doneEnsembl.append(ensemblID)
if isAmigo:
eGOs = amiGO.get(hugoID, [])
else:
eGOs = uniGO.get(ensemblID, [])
for termID in eGOs:
myGOs.setdefault(termID, []).append(ensemblID)
try:
myLevels.extend(list(levels[termID].keys()))
except KeyError:
#print >>sys.stderr, termID
continue
GOs[termID] = GOs.get(termID, 0) + 1
if not args.naive:
if termID not in GOadjusted:
GOadjusted[termID] = GO.getLevelIds(termID,
args.level, levels)
#print myLevels[-1], termID, GOadjusted[termID]
for adjustedID in GOadjusted[termID]:
myAdjusted[adjustedID] = myAdjusted.get(adjustedID, 0) + 1
myGOs.setdefault(adjustedID, []).append(ensemblID)
GOsCnt = []
myAdjustedCnt = []
for id, cnt in list(GOs.items()):
GOsCnt.append(id + "/" + str(cnt))
if not args.naive:
for id, cnt in list(myAdjusted.items()):
myAdjustedCnt.append(id)
myLevels = [str(x) for x in myLevels]
if not args.naive:
print("\t".join([str(chro), str(startPos), " ".join(GOsCnt),
" ".join(myLevels), " ".join(myAdjustedCnt)]))
import MEGA
from MEGA import GO
import pickle
import bz2
onts = {}
isa = {}
levels = {}
namespaces = {}
for rec in GO.parse(bz2.open(MEGA.GOFile, 'rt', encoding='utf-8')):
id = rec["id"][0]
onts[id] = rec
namespaces.setdefault(rec["namespace"][0], []).append(id)
if "is_a" in rec:
for ref in rec["is_a"]:
isa.setdefault(id, []).append(ref[0])
else:
levels[id] = {0: set()}
cisa = dict(isa)
while len(cisa) > 0:
dels = []
for id, owners in list(cisa.items()):
levels.setdefault(id, {})
for owner in owners:
if owner not in cisa:
ownerLevels = list(levels[owner].keys())
for level in ownerLevels:
levels[id].setdefault(level + 1, set()).add(owner)
cisa[id].remove(owner)
if len(cisa[id]) == 0: