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#!/usr/bin/python3
import networkx as nx
import sys
from collections import Counter
import json
LENGTH_THRESHOLD=10 #Connected components with less than LENGTH_THRESHOLD reads are thrown away
def merge_simple_path(g):
for node in g.nodes():
#print g.in_degree(node), g.out_degree(node)
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:
merge_path(g,in_node,node,out_node)
def merge_two_nodes(g):
for node in g.nodes():
if g.in_degree(node) == 1 and g.out_degree(node) == 0:
in_node = g.in_edges(node)[0][0]
if g.out_degree(in_node) == 1:
if in_node != node:
node_id = g.graph['aval']
g.graph['aval'] += 1
g.add_node(str(node_id),
count = g.node[in_node]['count'] + g.node[node]['count'],
read = g.node[in_node]['read'] + ':' + g.node[node]['read'],
#aln_chr = g.node[node]['aln_chr']
)
g.remove_node(in_node)
g.remove_node(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:]
g.add_node(str(node_id),
count = g.node[in_node]['count'] + g.node[node]['count'] + g.node[out_node]['count'],
read = g.node[in_node]['read'] + ':' + g.node[node]['read'] + ':' +g.node[out_node]['read'],
#aln_chr = g.node[node]['aln_chr']
)
#g.add_node(str(node_id)+'-', bases = reverse_comp_bases(bases), length = length, cov = cov)
#print g.node[str(node_id)]['chr']
for edge in g.in_edges(in_node):
g.add_edge(edge[0],str(node_id))
for edge in g.out_edges(out_node):
g.add_edge(str(node_id),edge[1])
g.remove_node(in_node)
g.remove_node(node)
g.remove_node(out_node)
def input1(flname):
g = nx.DiGraph()
with open (flname) as f:
for lines in f:
lines1=lines.split()
#print lines1
if len(lines1) < 5:
continue
#print lines1
g.add_edge(lines1[0] + "_" + lines1[3], lines1[1] + "_" + lines1[4], hinge_edge=int(lines1[5]))
g.add_edge(lines1[1] + "_" + str(1-int(lines1[4])), lines1[0] + "_" + str(1-int(lines1[3])),hinge_edge=int(lines1[5]))
return g
def input2(flname):
g = nx.DiGraph()
with open (flname) as f:
for lines in f:
lines1=lines.split()
#print lines1
g.add_edge(lines1[0], lines1[1])
return g
def run(filename, gt_file, n_iter):
f=open(filename)
line1=f.readline()
print(line1)
f.close()
if len(line1.split()) !=2:
g=input1(filename)
else:
g=input2(filename)
print(str(len(g.nodes())) + " vertices in graph to begin with.")
connected_components=[x for x in nx.weakly_connected_components(g)]
for component in connected_components:
if len(component) < 10:
g.remove_nodes_from(component)
print(str(len(g.nodes())) + " vertices in graph after removing components of at most "+str(LENGTH_THRESHOLD)+ " nodes.")
read_to_chr_map={}
if gt_file.split('.')[-1]=='json':
with open(gt_file,'r') as f:
tmp_map=json.load(f)
for read in tmp_map:
readid=int(read.strip("'"))
read_to_chr_map[readid] = int(tmp_map[read][0][2])
else:
with open(gt_file,'r') as f:
for num, line in enumerate(f.readlines()):
m = list(map(int, line.strip().split()))
read_to_chr_map[m[0]]=m[1]
nodes_seen=set([x.split("_")[0] for x in g.nodes()])
for node in nodes_seen:
read_to_chr_map.setdefault(int(node),-1)
#print nx.info(g)
print("Num reads read : "+str(len(read_to_chr_map)))
for node in g.nodes():
nodeid=int(node.split('_')[0])
g.node[node]['count'] = 1
g.node[node]['read'] = node
#print str(nodeid), node,g.node[node]['chr']
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.in_degree(node) == 0:
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))
h=nx.DiGraph()
h.add_nodes_from(g)
h.add_edges_from(g.edges())
for node in g.nodes():
reads_in_node=[int(x.split('_')[0]) for x in g.node[node]['read'].split(':')]
try:
chr_in_node=[read_to_chr_map[x] for x in reads_in_node]
except:
print(reads_in_node,g.node[node]['read'])
return
chr_in_node_set=set(chr_in_node)
if len(chr_in_node_set) ==1:
h.node[node]['chr']=chr_in_node[0]
else:
h.node[node]['chr']=':'.join(map(str,chr_in_node))
h.node[node]['count']=g.node[node]['count']
try:
h.node[node]['read']=g.node[node]['read']
except:
pass
nx.write_graphml(h, filename.split('.')[0]+'_condensed_annotated.graphml')
print(nx.number_weakly_connected_components(h))
print(nx.number_strongly_connected_components(h))
#
filename = sys.argv[1]
gt_file=sys.argv[2]
run(filename, gt_file,5)
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