#!/usr/bin/env python3.7

# Author: Roujia Li
# email: Roujia.li@mail.utoronto.ca

import argparse
import os
from TileSeqMut.random_ds import random_lines

parser = argparse.ArgumentParser()

parser.add_argument("-input", help="input folder contains original fastq files")
parser.add_argument("-n", help="number of lines to downsample to", type=int)

args = parser.parse_args()

n = args.n

for f in os.listdir(args.input):
    if (".fastq" in f) and ("_R1_" in f):
        r2 = f.replace("_R1_", "_R2_")

        r1 = os.path.join(args.input, f)
        r2 = os.path.join(args.input, r2)

        if f.endswith(".fastq.gz"):
            os.system("gunzip " + r1)
            os.system("gunzip " + r2)
            r1 = r1.replace(".gz", "")
            r2 = r2.replace(".gz", "")

        random_lines(r1, r2, n)

