[Biopython] SQL Alchemy based BioSQL

[Peter]

On Wed, Aug 26, 2009 at 10:38 PM, Kyle Ellrott<kellrott at gmail.com> wrote:
>> Is this idea just a shortcut for explicitly loading the GenBank
>> file into a BioSQL database (which hopefully will include an
>> SQLite backend option soon), and then iterating over its
>> records? e.g.
>
> Yes, it would also have a copy of the biodb-sqlite schema stored as a
> string in the module, so it could build an in-RAM database on demand.
> Make the setup and loading automatic.  It would appear to be just like
> a regular file parser.

I would agree that once we have SQLite support in BioSQL officially,
we can probably ship the schema within Biopython and make using
it much more straightforward than the other BioSQL backends (which
require the database software and schema to be installed manually).
However, I would put the SQLite database on disk, not in RAM.

> That way, if we start writing crazy feature
> filters methods based on SQL queries, they can be easily reapplied to
> file based usage.  And we wouldn't have to write a feature filter for
> the database objects and another for file based objects.

If we are just talking about filtering the feature list (see thread
http://lists.open-bio.org/pipermail/biopython-dev/2009-August/006700.html
) then we don't need BioSQL - it seems like overkill.

Peter