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#!/usr/bin/env python
#Author: Duy Tin Truong (duytin.truong@unitn.it)
# at CIBIO, University of Trento, Italy
import sys
import argparse
def read_params():
p = argparse.ArgumentParser()
p.add_argument('--input_file', required=True, default='-', type=str)
return vars(p.parse_args())
def fix_AF1(ifn):
if ifn == '-':
ifile = sys.stdin
else:
ifile = open(ifn, 'r')
for line in ifile:
if line[0] != '#':
if 'AF1=0' in line:
spline = line.split()
if spline[3] != spline[4] and spline[4].upper() in ['A', 'T', 'C', 'G']:
line = line.replace('AF1=0', 'AF1=1')
sys.stdout.write(line)
if ifn != '-':
ifile.close()
if __name__ == "__main__":
args = read_params()
fix_AF1(args['input_file'])
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