def test_serialization(self):
a = HPOSet.from_queries([
'Test child level 1-1', 'Test child level 2-1',
'Test child level 4'
])
self.assertEqual(a.serialize(), '11+21+41')
self.assertEqual(HPOSet.from_serialized('11+21+41'), a)
def test_omim_enrichment(self):
hposet = HPOSet.from_queries('HP:0007401,HP:0010885'.split(','))
res = self.omim_model.enrichment('hypergeom', hposet)
self.assertIsInstance(res, list)
self.assertIn('item', res[0])
self.assertIn('count', res[0])
self.assertIn('enrichment', res[0])
self.assertIsInstance(res[0]['item'], an.OmimDisease)
self.assertIsInstance(res[0]['count'], int)
self.assertIsInstance(res[0]['enrichment'], float)
def test_set(self):
full_set = HPOSet.from_queries([int(x) for x in self.terms])
self.assertEqual(len(full_set), len(self.terms))
phenoterms = full_set.remove_modifier()
self.assertLess(len(phenoterms), len(full_set))
self.assertGreater(len(phenoterms), 0)
self.assertIn(self.terms[5], full_set)
self.assertNotIn(self.terms[5], phenoterms)
def test_remove_modifier(self):
terms = mo.make_ontology_with_modifiers()
normal_term_ids = set([1, 11, 12, 21, 31, 41, 13])
modifier_term_ids = set([5, 12823, 5000001, 5000002, 5100001])
self.assertEqual(len(terms),
(len(normal_term_ids | modifier_term_ids)))
full_set = HPOSet.from_queries(normal_term_ids | modifier_term_ids)
self.assertEqual(len(full_set),
len(normal_term_ids | modifier_term_ids))
set_2 = full_set.remove_modifier()
self.assertEqual(len(set_2), len(normal_term_ids))
self.assertEqual((normal_term_ids | modifier_term_ids),
{int(x)
for x in full_set})
self.assertEqual(normal_term_ids, {int(x) for x in set_2})
def test_set_from_queries(self):
a = HPOSet.from_queries([
'Test child level 1-1', 'Test child level 2-1',
'Test child level 4'
])
assert len(a) == 3