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#!/usr/bin/env python
import sys
import numpy as np
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-i",
"--bedpe",
dest="bedpe",
help="BEDPE file")
parser.add_option("-n",
"--name",
default="LUMPY BedGraph",
dest="name",
help="Name")
(options, args) = parser.parse_args()
if not options.bedpe:
parser.error('BEDPE file not given')
f = open(options.bedpe,'r')
print('track type=bedGraph name="' + options.name + '"')
for line in f:
if line[0] == '#':
continue
v = line.rstrip().split('\t')
info = dict()
for s in v[12].split(';'):
s_v = s.split('=')
if len(s_v) == 2:
info[s_v[0]] = s_v[1]
L=[float(x) for x in info['PRPOS'].split(',')]
R=[float(x) for x in info['PREND'].split(',')]
l_chr = v[0]
l_start = int(v[1])
r_chr = v[3]
r_start = int(v[4])
c = 0
for p in L:
print('\t'.join( [l_chr,
str(l_start + c),
str(l_start + c + 1),
str(p)]))
c+=1
c = 0
for p in R:
print('\t'.join( [r_chr,
str(r_start + c),
str(r_start + c + 1),
str(p)]))
c+=1
f.close()
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