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OpenVariant is a comprehensive Python package that provides different functionalities to read, parse and operate different multiple input file formats (e. g. tsv, csv, vcf, maf, bed), being able to customize the output.

Its aim is being able to manage a ton of data represented in multiple ways and be able to build an unified output with a proper annotation file structure. This package was thought to work with any kind of data that can be represented as a table.

Documentation: https://openvariant.readthedocs.io

Features

OpenVariant offers a toolkit to transform and operate the parsed input data. We will be able to apply different functionalities on our parsed result some of them are the following ones:

Find files
Read and save
Cat
Group by
Count
Command-line interface (CLI)
Plugins

Check User guide in OpenVariant's documentation to find all the information about how it works and how can be applied the different functionalities.

Installation

It requires Python 3 or higher and can be installed as PyPI package with:

pip install open-variant

For more details check our Installation section.

Running with Docker

You can quickly build and run OpenVariant using Dockerfile without installing dependencies locally:

docker build -t openvariant .
docker run --rm openvariant openvar --help

Examples

We provide a variety of examples to help to understand how OpenVariant can be applied. Explore the Examples section in OpenVariant's documentation for more details.

As well, we present a small dataset for hands-on use with OpenVariant, allowing users to test the tool's functionalities. It may be found at Zenodo and it can be downloaded using the following commands:

pip install zenodo_get                      
zenodo_get 14215914

Contributing

You're welcome to contribute to the code as much as you'd like!

Please review the guidelines outlined in the Contributing document and adhere to the standards of conduct detailed in the Code of Conduct.

License

The software is licensed under BSD-3-Clause.

Reference

If you use OpenVariant in your research, please cite:

David Martínez-Millán, Federica Brando, Miguel L. Grau, Mònica Sánchez-Guixé, Carlos López-Elorduy, Iker Reyes-Salazar, Jordi Deu-Pons, Núria López-Bigas, Abel González-Pérez, OpenVariant: a toolkit to parse and operate multiple input file formats, Bioinformatics, Volume 40, Issue 12, December 2024, btae714, https://doi.org/10.1093/bioinformatics/btae714

License

bbglab/openvariant

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