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#!/usr/bin/env python2.7
import sys
import os
debug = os.environ.get("debug", False)
from subprocess import Popen
from subprocess import PIPE
def get_length(fn):
cmd = 'grep "^>" ' + fn + " -v | tr -d '\\n' | wc -c"
if debug:
print "loading sequence end points"
print "executing: " + cmd
points_fh = Popen(cmd, stdout=PIPE, shell=True)
return int(points_fh.stdout.readline())
if len(sys.argv) < 2:
print "filter_average_binding.py foreground.fa binding_distance"
exit()
foreground = sys.argv[1]
distance = int(sys.argv[2])
genome_length = get_length(foreground)
for line in sys.stdin:
(mer, count) = line.split()
if (genome_length / int(count)) < distance:
sys.stdout.write(line)
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