| Name | hgvs JSON |
| Version |
1.5.5
JSON |
| download |
| home_page | None |
| Summary | HGVS Parser, Formatter, Mapper, Validator |
| upload_time | 2025-07-14 00:13:27 |
| maintainer | None |
| docs_url | https://pythonhosted.org/hgvs/ |
| author | None |
| requires_python | >=3.10 |
| license | Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
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|
| keywords |
biocommons
bioinformatics
computational biology
genome variation
genomics
hgvs
variation
|
| VCS |
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| bugtrack_url |
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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
[](http://hgvs.readthedocs.io/) [](https://hgvs.readthedocs.io/en/stable/changelog/) [](https://hgvs.readthedocs.io/en/stable/getting_help.html) [](https://github.com/biocommons/hgvs/blob/main/LICENSE) [](https://mybinder.org/v2/gh/biocommons/hgvs/main?filepath=examples)
## Latest Release
[](https://github.com/biocommons/hgvs) [](https://pypi.org/project/hgvs/)
## Development
[](https://coveralls.io/github/biocommons/hgvs) [](https://github.com/biocommons/hgvs/issues)
[](https://github.com/biocommons/hgvs/pull/) [](https://github.com/biocommons/hgvs/graphs/contributors/) [](https://github.com/biocommons/hgvs/stargazers) [](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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"name": "hgvs",
"maintainer": null,
"docs_url": "https://pythonhosted.org/hgvs/",
"requires_python": ">=3.10",
"maintainer_email": null,
"keywords": "biocommons, bioinformatics, computational biology, genome variation, genomics, hgvs, variation",
"author": null,
"author_email": "HGVS Contributors <biocommons-dev@googlegroups.com>",
"download_url": "https://files.pythonhosted.org/packages/a6/8c/79b80ea8d5a21b71c94a9f8d042307f41a33813c591536eb83c3ce38e59e/hgvs-1.5.5.tar.gz",
"platform": null,
"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[](http://hgvs.readthedocs.io/) [](https://hgvs.readthedocs.io/en/stable/changelog/) [](https://hgvs.readthedocs.io/en/stable/getting_help.html) [](https://github.com/biocommons/hgvs/blob/main/LICENSE) [](https://mybinder.org/v2/gh/biocommons/hgvs/main?filepath=examples)\n\n## Latest Release\n\n[](https://github.com/biocommons/hgvs) [](https://pypi.org/project/hgvs/)\n\n## Development\n\n[](https://coveralls.io/github/biocommons/hgvs) [](https://github.com/biocommons/hgvs/issues)\n[](https://github.com/biocommons/hgvs/pull/) [](https://github.com/biocommons/hgvs/graphs/contributors/) [](https://github.com/biocommons/hgvs/stargazers) [](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,
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