fastq-handler 0.2.0

A python module to process minion fastq files by concatenating reads as they are generated

Fastq Handler

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.

Maintainers

• @xiaodre21
• @santosjgnd
• @insaflu