Does Anyone Know About A Biopython Package For Use With The Chado Db Schema?

Question

[Nicojo]

I am interested in using the Chado schema, which is actively developed and community supported, but it uses a BioPerl interface. I would rather use BioPython. Does anyone know of an active dev project or completed package for this?

Answer 1

[Raony Guimarães]

I believe the way to go would be by extending this tutorial:

http://gmod.org/wiki/Chado_Django_HOWTO

And looking at some code in Github:

https://github.com/search?q=chado+python

[Nicojo]

Thanks! I didn't pay much attention to the ChadoDjangoHOWTO because I don't know much about Django, and I thought it would only be useful for a webapp front for a DB. But I think I check now to see how it can be useful for my purposes... The Github link, as well as searches in Sourceforge and Google codes, tells me that there isn't much done for Chado and Python. Will have to work on it myself I guess.

Answer 2

[Peter]

I'm not aware of anyone looking at a CHADO interface for Biopython, but it would be a good idea. Are you interested in working on this?

See also: http://lists.open-bio.org/pipermail/biopython-dev/2011-April/008789.html - Jose might have some Python code that could be useful (and he sounded receptive to re-licensing which would be required to include it in Biopython)

[Nicojo]

Thanks for the link! And to answer your question, yes, I am interested in working on this. The only problem is that I am a beginner at programming (mostly did wet lab before), and I'm working with Python 3.x, which might be another limitation. In any case, I'll look into Jose's project, and eventually contact him...

Answer 3

[Neto]

There's machado https://github.com/lmb-embrapa/machado if you're still interested...