Overview

RHP KB Api returns pathogenecity status of a variant based on rules defined here: https://docs.google.com/spreadsheets/d/1xZWM2oTDntcLY9GkwoKPIHK4exlzJQGJ6i3OPMMbowg/edit#gid=0

Installation

1) clone repository

git clone THIS-REPO

2) create virtual environment

virtualenv ENV-NAME
. ENV-NAME/bin/activate
cd coleman_kb

3) install dependencies

pip install -r requirements.txt

5) Run the app

python app.py

5) Test on Browser

http://localhost:4848/annotate?gene=BRAF&protein_change=V600E&variant_type=MISSENSE http://localhost:4848/annotate?gene=CEBPA&protein_change=V600E&variant_type=INFRAME_INDEL&exac=0.0001 http://localhost:4848/annotate?gene=CEBPA&protein_change=V600E&variant_type=INFRAME_INDEL&exac=0.005