def test_root_term(self):
a = parse_obo_section(self.a1)
self.assertEqual(a['id'], 'HP:0000001')
self.assertEqual(a['name'], 'All')
self.assertEqual(
a['comment'],
'Root of all terms in the Human Phenotype Ontology.'
)
self.assertEqual(a['definition'], '')
self.assertEqual(a['is_obsolete'], False)
self.assertEqual(a['replaced_by'], '')
self.assertEqual(a['xref'], ['UMLS:C0444868'])
term = HPOTerm(**a)
self.assertEqual(
term.index,
1
)
self.assertEqual(
term.id,
'HP:0000001'
)
self.assertEqual(
term.name,
'All'
)
def setUp(self):
self.term = HPOTerm(**parse_obo_section(TEST_HPO))
self.t1 = HPOTerm(id='HP:001', name='HP1')
self.t1.Config.allow_mutation = True
self.t1.information_content = {'omim': 1, 'gene': 11}
self.t2 = HPOTerm(id='HP:002', name='HP2')
self.t2.Config.allow_mutation = True
self.t2.information_content = {'omim': 3, 'gene': 33}
self.t3 = HPOTerm(id='HP:003', name='HP3')
self.t3.Config.allow_mutation = True
self.t3.information_content = {'omim': 2, 'gene': 22}
def setUp(self):
self.term = HPOTerm(**parse_obo_section(TEST_HPO))