def filter_stmts_sampling(g, source, target, max_depth):
f_level, b_level = pg.get_reachable_sets(g, source, target,
max_depth=max_depth, signed=False)
for length in range(1, max_depth+1):
#print("Generating paths_graph for length %d" % length)
this_pg = pg.paths_graph(g, source, target, length, f_level, b_level,
signed=False)
def filter_stmts(g,
source,
target,
max_depth=6,
signed=False,
target_polarity=None):
f_level, b_level = pg.get_reachable_sets(g,
source,
target,
max_depth=max_depth,
signed=signed)
stmt_uuids = set()
stmt_nodes = set()
stmt_uuid_nums = []
stmt_node_nums = []
# Iterate over various path lengths
for length in range(1, max_depth + 1):
#print("Generating paths_graph for length %d" % length)
this_pg = pg.paths_graph(g,
source,
target,
length,
f_level,
b_level,
signed=signed,
target_polarity=target_polarity)
if this_pg and len(this_pg) < 100:
draw(this_pg, 'pybel_pg_%d.pdf' % length)
# Get nodes for this length PG
nodes_this_length = set([n[1] for n in this_pg])
# Get stmt UUIDs for this length PG
stmt_uuids_this_length = set()
"""
for u, v in this_pg.edges():
u_name, v_name = (u[1], v[1])
multiedge_data = g.get_edge_data(u_name, v_name)
for edge_data in multiedge_data.values():
stmt_uuids_this_length.add((u_name, edge_data['uuid'], v_name))
stmt_uuids |= stmt_uuids_this_length
"""
# Get counts for this depth
# Terminate the loop if we've saturated the number of edges
#if stmt_nodes and stmt_nodes == nodes_this_length:
# break
stmt_nodes |= nodes_this_length
stmt_uuid_nums.append(len(stmt_uuids))
stmt_node_nums.append(len(stmt_nodes))
return (stmt_uuids, stmt_nodes, stmt_node_nums, stmt_uuid_nums)
def sample_paths(g, source, target, max_depth, target_polarity=None,
num_paths=1000):
print('Source: %s' % source)
signed = True if target_polarity is not None else False
(f_level, b_level) = paths_graph.get_reachable_sets(
g, source, target, max_depth=10, signed=signed)
all_paths = []
for length in range(1, max_depth):
print("Path length: %d" % length)
pg_raw = paths_graph.paths_graph(g, source, target, length, f_level,
b_level, signed=signed,
target_polarity=target_polarity)
# Append depths to our source and target nodes
src = (0, (source, 0))
tgt = (length, (target, target_polarity))
dic_PG = cycle_free_paths_graph(pg_raw, src, tgt, length)
G_cf, T = dic_PG[length-1]
try:
P = sample_many_paths(src, tgt, G_cf, T, num_paths)
all_paths.extend(P)
except IndexError:
pass
return all_paths
dic_PG = cycle_free_paths_graph(pg_raw, src, tgt, length)
G_cf, T = dic_PG[length-1]
try:
P = sample_many_paths(src, tgt, G_cf, T, num_paths)
all_paths.extend(P)
except IndexError:
pass
return all_paths
if __name__ == '__main__':
G_0 = paths_graph.get_edges('korkut_im.sif')
source = 'BLK_phosphoY389_phosphorylation_PTK2_Y397'
target = 'EIF4EBP1_T37_p_obs'
(f_level, b_level) = paths_graph.get_reachable_sets(G_0, source, target,
max_depth=10, signed=False)
length = 8
pg_raw = paths_graph.paths_graph(G_0, source, target, length, f_level,
b_level, signed=False, target_polarity=0)
# Append depths to our source and target nodes
src = (0, source)
tgt = (length, target)
dic_PG = cycle_free_paths_graph(pg_raw, src, tgt, length)
G_cf, T = dic_PG[7]
P = sample_many_paths(src, tgt, G_cf, T, 1000)
#print("--- %s seconds ---" % (time.time() - start_time))