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# external
import pytest
# project
import textdistance
ALG = textdistance.Gotoh
# https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
NW_MATRIX = {
('A', 'A'): 10,
('G', 'G'): 7,
('C', 'C'): 9,
('T', 'T'): 8,
('A', 'G'): -1,
('A', 'C'): -3,
('A', 'T'): -4,
('G', 'C'): -5,
('G', 'T'): -3,
('C', 'T'): 0,
}
def sim_ident(x, y):
if x == y:
return 1
else:
return -1
@pytest.mark.parametrize('left, right, expected', [
('GATTACA', 'GCATGCU', 0),
])
def test_distance_ident(left, right, expected):
actual = ALG(gap_open=1, gap_ext=1, sim_func=sim_ident)(left, right)
assert actual == expected
@pytest.mark.parametrize('left, right, expected', [
('GATTACA', 'GCATGCU', 0),
('AGACTAGTTAC', 'TGACGSTGC', 1.5),
('AGACTAGTTAC', 'CGAGACGT', 1),
])
def test_distance_ident_with_gap_05(left, right, expected):
actual = ALG(gap_open=1, gap_ext=.5, sim_func=sim_ident)(left, right)
assert actual == expected
@pytest.mark.parametrize('left, right, expected', [
('AGACTAGTTAC', 'CGAGACGT', -15),
])
def test_distance_ident_with_gap_5(left, right, expected):
actual = ALG(gap_open=5, gap_ext=5, sim_func=sim_ident)(left, right)
assert actual == expected
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