Random sample of a FASTQ file

fastq_sample.py

#Take a fraction of random sequence reads from a fastq file
from sh import wc
import argparse
import random

def first_word(string):
    return string.strip().split()[0]

#read a file in chunks of deflines
def read_segments(filename,deflines):
    data = []
    with open(filename) as handle:
	line = handle.readline()
	while line != "":
	    chunk = []
	    for i in range(deflines):
		chunk.append(line)
		line = handle.readline()
	    data.append("".join(chunk))
    return data

parser = argparse.ArgumentParser()
parser.add_argument("input_file",type=str,help="input fastq file")
parser.add_argument("output_signature",type=str,help="output fastq file signature")
parser.add_argument("fractions",type=int,nargs="+",help="fraction of the file to be used")
args = parser.parse_args()

#number of lines that contain a complete fastq record
deflines = 4
length = int(first_word(wc("-l",args.input_file)))
seq_reads = read_segments(args.input_file,deflines)
for n in args.fractions:
    nlines = int(length/n/deflines)
    sample = random.sample(seq_reads,nlines)
    output_file = args.output_signature+"_"+str(n)
    with open(output_file,"w") as handle:
	for seq in sample:
	    handle.write(seq)