def test_edit_distance_affine_bytes():
for mismatch_cost in [1, 10, 20, 30, 40, 50]:
for gap_start in [1, 10, 20, 30, 40, 50]:
assert ed_aff(b"", b"", [], gap_start, 10) == 0
assert ed_aff(b"", b"A", [], gap_start, 10) == gap_start
assert ed_aff(b"A", b"B", [mismatch_cost], gap_start, 10) == min(
gap_start * 2, mismatch_cost
)
assert ed_aff(b"A", b"A", [mismatch_cost], gap_start, 10) == 0
assert ed_aff(b"A", b"AB", [mismatch_cost], gap_start, 10) == gap_start
assert ed_aff(b"BA", b"AB", [mismatch_cost] * 2, gap_start, 100) == min(
2 * mismatch_cost, 2 * gap_start
)
for s, t in STRING_PAIRS:
s = s.encode("ascii")
t = t.encode("ascii")
if s != b"":
assert (
ed_aff(s, b"", [mismatch_cost] * len(s), gap_start, 10)
== gap_start + (len(s) - 1) * 10
)
assert ed_aff(b"", s, [], gap_start, 10) == gap_start + (len(s) - 1) * 10
assert ed_aff(s, t, [mismatch_cost] * len(s), gap_start, 10) == ed_aff(
t, s, [mismatch_cost] * len(t), gap_start, 10
)
def test_mismatches():
for i in range(10):
rand_costs = [randint(10, 70) for j in range(5)]
assert ed_aff('AAAAA', 'TTTTT', rand_costs, 100,
100) == sum(rand_costs)
assert ed_aff('ATGCT', 'ATCCT', rand_costs, 100, 100) == rand_costs[2]
assert ed_aff('ATGGA', 'ATGTTCA', rand_costs, 80,
10) == rand_costs[3] + 80 + 10
def test_edit_distance_affine():
for mismatch_cost in [1, 10, 30, 40, 50]:
for gap_start in [1, 10, 30, 40, 50]:
assert ed_aff('', '', [], gap_start, 10) == 0
assert ed_aff('', 'A', [], gap_start, 10) == gap_start
assert ed_aff('A', 'B', [mismatch_cost], gap_start,
10) == min(gap_start * 2, mismatch_cost)
assert ed_aff('A', 'A', [mismatch_cost], gap_start, 10) == 0
assert ed_aff('A', 'AB', [mismatch_cost], gap_start,
10) == gap_start
assert ed_aff('BA', 'AB', [mismatch_cost] * 2, gap_start,
100) == min(2 * mismatch_cost, 2 * gap_start)
for s, t in STRING_PAIRS:
if s != '':
assert ed_aff(s, '', [mismatch_cost] * len(s), gap_start,
10) == gap_start + (len(s) - 1) * 10
assert ed_aff('', s, [], gap_start,
10) == gap_start + (len(s) - 1) * 10
assert ed_aff(s, t, [mismatch_cost] * len(s), gap_start,
10) == ed_aff(t, s, [mismatch_cost] * len(t),
gap_start, 10)
def test_edit_distance_affine():
for mismatch_cost in [1, 10, 30, 40, 50]:
for gap_start in [1, 10, 30, 40, 50]:
assert ed_aff("", "", [], gap_start, 10) == 0
assert ed_aff("", "A", [], gap_start, 10) == gap_start
assert ed_aff("A", "B", [mismatch_cost], gap_start, 10) == min(
gap_start * 2, mismatch_cost
)
assert ed_aff("A", "A", [mismatch_cost], gap_start, 10) == 0
assert ed_aff("A", "AB", [mismatch_cost], gap_start, 10) == gap_start
assert ed_aff("BA", "AB", [mismatch_cost] * 2, gap_start, 100) == min(
2 * mismatch_cost, 2 * gap_start
)
for s, t in STRING_PAIRS:
if s != "":
assert (
ed_aff(s, "", [mismatch_cost] * len(s), gap_start, 10)
== gap_start + (len(s) - 1) * 10
)
assert ed_aff("", s, [], gap_start, 10) == gap_start + (len(s) - 1) * 10
assert ed_aff(s, t, [mismatch_cost] * len(s), gap_start, 10) == ed_aff(
t, s, [mismatch_cost] * len(t), gap_start, 10
)
def test_edit_distance_affine_bytes():
for mismatch_cost in [1, 10, 20, 30, 40, 50]:
for gap_start in [1, 10, 20, 30, 40, 50]:
assert ed_aff(b'', b'', [], gap_start, 10) == 0
assert ed_aff(b'', b'A', [], gap_start, 10) == gap_start
assert ed_aff(b'A', b'B', [mismatch_cost], gap_start,
10) == min(gap_start * 2, mismatch_cost)
assert ed_aff(b'A', b'A', [mismatch_cost], gap_start, 10) == 0
assert ed_aff(b'A', b'AB', [mismatch_cost], gap_start,
10) == gap_start
assert ed_aff(b'BA', b'AB', [mismatch_cost] * 2, gap_start,
100) == min(2 * mismatch_cost, 2 * gap_start)
for s, t in STRING_PAIRS:
s = s.encode('ascii')
t = t.encode('ascii')
if s != b'':
assert ed_aff(s, b'', [mismatch_cost] * len(s), gap_start,
10) == gap_start + (len(s) - 1) * 10
assert ed_aff(b'', s, [], gap_start,
10) == gap_start + (len(s) - 1) * 10
assert ed_aff(s, t, [mismatch_cost] * len(s), gap_start,
10) == ed_aff(t, s, [mismatch_cost] * len(t),
gap_start, 10)
def test_compare_to_edit_dist():
for s, t in STRING_PAIRS:
assert ed(s, t) == ed_aff(s, t, [1] * len(s), 1, 1)
def test_small_examples():
assert ed_aff("AGTCCGGTG", "AGTCCATCGGTC", [30, 40, 20, 20, 50, 60, 10, 20, 5], 40, 10) == 65
assert ed_aff("ATGGCCG", "ATCGCTG", [40, 50, 10, 40, 50, 10, 40], 20, 10) == 20
assert ed_aff("ATCCTC", "ATCGGGCTC", [50] * 6, 10, 5) == 20