Needleman-Wunsh algorithm

Project in Python language for Bioinformatics course starting october '20, aimed at implementing Needleman-Wunsh algorithm.

System requirements

Python 3.x, packages numpy, sys, getopt, unittest.

How to download the program

There are two ways to download the program, directly from github and by terminal.

Github

1. Click button Clone or download.

2. Click button Download ZIP.

3. Extract all files from the .zip file.

Terminal

1. Copy link https://github.com/paldynaagata/Needleman-Wunsh_algorithm.

2. In terminal write command git clone and paste above link.

How to run the program

In terminal by python from catalog src run file run.py with parameters that are paths to files, according to the following formula:

run.py [path_to_seq_1] [path_to_seq_2] [path_to_config_file] [path_to_output_file]

e.g.:

/opt/anaconda/bin/python run.py -a ../data/seq1.txt -b ../data/seq2.txt -c ../configs/config.txt -o ../results/output.txt

How to run the tests

In terminal by python from catalog src run the following command:

/opt/anaconda/bin/python -m unittest tests.test_needleman_wunsch_algorithm -v