Saturday, December 4, 2010

Gene Ontology: showing the graph 2

A brief final update on the GO project. I modified to remember both the child and parent in moving up the tree: handle_request(D,target,debug=False) returns a list of pairs which are of the form

('GO:0006139', 'GO:0034641').

Having the GO data in memory, it's easy to find the corresponding names.

Now what we need is some graphing code that can obtain the name from the go_id and make the plot. Without worrying about it too much yet, I found some old code that works, and used that. I remember that it was hard to parse everything to make the labels, so I wasn't eager to revisit the logic behind it yet. Here is the graph for a transcription factor, I think it was GAL4 but I've lost track. Zipped project files here. Hope this helps someone.