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fast_scaled_scores.py
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fast_scaled_scores.py
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#!/usr/bin/env python2
import networkx as nx
import sys
import argparse
G = nx.Graph()
parser = argparse.ArgumentParser()
parser.add_argument("-i","--iteration", help="iteration number")
parser.add_argument("-d",'--directory',help="output directory")
args = parser.parse_args()
iteration = int(args.iteration)
def get_max_incident(start, end):
max=0
try:
for e in G.successors(start):
if (e != end and G[start][e]['weight'] > max):
max = G[start][e]['weight']
for e in G.predecessors(start):
if (e != end and G[e][start]['weight'] > max):
max = G[start][e]['weight']
except:
for e in G.neighbors(start):
if (e != end and G[start][e]['weight'] > max):
max = G[start][e]['weight']
return max
#map for node to max edge weight for it
node2weight = {}
def get_max_weight(start,end):
return max(get_max_incident(start, end), get_max_incident(end, start))
f = open(args.directory+'/contig_links_iteration_'+str(args.iteration),'r')
for line in f:
line = line.strip().split()
#LNK tig00001320_pilon tig00019085_pilon E:B 103.138095238 21659 True True True
#LNK tig00006867_pilon tig00009112_pilon E:E 0.214285714286 1 True True True
# if line[0] != "LNK":
# continue
# edgeType=line[3].split(":")
G.add_node(line[0])
G.add_node(line[1])
if line[0] not in node2weight:
node2weight[line[0]] = float(line[2])
else:
if float(line[2]) >= node2weight[line[0]]:
node2weight[line[0]] = float(line[2])
if line[1] not in node2weight:
node2weight[line[1]] = float(line[2])
else:
if float(line[2]) >= node2weight[line[1]]:
node2weight[line[1]] = float(line[2])
G.add_edge(line[0], line[1], weight=float(line[2]),isNeighbor="False", isGood="False",links=int(line[3]))
f.close()
ofile = open(args.directory+'/contig_links_scaled_iteration_'+str(args.iteration),'w')
#print 'Graph Loaded Done'
f1 = open(args.directory+'/contig_links_iteration_'+str(args.iteration),'r')
for line in f1:
#bestAlt=get_max_weight(u, v)
attrs = line.strip().split()
#print 'here'
u = attrs[0]
v = attrs[1]
w = float(attrs[2])
max_u = 0
max_v = 0
if u in node2weight:
max_u = node2weight[u]
if v in node2weight:
max_v = node2weight[v]
bestAlt = max(max_u,max_v)
if bestAlt == w:
#print 'here'
bestAlt=get_max_weight(u, v)
if bestAlt==0:
bestAlt=1
ofile.write(str(u)+'\t'+str(v)+'\t'+str(w)+'\t'+str(bestAlt)+'\t'+str(w/bestAlt)+'\t'+str(G[u][v]['links'])+'\t'+str(G[u][v]['isNeighbor'])+'\t'+str(G[u][v]['isGood'])+'\n')
#print str(u)+'\t'+str(v)+'\t'+str(w)+'\t'+str(bestAlt)+'\t'+str(w/bestAlt)+'\t'+str("FALSE")+'\t'+str("FALSE")+'\t'+str("FALSE")
#print "%s %s %f %f %f %d %s %s"%(u, v, d, bestAlt, d/bestAlt, G[u][v]['links'],G[u][v]['isNeighbor'], G[u][v]['isGood'])
ofile.close()
f1.close()