[Biopython] Gene ontology parsing

[Bartek Wilczynski]

hi Timothy,

I, for one, would be interested in Gene Ontology parsing. I could also help
with reviewing the code if you worry about whether it fits to the rest of
biopython.

I think the easiest for all would be if you could make a branch of biopython
on github including your proposed enhancements. This would allow everybody
to see what's in there and also make changes and finally mergi it into the
trunk.

thanks for your offer

Bartek
On Fri, Jul 23, 2010 at 9:04 AM, Timothy Wu <2huggie at gmail.com> wrote:

> Hi
>
> Is there a parser in BioPython for OBO v1.2?
>
> If there isn't (at least I couldn't find it a while back), maybe I could
> contribute a little. I've casually wrote an OntologyIO package with
> "OboRecord", a scanner and consumer files. I may have not handles all the
> stuff written on http://www.geneontology.org/GO.format.obo-1_2.shtml, but
> it
> did suit my own purpose before. I don't know if anyone in the project will
> be interested in it. I also do not know if my code will pass the quality
> standard set forth by BioPython. I've also wrote a GoGraph structure that
> allow me to look for stuff in the DAG, treating it much like a tree,
> looking
> for "common ancestor" given two nodes, parent, child, etc. I've never
> contributed code to any project before, so if these code can indeed be
> contributed, perhaps some help from someone in the project would be needed,
> thanks.
>
> Timothy
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>


-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
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