def test_collapse_probes_donors(testfiles, donor_probes): out = probes_.collapse_probes(flatten_dict(testfiles, 'microarray'), flatten_dict(testfiles, 'annotation'), first_entry(testfiles, 'probes'), method='max_intensity', donor_probes=donor_probes) out = list(out.values()) assert len(out) == 2 # number of donors assert np.all([len(exp) == n_samp for exp, n_samp in zip(out, [363, 470])]) assert np.all([len(exp.columns) == 29131 for exp in out])
def test_collapse_probes(testfiles, method): # we've aleady tested the underlying methods so here we just want to do # some smoke tests to make sure the function returns what we expected # regardless of the provided method out = probes_.collapse_probes(flatten_dict(testfiles, 'microarray'), flatten_dict(testfiles, 'annotation'), first_entry(testfiles, 'probes'), method=method) out = list(out.values()) assert len(out) == 2 # number of donors assert np.all([len(exp) == n_samp for exp, n_samp in zip(out, [363, 470])]) assert np.all([len(exp.columns) == 29131 for exp in out])
def test_collapse_probes_errors(testfiles): with pytest.raises(ValueError): probes_.collapse_probes(flatten_dict(testfiles, 'microarray'), flatten_dict(testfiles, 'annotation'), first_entry(testfiles, 'probes'), method='notamethod')