querynator 0.2.0

Python package to query cancer variant databases

Python package to query cancer variant databases

• Free software: MIT license

• Documentation: https://querynator.readthedocs.io.

Features

• Command-line tool to query the cancergenomeinterpreter via its REST API

• Command-line tool to query the Clinical Interpretation of Variants in Cancer (CIViC) Knowledgebase using CIViCpy

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.

Changelog

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