Metadata-Version: 2.1
Name: querynator
Version: 0.2.1
Summary: Python package to query cancer variant databases
Home-page: https://github.com/qbic-pipelines/querynator
Author: Susanne Jodoin, Mark Polster
Author-email: susanne.jodoin@qbic.uni-tuebingen.de, mark.polster@uni-tuebingen.de
License: MIT license
Keywords: querynator
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.8,<3.11
License-File: LICENSE

==========
querynator
==========


.. image:: https://img.shields.io/pypi/v/querynator.svg
        :target: https://pypi.python.org/pypi/querynator

.. image:: https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2Fqbic-pipelines%2Fquerynator%2Fbadge%3Fref%3Dmaster&style=flat-square
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.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
        :target: https://github.com/psf/black

.. image:: https://img.shields.io/badge/code%20style-prettier-ff69b4.svg
        :target: https://github.com/prettier/prettier

.. image:: https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336
        :target: https://pycqa.github.io/isort

.. image:: https://readthedocs.org/projects/querynator/badge/?version=latest
        :target: https://querynator.readthedocs.io/en/latest/?version=latest
        :alt: Documentation Status




Python package to query cancer variant databases


* Free software: MIT license
* Documentation: https://querynator.readthedocs.io.


Features
--------

* Command-line tool to query the `cancergenomeinterpreter <https://www.cancergenomeinterpreter.org/home>`_ via its REST API
* Command-line tool to query the `Clinical Interpretation of Variants in Cancer (CIViC) Knowledgebase <https://civicdb.org/>`_ using `CIViCpy <https://docs.civicpy.org/en/latest/>`_

Credits
-------

This package uses the cancergenomeinterpreter.org REST API for data retrieval.

* Muiños, F., Martínez-Jiménez, F., Pich, O. et al. In silico saturation mutagenesis of cancer genes. Nature 596, 428–432 (2021). https://doi.org/10.1038/s41586-021-03771-1
* Tamborero, D. Rubio-Perez, C., Deu-Pons, J. et al., Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations. Genome Medicine 10, (2018). doi: https://doi.org/10.1101/140475

This package uses the CIViCpy package for data retrieval from the CIViC database.

* Wagner, Alex H., et al. "CIViCpy: a python software development and analysis toolkit for the CIViC knowledgebase." JCO Clinical Cancer Informatics 4 (2020): 245-253. doi: https://doi.org/10.1200/CCI.19.00127
* Griffith, M., Spies, N., Krysiak, K. et al. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet 49, 170–174 (2017). doi: https://doi.org/10.1038/ng.3774

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage




Changelog
============

0.2.1 - Sour Venus  (2023-02-16)
---------------------------------------------

**Added**

**Fixed**

* Rendering API docs

**Dependencies**

**Deprecated**

0.2.0 - Sour Venus  (2023-02-07)
---------------------------------------------

**Added**

* Added functionality to query the Clinical Interpretation of Variants in Cancer (CIViC) Knowledgebase
* Added possibility to query bgzipped files

**Fixed**

**Dependencies**

**Deprecated**

0.1.3 - Diamond Neptune  (2022-11-21)
---------------------------------------------

**Added**

**Fixed**

* Fix including module

**Dependencies**

**Deprecated**

0.1.2 - Diamond Neptune  (2022-11-18)
---------------------------------------------

**Added**

**Fixed**

* Fix installing requirements

**Dependencies**

**Deprecated**

0.1.1 -  Methane Titan (2022-11-18)
---------------------------------------------

**Added**

**Fixed**

* Github Actions publishing to PyPI
* Fix docs

**Dependencies**

**Deprecated**


0.1.0 - initial release (2022-11-18)
---------------------------------------------

**Added**

* First release on PyPI
* Created the package template with cookiecutter
* Functions to query the cancergenomeinterpreter REST API

**Fixed**

**Dependencies**

**Deprecated**
