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#!/usr/local/bin/python
import sys
import subprocess
import os
import numpy as np
if len(sys.argv) < 3:
print('usage:' + sys.argv[0] + ' <max> <out file> <in bam 1> <in bam 2> <..>')
exit(1)
max_c = int(sys.argv[1])
out_file = sys.argv[2]
o = open('.exclude.tmp','w')
for i in range(3,len(sys.argv)):
bam_file = sys.argv[i]
coverage_file = bam_file + '.coverage'
f = open(coverage_file, 'r')
for l in f:
a = l.rstrip().split('\t')
if (int(a[3]) > max_c):
o.write(l)
f.close()
o.close()
p = subprocess.Popen(\
'cat .exclude.tmp | ' \
'sort -S 20G -k1,1 -k2,2n | ' \
'bedtools merge -i stdin -d 50 ' \
'> ' + out_file, shell=True)
os.waitpid(p.pid, 0)
os.unlink('.exclude.tmp')
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