qualmask.py

#!/usr/bin/env python3
"""
Mask low-quality bases in a FASTQ file with 'N'.
Adjust cutoff_front and cutoff_back below to use
different thresholds (currently: 20 at 5' end,
0 at 3' end).

Usage:
  python3 qualmask.py input.fastq.gz > output.fastq

Or with compression:
  python3 qualmask.py input.fastq.gz | gzip > output.fastq.gz
"""
from __future__ import print_function
from cutadapt.qualtrim import quality_trim_index
from cutadapt.seqio import open as openseq
import sys

masked = 0
with openseq(sys.argv[1]) as reader:
	with openseq(sys.stdout, mode='w', fileformat='fastq') as writer:
		for read in reader:
			# (start, stop) describes where the good-quality part of the read is
			start, stop = quality_trim_index(read.qualities, cutoff_front=20, cutoff_back=0)
			read.sequence = 'N' * start + read.sequence[start:stop] + 'N' * (len(read.sequence) - stop)
			masked += stop - start
			writer.write(read)
print('Masked', masked, 'bases', file=sys.stderr)