def _make_activity_graph(self):
self.activity_graph = networkx.DiGraph()
for a1, a2 in itertools.combinations(self.activity_types, 2):
if bio_ontology.isa('INDRA_ACTIVITIES', a1, 'INDRA_ACTIVITIES',
a2):
self.activity_graph.add_edge(a2, a1)
if bio_ontology.isa('INDRA_ACTIVITIES', a2, 'INDRA_ACTIVITIES',
a1):
self.activity_graph.add_edge(a1, a2)
def isa_cmp(a, b):
"""Compare two entries based on isa relationships for sorting."""
if not a.startswith('CHEBI:'):
a = 'CHEBI:%s' % a
if not b.startswith('CHEBI:'):
b = 'CHEBI:%s' % b
if bio_ontology.isa('CHEBI', a, 'CHEBI', b):
return -1
if bio_ontology.isa('CHEBI', b, 'CHEBI', a):
return 1
return 0
def test_erk_isa():
assert bio_ontology.isa('HGNC', '6871', 'FPLX', 'MAPK')
assert not bio_ontology.isa('HGNC', '6871', 'FPLX', 'JNK')
def test_isa_activity_not():
assert not bio_ontology.isa('INDRA_ACTIVITIES', 'kinase',
'INDRA_ACTIVITIES', 'phosphatase')
def test_isa_entity():
assert bio_ontology.isa('HGNC', '1097', 'FPLX', 'RAF')
def test_isa_mod_not():
assert not bio_ontology.isa('INDRA_MODS', 'phosphorylation', 'INDRA_MODS',
'ubiquitination')
def test_isa_activity():
assert bio_ontology.isa('INDRA_ACTIVITIES', 'kinase', 'INDRA_ACTIVITIES',
'activity')
def test_isa_mod():
assert bio_ontology.isa('INDRA_MODS', 'phosphorylation', 'INDRA_MODS',
'modification')
def test_isa_entity3():
assert not bio_ontology.isa('FPLX', 'RAF', 'HGNC', '1097')
def test_chebi_isa():
assert bio_ontology.isa('CHEBI', 'CHEBI:87307', 'CHEBI', 'CHEBI:36962')
def test_isa_entity2():
assert not bio_ontology.isa('HGNC', '1097', 'HGNC', '646')
def test_eccode_isa():
parents = set(bio_ontology.get_parents('ECCODE', '1.1.1.1'))
assert parents == {('ECCODE', '1.1.1'), ('ECCODE', '1.1'),
('ECCODE', '1')}, parents
assert bio_ontology.isa('ECCODE', '1.1.1.1', 'ECCODE', '1.1.1')