==========
querynator
==========
.. image:: https://img.shields.io/pypi/v/querynator.svg
:target: https://pypi.python.org/pypi/querynator
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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
============
0.4.1 - Stormy Saturn (2023-06-13)
---------------------------------------------
**Added**
**Fixed**
* Bug fixes to include all evidence of CIViC
**Dependencies**
**Deprecated**
0.4.0 - Stormy Saturn (2023-05-31)
---------------------------------------------
**Added**
**Fixed**
* Fixed functionality for new CGI file structure
* Fixed case when CIViC has no hits
**Dependencies**
**Deprecated**
0.3.3 - Iron Mercury (2023-05-05)
---------------------------------------------
**Added**
**Fixed**
* Fixed API docs
**Dependencies**
**Deprecated**
0.3.2 - Iron Mercury (2023-05-05)
---------------------------------------------
**Added**
**Fixed**
* Fixed version bump
**Dependencies**
**Deprecated**
0.3.1 - Iron Mercury (2023-05-05)
---------------------------------------------
**Added**
**Fixed**
* Fixed import of site-packages in setup.py
**Dependencies**
**Deprecated**
0.3.0 - Iron Mercury (2023-05-04)
---------------------------------------------
**Added**
* Added functionality to combine the results of the Knowledgebases in an HTML report
* Added possibility to have non-numerical chromosome columns in the input vcf
* Added deletion of CGI jobs from CGI Server after completion
**Fixed**
**Dependencies**
**Deprecated**
0.2.2 - Sour Venus (2023-03-16)
---------------------------------------------
**Added**
* Optional VEP annotation based filtering
* Additional metadata
* Usage of pyVCF3 to read vcf files
* Querynator ID added for filtered vcf files
* All possible reference genomes for CIViC
**Fixed**
**Dependencies**
**Deprecated**
* Usage of pysam to read vcf files
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**
Raw data
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"description": "==========\nquerynator\n==========\n\n\n.. image:: https://img.shields.io/pypi/v/querynator.svg\n :target: https://pypi.python.org/pypi/querynator\n\n.. image:: https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2Fqbic-pipelines%2Fquerynator%2Fbadge%3Fref%3Dmaster&style=flat-square\n :target: https://actions-badge.atrox.dev/qbic-pipelines/querynator/goto?ref=master\n\n.. image:: https://img.shields.io/badge/code%20style-black-000000.svg\n :target: https://github.com/psf/black\n\n.. image:: https://img.shields.io/badge/code%20style-prettier-ff69b4.svg\n :target: https://github.com/prettier/prettier\n\n.. image:: https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336\n :target: https://pycqa.github.io/isort\n\n.. image:: https://readthedocs.org/projects/querynator/badge/?version=latest\n :target: https://querynator.readthedocs.io/en/latest/?version=latest\n :alt: Documentation Status\n\n\n\n\nPython package to query cancer variant databases\n\n\n* Free software: MIT license\n* Documentation: https://querynator.readthedocs.io.\n\n\nFeatures\n--------\n\n* Command-line tool to query the `cancergenomeinterpreter <https://www.cancergenomeinterpreter.org/home>`_ via its REST API\n* 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/>`_\n\nCredits\n-------\n\nThis package uses the cancergenomeinterpreter.org REST API for data retrieval.\n\n* Mui\u00f1os, F., Mart\u00ednez-Jim\u00e9nez, F., Pich, O. et al. In silico saturation mutagenesis of cancer genes. Nature 596, 428\u2013432 (2021). https://doi.org/10.1038/s41586-021-03771-1\n* 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\n\nThis package uses the CIViCpy package for data retrieval from the CIViC database.\n\n* 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\n* Griffith, M., Spies, N., Krysiak, K. et al. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. 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