def test_common_ancestors(self):
ontology = make_ontology()
ca = ontology[31].common_ancestors(ontology[41])
assert ontology[12] in ca
assert ontology[21] in ca
assert ontology[11] in ca
assert ontology[1] in ca
assert ontology[31] in ca
assert len(ca) == 5
def setUp(self):
self.ontology = make_ontology()
genes = make_genes(4)
genes[0].hpo.add(self.ontology[1].index)
genes[0].hpo.add(self.ontology[11].index)
genes[1].hpo.add(self.ontology[1].index)
genes[2].hpo.add(self.ontology[11].index)
genes[3].hpo.add(self.ontology[31].index)
omim = make_omim(5)
omim[0].hpo.add(self.ontology[1].index)
omim[0].hpo.add(self.ontology[11].index)
omim[1].hpo.add(self.ontology[1].index)
omim[2].hpo.add(self.ontology[11].index)
omim[3].hpo.add(self.ontology[31].index)
omim[4].hpo.add(self.ontology[41].index)
self.ontology._genes = set(genes)
self.ontology._omim_diseases = set(omim)
def setUp(self):
Orpha.clear()
self.ontology = make_ontology()
self.orpha_diseases = make_orpha(5)
def setUp(self):
Decipher.clear()
self.ontology = make_ontology()
self.decipher_diseases = make_decipher(5)
def setUp(self):
self.ontology = make_ontology()
self.genes = make_genes(5)
def setUp(self):
Omim.clear()
self.ontology = make_ontology()
self.omim_diseases = make_omim(5)
def setUp(self):
self.ontology = mo.make_ontology()
self.ci = HPOSet([term for term in self.ontology])
def test_add_parent_term(self):
ontology = mo.make_ontology()
ci = BasicHPOSet([ontology[11], ontology[21], ontology[1]])
assert ci == set([ontology[21]])
def test_remove_duplicate_terms(self):
ontology = mo.make_ontology()
ci = BasicHPOSet([term for term in ontology] + [ontology[41]])
self.assertEqual(ci, set([ontology[41], ontology[13]]))
def test_init(self):
ontology = mo.make_ontology()
ci = BasicHPOSet([term for term in ontology])
self.assertEqual(ci, set([ontology[41], ontology[13]]))