问在python中实现Smith-Waterman局部比对算法

EN

# ...
SmithWaterman(X, Y, score)
print(matrix)
# ...

def zeros(X: int, Y: int):
    #        ^       ^  incorrect type annotations. should be str
    lenX = len(X) + 1
    lenY = len(Y) + 1
    matrix = []
    for i in range(lenX):
        matrix.append([0] * lenY)
    # A more "pythonic" way of expressing the above would be:
    # matrix = [[0] * len(Y) + 1 for _ in range(len(x) + 1)]
    
    def score(X, Y):
        #     ^  ^ shadowing variables from outer scope. this is not a bug per se but it's considered bad practice
        if X[n] == Y[m]: return 4
        #    ^       ^  variables not defined in scope
        if X[n] == '-' or Y[m] == '-': return -4
        #    ^              ^  variables not defined in scope
        else: return -2

    def SmithWaterman(X, Y, score): # this function is never called
        #                   ^ unnecessary function passed as parameter. function is defined in scope
        for n in range(1, len(X) + 1):
            for m in range(1, len(Y) + 1):
                align = matrix[n-1, m-1] + (score(X[n-1], Y[m-1]))
                #                 ^ invalid list lookup. should be: matrix[n-1][m-1]
                indelX = matrix[n-1, m] + (score(X[n-1], Y[m]))
                #                                          ^ out of bounds error when m == len(Y)
                indelY = matrix[n, m-1] + (score(X[n], Y[m-1]))
                #                                  ^ out of bounds error when n == len(X)
        matrix[n, m] = max(align, indelX, indelY, 0)
        # this should be nested in the inner for-loop. m, n, indelX, and indelY are not defined in scope here
    print(matrix)

zeros("ACGT", "ACGT")