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open-variant

Read, parse and operate different multiple input file formats with OpenVariant

https://github.com/bbglab/openvariant

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.8%) to scientific vocabulary

Keywords

bbglab bioinformatics openvar openvariant python
Last synced: 6 months ago · JSON representation ·

Repository

Read, parse and operate different multiple input file formats with OpenVariant

Basic Info
Statistics
  • Stars: 13
  • Watchers: 6
  • Forks: 3
  • Open Issues: 4
  • Releases: 38
Topics
bbglab bioinformatics openvar openvariant python
Created over 4 years ago · Last pushed 9 months ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md



License PyPi Test Coverage Documentation Status

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:

bash 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:

bash 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: 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 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

Owner

  • Name: BBGLab - Barcelona Biomedical Genomics Lab
  • Login: bbglab
  • Kind: organization
  • Email: bbglab@irbbarcelona.org
  • Location: Barcelona

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use OpenVariant in your research, please cite it as below."
title: "OpenVariant: a toolkit to parse and operate multiple input file formats"
authors:
  - family-names: "Martínez-Millán"
    given-names: "David"
    orcid: "https://orcid.org/0000-0002-4903-029X"
  - family-names: "Brando"
    given-names: "Federica"
    orcid: "https://orcid.org/0000-0003-0537-0281"
  - family-names: "L. Grau"
    given-names: "Miguel"
    orcid: "https://orcid.org/0000-0002-5137-9976"
  - family-names: "Sánchez-Guixé"
    given-names: "Mònica"
    orcid: "https://orcid.org/0000-0002-9430-4413"
  - family-names: "López-Elorduy"
    given-names: "Carlos"
    orcid: "https://orcid.org/0000-0001-8971-9051"
  - family-names: "Reyes-Salazar"
    given-names: "Iker"
  - family-names: "Deu-Pons"
    given-names: "Jordi"
    orcid: "https://orcid.org/0000-0002-1150-1586"
  - family-names: "López-Bigas"
    given-names: "Núria"
    orcid: "https://orcid.org/0000-0003-4925-8988"
  - family-names: "González-Pérez"
    given-names: "Abel"
    orcid: "https://orcid.org/0000-0002-8582-4660"
date-released: "2024-12-02"
version: "1.0.0"
doi: "10.1093/bioinformatics/btae714"
url: "https://doi.org/10.1093/bioinformatics/btae714"
journal: "Bioinformatics"
volume: "40"
issue: "12"
license: "CC-BY-4.0"
preferred-citation:
  type: article
  authors:
  - family-names: "Martínez-Millán"
    given-names: "David"
    orcid: "https://orcid.org/0000-0002-4903-029X"
  - family-names: "Brando"
    given-names: "Federica"
    orcid: "https://orcid.org/0000-0003-0537-0281"
  - family-names: "L. Grau"
    given-names: "Miguel"
    orcid: "https://orcid.org/0000-0002-5137-9976"
  - family-names: "Sánchez-Guixé"
    given-names: "Mònica"
    orcid: "https://orcid.org/0000-0002-9430-4413"
  - family-names: "López-Elorduy"
    given-names: "Carlos"
    orcid: "https://orcid.org/0000-0002-9430-4413"
  - family-names: "Reyes-Salazar"
    given-names: "Iker"
  - family-names: "Deu-Pons"
    given-names: "Jordi"
    orcid: "https://orcid.org/0000-0002-1150-1586"
  - family-names: "López-Bigas"
    given-names: "Núria"
    orcid: "https://orcid.org/0000-0003-4925-8988"
  - family-names: "González-Pérez"
    given-names: "Abel"
    orcid: "https://orcid.org/0000-0002-8582-4660"
  title: "OpenVariant: a toolkit to parse and operate multiple input file formats"
  doi: "10.1093/bioinformatics/btae714"
  journal: "Bioinformatics"
  volume: "40"
  issue: "12"
  year: 2024

GitHub Events

Total
  • Fork event: 2
  • Create event: 22
  • Release event: 2
  • Issues event: 11
  • Watch event: 12
  • Delete event: 19
  • Member event: 1
  • Issue comment event: 32
  • Push event: 78
  • Pull request review comment event: 13
  • Gollum event: 3
  • Pull request review event: 31
  • Pull request event: 38
Last Year
  • Fork event: 2
  • Create event: 22
  • Release event: 2
  • Issues event: 11
  • Watch event: 12
  • Delete event: 19
  • Member event: 1
  • Issue comment event: 32
  • Push event: 78
  • Pull request review comment event: 13
  • Gollum event: 3
  • Pull request review event: 31
  • Pull request event: 38

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 241
  • Total Committers: 7
  • Avg Commits per committer: 34.429
  • Development Distribution Score (DDS): 0.116
Top Committers
Name Email Commits
David Martinez d****z@i****g 213
David Martínez 1****n@u****m 7
CarlosLopezElorduy c****z@i****g 7
Carlos López Elorduy 1****y@u****m 5
dependabot[bot] 4****]@u****m 3
Federica Brando f****o@i****g 3
David d****n@h****m 3
Committer Domains (Top 20 + Academic)
irbbarcelona.org: 3

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 21
  • Total pull requests: 30
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 16 days
  • Total issue authors: 5
  • Total pull request authors: 4
  • Average comments per issue: 2.05
  • Average comments per pull request: 0.93
  • Merged pull requests: 26
  • Bot issues: 0
  • Bot pull requests: 12
Past Year
  • Issues: 6
  • Pull requests: 21
  • Average time to close issues: 26 days
  • Average time to close pull requests: 3 days
  • Issue authors: 5
  • Pull request authors: 3
  • Average comments per issue: 3.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 9
View more stats
Top Authors
Issue Authors
  • dmartmillan (10)
  • FedericaBrando (7)
  • CarlosLopezElorduy (3)
  • ScarpettaDavide (1)
  • Benoitdw (1)
Pull Request Authors
  • dependabot[bot] (21)
  • FedericaBrando (16)
  • dmartmillan (15)
  • CarlosLopezElorduy (2)
Top Labels
Issue Labels
bug (6) enhancement (6) documentation (2) test (1)
Pull Request Labels
dependencies (25) enhancement (12) bug (9) documentation (6) test (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 197 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 74
  • Total maintainers: 2
pypi.org: open-variant

OpenVariant provides different functionalities to read, parse and operate different multiple input file formats, being able to customize the output.

  • Homepage: https://github.com/bbglab/openvariant
  • Documentation: https://openvariant.readthedocs.io/
  • 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.
  • Latest release: 1.1.0
    published 11 months ago
  • Versions: 74
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 197 Last month
Rankings
Dependent packages count: 10.0%
Downloads: 10.6%
Average: 19.4%
Dependent repos count: 21.7%
Forks count: 22.6%
Stargazers count: 31.9%
Maintainers (2)
bbglab FBrando
Last synced: 6 months ago

Dependencies

.github/workflows/openvariant_tester.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
  • codecov/codecov-action v3 composite
pyproject.toml pypi
uv.lock pypi
  • alabaster 0.7.12
  • appdirs 1.4.4
  • asttokens 2.0.5
  • attrs 22.1.0
  • babel 2.10.3
  • backcall 0.2.0
  • beautifulsoup4 4.11.1
  • bleach 5.0.1
  • certifi 2024.8.30
  • cffi 1.17.1
  • charset-normalizer 2.1.0
  • click 8.1.3
  • colorama 0.4.6
  • coverage 7.6.9
  • decorator 5.1.1
  • defusedxml 0.7.1
  • docutils 0.17.1
  • entrypoints 0.4
  • exceptiongroup 1.2.2
  • executing 0.9.1
  • fastjsonschema 2.16.1
  • flake8 7.1.1
  • idna 3.7
  • imagesize 1.4.1
  • iniconfig 2.0.0
  • ipython 8.18.0
  • jedi 0.18.1
  • jinja2 3.1.4
  • jsonschema 4.8.0
  • jupyter-client 7.3.4
  • jupyter-core 4.11.2
  • jupyterlab-pygments 0.2.2
  • latexcodec 3.0.0
  • markupsafe 2.1.1
  • matplotlib-inline 0.1.3
  • mccabe 0.7.0
  • mistune 2.0.3
  • nbclient 0.6.6
  • nbconvert 7.0.0rc0
  • nbformat 5.4.0
  • nbsphinx 0.8.9
  • nest-asyncio 1.5.5
  • open-variant *
  • packaging 21.3
  • pandocfilters 1.5.0
  • parso 0.8.3
  • pexpect 4.8.0
  • pickleshare 0.7.5
  • pluggy 1.5.0
  • prompt-toolkit 3.0.30
  • ptyprocess 0.7.0
  • pure-eval 0.2.2
  • pybtex 0.24.0
  • pybtex-docutils 1.0.3
  • pycodestyle 2.12.1
  • pycparser 2.22
  • pydata-sphinx-theme 0.8.1
  • pyflakes 3.2.0
  • pygments 2.15.0
  • pyliftover 0.4.1
  • pyparsing 3.0.9
  • pyrsistent 0.18.1
  • pytest 8.3.4
  • pytest-cov 6.0.0
  • python-dateutil 2.8.2
  • pytz 2022.1
  • pywin32 308
  • pyyaml 6.0.1
  • pyzmq 26.2.0
  • requests 2.32.2
  • ruamel-yaml 0.16.13
  • ruff 0.8.3
  • setuptools 58.2.0
  • six 1.16.0
  • snowballstemmer 2.2.0
  • soupsieve 2.3.2.post1
  • sphinx 4.5.0
  • sphinx-copybutton 0.5.0
  • sphinx-gallery 0.10.1
  • sphinx-panels 0.6.0
  • sphinxcontrib-applehelp 1.0.2
  • sphinxcontrib-autoyaml 1.0.0
  • sphinxcontrib-bibtex 2.6.3
  • sphinxcontrib-devhelp 1.0.2
  • sphinxcontrib-htmlhelp 2.0.0
  • sphinxcontrib-jsmath 1.0.1
  • sphinxcontrib-qthelp 1.0.3
  • sphinxcontrib-serializinghtml 1.1.5
  • stack-data 0.3.0
  • tinycss2 1.1.1
  • tomli 2.2.1
  • tornado 6.4.2
  • tqdm 4.66.3
  • traitlets 5.3.0
  • urllib3 1.26.19
  • wcwidth 0.2.5
  • webencodings 0.5.1
Dockerfile docker
  • ghcr.io/astral-sh/uv 0.5-python3.13-bookworm build
  • python 3.13-bookworm build