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#!/usr/bin/env python3
"""
Read a SAM file from standard input, replace all characters in all reads
that are not one of {a, c, g, t, n, A, C, G, T, N} with the character 'N'.
Write the modified SAM file to standard output.
This is approx. 8 times faster than an equivalent awk line using the gsub()
function.
"""
import sys
from os.path import join, dirname, realpath, isfile
from sqt import HelpfulArgumentParser
def main():
parser = HelpfulArgumentParser(usage=__doc__)
args = parser.parse_args()
tab = [ord('N')] * 256
for c in b'ACGTNacgtn':
tab[c] = c
trans = bytes(tab)
for line in sys.stdin.buffer:
if line.startswith(b'@'):
sys.stdout.buffer.write(line)
else:
fields = line.split(b'\t')
fields[9] = fields[9].translate(trans)
sys.stdout.buffer.write(b'\t'.join(fields))
if __name__ == '__main__':
main()
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