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#!/usr/bin/env python

from Bio.SeqIO.QualityIO import FastqGeneralIterator as FqI

import argparse

if __name__ == '__main__':

    parser = argparse.ArgumentParser(description='Preprocesses data from basecalled fast5 files')

    parser.add_argument('-f', '--fastq', help='path to FASTQ file to extract')

    parser.add_argument('-o', '--output', help='desired path and name of output file')

    args = parser.parse_args()

    with open(args.output, 'w+') as output:

        for title, seq, qual in FqI(args.fastq):

            readID = str(title).split(' ')[0]

            print(readID, file=output)

exit()

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