[BioPython] GFF parser, other than Bio.GFF

[Giovanni Marco Dall'Olio]

Hi!
I'm currently working with some gene annotations in GFF format[1], and
I've noticed there is not any GFF parser in the current biopython
distribution. Am I wrong?

I've found the Bio.GFF module, but it doesn't actually do what I want
to do (read [2]), as it gets informations from a MySQL database (?),
while I'm searching for a module to parse a gff file and transform it
to dictionary, maybe like SeqIO.

Well, I wrote a few scripts to parse my GFF files.. I thought I can
contribute with some code if somebody can help me in refining and
adapting them (there is still a lot of work to do).

So why there is still not any gff parser in biopython? Is this format
too outdated, or maybe nobody is using it? Or maybe I'm missing it? Or
there is some other problem?

Thanks!
Giovanni




[1] http://www.sanger.ac.uk/Software/formats/GFF/ (gff),
http://mblab.wustl.edu/GTF22.html (gtf 2.2)
[2] http://portal.open-bio.org/pipermail/biopython/2004-May/002099.html

-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://dalloliogm.wordpress.com