def testEasyAssembly(self): reads = ["Hello", "o_my_friend", "d_its_me"] nodes = [Node(str) for str in reads] graph = Graph(nodes) assembled = graph.assemble() self.assertEqual(assembled, "Hello_my_friend_its_me")
def main(): parser = argparse.ArgumentParser( description = (" An implemention of a greedy sequence assembler using Graphs / Ham Paths"), ) parser.add_argument("--reads") parser.add_argument("--fastq", help="Option to process reads as a fastq file") opts = parser.parse_args() log.info("Starting Greedy Assembly") log.info("Read file: %s", opts.reads) if opts.reads: nodes = read_file_to_node_set(opts.reads) graph = Graph(nodes) print(graph.assemble()) elif opts.fastq: nodes = fastq_file_to_node_set(opts.fastq) graph = Graph.Graph(nodes) print(graph.assemble())
def testSampleAssembly(self): read_file = "test/test.reads" nodes = [] with open(read_file) as fh: for line in fh: nodes.append(Node(line.rstrip())) graph = Graph(nodes) assembled = graph.assemble() answer = "the_quick_brown_fox_jumps_over_the_lazy_dog" self.assertEqual(assembled, answer)