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#!/usr/bin/env python
#Author: Duy Tin Truong (duytin.truong@unitn.it)
# at CIBIO, University of Trento, Italy
__author__ = 'Duy Tin Truong (duytin.truong@unitn.it)'
__version__ = '0.1'
__date__ = '18 Jul 2015'
import sys
import os
import argparse
def read_params():
p = argparse.ArgumentParser()
p.add_argument(
'--input_file',
required=False,
default=None,
type=str,
help='The input sam file.')
p.add_argument(
'--min_align_score',
required=True,
default=None,
type=int,
help='The sam records with alignment score smaller than this value '
'will be discarded.')
p.add_argument(
'--verbose',
required=False,
dest='quiet',
action='store_false',
help='Show all information. Default "not set".')
p.set_defaults(quiet=True)
return p.parse_args()
def main(args):
if args.input_file == None:
ifile = sys.stdin
else:
ifile = open(args.input_file, 'r')
for line in ifile:
if line[0] == '@':
sys.stdout.write(line)
else:
spline = line.split()
read_length = len(spline[9])
align_score = float(spline[11].replace('AS:i:', ''))
if align_score >= args.min_align_score * read_length / 100.0:
sys.stdout.write(line)
if __name__ == "__main__":
args = read_params()
main(args)
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