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)