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")