def test_make_roi_targeted_mz(simulated_experiment):
# the first three m/z values generated by simulated experiment are used
targeted_mz = simulated_experiment.mz_params[:, 0][:3]
roi_list = lcms.make_roi(simulated_experiment, tolerance=0.005,
max_missing=0, min_length=0, min_intensity=0,
multiple_match="reduce", targeted_mz=targeted_mz)
assert len(roi_list) == targeted_mz.size
def test_make_roi_end(simulated_experiment):
end = 10
roi_list = lcms.make_roi(simulated_experiment, tolerance=0.005,
max_missing=0, min_length=0, min_intensity=0,
multiple_match="reduce", end=end)
n_sp = simulated_experiment.getNrSpectra()
for r in roi_list:
assert r.mz.size == end
def test_make_roi_min_intensity(simulated_experiment):
min_intensity = 15
roi_list = lcms.make_roi(simulated_experiment, tolerance=0.005,
max_missing=0, min_length=0,
min_intensity=min_intensity,
multiple_match="reduce")
# only two roi should have intensities greater than 15
assert len(roi_list) == 2
def test_make_roi_multiple_match_reduce_merge(simulated_experiment):
# set a tolerance such that two mz values are merged
# test is done in targeted mode to force a multiple match by removing
# one of the mz values
targeted_mz = simulated_experiment.mz_params[:, 0]
targeted_mz = np.delete(targeted_mz, 3)
tolerance = 31
roi_list = lcms.make_roi(simulated_experiment, tolerance=tolerance,
max_missing=0, min_length=0, min_intensity=0,
multiple_match="reduce", targeted_mz=targeted_mz)
assert len(roi_list) == (simulated_experiment.mz_params.shape[0] - 1)
def test_make_roi_invalid_multiple_match(simulated_experiment):
with pytest.raises(ValueError):
lcms.make_roi(simulated_experiment, tolerance=0.005, max_missing=0,
min_length=0, min_intensity=0,
multiple_match="invalid-value")
def test_make_roi_multiple_match_reduce_custom_sp_reduce(simulated_experiment):
sp_reduce = lambda x: 1
roi_list = lcms.make_roi(simulated_experiment, tolerance=0.005,
max_missing=0, min_length=0, min_intensity=0,
multiple_match="reduce", sp_reduce=sp_reduce)
assert len(roi_list) == simulated_experiment.mz_params.shape[0]
def test_make_roi_multiple_match_closest(simulated_experiment):
roi_list = lcms.make_roi(simulated_experiment, tolerance=0.005,
max_missing=0, min_length=0, min_intensity=0,
multiple_match="closest")
assert len(roi_list) == simulated_experiment.mz_params.shape[0]