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Convert USCS refFlat.txt to BED format
#!/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()
@afrendeiro

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@afrendeiro afrendeiro commented Aug 16, 2019

Very nice, thank you!

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