Package: querynator
Python package to query cancer variant databasesFree software: MIT licenseDocumentation:https://querynator.readthedocs.io.FeaturesCommand-line tool to query thecancergenomeinterpretervia its REST APICommand-line tool to query theClinical Interpretation of Variants in Cancer (CIViC) KnowledgebaseusingCIViCpyCreditsThis 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/s41586-021-03771-1Tamborero, 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/10.1101/140475This 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.19.00127Griffith, 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.3774This package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.Changelog0.4.1 - Stormy Saturn  (2023-06-13)AddedFixedBug fixes to include all evidence of CIViCDependenciesDeprecated0.4.0 - Stormy Saturn  (2023-05-31)AddedFixedFixed functionality for new CGI file structureFixed case when CIViC has no hitsDependenciesDeprecated0.3.3 - Iron Mercury  (2023-05-05)AddedFixedFixed API docsDependenciesDeprecated0.3.2 - Iron Mercury  (2023-05-05)AddedFixedFixed version bumpDependenciesDeprecated0.3.1 - Iron Mercury  (2023-05-05)AddedFixedFixed import of site-packages in setup.pyDependenciesDeprecated0.3.0 - Iron Mercury  (2023-05-04)AddedAdded functionality to combine the results of the Knowledgebases in an HTML reportAdded possibility to have non-numerical chromosome columns in the input vcfAdded deletion of CGI jobs from CGI Server after completionFixedDependenciesDeprecated0.2.2 - Sour Venus  (2023-03-16)AddedOptional VEP annotation based filteringAdditional metadataUsage of pyVCF3 to read vcf filesQuerynator ID added for filtered vcf filesAll possible reference genomes for CIViCFixedDependenciesDeprecatedUsage of pysam to read vcf files0.2.1 - Sour Venus  (2023-02-16)AddedFixedRendering API docsDependenciesDeprecated0.2.0 - Sour Venus  (2023-02-07)AddedAdded functionality to query the Clinical Interpretation of Variants in Cancer (CIViC) KnowledgebaseAdded possibility to query bgzipped filesFixedDependenciesDeprecated0.1.3 - Diamond Neptune  (2022-11-21)AddedFixedFix including moduleDependenciesDeprecated0.1.2 - Diamond Neptune  (2022-11-18)AddedFixedFix installing requirementsDependenciesDeprecated0.1.1 -  Methane Titan (2022-11-18)AddedFixedGithub Actions publishing to PyPIFix docsDependenciesDeprecated0.1.0 - initial release (2022-11-18)AddedFirst release on PyPICreated the package template with cookiecutterFunctions to query the cancergenomeinterpreter REST APIFixedDependenciesDeprecated