def process_ontology(self, obo_file):
obo_dag = GODag(obo_file)
obo_dag.populate_terms()
diseases = self.diseases
ontology_map = {}
self.category_map = defaultdict(list)
for item_id, item in obo_dag.items():
# Considers those diseases whose names are subsets of the disease ontology names
correlated_diseases = [
disease for disease in diseases if disease in item.name
]
if len(correlated_diseases) > 0:
d = {}
for parent in (obo_dag.paths_to_top(item.id)[0]):
d[parent.level] = parent.name
for corr_disease in correlated_diseases:
self.category_map[parent.name] += [corr_disease]
for corr_disease in correlated_diseases:
# Chooses the most specific disease mapping
if corr_disease in ontology_map:
if len(ontology_map[corr_disease]) > len(d):
continue
ontology_map[corr_disease] = d
self.dag = obo_dag
self.disease_class_map = ontology_map
def test_paths_to_top():
dag = GODag(ROOT + "mini_obo.obo")
expected_paths = [['GO:0000001', 'GO:0000002', 'GO:0000005', 'GO:0000010'],
['GO:0000001', 'GO:0000003', 'GO:0000005', 'GO:0000010'],
['GO:0000001', 'GO:0000003', 'GO:0000006', 'GO:0000008', 'GO:0000010']]
actual_paths = dag.paths_to_top("GO:0000010")
chk_results(actual_paths, expected_paths)
print_paths(actual_paths)
def test_paths_to_top():
#dag = GODag("./tests/data/mini_obo.obo")
dag = GODag("./data/mini_obo.obo")
expected_paths = [
['GO:0000001', 'GO:0000002', 'GO:0000005', 'GO:0000010'],
['GO:0000001', 'GO:0000003', 'GO:0000005', 'GO:0000010'],
['GO:0000001', 'GO:0000003', 'GO:0000006', 'GO:0000008', 'GO:0000010'] ]
actual_paths = dag.paths_to_top("GO:0000010")
chk_results(actual_paths, expected_paths)
prt_paths(actual_paths)
def test_paths_to_top():
#dag = GODag("./tests/data/mini_obo.obo")
dag = GODag("./data/mini_obo.obo")
expected_paths = [['GO:0000001', 'GO:0000002', 'GO:0000005', 'GO:0000010'],
['GO:0000001', 'GO:0000003', 'GO:0000005', 'GO:0000010'],
[
'GO:0000001', 'GO:0000003', 'GO:0000006',
'GO:0000008', 'GO:0000010'
]]
actual_paths = dag.paths_to_top("GO:0000010")
chk_results(actual_paths, expected_paths)
prt_paths(actual_paths)
