#!/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()