def test_append_matrix(self):
in_fpath = join(TEST_DATA_DIR, '1000snps.hdf5')
array = numpy.array([[1, 1, 1], [2, 2, 2]])
expected = ([[1, 8, 5], [3, 5, 3], [6, 0, 4], [7, 4, 2], [4, 2, 3],
[1, 1, 1], [2, 2, 2]])
expected2 = [[1, 1, 1], [2, 2, 2], [1, 8, 5], [3, 5, 3], [6, 0, 4],
[7, 4, 2], [4, 2, 3], [1, 1, 1], [2, 2, 2], [1, 8, 5],
[3, 5, 3], [6, 0, 4], [7, 4, 2], [4, 2, 3], [1, 1, 1],
[2, 2, 2]]
with NamedTemporaryFile(suffix='.h5') as fhand_out:
shutil.copy(in_fpath, fhand_out.name)
hdf5 = VariationsH5(fhand_out.name, mode='r+')
dset = hdf5['/calls/DP']
orig_array = dset[()]
append_matrix(dset, array)
assert numpy.all(dset[()] == expected)
append_matrix(dset, dset)
array2 = numpy.array([[1, 1, 1], [2, 2, 2]])
append_matrix(array2, dset[()])
assert numpy.all(expected2 == array2)
append_matrix(orig_array, array)
assert numpy.all(orig_array == expected)
def _get_mats_for_chunk(self, variations):
field_paths = variations.keys()
diff_fields = set(self.keys()).difference(set(field_paths))
if diff_fields:
msg = 'Previous matrices do not match matrices in chunk'
raise ValueError(msg)
matrices = {}
for field in field_paths:
mat1 = variations[field]
mat2 = self[field]
self._check_shape_matches(mat1, mat2, field)
append_matrix(mat2, mat1)
matrices[field] = mat2
return matrices
def put_chunks(self, chunks, kept_fields=None, ignored_fields=None):
matrices = None
if chunks is None:
return
for chunk in chunks:
if matrices is None:
matrices = self._create_or_get_mats_from_chunk(chunk)
continue
# check all chunks have the same number of snps
nsnps = [chunk[path].data.shape[0]
for path in chunk.keys()]
num_snps = nsnps[0]
assert all(num_snps == nsnp for nsnp in nsnps)
for path in chunk.keys():
dset_chunk = chunk[path]
dset = matrices[path]
append_matrix(dset, dset_chunk)
self._index = None
if hasattr(self, 'flush'):
self._h5file.flush()
def test_append_matrix(self):
in_fpath = join(TEST_DATA_DIR, '1000snps.hdf5')
array = numpy.array([[1, 1, 1], [2, 2, 2]])
expected = ([[1, 8, 5],
[3, 5, 3],
[6, 0, 4],
[7, 4, 2],
[4, 2, 3],
[1, 1, 1],
[2, 2, 2]])
expected2 = [[1, 1, 1],
[2, 2, 2],
[1, 8, 5],
[3, 5, 3],
[6, 0, 4],
[7, 4, 2],
[4, 2, 3],
[1, 1, 1],
[2, 2, 2],
[1, 8, 5],
[3, 5, 3],
[6, 0, 4],
[7, 4, 2],
[4, 2, 3],
[1, 1, 1],
[2, 2, 2]]
with NamedTemporaryFile(suffix='.h5') as fhand_out:
shutil.copy(in_fpath, fhand_out.name)
hdf5 = VariationsH5(fhand_out.name, mode='r+')
dset = hdf5['/calls/DP']
orig_array = dset.value
append_matrix(dset, array)
assert numpy.all(dset.value == expected)
append_matrix(dset, dset)
array2 = numpy.array([[1, 1, 1], [2, 2, 2]])
append_matrix(array2, dset.value)
assert numpy.all(expected2 == array2)
append_matrix(orig_array, array)
assert numpy.all(orig_array == expected)
