fastq_parser.py

"""
This script will print (std out) the read_id, read_seq and read_qual from the input fastq file.

Input:
#######
    * -i : fastq file to print values from

Output:
#######
    * read_id, read_seq and read_qual

Usage:
#######
    * python fastq-parser.py --version

    *This is the option that show you the program's version.*

    * python fastq-parser.py -h

    *This can show you some help information.*

    * python fastq-parser.py -i <filename.fastq>

    *Runs program with specified fastq file*
"""
import sys
from argparse import ArgumentParser
from Bio import SeqIO   # pylint: disable=import-error

__version__ = "1.0"
__status__ = "Dev"


def main():
    """Print read_id, read_seq and read_qual"""
    usage = "\n%prog  [options]"
    parser = ArgumentParser(description=usage)
    parser.add_argument('--version', '-V', action='version',
                        version="%(prog)s " + __version__)
    parser.add_argument("-i", "--fastqFile", action="store", dest="fastqFile",
                        help="Input fastqFile")

    options = parser.parse_args()
    for file in [options.fastqFile]:
        if not file:
            parser.print_help()
            sys.exit(0)

    fastq_file = options.fastqFile

    # qual_sum = 0
    # n = 0
    # c_count, g_count = 0, 0
    for record in SeqIO.parse(fastq_file, "fastq"):
        read_id = record.id
        read_seq = str(record.seq)
        read_qual = record.letter_annotations["phred_quality"]
        print(read_id)
        print(read_seq)
        print(read_qual)
        print("\n")

        # c_count += len(re.findall(r"C",read_seq))
        # g_count += len(re.findall(r"G",read_seq))
        # qual_sum +=  int(read_qual)
        # n += 1
    # average = qual_sum/n

    # print "total quality for the first position %s for %s reads" % (qual_sum, n)
    # print "average quality %s " %(average)
    # print c_count + g_count


if __name__ == '__main__':
    main()