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 testPaths(self):
nodes = [ Node(read) for read in ["AAA", "AGG", "GTT", "TCA"]]
graph = Graph(nodes)
edge = Edge(1, nodes[0], nodes[1])
self.assertFalse(graph.will_create_cycle(edge))
nodes[0].out_edges.append(edge)
nodes[1].in_edges.append(edge)
other_edge = Edge(0, nodes[1], nodes[0])
self.assertTrue(graph.will_create_cycle(other_edge))
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)
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 testWillCycle(self):
reads = ["AAA", "AGG", "GTT"]
first_node = Node("AAA")
second_node = Node("AGG")
third_node = Node("GGT")
graph = Graph([first_node, second_node, third_node])
# add edges
fs_edge = Edge(0, first_node, second_node)
first_node.out_edges.append(fs_edge)
second_node.in_edges.append(fs_edge)
st_edge = Edge(0, second_node, third_node)
second_node.out_edges.append(st_edge)
third_node.in_edges.append(st_edge)
# cycle edge
tf_edge = Edge(0, third_node, first_node)
self.assertTrue(graph.will_create_cycle(tf_edge))