Variant Normalization

Services and guidelines for normalizing variant terms

Backend Services

Variant Normalization relies on some local data caches which you will need to set up. It uses pipenv to manage its environment, which you will also need to install.

Installation

From the variant directory of the repository:

pipenv sync
curl ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/non_alt_loci_set.txt > data/gene_symbols.txt
pip install seqrepo
mkdir -p data/seqrepo
seqrepo -r data/seqrepo pull -i 2020-11-27
chmod -R u+w data/seqrepo
cd data/seqrepo
seqrepo_date_dir=$(ls -d */)
mv $seqrepo_date_dir latest

Setting up Gene Normalizer

Variant Normalization normalize endpoint relies on data from Gene Normalization. To install:

pip install gene-normalizer

To setup, follow the instructions from the Gene Normalization README.

You must have the Gene Normalizer DynamoDB running for the variant normalize endpoint to work.

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

Testing

From the root directory of the repository:

pytest tests/

Starting the Variant Normalization Service

From the root directory of the repository:

uvicorn variant.main:app --reload

Next, view the OpenAPI docs on your local machine: http://127.0.0.1:8000/variant