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")