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vrs-python provides Python language support for the [GA4GH VariationRepresentation Specification(VRS)](https://github.com/ga4gh/vr-spec).

This repository contains several related components:

• ga4gh.vrs package Python language support for the spec.
• ga4gh.vrs.extras package Python language support for additionalfunctionality, including translating from and to other variantformats and a REST service to similar functionality.ga4gh.vrs.extras requires access to supporting data, as describedbelow.
• Jupyter notebooks Demonstrations of the functionality ofga4gh.vrs and ga4gh.vrs.extras in the form of easy-to-readnotebooks.

$ pip install ga4gh.vrs[extras]

The [extras] argument tells pip to install packages to fullfill thedependencies of the ga4gh.vrs.extras package.

The following instructions are for Ubuntu 18.04+ and MacOS.vrs-python is unlikely to work on Windows due to dependencies.

$ git clone --recurse-submodules https://github.com/ga4gh/vrs-python.git$ cd vrs-python$ make devready

(Python 3.5 and 3.6 should also work.)

The ga4gh.vrs.extras modules are not part of the VR spec per se.They are bundled with ga4gh.vrs for development and installationconvenience. These modules depend directly and indrectly on externaldata sources of sequences, transcripts, and genome-transcriptalignments. This section recommends one way to install the biocommonstools that provide these data.

$ docker volume create --name=uta_vol$ docker volume create --name=seqrepo_vol$ docker-compose -f misc/stack/docker-compose.yml up

This should start three containers:* [seqrepo](https://github.com/biocommons/seqrepo): a non-redundant archive of sequences* [seqrepo-rest-service](https://github.com/biocommons/seqrepo-rest-service): a REST service on seqrepo (localhost:5000)* [uta](https://github.com/biocommons/uta): a database of transcripts and alignments (localhost:5432)

The seqrepo container will exit as soon as the data are downloaded.

$ docker psCONTAINER ID        IMAGE                                    //  NAMES86e872ab0c69        biocommons/seqrepo-rest-service:latest   //  stack_seqrepo-rest-service_1a40576b8cf1f        biocommons/uta:uta_20180821              //  stack_uta_1

Once installed as described above, type:

$ source venv/3.7/bin/activate$ jupyter notebook --notebook-dir notebooks/

The following jupyter extensions are recommended but not required:

$ pip install jupyter_contrib_nbextensions$ jupyter contrib nbextension install --user$ jupyter nbextension enable toc2/main

A stand-alone security review has been performed on the specificationitself. This implementation is offered as-is, and without anysecurity guarantees. It will need an independent security reviewbefore it can be considered ready for use in security-criticalapplications. If you integrate this code into your application it isAT YOUR OWN RISK AND RESPONSIBILITY to arrange for a security audit.