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#!/usr/bin/env python
import sys
import numpy as np
from operator import itemgetter
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-b",
"--bedpe_file",
dest="bedpe_file",
help="BEDPE file")
parser.add_option("-g",
"--genome_file",
dest="genome_file",
help="Genome file")
(options, args) = parser.parse_args()
if not options.bedpe_file:
parser.error('BEDPE file not given')
f = open(options.bedpe_file,'r')
B = {}
for l in f:
A = l.rstrip().split('\t')
if not A[0] in B:
B[A[0]] = []
B[A[0]].append([int(A[1]), l.rstrip()])
f.close()
order=[]
if options.genome_file:
f = open(options.genome_file,'r')
for l in f:
A = l.rstrip().split('\t')
order.append(A[0])
f.close()
else:
order = sorted(B.keys())
for c in order:
if c in B:
for l in sorted(B[c], key=itemgetter(0)):
print(l[1])
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