Metadata-Version: 2.1
Name: variant-normalizer
Version: 0.2.2
Summary: VICC normalization routine for variants
Home-page: https://github.com/cancervariants/variant-normalization
Author: VICC
Author-email: help@cancervariants.org
License: MIT
Description: # 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
        Variant Normalization relies on [seqrepo](https://github.com/biocommons/biocommons.seqrepo), which you must download yourself.
        
        From the _variant_ directory of the repository:
        ```
        pipenv sync
        pip install seqrepo
        mkdir -p data/seqrepo
        seqrepo -r data/seqrepo pull -i 2021-01-29
        sudo chmod -R u+w data/seqrepo
        cd data/seqrepo
        seqrepo_date_dir=$(ls -d */)
        sudo mv $seqrepo_date_dir latest
        ```
        
        ### Data
        Variant Normalization uses [Ensembl BioMart](http://www.ensembl.org/biomart/martview) to retrieve `variant/data/transcript_mappings.tsv`. We currently use `Human Genes (GRCh38.p13)` for the dataset and the following attributes we use are: Gene stable ID, Gene stable ID version, Transcript stable ID, Transcript stable ID version, Protein stable ID, Protein stable ID version, RefSeq match transcript (MANE Select), Gene name. 
        
        ![image](biomart.png)
        
        ### Setting up Gene Normalizer
        Variant Normalization `normalize` endpoint relies on data from Gene Normalization. To install:
        ```shell script
        pip install gene-normalizer
        ```
        
        To setup, follow the instructions from the [Gene Normalization README](https://github.com/cancervariants/gene-normalization). 
        
        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](https://github.com/PyCQA/flake8) and checked prior to commit.
        
        We use [pre-commit](https://pre-commit.com/#usage) 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
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=3.7
Description-Content-Type: text/markdown
