| Name | open-variant JSON |
| Version |
1.0.1
JSON |
| download |
| home_page | None |
| Summary | OpenVariant provides different functionalities to read, parse and operate different multiple input file formats, being able to customize the output. |
| upload_time | 2024-12-16 13:02:26 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | BSD 3-Clause License Copyright (c) 2021, BBGLab - Barcelona Biomedical Genomics Lab All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
bbglab
bioinformatics
openvar
openvariant
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<div align="center">
<a href="https://openvariant.readthedocs.io/">
<img src="https://github.com/bbglab/openvariant/raw/master/logo.png" width="590" height="350">
</a>
<br>
<br>
<a href="https://opensource.org/licenses/BSD-3-Clause">
<img alt="License" src="https://img.shields.io/github/license/bbglab/openvariant">
</a>
<a href="https://pypi.org/project/open-variant/">
<img alt="PyPi" src="https://img.shields.io/pypi/v/open-variant">
</a>
<a href="https://github.com/bbglab/openvariant/actions/workflows/openvariant_tester.yml">
<img alt="Test" src="https://github.com/bbglab/openvariant/actions/workflows/openvariant_tester.yml/badge.svg">
</a>
<a href="https://codecov.io/gh/bbglab/openvariant" >
<img alt="Coverage" src="https://codecov.io/gh/bbglab/openvariant/branch/develop/graph/badge.svg?token=N6HUMWS9U5"/>
</a>
<a href="https://openvariant.readthedocs.io/en/latest/?badge=latest">
<img alt="Documentation Status" src="https://readthedocs.org/projects/openvariant/badge/?version=latest">
</a>
<br>
<br>
</div>
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](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
<div align="center">
<a href="https://openvariant.readthedocs.io/en/latest/user_guide.html">
<img src="https://github.com/bbglab/openvariant/raw/master/workflow.gif" width="600" height="352">
</a>
</div>
Check [User guide](https://openvariant.readthedocs.io/en/latest/user_guide.html) 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](https://pypi.org/project/open-variant/) with:
```bash
pip install open-variant
```
For more details check our [Installation](https://openvariant.readthedocs.io/en/latest/installation.html) section.
## Examples
We provide a variety of [examples](https://github.com/bbglab/openvariant/tree/master/examples) to help to understand how OpenVariant can be applied. Explore the
[Examples](https://openvariant.readthedocs.io/en/latest/examples.html) 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](https://zenodo.org/records/14215914) and it can be downloaded using the following commands:
```bash
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](https://github.com/bbglab/openvariant/blob/master/CONTRIBUTING.md) document and adhere to the standards of conduct detailed in the [Code of Conduct](https://github.com/bbglab/openvariant/blob/master/CODE_OF_CONDUCT.md).
## License
The software is licensed under [BSD-3-Clause](https://github.com/bbglab/openvariant/blob/master/LICENSE).
## 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](https://doi.org/10.1093/bioinformatics/btae714)
Raw data
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