[Biopython-dev] Ortholog module (InParanoid and RoundUp)

[Andrew Gallant]

Hello,

I am a graduate student, and for a course project, I wrote an Ortholog
module for Biopython. It currently provides two orthology database wrappers
(InParanoid and RoundUp) along with a class hierarchy to contain the data.

It completely implements InParanoid's "gene search," and RoundUp's "browse"
(gene search) and "retrieve" (clustering) functions, with some rudimentary
error detection. RoundUp's clustering makes finding all orthologs between a
set of species very easy.

I haven't contributed to Biopython before, but assuming this module is
desirable, how might I start that process? I have the changes in a forked
git repository (which is updated with upstream changes) here [1]. I followed
the style guide and included doc strings for all functions/modules/classes.
However, I have *not* written any unit tests yet, but certainly will.

Please let me know if I've missed anything!

Thanks!
- Andrew Gallant

[1] - https://github.com/BurntSushi/biopython/tree/me