[Biopython] SQL Alchemy based BioSQL

[Peter]

On Thu, Aug 20, 2009 at 9:57 PM, Kyle Ellrott<kellrott at gmail.com> wrote:
>
>> Sounds interesting - but can you explain your motivation?
>
> The primary motivation is Jython compatibility (which is the main
> purpose of the branch).  MySQLdb depends on some C extensions which
> make it hard to port to Jython.  I don't keep track of IronPython, but
> I would imagine it would be a similar situation on the .Net platform.
> Beta SQLAlchemy 0.6 ( available on the SVN right now, but soon to be
> released ) supports the MySQL Connector/Java interface, so it works
> with Jython.  Using this combination was the only way I could get a
> Jython BioPython to connect to a database.

Ah. That ties in with the other changes on your github tree (to
work nicely with Jython) which had seemed unrelated to me.

I guess MySQLdb etc uses C code which means it won't
work under Jython. I don't know enough about Jython to say
if there are any other alternatives to using SQLAlchemy.

> As a technical note, now that this works, it means that you can
> use BioPython and BioJava in the same memory space.  I
> used BioPython's SQL code to get the data, and the passed
> it to BioJava's Smith-Waterman alignment code to calculate
> alignments, all in one script.

This might be a silly question, but why not just use BioJava to
talk to BioSQL instead? Or use Biopython's pairwise alignment
code. Was the point just to demonstrate things working together?

Peter