def make_cyjs_network(results, model, stmts):
path_stmts = get_path_stmts(results, model, stmts)
path_genes = get_path_genes(path_stmts)
path_uuids = [list(path.keys()) for path in path_stmts]
all_path_uuids = []
for p in path_uuids:
all_path_uuids += p
print(json.dumps(path_uuids, indent=1))
#filtered_stmts = ac.filter_gene_list(stmts, path_genes, 'one')
filtered_stmts = ac.filter_uuid_list(stmts, all_path_uuids)
ca = CyJSAssembler(filtered_stmts)
cm = ca.make_model()
ca.set_CCLE_context(['SKMEL28_SKIN'])
ca.save_json('output/korkut_model')
def make_cyjs_network(results, model, stmts):
path_stmts = get_path_stmts(results, model, stmts)
path_genes = get_path_genes(path_stmts)
# Get UUIDs to use as filter
path_uuids = [list(path.keys()) for path in path_stmts]
all_path_uuids = []
for p in path_uuids:
all_path_uuids += p
#filtered_stmts = ac.filter_gene_list(stmts, path_genes, 'one')
filtered_stmts = ac.filter_uuid_list(stmts, all_path_uuids)
ac.dump_statements(filtered_stmts, 'output/korkut_cyjs_model.pkl')
ca = CyJSAssembler(filtered_stmts)
cm = ca.make_model()
ca.set_CCLE_context(['SKMEL28_SKIN'])
ca.save_json('output/korkut_model')
def remove_kappa_dead_rules(stmts, model, dead_rules):
# FIXME: we should probably check that a statement we remove has all its
# generated rules recognized as dead. If it has at least one live rule
# coming from it, we shouldn't remove it. But the dead rules should still
# be removed somehow from the final model.
dead_uuids = set()
for rule in dead_rules:
for ann in model.annotations:
if ann.subject == rule and ann.predicate == 'from_indra_statement':
dead_uuids.add(ann.object)
all_uuids = {stmt.uuid for stmt in stmts}
live_uuids = all_uuids - dead_uuids
stmts = ac.filter_uuid_list(stmts, live_uuids)
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model()
return stmts, model
def test_filter_uuid_list():
st_out = ac.filter_uuid_list([st1, st4], [st1.uuid])
assert len(st_out) == 1
def remove_contradicts(stmts, conflicts):
remove_stmts = []
for s1, s2 in conflicts:
remove_stmts.append(s1.uuid if s1.belief < s2.belief else s2.uuid)
stmts = ac.filter_uuid_list(stmts, remove_stmts, invert=True)
return stmts