def test_json(self):
g = Omim(diseaseid=1, name='Foo')
self.assertEqual(g.toJSON(), {'id': 1, 'name': 'Foo'})
self.assertEqual(g.toJSON(verbose=True), {
'id': 1,
'name': 'Foo',
'hpo': set()
})
def make_ontology_with_annotation() -> pyhpo.ontology.OntologyClass:
"""
Generates the following Ontology
- HP:0001
- HP:0011
- HP:0021 <- Gene/Disease 0 / Negative Disease 2
- HP:0031(*)
- HP:0012 <- Gene/Disease 1
- HP:0031(*)
- HP:0041
- HP:0013
"""
Gene.clear()
Omim.clear()
Orpha.clear()
Decipher.clear()
items = make_terms()
terms = Ontology(from_obo_file=False)
for item in items:
terms._append(item)
terms._connect_all()
genes = make_genes(2)
genes[0].hpo.add(21)
genes[1].hpo.add(12)
omim = make_omim(3)
omim[0].hpo.add(21)
omim[1].hpo.add(12)
omim[2].negative_hpo.add(21)
decipher = make_decipher(3)
decipher[0].hpo.add(21)
decipher[1].hpo.add(12)
decipher[2].negative_hpo.add(21)
orpha = make_orpha(3)
orpha[0].hpo.add(21)
orpha[1].hpo.add(12)
orpha[2].negative_hpo.add(21)
ds._add_omim_to_ontology(terms)
ds._add_decipher_to_ontology(terms)
ds._add_orpha_to_ontology(terms)
_add_genes_to_ontology(terms)
return terms
def test_indexing(self):
def subindex_length(x):
return (
len(x.keys()),
len(x._indicies.keys()),
)
self.assertEqual(subindex_length(Omim), (0, 0))
_ = Omim(diseaseid=1, name='Gaucher')
self.assertEqual(subindex_length(Omim), (1, 1))
_ = Omim(diseaseid=2, name='Fabry')
self.assertEqual(subindex_length(Omim), (2, 2))
Omim.clear()
self.assertEqual(subindex_length(Omim), (0, 0))
def compare_set(diseases):
gaucher = Omim([None, 230800, None])
set1 = BasicHPOSet.from_queries(gaucher.hpo)
for x in diseases:
set2 = BasicHPOSet.from_queries(x.hpo)
_ = set1.similarity(set2)
return None
def test_singleton_handling(self):
d1a = Omim(diseaseid=1, name='Gaucher')
# ID present, will be used
d1b = Omim(diseaseid=1, name='Fabry')
# No name present, ID will be used as well
d1c = Omim(diseaseid=1, name=None)
# New ID, new Name => New Disease
d2a = Omim(diseaseid=2, name='Fabry')
# ID present, Matching by ID
d2b = Omim(diseaseid=2, name='Gaucher')
# ID present, Matching by ID
d2c = Omim(diseaseid=2, name=None)
# New ID but existing name => New disease
d3a = Omim(diseaseid=3, name='Gaucher')
self.assertIs(d1a, d1b)
self.assertIs(d1a, d1c)
self.assertIsNot(d1a, d2a)
self.assertIs(d2a, d2b)
self.assertIs(d2a, d2c)
self.assertIsNot(d1a, d3a)
self.assertIsNot(d2a, d3a)
def test_get_omim(self):
d1 = Omim(diseaseid=1, name='Gaucher')
d2 = Omim(diseaseid=2, name='Fabry')
self.assertEqual(Omim.get(1), d1)
self.assertEqual(Omim.get(2), d2)
self.assertEqual(Omim.get('1'), d1)
self.assertRaises(ValueError, lambda: Omim.get('Fabry'))
self.assertRaises(KeyError, lambda: Omim.get(12))
def test_set_with_one_annotation(self):
ci = HPOSet([self.ontology[11], self.ontology[13], self.ontology[31]])
assert len(ci.all_genes()) == 1
assert len(ci.omim_diseases()) == 1
assert len(ci.orpha_diseases()) == 1
assert len(ci.decipher_diseases()) == 1
assert ci.all_genes() == set([Gene.get(0)])
assert ci.omim_diseases() == set([Omim.get(0)])
assert ci.orpha_diseases() == set([Orpha.get(0)])
assert ci.decipher_diseases() == set([Decipher.get(0)])
def tearDown():
Gene.clear()
Omim.clear()
Orpha.clear()
Decipher.clear()
def make_omim(n) -> List[pyhpo.annotations.DiseaseSingleton]:
Omim.clear()
return [Omim(diseaseid=i, name='Omim{}'.format(i)) for i in range(n)]
def setUp(self):
Omim.clear()
self.ontology = make_ontology()
self.omim_diseases = make_omim(5)
def test_string_representation(self):
d = Omim(diseaseid=1, name='Foo')
self.assertEqual(str(d), 'Foo')
def test_equality(self):
g = Omim(diseaseid=1, name='Foo')
self.assertEqual(g, 1)
self.assertEqual(g, 'Foo')
def test_omim_disease_building(self):
a = Omim(diseaseid=1, name='Gaucher type I')
self.assertEqual(a.name, 'Gaucher type I')
self.assertEqual(a.id, 1)
self.assertEqual(a.hpo, set())
def tearDown(self):
Omim.clear()
def setUp(self):
Omim.clear()
def all_omim_diseases() -> Set['OmimDisease']:
return set(Omim.keys())