Biovalid

Quick validation of bioinformatics files

Pipeline information

• Author(s): Gino Raaijmakers
• Organization: Rijksinstituut voor Volksgezondheid en Milieu (RIVM)
• Department: Infektieziekteonderzoek, Diagnostiek en Laboratorium Surveillance (IDS), Informatiebeheer (IBR)
• Start date: 23 - 07 - 2025

About this project

Biovalid is a lightweight Python library and CLI tool for fast, robust validation of bioinformatics files such as BAM, FASTA, and FASTQ. It checks file integrity, headers, and format compliance, helping users catch common issues before downstream analysis.

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Features

• File Format Support: Validate BAM, FASTA, and FASTQ files.
• Lightweight: No dependencies.
• Dual Usage: Use as a CLI tool or import as a Python library.
• Customizable: Enable verbose logging, save logs to a file, or return boolean results.
• Extensible: Designed to support additional file formats in the future.

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Installation

Conda

conda create -n biovalid python>=3.10
conda activate biovalid
pip install biovalid

Pip

pip install biovalid

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Parameters & Usage

Command-line help

python3 -m biovalid --help

Required parameters

• -i, --input Path to the file or directory to validate

Optional parameters

• -v, --verbose Enable verbose logging
• -l, --log_file Path to a log file
• -b, --bool_mode Return True/False instead of raising exceptions

Example command

python3 -m biovalid -i /path/to/file.bam

Library usage

from biovalid import BioValidator

validator = BioValidator(file_paths="/path/to/file.bam", verbose=True)
validator.validate_files()

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Output

• Logging: Validation results and errors are printed to the console and optionally saved to a log file.
• Return values: In bool mode, returns True if all files are valid, False otherwise.

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Issues

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Future ideas

• Add support for more file formats (e.g., VCF, GFF).
• Improve error messages and reporting.
• Make the tool more user-friendly for external users.

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License

This project is licensed under the AGPL-3.0 license. See the LICENSE file for details.

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Contact

• Contact person: Gino Raaijmakers
• Email: [email protected]

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Acknowledgements

Thanks to the IDS and IBR teams at RIVM for their support and feedback.