fastq-handler (original) (raw)
Project description
A python module to process ONT fastq files by concatenating reads as they are generated during a sequencing run
INTRODUCTION
The fastqc-handler module screens folders and subfolders for fastq (fastq or fastq.gz format) files and concatenates them iteratively. This is useful for merging same-sample reads that are split into multiple files, as commonly obtained in ONT sequencing. The output is a one file per output fastq.gz, containing all reads from the previous files. The output directory structure is maintained.
INPUT
A directory containing fastq files. The files can be in subfolders (each representing a different sample). The files can be gzipped or not.
API
usage: fastq_handler [-h] -i IN_DIR -o OUT_DIR [-s SLEEP] [-n TAG] [--keep_names] [--monitor] [--max-size MAX_SIZE] [--downsize] [--merge]
Process fastq files.
optional arguments: -h, --help show this help message and exit -i IN_DIR, --in_dir IN_DIR Input directory -o OUT_DIR, --out_dir OUT_DIR Output directory -s SLEEP, --sleep SLEEP Sleep time -n TAG, --tag TAG name tag, if given, will be added to the output file names --keep_names keep original file names --monitor run indefinitely --max-size MAX_SIZE max size of the output file, in kilobytes --downsize downsize fastq files to max-size --merge merge files
REQUIREMENTS
Modules
- dataclasses==0.6
- natsort==8.3.1
- pandas==1.5.3
- setuptools==57.4.0
- xopen==1.7.0
INSTALLATION
python -m venv .venv source .venv/bin/activate python -m pip install fastq-handler
MAIN OUTPUTS
Note: The output directory structure is maintained.
- fastq.gz files containing all reads from the previous files.
- log.txt file containing the concatenation process.
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