def make_protein_complex_descendents_if_not_present(
self, ontology: Optional[ontol.Ontology]) -> Set:
if ontology is not None and self.protein_containing_complex_descendents is None:
closure = gafparser.protein_complex_sublcass_closure(ontology)
self.protein_containing_complex_descendents = closure
return {} if self.protein_containing_complex_descendents is None else self.protein_containing_complex_descendents
def test_gaf_2_1_creates_cell_component_closure():
ontology = OntologyFactory().create("tests/resources/goslim_generic.json")
closure = gafparser.protein_complex_sublcass_closure(ontology)
# "GO:1902494" as an example that should be in the set
assert "GO:0005840" in closure
p = GafParser(config=assocparser.AssocParserConfig(ontology=ontology))
with open("tests/resources/pombase_single.gaf") as gaf:
# First line will be version declaration, triggering closure computation
p.parse_line(gaf.readline())
assert "GO:0005840" in p.cell_component_descendants_closure