This is the answer to hw1 for CBB752 class at Yale University. The programming task is to implement the Smith-Waterman local alignment algorithm for protein sequences. To be mentioned, the affine gap penalty is applied to this code.
The script is written with Python3.6, using Numpy1.19.2 and Pandas1.1.3 packages
Installing these two packages, pip3 install numpy, pip3 install pandas
pip install git+https://https://github.com/chang0704/SW-algorithm.git
By running the script, you can use the following line:
python hw1.py -i <input file> -s <score file> -out <output file>