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#!/usr/bin/python3
import networkx as nx
import sys
import itertools
filename = sys.argv[1]
outfile = filename.split('.')[0] + ".edges.list"
g = nx.read_graphml(filename)
print(nx.info(g))
def get_circle(g,node,vertices_of_interest):
cur_path = [node]
cur_vertex = g.successors(node)[0]
i = 0
while cur_vertex != node:
cur_path.append(cur_vertex)
try:
assert len(g.successors(cur_vertex)) == 1
except:
print(g.successors(cur_vertex), cur_vertex, node)
print(cur_vertex in vertices_of_interest)
raise
successor = g.successors(cur_vertex)[0]
cur_vertex = successor
cur_path.append(cur_vertex)
return cur_path
def get_unitigs(g):
paths = []
num_paths = 0
node_set = set(g.nodes())
vertices_of_interest = set([x for x in g if g.in_degree(x) != 1 or g.out_degree(x) != 1])
vertices_used = set(vertices_of_interest)
for start_vertex in vertices_of_interest:
first_out_vertices = g.successors(start_vertex)
print(first_out_vertices)
for vertex in first_out_vertices:
cur_path = [start_vertex]
cur_vertex = vertex
while cur_vertex not in vertices_of_interest:
successor = g.successors(cur_vertex)[0]
cur_path.append(cur_vertex)
predecessor = cur_vertex
cur_vertex = successor
cur_path.append(cur_vertex)
vertices_used = vertices_used.union(set(cur_path))
paths.append(cur_path)
print(len(node_set))
print(len(vertices_used))
while len(node_set-vertices_used) > 0:
node = list(node_set-vertices_used)[0]
# print list(node_set-vertices_used)
# # print vertices_of_interest
# # print len(node_set-vertices_used)
# break
path = get_circle(g, node, vertices_of_interest)
vertices_used = vertices_used.union(set(path))
if len(path) > 1:
paths.append(path)
print(len(paths))
# print paths
print("paths")
return paths
paths = get_unitigs(g)
print(len(paths))
h = nx.DiGraph()
for i, path in enumerate(paths):
h.add_node(i)
h.node[i]['path'] = path
vertices_of_interest = set([x for x in g if g.in_degree(x) != 1 or g.out_degree(x) != 1])
for vertex in vertices_of_interest:
successors = [x for x in h.nodes() if h.node[x]['path'][0] == vertex]
predecessors = [x for x in h.nodes() if h.node[x]['path'][-1] == vertex]
print(successors,predecessors)
assert len(successors)==1 or len(predecessors)==1
for succ, pred in itertools.product(successors,predecessors):
h.add_edge(pred,succ)
# if vertex.split('_') == '0':
# if len(predecessors) == 1:
# for succ in successors:
# rel_suc = h.node[succ]['path'][1]
# d = g.get_edge_data(vertex,rel_suc)
# h.edge[predecessors[0]][succ]['start_pos'] = d['read_a_end']
# h.edge[predecessors[0]][succ]['weight'] = d['read_a_end_raw'] - d['read_a_start']
# if len(successors) == 1:
# for pred in predecessors:
# rel_pred = h.node[pred]['path'][-2]
# d = g.get_edge_data(rel_pred,vertex)
# h.edge[predecessors[0]][succ][''] = d['read_a_end_raw'] - d['read_a_start']
with open(outfile, 'w') as f:
for i,path in enumerate(paths):
f.write('>Unitig%d\n'%(i))
for j in range(len(path)-1):
nodeA = path[j].lstrip("B")
nodeB = path[j+1].lstrip("B")
d = g.get_edge_data(path[j],path[j+1])
f.write('%s %s %s %s %d %d %d %d %d\n'%(nodeA.split('_')[0],nodeA.split('_')[1] , nodeB.split('_')[0],
nodeB.split('_')[1], -d['read_a_start_raw'] + d['read_a_end_raw'] - d['read_b_start_raw'] + d['read_b_end_raw'],
d['read_a_start_raw'], d['read_a_end_raw'], d['read_b_start_raw'], d['read_b_end_raw']))
f.close()
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