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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.

Examples

We offer a bunch of Examples to we be able to understand how OpenVariant can be applied. Also, check Examples section in OpenVariant's documentation.

Contributing

Feel free to contribute as much as you want to the code.

See CONTRIBUTING for guidelines on contributing and respect your behaviour specified at CODE OF CONDUCT.

License

The software is licensed under BSD-3-Clause.