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.
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
Release files for open-variant 1.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| open_variant-1.1.0.tar.gz | 64.0 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| open_variant-1.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 64.0 MB
Release files / open_variant-1.1.0.tar.gz
| Download URL | open_variant-1.1.0.tar.gz |
|---|---|
| Size | 64.0 MB |
| Tags | Source |
|
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| Upload date | |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.10.14
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Release files / open_variant-1.1.0-py3-none-any.whl
| Download URL | open_variant-1.1.0-py3-none-any.whl |
|---|---|
| Size | 34.0 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.10.14
|
