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#!/usr/bin/python3
import networkx as nx
import sys
graphml_file = sys.argv[1]
groundtruth_file = sys.argv[2]
graphml_file_w_groundtruth = sys.argv[3]
try:
chromosome_to_consider= int(sys.argv[4])
except:
chromosome_to_consider=None
g = nx.read_graphml(graphml_file)
print(nx.info(g))
mapping_dict = {}
with open(groundtruth_file,'r') as f:
for num, line in enumerate(f.readlines()):
m = list(map(int, line.strip().split()))
# mapping_dict[num] = [min(m), max(m), int(m[0]>m[1])]
mapping_dict[num] = [m[2],m[3],m[1]]
#print mapping_dict
max_len=0
for num in list(mapping_dict.keys()):
max_len=max(max_len,len(str(m[3])))
pow_mov=10**(max_len+1)
for node in g.nodes():
#print node
try:
nodeid = int(node.split('_')[0])
#print nodeid
rev = int(node.split('_')[1])
if chromosome_to_consider != None:
g.node[node]['chromosome'] = 0
if mapping_dict[nodeid][2]==chromosome_to_consider:
g.node[node]['chromosome'] = mapping_dict[nodeid][2]+1
else:
g.node[node]['chromosome'] = mapping_dict[nodeid][2]+1
if rev == 0:
g.node[node]['aln_end'] = mapping_dict[nodeid][2]*pow_mov+ mapping_dict[nodeid][1]
g.node[node]['aln_start'] = mapping_dict[nodeid][2]*pow_mov + mapping_dict[nodeid][0]
# g.node[node]['aln_strand'] = mapping_dict[nodeid][2]
else:
g.node[node]['aln_end'] = mapping_dict[nodeid][2]*pow_mov + mapping_dict[nodeid][1]
g.node[node]['aln_start'] = mapping_dict[nodeid][2]*pow_mov+ mapping_dict[nodeid][0]
# g.node[node]['aln_strand'] = 1-mapping_dict[nodeid][2]
except:
pass
nx.write_graphml(g, graphml_file_w_groundtruth)
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