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#!/usr/bin/python3
import networkx as nx
import sys
from collections import Counter
# This script condenses the graph down, creates a gfa with for the condensed graph, and computes the contig N50
# python3 condense_graph_create_gfa_compute_n50.py ecoli.edges
# The conditions in lines 23 and 24 are meant to prevent nodes corresponding to different strands to be merged
# (and should be commented out if this is not desired, or if a json is not available)
def merge_simple_path(g):
for node in g.nodes():
if g.in_degree(node) == 1 and g.out_degree(node) == 1:
in_node = g.in_edges(node)[0][0]
out_node = g.out_edges(node)[0][1]
if g.out_degree(in_node) == 1 and g.in_degree(out_node) == 1:
if in_node != node and out_node != node and in_node != out_node:
if g.node[in_node]['aln_strand']==g.node[node]['aln_strand'] or max(g.node[in_node]['aln_strand'],g.node[node]['aln_strand']) == 5:
if g.node[out_node]['aln_strand']==g.node[node]['aln_strand'] or max(g.node[out_node]['aln_strand'],g.node[node]['aln_strand']) == 5:
#print in_node, node, out_node
merge_path(g,in_node,node,out_node)
def merge_path(g,in_node,node,out_node):
#ov1 = find_overlap(g.node[in_node]['bases'], g.node[node]['bases'])
#ov2 = find_overlap(g.node[node]['bases'], g.node[out_node]['bases'])
node_id = g.graph['aval']
g.graph['aval'] += 1
#length = g.node[node]['length'] + g.node[in_node]['length'] + g.node[out_node]['length'] - ov1 - ov2
#cov = (g.node[in_node]['cov'] * g.node[in_node]['length'] + g.node[node]['cov'] * g.node[node]['length'] + \
#g.node[out_node]['cov'] * g.node[out_node]['length'])/float(length)
#bases = g.node[in_node]['bases'][:-ov1] + g.node[node]['bases'] + g.node[out_node]['bases'][ov2:]
overlap1 = g.edge[in_node][node][0]['overlap']
overlap2 = g.edge[node][out_node][0]['overlap']
length0 = g.node[in_node]['length']
length1 = g.node[node]['length']
length2 = g.node[out_node]['length']
if overlap1 > min(length0,length1):
print("problem here:")
print(overlap1, length0, length1)
g.add_node(str(node_id),length = length0+length1+length2 - overlap1 - overlap2, aln_strand = g.node[node]['aln_strand'])
#g.add_node(str(node_id)+'-', bases = reverse_comp_bases(bases), length = length, cov = cov)
for cur_edge in g.in_edges(in_node):
# print g.edge[cur_edge[0]][cur_edge[1]][0]['overlap']
g.add_edge(cur_edge[0],str(node_id),overlap = g.edge[cur_edge[0]][cur_edge[1]][0]['overlap'])
for cur_edge in g.out_edges(out_node):
g.add_edge(str(node_id),cur_edge[1],overlap = g.edge[cur_edge[0]][cur_edge[1]][0]['overlap'])
g.remove_node(in_node)
g.remove_node(node)
g.remove_node(out_node)
def comp_n50(contig_vec):
if len(contig_vec) == 0:
return 0
sorted_lengths = sorted(contig_vec)
total_length = sum(contig_vec)
half_length = 0.5*total_length
min_n50 = sorted_lengths[-1]
max_n50 = 0
for i in range(len(sorted_lengths)):
#if len(sorted_lengths) % 2 == 0:
# sum_1 = sum(sorted_lengths[0:i])
# sum_2 = sum(sorted_lengths[i:])
#else:
# sum_1 = sum(sorted_lengths[0:i+1])
# sum_2 = sum(sorted_lengths[i:])
sum_1 = sum(sorted_lengths[0:i+1])
sum_2 = sum(sorted_lengths[i:])
if sum_1 >= half_length and sum_2 >= half_length:
min_n50 = min(sorted_lengths[i],min_n50)
max_n50 = max(sorted_lengths[i],max_n50)
# print "Min N50: "+str(min_n50)
# print "Max N50: "+str(max_n50)
return 0.5*(min_n50+max_n50)
def de_clip(filename, n_iter):
g = nx.MultiDiGraph()
# count = 0
with open(filename,'r') as f:
for line in f:
l = line.strip().split()
#print l2
g.add_edge(l[0],l[1],overlap=int(l[2])/2)
# if count < 10:
# print l[0], l[1], l[2]
# count += 1
node0start = int(l[7][1:])
node0end = int(l[8][:-1])
g.node[l[0]]['length'] = node0end - node0start
node1start = int(l[9][1:])
node1end = int(l[10][:-1])
g.node[l[1]]['length'] = node1end - node1start
print(nx.info(g))
try:
import ujson
mapping = ujson.load(open(filename.split('.')[0]+'.mapping.json'))
# print mapping
print('get mapping')
for node in g.nodes():
#print node
if node in mapping:
# alnstart = int(mapping[node][0])
# alnend = int(mapping[node][1])
# g.node[node]['length'] = abs(alnend-alnstart)
# print abs(alnend-alnstart)
g.node[node]['aln_strand'] = mapping[node][3]
# g.node[node]['aln_start'] = mapping[node][0]
# g.node[node]['aln_end'] = mapping[node][1]
# g.node[node]['aln_strand'] = mapping[node][2]
else:
# g.node[node]['length'] = 5000
g.node[node]['aln_strand'] = 5
# print "this happened"
# g.node[node]['aln_start'] = 0
# g.node[node]['aln_end'] = 0
# g.node[node]['aln_strand'] = 0
except:
pass
degree_sequence=sorted(list(g.degree().values()),reverse=True)
print(Counter(degree_sequence))
for i in range(n_iter):
for node in g.nodes():
if g.degree(node) < 2:
g.remove_node(node)
print(nx.info(g))
degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
print(Counter(degree_sequence))
degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
print(Counter(degree_sequence))
g.graph['aval'] = 1000000000
for i in range(5):
merge_simple_path(g)
degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
print(Counter(degree_sequence))
nx.write_graphml(g, filename.split('.')[0]+'.graphml')
print(nx.number_weakly_connected_components(g))
print(nx.number_strongly_connected_components(g))
# Next we create the gfa file
outputfile = filename.split('.')[0]+'.gfa'
with open(outputfile, 'w') as fout:
for cur_node in g.nodes():
node_length = g.node[cur_node]['length']
node_str = 'A'*node_length
node_str = node_str + '\n'
fout.write("NODE "+str(cur_node)+' 0 0 0 0 0\n')
fout.write(node_str)
fout.write(node_str)
# print "NODE "+str(node)
for arc in g.edges():
fout.write("ARC "+str(arc[0])+' '+str(arc[1])+' 0\n')
# Compute N50
contig_lengths = []
for cur_node in g.nodes():
contig_lengths.append(g.node[cur_node]['length'])
print("N50 = "+str(comp_n50(contig_lengths)))
filename = sys.argv[1]
de_clip(filename, 5)
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