sanjayboddu/python-gene-search repository overview

⁠Description

This is a simple application built using Flask - a micro web framework written in Python. It provides /gene_suggest/:species/:gene/:limit endpoint which responds with a list of suggested gene names for the given gene query and target species. You can limit the number of suggestion hits using limit parameter.

⁠Starting the service

There are two ways to run this application

1. Run in a docker container
2. Clone the repo and run directly on your local machine

⁠Docker

Docker allows you to run applications in virtualized "containers". A docker image for this application is available from DockerHub⁠

⁠Requirements: Docker v18.09.0

docker run -p 8000:8011 -d sanjayboddu/python-gene-search

You should now be able to access the service at http://localhost:8000/⁠ on your machine

⁠Local machine:

⁠Requirements: Python 3.x and Git

git clone https://github.com/sanjay-boddu/python-gene-search.git
cd python-gene-search/

# Install all the requirements for application
pip3 install --no-cache-dir -r requirements.txt

# Query Ensembl public MySQL server and create json files to use as data source
python dump_genes.py

# Start the app
python app.py 

You should now be able to access service at http://localhost:8011/⁠ on your machine