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 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 tearDown(self):
Omim.clear()
def setUp(self):
Omim.clear()