def test_count_alleles_subpops(self):
data = chunked.storage_registry['default'].array(diploid_genotype_data, chunklen=2)
g = GenotypeChunkedArray(data)
subpops = {'foo': [0, 2], 'bar': [1]}
ac_subpops = g.count_alleles_subpops(subpops)
for p in subpops.keys():
ac = g.take(subpops[p], axis=1).count_alleles()
aeq(ac, ac_subpops[p])
loc = np.array([True, False, True, False, True])
t = ac_subpops.compress(loc)
eq(3, len(t))
def test_constructor(self):
# missing data arg
with assert_raises(TypeError):
# noinspection PyArgumentList
GenotypeChunkedArray()
# data has wrong dtype
data = 'foo bar'
with assert_raises(TypeError):
GenotypeChunkedArray(data)
# data has wrong dtype
data = np.array([4., 5., 3.7])
with assert_raises(TypeError):
GenotypeChunkedArray(data)
# data has wrong dimensions
data = np.array([1, 2, 3])
with assert_raises(TypeError):
GenotypeChunkedArray(data)
# data has wrong dimensions
data = np.array([[1, 2], [3, 4]]) # use HaplotypeChunkedArray instead
with assert_raises(TypeError):
GenotypeChunkedArray(data)
# diploid data (typed)
g = self.setup_instance(np.array(diploid_genotype_data, dtype='i1'))
aeq(diploid_genotype_data, g)
eq(np.int8, g.dtype)
# polyploid data (typed)
g = self.setup_instance(np.array(triploid_genotype_data, dtype='i1'))
aeq(triploid_genotype_data, g)
eq(np.int8, g.dtype)
def setup_instance(self, data, dtype=None):
data = chunked.hdf5tmp_lzf_storage.array(data, dtype=dtype)
return GenotypeChunkedArray(data)
def setup_instance(self, data, **kwargs):
data = chunked.storage_registry['default'].array(data, chunklen=2, **kwargs)
return GenotypeChunkedArray(data)
def setup_instance(self, data, **kwargs):
data = chunked.zarrtmp_storage.array(data, **kwargs)
return GenotypeChunkedArray(data)