run_trimgalore.py

import os
import argparse
import subprocess

def ensure_dir_exists(dir_path):
    if not os.path.exists(dir_path):
        os.makedirs(dir_path)

def run_trimgalore(input_dir, output_dir, threads, length, quality):
    trimgalore_output_dir = os.path.join(output_dir, 'TrimGalore')
    ensure_dir_exists(trimgalore_output_dir)

    fastq_files = [f for f in os.listdir(input_dir) if f.endswith('.fastq.gz')]
    fastq_pairs = {}
    
    for fastq_file in fastq_files:
        if '_R1.fastq.gz' in fastq_file:
            base_name = fastq_file.replace('_R1.fastq.gz', '')
            fastq_pairs[base_name] = [fastq_file]
        elif '_R2.fastq.gz' in fastq_file:
            base_name = fastq_file.replace('_R2.fastq.gz', '')
            if base_name in fastq_pairs:
                fastq_pairs[base_name].append(fastq_file)
            else:
                fastq_pairs[base_name] = [fastq_file]

    for base_name, pair in fastq_pairs.items():
        if len(pair) == 2:
            r1_path = os.path.join(input_dir, pair[0])
            r2_path = os.path.join(input_dir, pair[1])
            cmd = [
                'trim_galore',
                '--paired',
                '--fastqc',
                '--quality', str(quality),
                '--length', str(length),
                '--adapter', 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC',
                '--adapter2', 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT',
                '--cores', str(threads),
                '--output_dir', trimgalore_output_dir,
                r1_path, r2_path
            ]
            subprocess.run(cmd, check=True)

def main():
    parser = argparse.ArgumentParser(description='Run TrimGalore on FASTQ files.')
    parser.add_argument('-i', '--input_dir', required=True, help='Directory containing input FASTQ files.')
    parser.add_argument('-o', '--output_dir', required=True, help='Directory to store output files.')
    parser.add_argument('-t', '--threads', type=int, default=1, help='Number of threads to use for TrimGalore.')
    parser.add_argument('--length', type=int, default=40, help='Minimum paired-end read length to allow retention. Default is 40')
    parser.add_argument('--quality', type=int, default=20, help='Trim low-quality ends from reads in addition to adapter removal. Default is 20.')
    args = parser.parse_args()

    input_dir = os.path.abspath(args.input_dir)
    output_dir = os.path.abspath(args.output_dir)

    ensure_dir_exists(output_dir)
    
    run_trimgalore(input_dir, output_dir, args.threads, args.length, args.quality)

if __name__ == "__main__":
    main()