def test_indexing(self): def subindex_length(x): return ( len(x.keys()), len(x._indicies.keys()), len(x._names.keys()) ) self.assertEqual( subindex_length(Gene), (0, 0, 0) ) _ = Gene(hgncid=1, symbol='EZH1') self.assertEqual( subindex_length(Gene), (1, 1, 1) ) _ = Gene(hgncid=2, symbol='EZH2') self.assertEqual( subindex_length(Gene), (2, 2, 2) ) Gene.clear() self.assertEqual( subindex_length(Gene), (0, 0, 0) )
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 tearDown(self): Gene.clear()
def setUp(self): Gene.clear()
def make_genes(n) -> List[pyhpo.annotations.GeneSingleton]: # Ensure to remove all items from Gene object Gene.clear() return [Gene(hgncid=i, symbol='Gene{}'.format(i)) for i in range(n)]
def tearDown(): Gene.clear() Omim.clear() Orpha.clear() Decipher.clear()