Randomly pick out some of the line triples in a fastq file and write to a new fastq file.

make_random_test_fastq.py

"""Randomly picks out some title / sequence / quality triples
from a given fastq file and writes them in to a new fastq file.

This is to generate rudimentary test data which doesn't take too long to run.

Usage: make_random_test_fastq.py <fastq_file> <target file size in MB>
"""
import os
import sys
from random import random
from optparse import OptionParser
from Bio.SeqIO.QualityIO import FastqGeneralIterator


def main(fastq, target_size):
    # File sizes are in terms of MB.
    big_file_size = float(os.path.getsize(fastq)) / 1048576.
    probability = target_size / big_file_size

    in_handle = open(fastq, "r")
    out_handle = open(fastq.split("_fastq.")[0] + \
                    "_random_sample_fastq.txt", "w+")

    for title, sequence, quality in FastqGeneralIterator(in_handle):
        if random() < probability:
            out_handle.write("@%s\n%s\n+\n%s\n" % (title, sequence, quality))

    in_handle.close()
    out_handle.close()

if __name__ == '__main__':
    parser = OptionParser()
    _, args = parser.parse_args()
    if len(args) == 2:
        fastq, target_size = args
    else:
        print(__doc__)
        sys.exit()

    main(fastq, float(target_size))