def test_out_of_range_probe_counts_throws(self, capsys):
with pytest.raises(ValueError):
results = ArrayType.from_probe_count(100)
assert results is None
captured = capsys.readouterr()
assert captured.out == 'Unknown array type\n'
def _control_probe_selection(self):
""" checks that control sections of each manifest match the number of probes the model expects.
this TEST DOES NOT RUN because it would require downloading all 4 manifest files each time. """
array_type_filenames = manifests.ARRAY_TYPE_MANIFEST_FILENAMES # array_type : manifest_filename
files = {
array_type: Path(manifests.MANIFEST_DIR_PATH,
manifest_filename).expanduser()
for array_type, manifest_filename in array_type_filenames.items()
}
for array_type, filepath in files.items():
man = manifests.Manifest(array_type, filepath)
if ArrayType(
array_type
).num_controls != man._Manifest__control_data_frame.shape[0]:
raise AssertionError(
f'Control probes found ({man._Manifest__control_data_frame.shape[0]}) in file ({filepath}) does not match expected number: {ArrayType(array_type).num_controls}'
)
def test_epic_plus(self):
array_type = ArrayType.from_probe_count(1055583)
assert array_type == ArrayType.ILLUMINA_EPIC_PLUS
def test_epic_probe_counts_upper_bound(self):
array_type = ArrayType.from_probe_count(1053000)
assert array_type == ArrayType.ILLUMINA_EPIC
def test_450k_probe_counts_upper_bound(self):
array_type = ArrayType.from_probe_count(623000)
assert array_type == ArrayType.ILLUMINA_450K
def test_27k_probe_counts_upper_bound(self):
array_type = ArrayType.from_probe_count(56000)
assert array_type == ArrayType.ILLUMINA_27K
def test_no_probe_counts_throws(self):
with pytest.raises(TypeError):
ArrayType.from_probe_count()