def test_find_drugs_for_genes():
# SearchTerm for SRC
SRC = SearchTerm(type='gene',
name='SRC',
search_term='"SRC"',
db_refs={'HGNC': '11283'})
# drugs targeting KRAS
drug_terms = find_drugs_for_genes([SRC])
# make sure there are results
assert drug_terms
# make sure the result is a list of search terms
assert all(isinstance(term, SearchTerm) for term in drug_terms)
# something is wrong if there are fewer than 10 drugs
assert len(drug_terms) > 10
# test that some example drugs are included
drug_names = set(term.name for term in drug_terms)
example_drugs = set(['Dasatinib', 'Tozasertib', 'Ponatinib'])
assert example_drugs <= drug_names
def test_find_drugs_for_genes():
# SearchTerm for SRC
SRC = SearchTerm(type='gene',
name='SRC',
search_term='"SRC"',
db_refs={'HGNC': '11283'})
# drugs targeting KRAS
drug_terms = find_drugs_for_genes([SRC], [
Inhibition(Agent('Dasatinib', db_refs={'CHEBI': 'CHEBI:49375'}),
Agent('SRC', db_refs={'HGNC': '11283'})),
Inhibition(Agent('Ponatinib', db_refs={'CHEBI': 'CHEBI:78543'}),
Agent('SRC', db_refs={'HGNC': '11283'}))
])
# make sure there are results
assert drug_terms
# make sure the result is a list of search terms
assert all(isinstance(term, SearchTerm) for term in drug_terms)
# test that some example drugs are included
drug_names = set(term.name for term in drug_terms)
assert drug_names == set(['Dasatinib', 'Ponatinib'])
# If all the agents are gene names, this is an internal statement.
# We classify any statements with drugs in them as external.
return all([a.name in gene_names for a in stmt.real_agent_list()])
estmts = [
EmmaaStatement(stmt, datetime.datetime.now(), [],
{'internal': is_internal(stmt)}) for stmt in stmts
]
return estmts
if __name__ == '__main__':
cancer_types = (
'aml',
'brca',
'luad',
'paad',
'prad',
'skcm',
)
for ctype in cancer_types:
top_genes = get_top_genes(ctype, 5)
cancer_terms = make_prior_from_genes(top_genes)
drug_terms = find_drugs_for_genes(cancer_terms)
gene_names = [g.name for g in cancer_terms]
drug_names = [d.name for d in drug_terms]
terms = cancer_terms + drug_terms
save_config(ctype, terms)
prior_stmts = get_stmts_for_gene_list(gene_names, drug_names)
save_prior(ctype, prior_stmts)