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"GA4GH Variation Representation (VR) reference implementation (https://github.com/ga4gh/vr-python/)"

Project description

vr-python

ci_rel | cov | pypi_rel

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

This repository contains several related components:

  • ga4gh.vr package Python language support for the spec.
  • ga4gh.vr.extras package Python language support for additional functionality, including translating from and to other variant formats and a REST service to similar functionality. ga4gh.vr.extras requires access to supporting data, as described below.
  • Jupyter notebooks Demonstrations of the functionality of ga4gh.vr and ga4gh.vr.extras in the form of easy-to-read notebooks.

Installing ga4gh.vr

Installating with pip

$ pip install ga4gh.vr[extras]

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

Installing for development

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

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

(Python 3.5 and 3.6 should also work.)

Installing Dependencies for ga4gh.vr.extras

The ga4gh.vr.extras modules are not part of the VR spec per se. They are bundled with ga4gh.vr for development and installation convenience. These modules depend directly and indrectly on external data sources of sequences, transcripts, and genome-transcript alignments. This section recommends one way to install the biocommons tools 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 ps
CONTAINER ID        IMAGE                                    //  NAMES
86e872ab0c69        biocommons/seqrepo-rest-service:latest   //  stack_seqrepo-rest-service_1
a40576b8cf1f        biocommons/uta:uta_20180821              //  stack_uta_1

Running the Notebooks

Once installed as described above, type:

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

Security Note (from the GA4GH Security Team)

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

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