def test_path_graph_factory(): t_dict, locus = read_single_locus('path1.gtf') sgraph = SpliceGraph.create(t_dict.values()) pgraphfactory = PathGraphFactory(sgraph) g1 = pgraphfactory.create(k=1) assert len(g1) == 5 g2 = pgraphfactory.create(k=2) assert len(g2) == 6 gopt, k = pgraphfactory.create_optimal() assert k == 2 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_topological_sort(): G = Graph() G.add_path((G.SOURCE, 10, 20, 30, 40, G.SINK)) G.add_path((G.SOURCE, 10, 30, 40, G.SINK)) G.add_path((G.SOURCE, 10, G.SINK)) G.add_path((G.SOURCE, 20, G.SINK)) assert G.is_topological_sort(G.topological_sort()) t_dict, locus = read_single_locus('noc2l_locus.gtf') for sgraph in locus.create_splice_graphs(): pgf = PathGraphFactory(sgraph) G = pgf.create(k=1) assert G.is_topological_sort(G.topological_sort()) assert G.is_topological_sort(G.topological_sort_dfs())