AnyVar

AnyVar provides Python and REST interfaces to validate, normalize, generate identifiers, and register biological sequence variation according to the GA4GH Variation Representation standards.

Supported Variation Types

Alleles specified by HGVS, SPDI, beacon, or gnomad formats
Unparsed text variation
[future] Copy Number Variation
[future] Genotypes (composed of Haplotypes)
[future] Structural Variation/Translocations/Fusions

All types are assigned computed, digest-based identifiers based on the underlying data.

Architecture

The AnyVar package is comprised of two components. The AnyVar class is a façade over variation translation, validation, and storage services. It may be instantiated within any Python application. The AnyVar REST interface exposes the AnyVar class functionality through an OpenAPI-based REST interface.

The AnyVar class relies on external services for sequence data and object storage, both specified as abstract interfaces.

Sequences and sequence metadata "data proxy" (interface) provides data that are essential for translating identifiers and fetching sequence for normalization. The two available data proxies are SeqRepoDataProxy and SeqRepoRESTDataProxy, for local a local SeqRepo instance and a remote seqrepo-rest-service instance.
A storage interface for object storage. AnyVar must instantiated with a storage object that satisfies a collections.abc.MutableMapping interface. Three backends are common: 1) a dict, for emphemeral in-memory storage; 2) anyvar.storage.shelf, a dbm-based persistent storage mechanism that does not incur additional dependencies; 3) anyvar.storage.redisobjectstore, a Redis-backed storage interface that may be local or remote.

The AnyVar REST interface is implemented using the Connexion Python library. It may be deployed using any WSGI or ASGI framework. The default is currently to use the Flask development server, but this will change as the product matures.

Configuration

AnyVar should run without configuration. The following environment variables provide additional configuration:

GA4GH_VRS_DATAPROXY_URI is a URI used to instantiate a ga4gh.vrs.dataproxy instance. See ga4gh.vrs.dataproxy.create_dataproxy() for permissible values.
ANYVAR_STORAGE_URI configures storage used for AnyVar. Examples are memory:, file:///tmp/anyvar.dbm/ for shelf storage at /tmp/anyvar.dbm, or redis:///15 for redis database 15 on localhost.

Example for running with REST API:

    $ export GA4GH_VRS_DATAPROXY_URI=https://services.genomicmedlab.org/seqrepo
    $ export ANYVAR_STORAGE_URI="redis:///15"

Example for running with local SeqRepo:

    $ export SEQREPO_DIR=seqrepo+file:///usr/local/share/seqrepo/latest
    $ export ANYVAR_STORAGE_URI="redis:///15"

Developer installation

git clone https://github.com/biocommons/anyvar.git
cd anyvar
python3 -mvenv venv
source venv/bin/activate
pip install -U setuptools pip
pip install -e '.[dev]'

Or, more simply:

make devready
source venv/bin/activate

Then, start the REST server with:

python -m anyvar.restapi

In another terminal:

curl http://localhost:5000/info

Setting up Redis

A Redis-backed AnyVar installation may use any Redis instance, local or remote. The following instructions are for using a docker-based Redis instance.

$ docker volume create anyvar_redis_vol
$ docker run --name anyvar_redis -v anyvar_redis_vol:/data -d redis redis-server --appendonly yes
$ python3 -m anyvar.restapi

Deployment

Download docker-compose.yml.

Create a docker volume seqrepo_vol that contains a recent seqrepo release.

a. If you already have seqrepo locally, do this to copy your local instance to a new volume:

 $ docker run --rm \
   -v seqrepo_vol:/usr/local/share/seqrepo  \
   -v /usr/local/share/seqrepo:/tmp/seqrepo \
   alpine \
   cp -av /tmp/seqrepo /usr/local/share/

b. Otherwise, do this:

 $ docker run --rm \
 -v seqrepo_vol:/usr/local/share/seqrepo \
 biocommons/seqrepo:latest

Then, type:

$ docker-compose up

Verify that anyvar is running like this:

$ curl http://localhost:5000/info
{
  "anyvar": {
    "version": "0.1.2.dev0+d20190508"
  },
  "ga4gh.vrs": {
    "version": "0.2.0"
  }
}

NOTE: The authoritative and sole source for version tags is the repository. When a commit is tagged, that tag is automatically used as the Python __version__, the docker image tag, and the version reported at the /info endpoint.