def __init__(self, inputFileName, namespace='molecular_function'):
"""Constructor, reads and parses the ontology OBO file."""
debug("Reading ontology file %s... " % inputFileName)
self.root = None
self.namespace = namespace
ontology = defaultdict(lambda: defaultdict(list))
self.inputFileName = Path(inputFileName)
with self.inputFileName.open() as go:
terms = groupby(go.read().splitlines(), lambda x: x != '')
for b, term in terms:
term = list(term)
if not b or term[0] != '[Term]': continue
nonlists = ('id', 'def', 'name', 'namespace', 'is_obsolete')
# Do some deciphering here...
term = defaultdict(
list,
[(a, [y[1]
for y in b][0 if a in nonlists else slice(None)])
for a, b in groupby([x.split(': ', 1)
for x in term[1:]], lambda x: x[0])])
# Filter terms by namespace, discard obsolete terms
if term['namespace'] != namespace or term[
'is_obsolete'] == 'true':
continue
# Decide root node
if term['name'] == namespace:
assert self.root is None
self.root = term['id']
# Save the term to ontology
ontology[term['id']]['name'] = term['name'].replace(
'_', ' ') # FIXME KDYBY BLBLO, ODEBRAT replace
for ref in term['is_a']:
refid, refname = ref.split(' ! ')
ontology[refid]['children'].append(term['id'])
ontology[term['id']]['parents'].append(refid)
# This is used by Bayes nets
ontology[term['id']]['node'] = defaultdict(
dict) # fold : clfName : node
ontology[term['id']]['clf'] = defaultdict(
dict) # fold : clfName : Classifier
self.ontology = {**ontology}
self.associations = None
self.geneFactory = GeneFactory()
debug("Initialized ontology for file %s... " % inputFileName)
