OpenVariant provides different functionalities to read, parse and operate different multiple input file formats, being able to customize the output.
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
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:
Check User guide in OpenVariant's documentation to find all the information about how it works and how can be applied the different functionalities.
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.
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
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.
The software is licensed under BSD-3-Clause.
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
FAQs
OpenVariant provides different functionalities to read, parse and operate different multiple input file formats, being able to customize the output.
We found that open-variant demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
Research
Security News
Socket’s Threat Research Team has uncovered 60 npm packages using post-install scripts to silently exfiltrate hostnames, IP addresses, DNS servers, and user directories to a Discord-controlled endpoint.
Security News
TypeScript Native Previews offers a 10x faster Go-based compiler, now available on npm for public testing with early editor and language support.
Research
Security News
Malicious npm packages targeting React, Vue, Vite, Node.js, and Quill remained undetected for two years while deploying destructive payloads.