How to use the dtaidistance.alignment function in dtaidistance

matrix = read_substitution_matrix(
        Path(__file__).parent / "rsrc" / "substitution.txt"
    )
    substitution = alignment.make_substitution_fn(matrix)

    s1 = "CCAGG"
    s2 = "CCGA"

    value, matrix = alignment.needleman_wunsch(s1, s2)
    algn, s1a1, s2a1 = alignment.best_alignment(matrix, s1, s2, gap='-')
    algn_sol1 = [list("CCAGG"), list("CC-GA")]
    assert s1a1 == algn_sol1[0]
    assert s2a1 == algn_sol1[1]

    value, matrix = alignment.needleman_wunsch(s1, s2, substitution=substitution)
    algn, s1a2, s2a2 = alignment.best_alignment(matrix, s1, s2, gap='-')
    algn_sol2 = [list("CC-AGG"), list("CCGA--")]
    assert s1a2 == algn_sol2[0]
    assert s2a2 == algn_sol2[1]

def test_sequences_custom():

    matrix = read_substitution_matrix(
        Path(__file__).parent / "rsrc" / "substitution.txt"
    )
    substitution = alignment.make_substitution_fn(matrix)

    s1 = "CCAGG"
    s2 = "CCGA"

    value, matrix = alignment.needleman_wunsch(s1, s2)
    algn, s1a1, s2a1 = alignment.best_alignment(matrix, s1, s2, gap='-')
    algn_sol1 = [list("CCAGG"), list("CC-GA")]
    assert s1a1 == algn_sol1[0]
    assert s2a1 == algn_sol1[1]

    value, matrix = alignment.needleman_wunsch(s1, s2, substitution=substitution)
    algn, s1a2, s2a2 = alignment.best_alignment(matrix, s1, s2, gap='-')
    algn_sol2 = [list("CC-AGG"), list("CCGA--")]
    assert s1a2 == algn_sol2[0]
    assert s2a2 == algn_sol2[1]

def test_sequences_blosum():
    matrix = read_substitution_matrix(
        Path(__file__).parent / "rsrc" / "substitution.txt"
    )
    substitution = alignment.make_substitution_fn(matrix)
    s1 = "AGACTAGTTAC"
    s2 = "CGAGACGT"
    value, matrix = alignment.needleman_wunsch(s1, s2, substitution=substitution)
    algn, s1a1, s2a1 = alignment.best_alignment(matrix, s1, s2, gap='-')
    algn_sol1 = [list('--AGACTAGTTAC'),
                 list('CGAGAC--GT---')]
    assert s1a1 == algn_sol1[0]
    assert s2a1 == algn_sol1[1]

def test_sequences1():
    """Example from https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm . """
    s1 = "GATTACA"
    s2 = "GCATGCU"
    value, matrix = alignment.needleman_wunsch(s1, s2)
    algn, s1a1, s2a1 = alignment.best_alignment(matrix, s1, s2, gap='-')
    matrix_sol = [
        [-0., -1., -2., -3., -4., -5., -6., -7.],
        [-1.,  1., -0., -1., -2., -3., -4., -5.],
        [-2., -0., -0.,  1., -0., -1., -2., -3.],
        [-3., -1., -1., -0.,  2.,  1., -0., -1.],
        [-4., -2., -2., -1.,  1.,  1., -0., -1.],
        [-5., -3., -3., -1., -0., -0., -0., -1.],
        [-6., -4., -2., -2., -1., -1.,  1., -0.],
        [-7., -5., -3., -1., -2., -2., -0., -0.]]
    algn_sol1 = [['G', '-', 'A', 'T', 'T', 'A', 'C', 'A'], ['G', 'C', 'A', 'T', '-', 'G', 'C', 'U']]
    assert value == 0.0
    assert np.array_equal(matrix, matrix_sol)
    assert s1a1 == algn_sol1[0]
    assert s2a1 == algn_sol1[1]

def test_substitution_function():
    matrix = read_substitution_matrix(
        Path(__file__).parent / "rsrc" / "substitution.txt"
    )
    substitution = alignment.make_substitution_fn(matrix, gap=0.5)
    assert substitution('A', 'B') == (1, 0.5)
    assert substitution('A', 'A') == (-20.0, 0.5)
    assert substitution('A', 'C') == (3.0, 0.5)

    # test just changing gap function
    substitution2 = alignment.make_substitution_fn({}, gap=0.5)
    assert substitution2('A', 'A') == (-1, 0.5)
    assert substitution2('G', 'C') == (1, 0.5)
    assert alignment._default_substitution_fn('A', 'A') == (-1, 1)
    assert alignment._default_substitution_fn('G', 'C') == (1, 1)