calculate_information_content.py

import subprocess
from goatools.semantic import get_info_content
from goatools.base import get_godag
from goatools.semantic import TermCounts
from goatools.anno.factory import get_objanno


godag = get_godag("go-basic.obo")
return_code = subprocess.call("wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/goa_human.gpa.gz && gunzip goa_human.gpa.gz", shell=True)
anno = get_objanno('goa_human.gpa', 'gpad', godag=godag)
cnt = TermCounts(godag, anno.get_id2gos_nss())
tinf = {t: get_info_content(t, cnt) for t in godag.keys()}