cython_swa

Cython implementation of Smith Waterman Algorithm

Installation

If you don't have a C/C++ compiler installed, find the right one for your OS:

• Linux: run sudo apt-get install build-essential in the terminal
• MacOS: get XCode from https://developer.apple.com/
• Windows: find a suitable compiler from https://wiki.python.org/moin/WindowsCompilers

Once you have install a C/C++ compiler, run the following in the terminal/command prompt:

python -m venv venv
# Linux/MacOS
source .venv/bin/activate
# Windows
venv\Scripts\activate

python -m pip install -r requirements.txt
python setup.py build_ext --inplace

Run the demo

python main.py

# Output
Python SWA took 35.515625s
Cython SWA took 1.031250s
Cython speed up of 34.44x