def test_calculate_hwe(self):
variations = VariationsArrays()
gts = numpy.array([])
variations['/calls/GT'] = gts
variations['/variations/alt'] = gts
result = calc_hwe_chi2_test(variations, min_num_genotypes=0,
chunk_size=None)
assert result.shape[0] == 0
variations = VariationsArrays()
gts = numpy.array([[[0, 0], [0, 1], [0, 1], [0, 0], [0, 1], [0, 0],
[0, 0], [0, 1], [1, 1], [0, 0]],
[[0, 0], [1, 0], [0, 1], [0, 0], [0, 1], [0, 0],
[0, 0], [1, 0], [1, 1], [0, 0]]])
variations['/calls/GT'] = gts
variations._create_matrix('/variations/alt', shape=(1, 1),
dtype=numpy.int16, fillvalue=0)
expected = numpy.array([[1.25825397e+01, 1.85240619e-03],
[1.25825397e+01, 1.85240619e-03]])
result = calc_hwe_chi2_test(variations, min_num_genotypes=0,
chunk_size=None)
assert numpy.allclose(result, expected)
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
hwe_test1 = calc_hwe_chi2_test(hdf5, chunk_size=None)
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
hwe_test2 = calc_hwe_chi2_test(hdf5)
assert numpy.allclose(hwe_test1, hwe_test2, equal_nan=True)
def test_calculate_hwe(self):
variations = VariationsArrays()
gts = numpy.array([])
variations['/calls/GT'] = gts
variations['/variations/alt'] = gts
result = calc_hwe_chi2_test(variations, min_num_genotypes=0,
chunk_size=None)
assert result.shape[0] == 0
variations = VariationsArrays()
gts = numpy.array([[[0, 0], [0, 1], [0, 1], [0, 0], [0, 1], [0, 0],
[0, 0], [0, 1], [1, 1], [0, 0]],
[[0, 0], [1, 0], [0, 1], [0, 0], [0, 1], [0, 0],
[0, 0], [1, 0], [1, 1], [0, 0]]])
variations['/calls/GT'] = gts
variations._create_matrix('/variations/alt', shape=(1, 1),
dtype=numpy.int16, fillvalue=0)
expected = numpy.array([[1.25825397e+01, 1.85240619e-03],
[1.25825397e+01, 1.85240619e-03]])
result = calc_hwe_chi2_test(variations, min_num_genotypes=0,
chunk_size=None)
assert numpy.allclose(result, expected)
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
hwe_test1 = calc_hwe_chi2_test(hdf5, chunk_size=None)
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
hwe_test2 = calc_hwe_chi2_test(hdf5)
assert numpy.allclose(hwe_test1, hwe_test2, equal_nan=True)
