def test_to_hdf5(self):
# setup HDF5 file
tf = tempfile.NamedTemporaryFile(delete=False)
file_path = tf.name
tf.close()
# setup genotype array
node_path = 'test'
g = GenotypeCArray(diploid_genotype_data, dtype='i1')
# write using file path and node path
g.to_hdf5(file_path, node_path)
# test outcome
with h5py.File(file_path, mode='r') as h5f:
h5d = h5f[node_path]
aeq(g[:], h5d[:])
# write using group
with h5py.File(file_path, mode='w') as h5f:
g.to_hdf5(h5f, node_path)
# test outcome
with h5py.File(file_path, mode='r') as h5f:
h5d = h5f[node_path]
aeq(g[:], h5d[:])
def test_constructor(self):
# missing data arg
with assert_raises(ValueError):
# noinspection PyArgumentList
GenotypeCArray()
# data has wrong dtype
data = 'foo bar'
with assert_raises(TypeError):
GenotypeCArray(data)
# data has wrong dtype
data = [4., 5., 3.7]
with assert_raises(TypeError):
GenotypeCArray(data)
# data has wrong dimensions
data = [1, 2, 3]
with assert_raises(TypeError):
GenotypeCArray(data)
# data has wrong dimensions
data = [[1, 2], [3, 4]] # use HaplotypeCArray instead
with assert_raises(TypeError):
GenotypeCArray(data)
# diploid data (typed)
g = GenotypeCArray(diploid_genotype_data, dtype='i1')
aeq(diploid_genotype_data, g)
eq(np.int8, g.dtype)
# polyploid data (typed)
g = GenotypeCArray(triploid_genotype_data, dtype='i1')
aeq(triploid_genotype_data, g)
eq(np.int8, g.dtype)
# cparams
g = GenotypeCArray(diploid_genotype_data,
cparams=bcolz.cparams(clevel=10))
aeq(diploid_genotype_data, g)
eq(10, g.cparams.clevel)
def test_slice_types(self):
g = GenotypeCArray(diploid_genotype_data, dtype='i1')
# row slice
s = g[1:]
self.assertNotIsInstance(s, GenotypeCArray)
self.assertIsInstance(s, GenotypeArray)
# col slice
s = g[:, 1:]
self.assertNotIsInstance(s, GenotypeCArray)
self.assertIsInstance(s, GenotypeArray)
# row index
s = g[0]
self.assertNotIsInstance(s, GenotypeCArray)
self.assertNotIsInstance(s, GenotypeArray)
self.assertIsInstance(s, np.ndarray)
# col index
s = g[:, 0]
self.assertNotIsInstance(s, GenotypeCArray)
self.assertNotIsInstance(s, GenotypeArray)
self.assertIsInstance(s, np.ndarray)
# ploidy index
s = g[:, :, 0]
self.assertNotIsInstance(s, GenotypeCArray)
self.assertNotIsInstance(s, GenotypeArray)
self.assertIsInstance(s, np.ndarray)
# item
s = g[0, 0, 0]
self.assertNotIsInstance(s, GenotypeCArray)
self.assertNotIsInstance(s, GenotypeArray)
self.assertIsInstance(s, np.int8)
def setup_instance(self, data):
return GenotypeCArray(data)
