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#!/usr/bin/env python
# -*- coding: latin-1 -*-
'''Midpoint extend by 500 on either side of histone enhancers'''
EPILOG = '''
For more details:
%(prog)s --help
'''
import numpy
import pybedtools
import pybedtools.featurefuncs
import argparse
import os
from subprocess import Popen
def get_args():
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('-e', '--enhancers',
help="The enhancers",
required = True)
parser.add_argument('-o', '--outfile',
help="The outfile",
required = True)
args = parser.parse_args()
return args
def main():
args = get_args()
# Read in bedtools:
histone_bed = pybedtools.BedTool(args.enhancers)
chromsizes = pybedtools.helpers.chromsizes("hg19")
input_bed_mid = histone_bed.each(pybedtools.featurefuncs.midpoint)
input_extend = input_bed_mid.slop(b=500,g=chromsizes)
input_extend.saveas(args.outfile + '.bed')
if __name__ == '__main__':
main()