def scores(self, id1, id2):
"""Returns the score between two given GO terms.
:arg id1, identifier of a GO term (ie: GO:0043231, or whatever
identifier is in your ontology).
:arg id2, identifier of a GO term (ie: GO:0043229, or whatever
identifier is in your ontology).
"""
golib = PyGoLib(self.goterms)
goterm1 = self.goterms[id1]
path1 = golib.get_path(goterm1, pred=goterm1['id'], paths=[])
goterm2 = self.goterms[id2]
path2 = golib.get_path(goterm2, pred=goterm2['id'], paths=[])
# We use goterm['id'] instead of the id provided to take into
# account alt_id which are in the list of goterms but not in the
# paths. Via goterm['id'] we get the 'normal' GO term identifier.
scores = self.__score_parents(goterm1['id'], goterm2['id'], path1,
path2)
if scores:
score = min(scores)
self.log.debug("%s and %s are parents" % (id1, id2))
return (score, score)
else:
score = self.__score_cousins(goterm1['id'], goterm2['id'], path1,
path2)
return score
