smanurung
/ smith_waterman.py
Created
September 9, 2019 04:22
— forked from nornagon/smith_waterman.py
Smith-Waterman Python implementation
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| import numpy as np | |
| def smith_waterman(a: str, b: str, alignment_score: float = 1, gap_cost: float = 1) -> float: | |
| """ | |
| Compute the Smith-Waterman alignment score for two strings. | |
| See https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm#Algorithm | |
| This implementation has a fixed gap cost (i.e. extending a gap is considered | |
| free). In the terminology of the Wikipedia description, W_k = {c, c, c, ...}. | |
| This implementation also has a fixed alignment score, awarded if the relevant |