def test_ssl01_scan_f():
# 4 haplotypes,
h = np.array([[0, 0, 1, 1], [0, 0, 1, 1], [0, 0, 1, 1]])
expect0 = [1, 2, 3]
expect1 = [1, 2, 3]
actual0, actual1 = ssl01_scan(h, sum_ssl)
assert_array_equal(expect0, actual0)
assert_array_equal(expect1, actual1)
def test_ssl01_scan_c():
# 2 haplotypes, identical
h = np.array([[0, 0], [0, 0], [1, 1], [1, 1]])
expect0 = [1, 2, 0, 0]
expect1 = [0, 0, 3, 4]
actual0, actual1 = ssl01_scan(h, sum_ssl)
assert_array_equal(expect0, actual0)
assert_array_equal(expect1, actual1)
def test_ssl01_scan_e():
# 3 haplotypes, 3 pairs, identical
h = np.array([[0, 0, 0], [0, 0, 0], [0, 0, 0]])
expect0 = [3, 6, 9]
expect1 = [0, 0, 0]
actual0, actual1 = ssl01_scan(h, sum_ssl)
assert_array_equal(expect0, actual0)
assert_array_equal(expect1, actual1)
def test_ssl01_scan_d():
# 2 haplotypes, different
h = np.array([[0, 1], [0, 1], [1, 0], [1, 0]])
expect0 = [0, 0, 0, 0]
expect1 = [0, 0, 0, 0]
actual0, actual1 = ssl01_scan(h, sum_ssl)
assert_array_equal(expect0, actual0)
assert_array_equal(expect1, actual1)
def test_ssl01_scan_int8_b():
# 2 haplotypes, identical
h = np.array([[1, 1], [1, 1], [1, 1]], dtype='i1')
expect0 = [0, 0, 0]
expect1 = [1, 2, 3]
actual0, actual1 = ssl01_scan_int8(h, sum_ssl)
assert_array_equal(expect0, actual0)
assert_array_equal(expect1, actual1)
def test_ehh_decay():
h = [[0, 0, 1, 1], [0, 0, 1, 1], [0, 0, 0, 1], [0, 0, 0, 0], [0, 1, 0, 0]]
e = [2 / 6, 2 / 6, 1 / 6, 1 / 6, 0]
a = ehh_decay(h)
assert_array_equal(e, a)
# with multiallelics
h = [[0, 0, 2, 2], [0, 0, 1, 1], [0, 0, 0, 3], [0, 0, 0, 0], [0, 4, 0, 0]]
e = [2 / 6, 2 / 6, 1 / 6, 1 / 6, 0]
a = ehh_decay(h)
assert_array_equal(e, a)
def test_ssl01_scan_int8_f():
# 4 haplotypes,
h = np.array([[0, 0, 1, 1],
[0, 0, 1, 1],
[0, 0, 1, 1]], dtype='i1')
expect0 = [1, 2, 3]
expect1 = [1, 2, 3]
actual0, actual1 = ssl01_scan_int8(h, sum_ssl)
assert_array_equal(expect0, actual0)
assert_array_equal(expect1, actual1)
def test_ssl01_scan_int8_e():
# 3 haplotypes, 3 pairs, identical
h = np.array([[0, 0, 0],
[0, 0, 0],
[0, 0, 0]], dtype='i1')
expect0 = [3, 6, 9]
expect1 = [0, 0, 0]
actual0, actual1 = ssl01_scan_int8(h, sum_ssl)
assert_array_equal(expect0, actual0)
assert_array_equal(expect1, actual1)
def test_ssl01_scan_int8_b():
# 2 haplotypes, identical
h = np.array([[1, 1],
[1, 1],
[1, 1]], dtype='i1')
expect0 = [0, 0, 0]
expect1 = [1, 2, 3]
actual0, actual1 = ssl01_scan_int8(h, sum_ssl)
assert_array_equal(expect0, actual0)
assert_array_equal(expect1, actual1)
def test_ssl01_scan_int8_d():
# 2 haplotypes, different
h = np.array([[0, 1],
[0, 1],
[1, 0],
[1, 0]], dtype='i1')
expect0 = [0, 0, 0, 0]
expect1 = [0, 0, 0, 0]
actual0, actual1 = ssl01_scan_int8(h, sum_ssl)
assert_array_equal(expect0, actual0)
assert_array_equal(expect1, actual1)
def test_voight_painting():
h = [[0, 0, 1, 1],
[0, 0, 1, 1],
[0, 0, 0, 1],
[0, 0, 0, 0],
[0, 1, 0, 0]]
e = [[1, 1, 2, 2],
[1, 1, 2, 2],
[1, 1, 0, 0],
[1, 1, 0, 0],
[0, 0, 0, 0]]
a, _ = voight_painting(h)
assert_array_equal(e, a)
def test_ehh_decay():
h = [[0, 0, 1, 1], [0, 0, 1, 1], [0, 0, 0, 1], [0, 0, 0, 0], [0, 1, 0, 0]]
e = [2 / 6, 2 / 6, 1 / 6, 1 / 6, 0]
a = ehh_decay(h)
assert_array_equal(e, a)
