def test_create_ob_graph(self): run_argument_parser([ "create_ob_graph", "-o", "tests/testgraph.obg", "tests/vg_test_graph.json" ]) graph = GraphWithReversals.from_numpy_file("tests/testgraph.obg") self.assertEqual(graph, self.correct_ob_graph)
def find_linear_path_through_chromosome(chromosome, chromend, fasta_file_name, ob_graph_file_name, vg_graph_file_name): genome = Fasta(fasta_file_name) seq = str(genome[chromosome][0:50818468]).lower() logging.info("Creating sequence retriever") sequence_retriever = SequenceRetriever.from_vg_json_graph( vg_graph_file_name) graph = GraphWithReversals.from_numpy_file(ob_graph_file_name) start_nodes = graph.get_first_blocks() assert len(start_nodes) == 1, "Found %d start nodes" % start_nodes start_node = start_nodes[0] traverser = GraphTraverserUsingSequence(graph, seq, sequence_retriever) traverser.search_from_node(start_node) path = traverser.get_interval_found() path = IntervalCollection(path) path.to_file("22_path.intervalcollection", text_file=True) logging.info("Done")