querynator 0.6.0

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

0.6.0 - Keppler-452b Goldilocks (2024-10-10)

Added

• option –filter_evidence to filter CIViC evidences based on type, direction, status, level and significance

Fixed

Dependencies

• updated black to version 24.3.0 due to moderate vulnerability CVE-2024-21503

• updated requests to version 2.31.0 due to moderate vulnerabilities CVE-2023-32681 and CVE-2024-35195

Deprecated

0.5.5 - Sulfur Io (2024-09-09)

Added

Fixed

• [#52](https://github.com/qbic-pipelines/querynator/issues/52): issue that lead to an inconsitent number of fields for the CIViC evidences

• [#51](https://github.com/qbic-pipelines/querynator/issues/51): CGI evidences are now filtered by the specified cancer type

Dependencies

Deprecated

0.5.4 - Sulfur Io (2024-07-24)

Added

Fixed

• [#43](https://github.com/qbic-pipelines/querynator/issues/43): issue with disease ontology file path, which resurfaced in docker container

• evidences without specified disease are now excluded if –cancer is specified

Dependencies

Deprecated

0.5.3 - Sulfur Io (2024-07-20)

Added

Fixed

• [#43](https://github.com/qbic-pipelines/querynator/issues/43): added disease ontology file to the package

Dependencies

Deprecated

0.5.2 - Sulfur Io (2024-07-05)

Added

Fixed

• [#37](https://github.com/qbic-pipelines/querynator/issues/37): fixed bug in query-api-civic that caused the containerized tool to fail when querying CIViC.

Dependencies

• pinned pandas to version 1.5.3 to fix deprecation issues with pandas 2.x in querynator and civicpy.

Deprecated

0.5.1 - Sulfur Io (2024-07-03)

Added

Fixed

• fixed a severe bug in query-api-civic that made the tool unusable, the bug was introduced in v0.5.0.

Dependencies

Deprecated

0.5.0 - Sulfur Io (2024-06-23)

Added

• CL option to specify cancer type when querying CIViC (-c –cancer)

Fixed

Dependencies

• pinned numpy to version 1.24.4 to fix pandas bug with numpy-v2

Deprecated

0.4.2 - Stormy Saturn (2024-04-05)

Added

Fixed

• Bug fixes to handle new CGI wildtype biomarkers

• civicpy cache will only be updated when civic is queried

Dependencies

Deprecated

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