def test_from_hdf5_condition(self):
# setup HDF5 file
node_path = 'test'
tf = tempfile.NamedTemporaryFile(delete=False)
file_path = tf.name
tf.close()
with h5py.File(file_path, mode='w') as h5f:
h5f.create_dataset(node_path,
data=diploid_genotype_data,
chunks=(2, 3, 2))
# selection
condition = [False, True, False, True, False]
# file and node path
g = GenotypeCArray.from_hdf5(file_path, node_path, condition=condition)
expect = GenotypeArray(diploid_genotype_data).compress(condition,
axis=0)
aeq(expect, g)
# dataset
with h5py.File(file_path, mode='r') as h5f:
dataset = h5f[node_path]
g = GenotypeCArray.from_hdf5(dataset, condition=condition)
aeq(expect, g)
def test_from_hdf5_condition(self):
# setup HDF5 file
node_path = 'test'
tf = tempfile.NamedTemporaryFile(delete=False)
file_path = tf.name
tf.close()
with h5py.File(file_path, mode='w') as h5f:
h5f.create_dataset(node_path,
data=diploid_genotype_data,
chunks=(2, 3, 2))
# selection
condition = [False, True, False, True, False]
# file and node path
g = GenotypeCArray.from_hdf5(file_path, node_path, condition=condition)
expect = GenotypeArray(diploid_genotype_data).compress(condition,
axis=0)
aeq(expect, g)
# dataset
with h5py.File(file_path, mode='r') as h5f:
dataset = h5f[node_path]
g = GenotypeCArray.from_hdf5(dataset, condition=condition)
aeq(expect, g)
def test_from_hdf5(self):
# setup HDF5 file
node_path = 'test'
tf = tempfile.NamedTemporaryFile(delete=False)
file_path = tf.name
tf.close()
with h5py.File(file_path, mode='w') as h5f:
h5f.create_dataset(node_path,
data=diploid_genotype_data,
chunks=(2, 3, 2))
# file and node path
g = GenotypeCArray.from_hdf5(file_path, node_path)
aeq(diploid_genotype_data, g)
# dataset
with h5py.File(file_path, mode='r') as h5f:
dataset = h5f[node_path]
g = GenotypeCArray.from_hdf5(dataset)
aeq(diploid_genotype_data, g)
def test_from_hdf5(self):
# setup HDF5 file
node_path = 'test'
tf = tempfile.NamedTemporaryFile(delete=False)
file_path = tf.name
tf.close()
with h5py.File(file_path, mode='w') as h5f:
h5f.create_dataset(node_path,
data=diploid_genotype_data,
chunks=(2, 3, 2))
# file and node path
g = GenotypeCArray.from_hdf5(file_path, node_path)
aeq(diploid_genotype_data, g)
# dataset
with h5py.File(file_path, mode='r') as h5f:
dataset = h5f[node_path]
g = GenotypeCArray.from_hdf5(dataset)
aeq(diploid_genotype_data, g)
