#!/usr/bin/env python

# -*- coding: latin-1 -*-
'''Take an transcript file from GRO-seq and gets the short transcripts.'''

EPILOG = '''
For more details:
        %(prog)s --help
'''

import numpy
import pybedtools
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('-t', '--transcripts',
    	help="The transcripts file defined by gro-seq",
        required = True)
    args = parser.parse_args()
    return args



def main():
    args = get_args()
    # Read in bedtools:
    transcripts = pybedtools.BedTool(args.transcripts)

    # Sort if not sorted
    transcripts_sorted = transcripts.sort()

    # Sepertate into short
    short_t = transcripts_sorted.filter(lambda c: c.length <= 9000 and c.length >= 1)

    # Save Temp files
    short_t.saveas('short_transcripts.bed')


if __name__ == '__main__':
    main()