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_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)