CS466-Nussinov

Implementation of Nussinov's Algorithm for CS466

Installation

This program is designed to run using python 3.7+.

It is recommended you use a virtual environment when installing packages.

1. Clone the repository and cd into the directory
2. Create a virtual environment and activate it
3. Install the requirements

pip install -r requirements.txt

4. Create a .env file touch .env and add SECRET_KEY="<secret_key>", where secret key is a 32 character string.
5. Run python flask_app.py
6. Navigate to localhost:5000.

Docker

1. Run docker build
2. Run docker run -d -it --name nuss --rm -p 5000:5000 nussinov
3. Navigate to localhost:5000

Command Line interface

1. pip install numpy
2. python nussinov/nussinov.py Include either the -s option and a sequence string or -f and a filepath to your sequence.

Build and run C code

1. If you are on a mac, install argp: brew install argp-standalone
2. Compile: gcc -largp c_implimentaiton/nussinov.c -o nussinov.o
3. Run: ./nussinov.o -s <sequence>