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#!/usr/bin/python3
import networkx as nx
import random
import sys
from collections import Counter
# This script does a random condensation of the graph down to 2000 nodes
# python3 random_condensation.py ecoli.edges 2000
# It also keeps the ground truth on the graph through the condensation steps (if a json file is available)
def merge_path(g,in_node,node,out_node):
g.add_edge(in_node,out_node,hinge_edge = -1,false_positive = 0)
g.remove_node(node)
def input1(flname):
print("input1")
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):
print("input2")
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 input3(flname):
print("input3")
# g = nx.DiGraph()
g = nx.read_graphml(flname)
def de_clip(filename, n_nodes, hinge_list,gt_file):
n_iter = 5
f=open(filename)
line1=f.readline()
print(line1)
f.close()
extension = filename.split('.')[-1]
if extension == 'graphml':
g=input3(filename)
elif len(line1.split()) !=2:
g=input1(filename)
else:
g=input2(filename)
print(nx.info(g))
degree_sequence=sorted(list(g.degree().values()),reverse=True)
print(Counter(degree_sequence))
degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
print(Counter(degree_sequence))
try:
import ujson
mapping = ujson.load(open(gt_file))
print('getting mapping')
mapped_nodes=0
print(str(len(mapping)))
print(str(len(g.nodes())))
for node in g.nodes():
# print node
node_base=node.split("_")[0]
# print node_base
#print node
if node_base in mapping:
g.node[node]['aln_start'] = min (mapping[node_base][0][0],mapping[node_base][0][1])
g.node[node]['aln_end'] = max(mapping[node_base][0][1],mapping[node_base][0][0])
g.node[node]['chr'] = mapping[node_base][0][2]
mapped_nodes+=1
else:
# pass
g.node[node]['aln_start'] = 0
g.node[node]['aln_end'] = 0
g.node[node]['aln_strand'] = 0
for edge in g.edges_iter():
in_node=edge[0]
out_node=edge[1]
# print 'akjdfakjhfakljh'
if ((g.node[in_node]['aln_start'] < g.node[out_node]['aln_start'] and
g.node[out_node]['aln_start'] < g.node[in_node]['aln_end']) or
(g.node[in_node]['aln_start'] < g.node[out_node]['aln_end'] and
g.node[out_node]['aln_end'] < g.node[in_node]['aln_end'])):
g.edge[in_node][out_node]['false_positive']=0
else:
g.edge[in_node][out_node]['false_positive']=1
except:
raise
# print "json "+filename.split('.')[0]+'.mapping.json'+" not found. exiting."
print(hinge_list)
print(str(mapped_nodes)+" out of " +str(len(g.nodes()))+" nodes mapped.")
# for i in range(5):
# merge_simple_path(g)
# degree_sequence=sorted(nx.degree(g).values(),reverse=True)
# print Counter(degree_sequence)
in_hinges = set()
out_hinges = set()
num_iter=10000
iter_done=0
if hinge_list != None:
print("Found hinge list.")
with open(hinge_list,'r') as f:
for lines in f:
lines1=lines.split()
if lines1[2] == '1':
in_hinges.add(lines1[0]+'_0')
out_hinges.add(lines1[0]+'_1')
elif lines1[2] == '-1':
in_hinges.add(lines1[0]+'_1')
out_hinges.add(lines1[0]+'_0')
print(str(len(in_hinges))+' hinges found.')
for node in g.nodes():
if node in in_hinges and node in out_hinges:
g.node[node]['hinge']=100
elif node in in_hinges:
g.node[node]['hinge']=10
elif node in out_hinges:
g.node[node]['hinge']=-10
else:
g.node[node]['hinge']=0
while len(g.nodes()) > n_nodes and iter_done < num_iter :
node = g.nodes()[random.randrange(len(g.nodes()))]
iter_done+=1
# print iter_done
if g.in_degree(node) == 1 and g.out_degree(node) == 1:
base_node=node.split("_")[0]
orintation = node.split("_")[1]
# if orintation=='1':
# node2=base_node+'_0'
# else:
# node2=base_node+'_1'
# print node,node2
in_node = g.in_edges(node)[0][0]
out_node = g.out_edges(node)[0][1]
if g.node[node]['hinge']==0 and g.node[in_node]['hinge']==0 and g.node[out_node]['hinge']==0:
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:
bad_node=False
# print g.in_edges(node)
# print g.edge[g.in_edges(node)[0][0]][g.in_edges(node)[0][1]]
# print g.out_edges(node)
for in_edge in g.in_edges(node):
if g.edge[in_edge[0]][in_edge[1]]['false_positive']==1:
bad_node=True
for out_edge in g.out_edges(node):
if g.edge[out_edge[0]][out_edge[1]]['false_positive']==1:
bad_node=True
if not bad_node:
#print in_node, node, out_node
merge_path(g,in_node,node,out_node)
# print g.edge[edge1[0]][edge1[1]]['hinge_edge']
for nd in g.nodes():
if len(nd.split("_"))==1:
print(nd + " in trouble")
# in_node = g.in_edges(node2)[0][0]
# out_node = g.out_edges(node2)[0][1]
# if g.node[node2]['hinge']==0 and g.node[in_node]['hinge']==0 and g.node[out_node]['hinge']==0:
# if g.out_degree(in_node) == 1 and g.in_degree(out_node) == 1:
# if in_node != node2 and out_node != node2 and in_node != out_node:
# bad_node=False
# for in_edge in g.in_edges(node2):
# if g.edge[in_edge]==1:
# bad_node=True
# for out_edge in g.out_edges(node2):
# if g.edge[out_edge]==1:
# bad_node=True
# if not bad_node:
# #print in_node, node, out_node
# merge_path(g,in_node,node2,out_node)
# for nd in g.nodes():
# print nd
else:
while len(g.nodes()) > n_nodes:
node = g.nodes()[random.randrange(len(g.nodes()))]
if g.in_degree(node) == 1 and g.out_degree(node) == 1:
# assert g.in_degree(node2) == 1 and g.out_degree(node2) == 1
# edge_1 = g.out_edges(node)[0]
# edge_2 = g.in_edges(node)[0]
edge1 = g.out_edges(node)[0]
edge2 = g.in_edges(node)[0]
# print g.edge[edge1[0]][edge1[1]]['hinge_edge']
if (g.edge[edge1[0]][edge1[1]]['hinge_edge'] == -1 and g.edge[edge2[0]][edge2[1]]['hinge_edge'] == -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:
#print in_node, node, out_node
merge_path(g,in_node,node,out_node)
degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
print(Counter(degree_sequence))
nx.write_graphml(g, filename.split('.')[0]+'.sparse3.graphml')
print(nx.number_weakly_connected_components(g))
print(nx.number_strongly_connected_components(g))
if __name__ == "__main__":
filename = sys.argv[1]
try :
hinge_list=sys.argv[3]
print("Found hinge list.")
except:
hinge_list=None
print("in except "+hinge_list)
de_clip(filename, int(sys.argv[2]),hinge_list, sys.argv[4])
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