Convert USCS refFlat.txt to BED format

refFlat2Bed.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import argparse
import csv

def _main():
    parser = argparse.ArgumentParser(description="Convert RefFlat to BED format")
    parser.add_argument('refFlat', type=argparse.FileType('r'))
    parser.add_argument('outputBed', type=argparse.FileType('w'))
    parser.add_argument('-n', '--name', help='Name of Bed File', default='refflat')
    options = parser.parse_args()

    reader = csv.reader(options.refFlat, delimiter='\t', quotechar=None)
    writer = csv.writer(options.outputBed, delimiter='\t', quotechar=None)
    writer.writerow(['track name="{}"'.format(options.name)])

    for row in reader:
        writer.writerow((row[2], row[4], row[5], row[1]+'|'+row[0], 0, row[3], row[6], row[7], 0,
                         row[8],
                         ','.join([str(int(x) - int(y)) for x, y in zip(row[10].split(','), row[9].split(',')) if x and y]),
                         ','.join([str(int(x) - int(row[4])) for x in row[9].split(',') if x])))
    

if __name__ == '__main__':
    _main()

Very nice, thank you!