[Biopython] SQL Alchemy based BioSQL

[Kyle Ellrott]

> 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.

If you aren't using a layer of abstraction like SQLAlchemy, they you
can use the standard Java SQL interfaces (JDBC).  But code written for
that would only work within Jython and be useless for CPython.


> 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?

To prove that it could be done was part of the point.  But there is
also a 'cross training' aditude about it.  BioPython seems more
lightweight/easier to use, but has heavier requirements on installing
external applications. BioJava can be harder to use, but it has lots
more embedded functionality ( built in dynamic programming and HMM
code ).  If I can get both working in the same environment, then I get
the best of both worlds.


Kyle