convert_fastq_qual.py

#!/usr/bin/env python
from __future__ import print_function
import sys,os
import gzip
import argparse
from Bio import SeqIO

desc = 'Convert between quality fastq formats'
epi = """DESCRIPTION:
  Convert between fastq quality formats by using biopython.
  The input fastq can be gzip'ed.
  The output is written to STDOUT

  --Formats--
  * "fastq" means Sanger style FASTQ files using PHRED scores and an ASCII offset of 33 (e.g. from the NCBI Short Read Archive and Illumina 1.8+). These can potentially hold PHRED scores from 0 to 93.
  * "fastq-sanger" is an alias for "fastq".
  * "fastq-solexa" means old Solexa (and also very early Illumina) style FASTQ files, using Solexa scores with an ASCII offset 64. These can hold Solexa scores from -5 to 62.
  * "fastq-illumina" means newer Illumina 1.3 to 1.7 style FASTQ files, using PHRED scores but with an ASCII offset 64, allowing PHRED scores from 0 to 62.
"""
parser = argparse.ArgumentParser(description=desc, epilog=epi,
                                 formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('fastq_file', metavar='fastq_file', type=str,
                    help='Input fastq file')
parser.add_argument('-i', '--in-format', default='fastq', type=str,
                    help='Input fastq format (default: %(default)s)')
parser.add_argument('-o', '--out-format', default='fastq-sanger', type=str,
                    help='Output fastq format (default: %(default)s)')
parser.add_argument('--version', action='version', version='0.1.0')


def main(args):
    if args.fastq_file.endswith('.gz'):
        inF = gzip.open(args.fastq_file, 'rt')
    else:
        inF = open(args.fastq_file, 'r')
    for record in SeqIO.parse(inF, args.in_format):
        print(record.format(args.out_format))
    inF.close()


if __name__ == '__main__':
    args = parser.parse_args()
    main(args)