Randomly subsamples a directory of fastq.gz files, writes out subsampled fastq files to output directory

random_subsample_fastq.py

#!/usr/bin/env

from sys import argv
from random import random

#from gzip import open as gz_open
from glob import glob

import gzip
import os

from os.path import abspath, basename, exists, dirname, join, splitext, isfile


from skbio.util import remove_files, create_dir
from cogent.parse.fastq import MinimalFastqParser

threshold = 0.03 # random value between 0 and 1 to retain read, using 3% now
input_dir = argv[1]
output_dir = argv[2]

create_dir(output_dir)

fastq_files = []

fastq_files = glob(input_dir + "/*.fastq.gz")
        


for curr_file in fastq_files:

    if curr_file.endswith('.gz'):
        query_reads = gzip.open(curr_file, "rb")
    else:
        query_reads = open(curr_file, "U")
        
    curr_outfile = join(output_dir, basename(curr_file).replace(".fastq.gz", ".fastq"))
    

    out_f = open(curr_outfile, "w")
    for read_data in MinimalFastqParser(query_reads, strict=False):
        if random() < threshold:
            curr_read = "@%s\n" % read_data[0]
            curr_read += "%s\n" % read_data[1]
            curr_read += "+\n"
            curr_read += "%s\n" % read_data[2]
            out_f.write(curr_read)
            
    query_reads.close()
    out_f.close()