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