gene-normalizer 0.1.31

VICC normalization routine for genes

Gene Normalization

Services and guidelines for normalizing gene terms

Installing with pip:

pip install gene[dev]

The [dev] argument tells pip to install packages to fulfill the dependencies of the gene.etl package.

Developer instructions

Following are sections include instructions specifically for developers.

Installation

For a development install, we recommend using Pipenv. See the pipenv docs for direction on installing pipenv in your compute environment.

Once installed, from the project root dir, just run:

pipenv shell
pipenv lock && pipenv sync
pipenv install --dev

Gene Normalization relies on SeqRepo data, which you must download yourself.

From the root directory:

pip install seqrepo
sudo mkdir /usr/local/share/seqrepo
sudo chown $USER /usr/local/share/seqrepo
seqrepo pull -i 2021-01-29  # Replace with latest version using `seqrepo list-remote-instances` if outdated

If you get an error similar to the one below:

PermissionError: [Error 13] Permission denied: '/usr/local/share/seqrepo/2021-01-29._fkuefgd' -> '/usr/local/share/seqrepo/2021-01-29'

You will want to do the following:
(Might not be ._fkuefgd, so replace with your error message path)

sudo mv /usr/local/share/seqrepo/2021-01-29._fkuefgd /usr/local/share/seqrepo/2021-01-29
exit

Deploying DynamoDB Locally

We use Amazon DynamoDB for our database. To deploy locally, follow these instructions.

Init coding style tests

Code style is managed by flake8 and checked prior to commit.

We use pre-commit to run conformance tests.

This ensures:

• Check code style
• Check for added large files
• Detect AWS Credentials
• Detect Private Key

Before first commit run:

pre-commit install

Running unit tests

By default, tests will employ an existing DynamoDB database. For test environments where this is unavailable (e.g. in CI), the GENE_TEST environment variable can be set to initialize a local DynamoDB instance with miniature versions of input data files before tests are executed.

export GENE_TEST=true

Running unit tests is as easy as pytest.

pipenv run pytest

Updating the gene normalization database

Before you use the CLI to update the database, run the following in a separate terminal to start a local DynamoDB service on port 8000:

java -Djava.library.path=./DynamoDBLocal_lib -jar DynamoDBLocal.jar -sharedDb

To change the port, simply add -port value.

Update source(s)

The sources we currently use are: HGNC, Ensembl, and NCBI.

To update one source, simply set --normalizer to the source you wish to update.

From the project root, run the following to update the HGNC source:

python3 -m gene.cli --normalizer="hgnc"

To update multiple sources, you can use the --normalizer flag with the source names separated by spaces.

Update all sources

To update all sources, use the --update_all flag.

From the project root, run the following to update all sources:

python3 -m gene.cli --update_all

Specifying the database URL endpoint

The default URL endpoint is http://localhost:8000. There are two different ways to specify the database URL endpoint.

The first way is to set the --db_url flag to the URL endpoint.

python3 -m gene.cli --update_all --db_url="http://localhost:8001"

The second way is to set the GENE_NORM_DB_URL to the URL endpoint.

export GENE_NORM_DB_URL="http://localhost:8001"
python3 -m gene.cli --update_all

Starting the gene normalization service

From the project root, run the following:

 uvicorn gene.main:app --reload

Next, view the OpenAPI docs on your local machine:

http://127.0.0.1:8000/gene