I skyped with Prishanti and have her scripts for computing functional similarity working
on my system. I am currently working on puling annotations on a gene by gene basis from
phenoscape. I have been working with Jim on this but there is a lot to learn and a lot
of pieces that need to work together. He gave me some sample code that shows general
phenoscape access and I am creating my own script to tailor his sample to my needs.
I have posted some of the major scripts that I have used on another authorea document.
They include ways to fetch paralogs and orthologs from Ensembl, a script to get all
of the genes of an organism and a way to convert ensembl gene id's to MGI ZFIN ID's.
The codes that I have posted tend to be specific to one organism. I do have a version
for the the other organism when pertinent but I felt authorea would get too cluttered
with mostly redundant code. It would be rather easy to create a version for each
that allows the user to decide the input organisms, though even in the current form
it is very easy to alter the organism.