def test_gene_sets(self):
gs1 = GeneSet(
gs_id=self.test_gs_id,
name=self.test_name,
genes=self.test_genes,
hierarchy=self.test_hierarchy,
organism=self.test_organism,
link='',
)
gs2 = GeneSet(gs_id='test2',
name='test_name2',
hierarchy=('Test', 'test'),
organism='3702')
gs3 = GeneSet(gs_id='test3',
name='test_name3',
hierarchy=('Test', 'test'),
organism='3702')
sets = GeneSets([gs1, gs2, gs3])
self.assertIsNotNone(sets)
self.assertRaises(GeneSetException, sets.common_org)
self.assertRaises(GeneSetException, sets.common_hierarchy)
self.assertGreater(len(sets.hierarchies()), 1)
split_by_hierarchy = sets.split_by_hierarchy()
self.assertLess(len(split_by_hierarchy), len(sets))
def go_gene_sets(tax_id: str) -> None:
domain = 'go'
ontology = go.Ontology(filename=f'{data_path}/{domain}/gene_ontology.obo')
annotations = go.Annotations(tax_id,
filename=f'{data_path}/{domain}/{tax_id}.tab',
ontology=ontology)
def to_gene_set(term: go.Term) -> Optional[GeneSet]:
genes = annotations.get_genes_by_go_term(term.id)
if len(genes) > 0:
return GeneSet(
gs_id=term.id,
name=term.name,
genes=set(genes),
hierarchy=('GO', term.namespace),
organism=tax_id,
link=f'http://amigo.geneontology.org/amigo/term/{term.id}')
gene_sets = GeneSets([
gs for gs in [to_gene_set(term) for term in ontology.terms.values()]
if gs is not None
])
for gs_group in gene_sets.split_by_hierarchy():
hierarchy = gs_group.common_hierarchy()
gs_group.to_gmt_file_format(
f'{data_path}/gene_sets/{filename(hierarchy, tax_id)}')
