def test_path2():
t_dict, locus = read_single_locus('noc2l_locus.gtf')
for sgraph in locus.create_splice_graphs():
pgraphfactory = PathGraphFactory(sgraph)
pgraph, k = pgraphfactory.create_optimal()
paths = find_paths(pgraph)
return
def test_path1():
t_dict, locus = read_single_locus('path1.gtf')
transfrags = locus.get_transfrags(Strand.POS)
sgraph = SpliceGraph.create(transfrags)
k = 2
pgf = PathGraphFactory(sgraph)
pgraph = pgf.create(k)
paths = find_paths(pgraph)
return
def test_path2():
t_dict, locus = read_single_locus('noc2l_locus.gtf')
for sgraph in locus.create_splice_graphs():
K, k = create_optimal_path_graph(sgraph)
paths1 = find_paths(K, 'expr')
paths2 = cpathfinder.find_paths(K, 'expr')
assert len(paths1) == len(paths2)
for p1, p2 in zip(paths1, paths2):
p1, e1 = p1
p2, e2 = p2
assert p1 == p2
assert abs(e1 - e2) < 1e-5
def test_path2():
t_dict, locus = read_single_locus('noc2l_locus.gtf')
for sgraph in locus.create_splice_graphs():
K, k = create_optimal_path_graph(sgraph)
paths1 = find_paths(K, 'expr')
paths2 = cpathfinder.find_paths(K, 'expr')
assert len(paths1) == len(paths2)
for p1, p2 in zip(paths1, paths2):
p1, e1 = p1
p2, e2 = p2
assert p1 == p2
assert abs(e1-e2) < 1e-5
def test_path1():
t_dict, locus = read_single_locus('path1.gtf')
transfrags = locus.get_transfrags(Strand.POS)
sgraph = SpliceGraph.create(transfrags)
k = 2
K = create_path_graph(sgraph, k)
paths1 = find_paths(K, 'expr')
paths2 = cpathfinder.find_paths(K, 'expr')
assert len(paths1) == len(paths2)
for p1, p2 in zip(paths1, paths2):
p1, e1 = p1
p2, e2 = p2
assert p1 == p2
assert abs(e1 - e2) < 1e-8
return
def test_path1():
t_dict, locus = read_single_locus('path1.gtf')
transfrags = locus.get_transfrags(Strand.POS)
sgraph = SpliceGraph.create(transfrags)
k = 2
K = create_path_graph(sgraph, k)
paths1 = find_paths(K, 'expr')
paths2 = cpathfinder.find_paths(K, 'expr')
assert len(paths1) == len(paths2)
for p1, p2 in zip(paths1, paths2):
p1, e1 = p1
p2, e2 = p2
assert p1 == p2
assert abs(e1-e2) < 1e-8
return
