Skeleton for Smith-Waterman project.
- Implement Smith-Waterman algorithm.
- Optimize a scoring matrix using a simulated annealing algorithm.
All functions are contained within SmithWaterman.py.
To use the package, first run
conda install --yes --file requirements.txt
to install all the dependencies in requirements.txt
. Then the package's
main function (located in hw2skeleton/__main__.py
) can be run as
follows
python -m hw2skeleton -P data test.txt
Testing is as simple as running
python -m pytest
from the root directory of this project.
Original design by Scott Pegg. Refactored and updated by Tamas Nagy.