variant_search_app

Web application (backed by RESTful microservices and PostgreSQL DB) capable of querying genomic variants by Gene Name (e.g. BRCA1, CRY1, etc.) and reporting the information via an interactive results table.

Installation

Dependencies:

• PostgreSQL (>= 9.6)
• Python2.7 (Flask=0.12.2, psycopg2==2.7.3.2)
• jQuery, jQuery UI, MaterializeCSS, DataTables

Step 1: Clone repository:

git clone https://github.com/autovivification/variant_search.git
cd variant_search

Step 2: Initialise python virtualenv and install necessary dependencies:

$ virtualenv -p /usr/local/bin/python2 venv
$ . venv/bin/activate

(venv)$ pip install -r requirements.txt

Step 3: Initialize empty PostgreSQL database using schema defined in variant_search_db/schema.sql:

(venv)$ psql -U postgres -d postgres -f variant_search_db/schema.sql

Step 4: Execute database loading script, which downloads the variant_results.tsv dataset from Clinvitae and uses it to build the database:

(venv)$ python -m variant_search_db.build

Step 5: Start the Flask server:

(venv)$ python runserver.py

Usage

Flask webapp accessible at http://localhost:5000/

REST API endpoints (Flask routes) can be accessed as follows:

• Gene Name autocomplete (startswith): http://localhost:5000/genes/TRPV
• Gene Name autocomplete (contains): http://localhost:5000/genes/ARP/contains
• Variants by Gene Name: http://localhost:5000/variants/CRY1

Tests

Backend:

(venv)$ python -m variant_search_app.tests