def test_count_alleles(self):
hdf5 = VariationsH5(join(TEST_DATA_DIR, '1000snps.hdf5'), mode='r')
chunk = first(hdf5.iterate_chunks())
genotypes = chunk['/calls/GT']
expected = [[3, 3, 0], [5, 1, 0], [0, 2, 4], [6, 0, 0], [2, 3, 1]]
counts = counts_by_row(genotypes, missing_value=-1)
assert numpy.all(expected == counts)
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
chunks = hdf5.iterate_chunks(kept_fields=['/calls/GT'])
chunks = (chunk['/calls/GT'] for chunk in chunks)
matrix = first(chunks)
for _ in range(20):
extend_matrix(matrix, chunks)
counts = counts_by_row(matrix, missing_value=-1)
gts = [[[-1, -1], [-1, -1], [-1, -1], [0, 0], [0, 0], [0, 0]]]
gts = numpy.array(gts)
counts = counts_by_row(gts, missing_value=-1)
assert numpy.all(counts == [[6]])
gts = [[[0, 0], [0, 0], [0, 0]], [[0, 0], [0, 0], [0, 0]]]
gts = numpy.array(gts)
counts = counts_by_row(gts, missing_value=-1)
assert numpy.all(counts == [[6, 6]])
def test_count_alleles(self):
hdf5 = VariationsH5(join(TEST_DATA_DIR, '1000snps.hdf5'), mode='r')
chunk = first(hdf5.iterate_chunks())
genotypes = chunk['/calls/GT']
expected = [[3, 3, 0],
[5, 1, 0],
[0, 2, 4],
[6, 0, 0],
[2, 3, 1]]
counts = counts_by_row(genotypes, missing_value=-1)
assert numpy.all(expected == counts)
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
chunks = hdf5.iterate_chunks(kept_fields=['/calls/GT'])
chunks = (chunk['/calls/GT'] for chunk in chunks)
matrix = first(chunks)
for _ in range(20):
extend_matrix(matrix, chunks)
counts = counts_by_row(matrix, missing_value=-1)
gts = [[[-1, -1], [-1, -1], [-1, -1], [0, 0], [0, 0], [0, 0]]]
gts = numpy.array(gts)
counts = counts_by_row(gts, missing_value=-1)
assert numpy.all(counts == [[6]])
gts = [[[0, 0], [0, 0], [0, 0]],
[[0, 0], [0, 0], [0, 0]]]
gts = numpy.array(gts)
counts = counts_by_row(gts, missing_value=-1)
assert numpy.all(counts == [[6, 6]])
def test_extend(self):
mats = [
numpy.array([[1, 1], [2, 2]]),
numpy.array([[3, 3], [4, 4]]),
numpy.array([[5, 5]])
]
expected = ([[0, 0], [1, 1], [2, 2], [3, 3], [4, 4], [5, 5]])
array = numpy.zeros([1, 2], dtype=numpy.int)
extend_matrix(array, mats)
assert numpy.all(array == expected)
def test_extend(self):
mats = [numpy.array([[1, 1], [2, 2]]), numpy.array([[3, 3], [4, 4]]),
numpy.array([[5, 5]])]
expected = ([[0, 0],
[1, 1],
[2, 2],
[3, 3],
[4, 4],
[5, 5]])
array = numpy.zeros([1, 2], dtype=numpy.int)
extend_matrix(array, mats)
assert numpy.all(array == expected)