def test_c_reader_npz(self):
distreader = DistNpz(self.currentFolder + "/../examples/toydata10.dist.npz")
distdata = distreader.read(order='F',force_python_only=False)
snp_c = distdata.val
self.assertEqual(np.float64, snp_c.dtype)
self.assertTrue(np.allclose(self.dist_values[:,:10], snp_c, rtol=1e-05, atol=1e-05))
distreader1 = DistNpz(self.currentFolder + "/../examples/toydata10.dist.npz")
distreader2 = DistNpz(self.currentFolder + "/../examples/toydata.dist.npz")[:,:10]
self.assertTrue(np.allclose(distreader1.read().val, distreader2.read().val, rtol=1e-05, atol=1e-05))
distdata.val[1,2] = np.NaN # Inject a missing value to test writing and reading missing values
output = "tempdir/distreader/toydata10.dist.npz"
create_directory_if_necessary(output)
DistNpz.write(output,distdata)
snpdata2 = DistNpz(output).read()
np.testing.assert_array_almost_equal(distdata.val, snpdata2.val, decimal=10)
snpdata3 = distdata[:,0:0].read() #create distdata with no sids
output = "tempdir/distreader/toydata0.dist.npz"
DistNpz.write(output,snpdata3)
snpdata4 = DistNpz(output).read()
assert snpdata3 == snpdata4
def setUpClass(self):
self.currentFolder = os.path.dirname(os.path.realpath(__file__))
#TODO: get data set with NANs!
distreader = DistNpz(self.currentFolder +
"/../examples/toydata.dist.npz")
self.distdata = distreader.read(order='F', force_python_only=True)
self.dist_values = self.distdata.val
def test_write_x_x_cpp(self):
distreader = DistNpz(self.currentFolder + "/../examples/toydata.dist.npz")
for order in ['C','F']:
for dtype in [np.float32,np.float64]:
distdata = distreader.read(order=order,dtype=dtype)
distdata.val[-1,0] = float("NAN")
output = "tempdir/toydata.{0}{1}.cpp.dist.npz".format(order,"32" if dtype==np.float32 else "64")
create_directory_if_necessary(output)
DistNpz.write(output, distdata)
snpdata2 = DistNpz(output).read()
np.testing.assert_array_almost_equal(distdata.val, snpdata2.val, decimal=10)
def test_hdf5_case3(self):
distreader1 = DistHdf5(
self.currentFolder +
"/../examples/toydata.snpmajor.dist.hdf5")[::2, :]
distreader2 = DistNpz(self.currentFolder +
"/../examples/toydata.dist.npz")[::2, :]
self.assertTrue(
np.allclose(distreader1.read().val,
distreader2.read().val,
rtol=1e-05,
atol=1e-05))
def test_subset_view(self):
distreader2 = DistNpz(self.currentFolder + "/../examples/toydata.dist.npz")[:,:]
result = distreader2.read(view_ok=True)
self.assertFalse(distreader2 is result)
result2 = result[:,:].read()
self.assertFalse(np.may_share_memory(result2.val,result.val))
result3 = result[:,:].read(view_ok=True)
self.assertTrue(np.may_share_memory(result3.val,result.val))
result4 = result3.read()
self.assertFalse(np.may_share_memory(result4.val,result3.val))
result5 = result4.read(view_ok=True)
self.assertTrue(np.may_share_memory(result4.val,result5.val))
