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')