hgvs - manipulate biological sequence variants according to Human Genome Variation Society recommendations

Important: biocommons packages require Python 3.10+. More

The hgvs package provides a Python library to parse, format, validate, normalize, and map sequence variants according to Variation Nomenclature (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 for limitations.

Information

Latest Release

Development

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

Important Notes

You are encouraged to browse 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.

Installing HGVS Locally

Important: For more detailed installation and configuration instructions, see the HGVS readthedocs

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.

Create a virtual environment using your preferred method.

Example:
```
 python3 -m venv venv
```

Run the following commands in your virtual environment:

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

See Installation instructions for details, including instructions for installing Universal Transcript Archive (UTA) and SeqRepo locally.

Examples and Usage

See examples and readthedocs for usage.

Contributing

The hgvs package is intended to be a community project. Please see Contributing to get started in submitting source code, tests, or documentation. Thanks for getting involved!

davmlaw/hgvs