hgvs


Namehgvs JSON
Version 1.5.5 PyPI version JSON
download
home_pageNone
SummaryHGVS Parser, Formatter, Mapper, Validator
upload_time2025-07-14 00:13:27
maintainerNone
docs_urlhttps://pythonhosted.org/hgvs/
authorNone
requires_python>=3.10
licenseApache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. "License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. "Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. "Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. "You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. 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keywords biocommons bioinformatics computational biology genome variation genomics hgvs variation
VCS
bugtrack_url
requirements No requirements were recorded.
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            # *hgvs* - manipulate biological sequence variants according to Human Genome Variation Society recommendations

The *hgvs* package provides a Python library to parse, format, validate,
normalize, and map sequence variants according to [Variation
Nomenclature](http://varnomen.hgvs.org/) (aka Human Genome Variation
Society) recommendations.

Specifically, the hgvs package focuses on the subset of the HGVS
recommendations that precisely describe sequence-level variation
relevant to the application of high-throughput sequencing to clinical
diagnostics. The package does not attempt to cover the full scope of
HGVS recommendations. Please refer to
[issues](https://github.com/biocommons/hgvs/issues) for limitations.

## Information

[![rtd](https://img.shields.io/badge/docs-readthedocs-green.svg)](http://hgvs.readthedocs.io/) [![changelog](https://img.shields.io/badge/docs-changelog-green.svg)](https://hgvs.readthedocs.io/en/stable/changelog/)  [![getting_help](https://img.shields.io/badge/!-help%20me-red.svg)](https://hgvs.readthedocs.io/en/stable/getting_help.html)  [![GitHub license](https://img.shields.io/github/license/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/blob/main/LICENSE)  [![binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/biocommons/hgvs/main?filepath=examples)

## Latest Release

[![GitHub tag](https://img.shields.io/github/tag/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs) [![pypi_rel](https://img.shields.io/pypi/v/hgvs.svg)](https://pypi.org/project/hgvs/)

## Development

[![coveralls](https://img.shields.io/coveralls/github/biocommons/hgvs.svg)](https://coveralls.io/github/biocommons/hgvs) [![issues](https://img.shields.io/github/issues-raw/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/issues)
[![GitHub Open Pull Requests](https://img.shields.io/github/issues-pr/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/pull/) [![GitHub license](https://img.shields.io/github/contributors/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/graphs/contributors/) [![GitHub stars](https://img.shields.io/github/stars/biocommons/hgvs.svg?style=social&label=Stars)](https://github.com/biocommons/hgvs/stargazers) [![GitHub forks](https://img.shields.io/github/forks/biocommons/hgvs.svg?style=social&label=Forks)](https://github.com/biocommons/hgvs/network)

## Features

- Parsing is based on formal grammar.
- An easy-to-use object model that represents most variant types
  (SNVs, indels, dups, inversions, etc) and concepts (intronic
  offsets, uncertain positions, intervals)
- A variant normalizer that rewrites variants in canonical forms and
  substitutes reference sequences (if reference and transcript
  sequences differ)
- Formatters that generate HGVS strings from internal representations
- Tools to map variants between genome, transcript, and protein
  sequences
- Reliable handling of regions genome-transcript discrepancies
- Pluggable data providers support alternative sources of transcript
  mapping data
- Extensive automated tests, including those for all variant types and
  \"problematic\" transcripts
- Easily installed using remote data sources. Installation with local
  data sources is straightforward and completely obviates network
  access

## Citation

Wang M, Callenberg KM, Dalgleish R, Fedtsov A, Fox N, Freeman PJ, et al.
<br/>**hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.**
<br/>Hum Mutat. 2018. [doi:10.1002/humu.23615](https://doi.org/10.1002/humu.23615)

## Important Notes

- **You are encouraged to** [browse
  issues](https://github.com/biocommons/hgvs/issues). All known issues
  are listed there. Please report any issues you find.
- **Use a pip package specification to stay within minor releases.**
  For example, `hgvs>=1.5,<1.6`. hgvs uses [Semantic
  Versioning](http://semver.org/).

## Installing HGVS Locally

**Important:** For more detailed installation and configuration
instructions, see the [HGVS readthedocs](https://hgvs.readthedocs.io/)

### Prerequisites

    libpq
    python3
    postgresql

Examples for installation:

MacOS :

    brew install libpq
    brew install python3
    brew install postgresql@14

Ubuntu :

    sudo apt install gcc libpq-dev python3-dev

### Installation Steps

By default, hgvs uses remote data sources, which makes
installation easy. If you would like to use local instances of the data sources, see the [readthedocs](https://hgvs.readthedocs.io/).

1. Create a virtual environment using your preferred method.

    **Example:**

        python3 -m venv venv

2. Run the following commands in your virtual environment:

        source venv/bin/activate
        pip install --upgrade setuptools
        pip install hgvs

See [Installation
instructions](http://hgvs.readthedocs.org/en/stable/installation.html)
for details, including instructions for installing [Universal Transcript
Archive (UTA)](https://github.com/biocommons/uta/) and
[SeqRepo](https://github.com/biocommons/biocommons.seqrepo/) locally.

## Examples and Usage

See [examples](https://github.com/biocommons/hgvs/tree/main/examples) and [readthedocs](https://hgvs.readthedocs.io/) for usage.

## Contributing

The hgvs package is a community effort. Please see
[Contributing](http://hgvs.readthedocs.org/en/stable/contributing.html) to get
started in submitting source code, tests, or documentation. Thanks for getting
involved!

### Testing

Existing tests use a cache that is committed with the repo to ensure that tests do not require external networking.  To develop new tests, which requires loading the cache, you should install UTA and Seqrepo (and the rest service) locally.

    docker compose --project-name biocommons -f $PWD/misc/docker-compose.yml up

IMPORTANT: Loading the test caches is currently hampered b
[#551](https://github.com/biocommons/hgvs/issues/551),
[#760](https://github.com/biocommons/hgvs/issues/760), and
[#761](https://github.com/biocommons/hgvs/issues/761). To load reliably, use
`make test-relearn-iteratively` for now.

## See Also

Other packages that manipulate HGVS variants:

- [pyhgvs](https://github.com/counsyl/hgvs)
- [Mutalyzer](https://mutalyzer.nl/)

            

Raw data

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    "keywords": "biocommons, bioinformatics, computational biology, genome variation, genomics, hgvs, variation",
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    "author_email": "HGVS Contributors <biocommons-dev@googlegroups.com>",
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    "description": "# *hgvs* - manipulate biological sequence variants according to Human Genome Variation Society recommendations\n\nThe *hgvs* package provides a Python library to parse, format, validate,\nnormalize, and map sequence variants according to [Variation\nNomenclature](http://varnomen.hgvs.org/) (aka Human Genome Variation\nSociety) recommendations.\n\nSpecifically, the hgvs package focuses on the subset of the HGVS\nrecommendations that precisely describe sequence-level variation\nrelevant to the application of high-throughput sequencing to clinical\ndiagnostics. The package does not attempt to cover the full scope of\nHGVS recommendations. Please refer to\n[issues](https://github.com/biocommons/hgvs/issues) for limitations.\n\n## Information\n\n[![rtd](https://img.shields.io/badge/docs-readthedocs-green.svg)](http://hgvs.readthedocs.io/) [![changelog](https://img.shields.io/badge/docs-changelog-green.svg)](https://hgvs.readthedocs.io/en/stable/changelog/)  [![getting_help](https://img.shields.io/badge/!-help%20me-red.svg)](https://hgvs.readthedocs.io/en/stable/getting_help.html)  [![GitHub license](https://img.shields.io/github/license/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/blob/main/LICENSE)  [![binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/biocommons/hgvs/main?filepath=examples)\n\n## Latest Release\n\n[![GitHub tag](https://img.shields.io/github/tag/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs) [![pypi_rel](https://img.shields.io/pypi/v/hgvs.svg)](https://pypi.org/project/hgvs/)\n\n## Development\n\n[![coveralls](https://img.shields.io/coveralls/github/biocommons/hgvs.svg)](https://coveralls.io/github/biocommons/hgvs) [![issues](https://img.shields.io/github/issues-raw/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/issues)\n[![GitHub Open Pull Requests](https://img.shields.io/github/issues-pr/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/pull/) [![GitHub license](https://img.shields.io/github/contributors/biocommons/hgvs.svg)](https://github.com/biocommons/hgvs/graphs/contributors/) [![GitHub stars](https://img.shields.io/github/stars/biocommons/hgvs.svg?style=social&label=Stars)](https://github.com/biocommons/hgvs/stargazers) [![GitHub forks](https://img.shields.io/github/forks/biocommons/hgvs.svg?style=social&label=Forks)](https://github.com/biocommons/hgvs/network)\n\n## Features\n\n- Parsing is based on formal grammar.\n- An easy-to-use object model that represents most variant types\n  (SNVs, indels, dups, inversions, etc) and concepts (intronic\n  offsets, uncertain positions, intervals)\n- A variant normalizer that rewrites variants in canonical forms and\n  substitutes reference sequences (if reference and transcript\n  sequences differ)\n- Formatters that generate HGVS strings from internal representations\n- Tools to map variants between genome, transcript, and protein\n  sequences\n- Reliable handling of regions genome-transcript discrepancies\n- Pluggable data providers support alternative sources of transcript\n  mapping data\n- Extensive automated tests, including those for all variant types and\n  \\\"problematic\\\" transcripts\n- Easily installed using remote data sources. Installation with local\n  data sources is straightforward and completely obviates network\n  access\n\n## Citation\n\nWang M, Callenberg KM, Dalgleish R, Fedtsov A, Fox N, Freeman PJ, et al.\n<br/>**hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.**\n<br/>Hum Mutat. 2018. [doi:10.1002/humu.23615](https://doi.org/10.1002/humu.23615)\n\n## Important Notes\n\n- **You are encouraged to** [browse\n  issues](https://github.com/biocommons/hgvs/issues). All known issues\n  are listed there. Please report any issues you find.\n- **Use a pip package specification to stay within minor releases.**\n  For example, `hgvs>=1.5,<1.6`. hgvs uses [Semantic\n  Versioning](http://semver.org/).\n\n## Installing HGVS Locally\n\n**Important:** For more detailed installation and configuration\ninstructions, see the [HGVS readthedocs](https://hgvs.readthedocs.io/)\n\n### Prerequisites\n\n    libpq\n    python3\n    postgresql\n\nExamples for installation:\n\nMacOS :\n\n    brew install libpq\n    brew install python3\n    brew install postgresql@14\n\nUbuntu :\n\n    sudo apt install gcc libpq-dev python3-dev\n\n### Installation Steps\n\nBy default, hgvs uses remote data sources, which makes\ninstallation easy. If you would like to use local instances of the data sources, see the [readthedocs](https://hgvs.readthedocs.io/).\n\n1. Create a virtual environment using your preferred method.\n\n    **Example:**\n\n        python3 -m venv venv\n\n2. Run the following commands in your virtual environment:\n\n        source venv/bin/activate\n        pip install --upgrade setuptools\n        pip install hgvs\n\nSee [Installation\ninstructions](http://hgvs.readthedocs.org/en/stable/installation.html)\nfor details, including instructions for installing [Universal Transcript\nArchive (UTA)](https://github.com/biocommons/uta/) and\n[SeqRepo](https://github.com/biocommons/biocommons.seqrepo/) locally.\n\n## Examples and Usage\n\nSee [examples](https://github.com/biocommons/hgvs/tree/main/examples) and [readthedocs](https://hgvs.readthedocs.io/) for usage.\n\n## Contributing\n\nThe hgvs package is a community effort. Please see\n[Contributing](http://hgvs.readthedocs.org/en/stable/contributing.html) to get\nstarted in submitting source code, tests, or documentation. Thanks for getting\ninvolved!\n\n### Testing\n\nExisting tests use a cache that is committed with the repo to ensure that tests do not require external networking.  To develop new tests, which requires loading the cache, you should install UTA and Seqrepo (and the rest service) locally.\n\n    docker compose --project-name biocommons -f $PWD/misc/docker-compose.yml up\n\nIMPORTANT: Loading the test caches is currently hampered b\n[#551](https://github.com/biocommons/hgvs/issues/551),\n[#760](https://github.com/biocommons/hgvs/issues/760), and\n[#761](https://github.com/biocommons/hgvs/issues/761). To load reliably, use\n`make test-relearn-iteratively` for now.\n\n## See Also\n\nOther packages that manipulate HGVS variants:\n\n- [pyhgvs](https://github.com/counsyl/hgvs)\n- [Mutalyzer](https://mutalyzer.nl/)\n",
    "bugtrack_url": null,
    "license": "Apache License\n                                   Version 2.0, January 2004\n                                http://www.apache.org/licenses/\n        \n           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n        \n           1. Definitions.\n        \n              \"License\" shall mean the terms and conditions for use, reproduction,\n              and distribution as defined by Sections 1 through 9 of this document.\n        \n              \"Licensor\" shall mean the copyright owner or entity authorized by\n              the copyright owner that is granting the License.\n        \n              \"Legal Entity\" shall mean the union of the acting entity and all\n              other entities that control, are controlled by, or are under common\n              control with that entity. For the purposes of this definition,\n              \"control\" means (i) the power, direct or indirect, to cause the\n              direction or management of such entity, whether by contract or\n              otherwise, or (ii) ownership of fifty percent (50%) or more of the\n              outstanding shares, or (iii) beneficial ownership of such entity.\n        \n              \"You\" (or \"Your\") shall mean an individual or Legal Entity\n              exercising permissions granted by this License.\n        \n              \"Source\" form shall mean the preferred form for making modifications,\n              including but not limited to software source code, documentation\n              source, and configuration files.\n        \n              \"Object\" form shall mean any form resulting from mechanical\n              transformation or translation of a Source form, including but\n              not limited to compiled object code, generated documentation,\n              and conversions to other media types.\n        \n              \"Work\" shall mean the work of authorship, whether in Source or\n              Object form, made available under the License, as indicated by a\n              copyright notice that is included in or attached to the work\n              (an example is provided in the Appendix below).\n        \n              \"Derivative Works\" shall mean any work, whether in Source or Object\n              form, that is based on (or derived from) the Work and for which the\n              editorial revisions, annotations, elaborations, or other modifications\n              represent, as a whole, an original work of authorship. For the purposes\n              of this License, Derivative Works shall not include works that remain\n              separable from, or merely link (or bind by name) to the interfaces of,\n              the Work and Derivative Works thereof.\n        \n              \"Contribution\" shall mean any work of authorship, including\n              the original version of the Work and any modifications or additions\n              to that Work or Derivative Works thereof, that is intentionally\n              submitted to Licensor for inclusion in the Work by the copyright owner\n              or by an individual or Legal Entity authorized to submit on behalf of\n              the copyright owner. For the purposes of this definition, \"submitted\"\n              means any form of electronic, verbal, or written communication sent\n              to the Licensor or its representatives, including but not limited to\n              communication on electronic mailing lists, source code control systems,\n              and issue tracking systems that are managed by, or on behalf of, the\n              Licensor for the purpose of discussing and improving the Work, but\n              excluding communication that is conspicuously marked or otherwise\n              designated in writing by the copyright owner as \"Not a Contribution.\"\n        \n              \"Contributor\" shall mean Licensor and any individual or Legal Entity\n              on behalf of whom a Contribution has been received by Licensor and\n              subsequently incorporated within the Work.\n        \n           2. Grant of Copyright License. Subject to the terms and conditions of\n              this License, each Contributor hereby grants to You a perpetual,\n              worldwide, non-exclusive, no-charge, royalty-free, irrevocable\n              copyright license to reproduce, prepare Derivative Works of,\n              publicly display, publicly perform, sublicense, and distribute the\n              Work and such Derivative Works in Source or Object form.\n        \n           3. Grant of Patent License. Subject to the terms and conditions of\n              this License, each Contributor hereby grants to You a perpetual,\n              worldwide, non-exclusive, no-charge, royalty-free, irrevocable\n              (except as stated in this section) patent license to make, have made,\n              use, offer to sell, sell, import, and otherwise transfer the Work,\n              where such license applies only to those patent claims licensable\n              by such Contributor that are necessarily infringed by their\n              Contribution(s) alone or by combination of their Contribution(s)\n              with the Work to which such Contribution(s) was submitted. If You\n              institute patent litigation against any entity (including a\n              cross-claim or counterclaim in a lawsuit) alleging that the Work\n              or a Contribution incorporated within the Work constitutes direct\n              or contributory patent infringement, then any patent licenses\n              granted to You under this License for that Work shall terminate\n              as of the date such litigation is filed.\n        \n           4. Redistribution. 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