (using MySQLdb),
> PostgreSQL (using either Psycopg or Psycopg2).  In theory it could be
> extended to use any supported BioSQL database (provided there are
> python bindings for the database software, in the case of SQLite using
> pysqlite would probably fine).

We have a proof of principle implementation of the Biopython BioSQL
bindings working with BioSQL on SQLite, see enhancement Bug 2866:
http://bugzilla.open-bio.org/show_bug.cgi?id=2866

Peter