Python implementation of Smith Waterman's Local Sequence Alignment Algorithm by Leonardo Golinelli This tool was created for the course Bionformatics Algorithms held by Prof. E.Blanzieri @ CIBIO dept, University of Trento, Italy
Instructions:
- Make sure numpy is installed
- Fastest way to run: use the jupyter notebook "notebook.ipynb": select scoring system and sequences to be aligned then run the cell.
- Alternatively: run the file "run.py" from command line, making sure to use the right shebang, interpreter and environment. If flags are not specified, default values are chosen. Sequences can be either fed to the command line or added to a .txt file.
To check flags, run python run.py -h or ./run.py -h
options: -h, --help show this help message and exit
--match MATCH Score for a match
--mismatch MISMATCH Score for a mismatch
--gap GAP Score for a gap
--top_sequence TOP_SEQUENCE Top sequence
--bottom_sequence BOTTOM_SEQUENCE Bottom sequence
--sequence_file SEQUENCE_FILE Path to file containing sequences, The first row should contain the top sequence, whereas the second row should contain the bottom sequence