def test_sampling_example_graph2():
sif_file = join(dirname(__file__), 'korkut_stmts.sif')
g = pg.load_signed_sif(sif_file)
source = 'BLK'
target = 'EIF4EBP1'
enum_cf_paths = set(
pg.enumerate_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
cycle_free=True))
sampled_cf_paths = set(
pg.sample_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
num_samples=10000,
cycle_free=True))
count_cf_paths = pg.count_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
cycle_free=True)
# The sampled paths should be a subset of the enumerated paths
assert sampled_cf_paths.intersection(enum_cf_paths) == sampled_cf_paths
def test_enumerate_example_graph2():
sif_file = join(dirname(__file__), 'korkut_stmts.sif')
g = pg.load_signed_sif(sif_file)
source = 'BLK'
target = 'EIF4EBP1'
enum_paths = pg.enumerate_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
cycle_free=False)
assert len(enum_paths) == len(set(enum_paths))
enum_paths = set(enum_paths)
count_paths = pg.count_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
cycle_free=False)
enum_cf_paths = pg.enumerate_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
cycle_free=True)
assert len(enum_cf_paths) == len(set(enum_cf_paths))
enum_cf_paths = set(enum_cf_paths)
count_cf_paths = pg.count_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
cycle_free=True)
# Check that the counts match the enumeratio
assert len(enum_paths) == count_paths
assert len(enum_cf_paths) == count_cf_paths
# All of the cycle-free paths should be contained in the set of paths
# with cycles
assert enum_paths.intersection(enum_cf_paths) == enum_cf_paths
# Check that all paths in the set difference contain cycles
for path in enum_paths.difference(enum_cf_paths):
assert len(set(path)) < len(path)
def test_uniform_sampling_example_graph1():
sif_file = join(dirname(__file__), 'korkut_im.sif')
g = pg.load_signed_sif(sif_file)
source = 'BLK_phosphoY389_phosphorylation_PTK2_Y397'
target = 'EIF4EBP1_T37_p_obs'
target_polarity = 0
length = 8
cfpg = pg.CFPG.from_graph(g,
source,
target,
length,
signed=True,
target_polarity=0)
os.environ['TEST_FLAG'] = 'TRUE'
np.random.seed(1)
# Count paths
# Now, re-weight for uniformity and re-sample
num_samples = cfpg.count_paths() * 1000
cfpg.set_uniform_path_distribution()
sampled_paths_uni = cfpg.sample_paths(num_samples=num_samples)
ctr_uni = Counter(sampled_paths_uni)
for path, count in ctr_uni.items():
assert count > 900 and count < 1100
def test_example_graph1():
sif_file = join(dirname(__file__), 'korkut_im.sif')
g = pg.load_signed_sif(sif_file)
source = 'BLK_phosphoY389_phosphorylation_PTK2_Y397'
target = 'EIF4EBP1_T37_p_obs'
target_polarity = 0
enum_paths = pg.enumerate_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
cycle_free=False)
assert len(enum_paths) == len(set(enum_paths))
enum_paths = set(enum_paths)
sampled_paths = set(
pg.sample_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
num_samples=10000,
cycle_free=False))
count_paths = pg.count_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
cycle_free=False)
assert len(sampled_paths) == len(enum_paths)
assert len(sampled_paths) == count_paths
assert sampled_paths == enum_paths
enum_cf_paths = pg.enumerate_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
cycle_free=True)
assert len(enum_cf_paths) == len(set(enum_cf_paths))
enum_cf_paths = set(enum_cf_paths)
sampled_cf_paths = set(
pg.sample_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
num_samples=10000,
cycle_free=True))
count_cf_paths = pg.count_paths(g,
source,
target,
signed=True,
target_polarity=0,
max_depth=8,
cycle_free=True)
assert len(sampled_cf_paths) == len(enum_cf_paths)
assert len(sampled_cf_paths) == count_cf_paths
assert sampled_cf_paths == enum_cf_paths
# 101 cycle free paths
assert count_cf_paths == 101
# All of the cycle-free paths should be contained in the set of paths
# with cycles
assert sampled_paths.intersection(sampled_cf_paths) == sampled_cf_paths
# Check that all paths in the set difference contain cycles
for path in sampled_paths.difference(sampled_cf_paths):
assert len(set(path)) < len(path)