[Biopython-dev] GTF (T not F)

[Tiago Antão]

Hi,

I've been noticing that there has been some work with GFF files around here.
I've done a parser for GTF files ( http://mblab.wustl.edu/GTF22.html )
and I was wondering if someone would find interest in it?
My knowledge of use cases of GTF/GFF is quite limited. I've done this
to support reading Ensembl data in the context of supporting my work
with HapMap datasets (The related project is this:
http://popgen.eu/soft/interPop/ ) , but I really do not know the "big
picture" of use cases.

Anyway, I would be willing to donate the code if there is interest.
Also adapt it to support more general use cases
The code is available here
http://bazaar.launchpad.net/~tiagoantao/interpopula/trunk/annotate/head%3A/src/interPopula/Ensembl/GTF.py
But as you will notice it is wrapped in lots of SQL stuff (which would
have to be removed/adapted).

I could remove my SQL fluff and just produce a simple parser if
somebody would tell me how should the design be done to support more
general use cases.
The format is not very complex, anyway.


Tiago


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