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Concatenate demultiplexed ONT FASTQs by barcode (for one or more runs)
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| """ | |
| Purpose: Concatenate demultiplexed FASTQs by barcode for one or more ONT runs | |
| Usage: python concat_by_barcode.py run1/fastq_pass run2/fastq_pass -o output/ | |
| Author: Bede Constantinides | |
| """ | |
| import subprocess | |
| import sys | |
| import argparse | |
| from collections import defaultdict | |
| from pathlib import Path | |
| def concatenate_fastqs_by_barcode(fastq_pass_dirs: [list[Path]], output_dir: Path): | |
| barcodes_paths = defaultdict(list) | |
| fq_ext = ".fastq.gz" | |
| barcodes = [f"barcode{str(i).zfill(2)}" for i in range(1, 97)] | |
| for barcode in barcodes: | |
| for d in fastq_pass_dirs: | |
| barcode_dir = d / barcode | |
| if barcode_dir.exists(): | |
| fastq_paths = [f for f in barcode_dir.iterdir() if str(f).endswith(fq_ext)] | |
| barcodes_paths[barcode].extend(list(map(str, fastq_paths))) | |
| output_dir.mkdir(parents=True, exist_ok=True) | |
| for barcode, fastq_paths in barcodes_paths.items(): | |
| if fastq_paths: | |
| output_path = output_dir / f"{barcode}{fq_ext}" | |
| if output_path.exists(): | |
| output_path.unlink() | |
| subprocess.run(f"cat {' '.join(fastq_paths)} > {output_path}", shell=True) | |
| print(f"Created {output_path} from files {fastq_paths}", file=sys.stderr) | |
| if __name__ == "__main__": | |
| parser = argparse.ArgumentParser(description='Concatenate demultiplexed FASTQs by barcode for one or more ONT runs.') | |
| parser.add_argument('fastq_pass_dirs', nargs='+', type=Path, help='Directories containing FASTQ files.') | |
| parser.add_argument('-o', '--output-dir', type=Path, default=Path('.'), help='Output directory for concatenated FASTQ files.') | |
| args = parser.parse_args() | |
| concatenate_fastqs_by_barcode(args.fastq_pass_dirs, args.output_dir) |
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