def test_snp_kernel2(self):
logging.info("in test_snp_kernel2")
snpreader = Bed(self.currentFolder + "/../examples/toydata.5chrom.bed",
count_A1=False)
snpkernel = SnpKernel(snpreader, standardizer=stdizer.Beta(1, 25))
s = str(snpkernel)
_fortesting_JustCheckExists().input(snpkernel)
def test_merge_std(self):
#unit vs beta
for std in [stdizer.Beta(2, 10), stdizer.Unit()]:
np.random.seed(0)
sid_count = 20
snpreader = SnpData(iid=[["0", "0"], ["1", "1"], ["2", "2"]],
sid=[str(i) for i in range(sid_count)],
val=np.array(np.random.randint(
3, size=[3, sid_count]),
dtype=np.float64,
order='F'))
kerneldata0, trained0, diag0 = SnpKernel(
snpreader, std,
block_size=1)._read_with_standardizing(to_kerneldata=True,
return_trained=True)
kerneldata1, trained1, diag1 = SnpKernel(
snpreader, std,
block_size=None)._read_with_standardizing(to_kerneldata=True,
return_trained=True)
np.testing.assert_array_almost_equal(kerneldata0.val,
kerneldata1.val,
decimal=10)
np.testing.assert_array_almost_equal(trained0.stats,
trained1.stats,
decimal=10)
assert abs(diag0.factor - diag1.factor) < 1e-7
def test_respect_inputs(self):
np.random.seed(0)
for dtype_start, decimal_start in [(np.float32, 5), (np.float64, 10)]:
for order_start in ['F', 'C', 'A']:
for sid_count in [20, 2]:
snpdataX = SnpData(
iid=[["0", "0"], ["1", "1"], ["2", "2"]],
sid=[str(i) for i in range(sid_count)],
val=np.array(np.random.randint(3, size=[3, sid_count]),
dtype=dtype_start,
order=order_start))
for stdx in [
stdizer.Beta(1, 25),
stdizer.Identity(),
stdizer.Unit()
]:
for snpreader0 in [snpdataX, snpdataX[:, 1:]]:
snpreader1 = snpreader0[1:, :]
refdata0, trained_standardizer = snpreader0.read(
).standardize(stdx,
return_trained=True,
force_python_only=True)
refval0 = refdata0.val.dot(refdata0.val.T)
refdata1 = snpreader1.read().standardize(
trained_standardizer, force_python_only=True
) #LATER why aren't these used?
refval1 = refdata0.val.dot(
refdata1.val.T) #LATER why aren't these used?
for dtype_goal, decimal_goal in [(np.float32, 5),
(np.float64, 10)]:
for order_goal in ['F', 'C', 'A']:
k = snpreader0.read_kernel(
standardizer=stdx,
block_size=1,
order=order_goal,
dtype=dtype_goal)
PstReader._array_properties_are_ok(
k.val, order_goal, dtype_goal)
np.testing.assert_array_almost_equal(
refval0,
k.val,
decimal=min(decimal_start,
decimal_goal))
def test_cpp_std(self):
#Order C vs F
for order in ['C', 'F']:
#32 vs 64
for dtype in [np.float64, np.float32]:
#unit vs beta
for std in [stdizer.Unit(), stdizer.Beta(2, 10)]:
np.random.seed(0)
sid_count = 20
snpreader0 = SnpData(
iid=[["0", "0"], ["1", "1"], ["2", "2"]],
sid=[str(i) for i in range(sid_count)],
val=np.array(np.random.randint(3, size=[3, sid_count]),
dtype=dtype,
order=order))
snpreader1 = SnpData(
iid=[["3", "3"], ["4", "4"]],
sid=[str(i) for i in range(sid_count)],
val=np.array(np.random.randint(3, size=[2, sid_count]),
dtype=dtype,
order=order))
#has SNC
for has_SNC_in_train in [False, True]:
if has_SNC_in_train:
snpreader0.val[:, 1] = 0
#missing data
for has_missing_data in [False, True]:
if has_missing_data:
snpreader0.val[0, 2] = np.nan
snpreader1.val[0, 2] = np.nan
#gather stats vs not
cppa, stdcppa = snpreader0.read(
order=order, dtype=dtype).standardize(
std,
return_trained=True,
force_python_only=False)
pya, stdpya = snpreader0.read(
order=order, dtype=dtype).standardize(
std,
return_trained=True,
force_python_only=True)
np.testing.assert_array_almost_equal(
cppa.val,
pya.val,
decimal=10 if dtype == np.float64 else 5)
np.testing.assert_array_almost_equal(
stdcppa.stats,
stdpya.stats,
decimal=10 if dtype == np.float64 else 5)
assert (np.inf
in stdcppa.stats[:, 1]) == has_SNC_in_train
assert (np.inf
in stdpya.stats[:, 1]) == has_SNC_in_train
if has_SNC_in_train:
assert np.array_equal(
cppa.val[:, 1],
np.zeros([cppa.val.shape[0]]))
assert np.array_equal(
pya.val[:, 1],
np.zeros([pya.val.shape[0]]))
if has_missing_data:
assert 0 == cppa.val[0, 2]
assert 0 == pya.val[0, 2]
#uses stats
cppb = snpreader1.read(order=order,
dtype=dtype).standardize(
stdcppa,
force_python_only=False)
pyb = snpreader1.read(order=order,
dtype=dtype).standardize(
stdpya,
force_python_only=True)
np.testing.assert_array_almost_equal(
cppb.val,
pyb.val,
decimal=10 if dtype == np.float64 else 5)
np.testing.assert_array_almost_equal(
stdcppa.stats,
stdpya.stats,
decimal=10 if dtype == np.float64 else 5
) #Make sure we haven't messed up the train stats
if has_SNC_in_train:
assert np.array_equal(
cppb.val[:, 1],
np.zeros([cppb.val.shape[0]]))
assert np.array_equal(
pyb.val[:, 1],
np.zeros([pyb.val.shape[0]]))
if has_missing_data:
assert cppb.val[0, 2] == 0
assert pyb.val[0, 2] == 0
logging.info("done with 'test_cpp_std'")