def test_write(self, stool_biom, tmpdir): otu_inst = Otu(stool_biom) fol = tmpdir.mkdir("results") otu_inst.write("biom_test", str(fol)) otu_load1 = Otu.load_data(fol.join("biom_test.biom")) assert otu_inst.otu_data.shape == otu_load1.otu_data.shape otu_inst.write("tsv_test", str(fol), "tsv") otu_load2 = Otu.load_data( fol.join("tsv_test_otu.tsv"), fol.join("tsv_test_sample_metadata.tsv"), fol.join("tsv_test_obs_metadata.csv"), dtype="tsv", ) assert otu_inst.otu_data.shape == otu_load2.otu_data.shape
def test_load_data_tsv(self, tsv_files): for otu, sample, tax in tsv_files["good"]: otu_inst = Otu.load_data(otu, sample, tax, dtype="tsv") assert hasattr(otu_inst, "otu_data") assert hasattr(otu_inst, "sample_metadata") assert hasattr(otu_inst, "obs_metadata")
def test_load_data_biom(self, biom_files): for biom in biom_files["good"]: otu_inst = Otu.load_data(biom) assert hasattr(otu_inst, "otu_data") assert hasattr(otu_inst, "sample_metadata") assert hasattr(otu_inst, "obs_metadata")