json_dict[drug] = {}
if json_dict[drug].get(ab) is None:
json_dict[drug][ab] = {}
for idx, path in enumerate(paths):
path_stmts = []
for rule_name, sign in path[:-1]:
stmt = _stmt_from_rule(model, rule_name, stmts)
path_stmts.append(stmt.uuid)
json_dict[drug][ab][idx] = path_stmts
return json_dict
if __name__ == '__main__':
print("Processing data")
data = process_data.read_data(process_data.data_file)
data_genes = process_data.get_all_gene_names(data)
ab_map = process_data.get_antibody_map(data)
print('Loading data statements.')
data_stmts, data_values = make_stmts.run(dec_thresh=0.5, inc_thresh=1.5)
all_data_stmts = [values.values() for values in data_stmts.values()]
all_data_stmts = itertools.chain.from_iterable(all_data_stmts)
all_data_stmts = list(itertools.chain.from_iterable(all_data_stmts))
print('We will check the following drug-ab combinations:\n============')
for drug, stmtd in data_stmts.items():
print(drug)
for ab in stmtd.keys():
print('-'+ ab)
agent_obs = list(itertools.chain.from_iterable(ab_map.values()))
trips_stmts = process_trips.read_stmts(process_trips.base_folder)
sparser_stmts = process_sparser.read_stmts(process_sparser.base_folder)
r3_stmts = process_r3.read_stmts(process_r3.active_forms_file)
stmts = trips_stmts + sparser_stmts + r3_stmts
return stmts
def get_prior_genes(fname):
"""Get the list of prior genes."""
with open(fname, 'rt') as fh:
genes = fh.read().strip().split('\n')
return genes
if __name__ == '__main__':
outf = 'output/'
data = process_data.read_data(process_data.data_file)
data_genes = process_data.get_all_gene_names(data)
reassemble = False
if not reassemble:
stmts = ac.load_statements(pjoin(outf, 'preassembled.pkl'))
#stmts = ac.load_statements(pjoin(outf, 'prior.pkl'))
else:
#prior_stmts = build_prior(data_genes, pjoin(outf, 'prior.pkl'))
prior_stmts = ac.load_statements(pjoin(outf, 'prior.pkl'))
prior_stmts = ac.map_grounding(prior_stmts,
save=pjoin(outf, 'gmapped_prior.pkl'))
reading_stmts = ac.load_statements(pjoin(outf, 'phase3_stmts.pkl'))
reading_stmts = ac.map_grounding(reading_stmts,
save=pjoin(outf, 'gmapped_reading.pkl'))
stmts = prior_stmts + reading_stmts
stmts = ac.filter_grounded_only(stmts)
