I want to figure out how to use Python to get all genes associated with a GO Term. I was trying to Biomart Python API but it's really weird and Retrieve All Genes Associated With A Go Term is for R. I'm trying to use mygene but there's no GO for the scopes (the input term) only in the fields (output terms) Gene Id Conversion Tool I need to do it for ~6000 GO pathways. I got it to work using bioservices db2db but I get timed out. Set a pause for 5 seconds between each search and I'm still getting the timeout. (http://pythonhosted.org/bioservices/references.html#module-bioservices.biodbnet if anyone wants to know how to use this...really useful)
Does anyone know a tool in Python I can use to do this that won't time me out?