def test_rm_sparse_samples(self, stool_biom):
otu_inst = Otu(stool_biom)
rm_samples_otu = otu_inst.rm_sparse_samples()
assert otu_inst.otu_data.shape[0] == rm_samples_otu.otu_data.shape[0]
assert otu_inst.otu_data.shape[1] > rm_samples_otu.otu_data.shape[1]
assert otu_inst.otu_data.shape[1] - rm_samples_otu.otu_data.shape[
1] == 1
norm_otu = otu_inst.normalize()
with pytest.raises(ValueError):
norm_otu.rm_sparse_samples()
def test_normalize(self, stool_biom):
otu_inst = Otu(stool_biom)
sample_norm = otu_inst.normalize()
assert (otu_inst.otu_data.to_dataframe().sum(axis=0) > 1).all()
assert np.isclose(sample_norm.otu_data.to_dataframe().sum(axis=0),
1.0).all()
assert sample_norm.is_norm(axis="sample")
obs_norm = otu_inst.normalize(axis="observation")
assert (otu_inst.otu_data.to_dataframe().sum(axis=1) > 1).all()
assert obs_norm.is_norm(axis="observation")
assert np.isclose(obs_norm.otu_data.to_dataframe().sum(axis=1),
1.0).all()
with pytest.raises(ValueError):
otu_inst.normalize(method="random_method")
with pytest.raises(NotImplementedError):
otu_inst.normalize(method="css")
with pytest.raises(NotImplementedError):
otu_inst.normalize(method="rarefy")