[Biopython] SQL Alchemy based BioSQL
Kyle Ellrott
kellrott at gmail.com
Thu Aug 20 21:59:08 UTC 2009
> 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
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