def test_remove_peaks_around_precursor_with_wrong_precursor_mz(spectrum_in):
"""Test if correct assert error is raised for precursor-mz as string."""
spectrum_in.set("precursor_mz", "445.0")
with pytest.raises(AssertionError) as msg:
_ = remove_peaks_around_precursor_mz(spectrum_in)
assert "Expected 'precursor_mz' to be a scalar number." in str(msg.value)
def test_remove_peaks_around_precursor_mz_tolerance_20(spectrum_in):
"""Set mz_tolerance to 20."""
spectrum = remove_peaks_around_precursor_mz(spectrum_in, mz_tolerance=20)
assert len(spectrum.peaks) == 3, "Expected 3 peaks to remain."
assert spectrum.peaks.mz.tolist() == [
10., 20., 30.
], "Expected different peaks to remain."
def test_remove_peaks_around_precursor_without_precursor_mz(spectrum_in):
"""Test if correct assert error is raised for missing precursor-mz."""
spectrum_in.metadata = {}
with pytest.raises(AssertionError) as msg:
_ = remove_peaks_around_precursor_mz(spectrum_in)
assert str(msg.value
) == "Precursor mz absent.", "Expected different error message."
def test_if_spectrum_is_cloned():
"""Test if filter is correctly cloning the input spectrum."""
spectrum_in = SpectrumBuilder().with_metadata({"precursor_mz": 1.}).build()
spectrum = remove_peaks_around_precursor_mz(spectrum_in)
spectrum.set("testfield", "test")
assert not spectrum_in.get(
"testfield"), "Expected input spectrum to remain unchanged."
def test_remove_peaks_around_precursor_mz_no_params():
"""Using defaults with precursor mz present."""
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([0, 1, 10, 100], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum_in.set("precursor_mz", 60.)
spectrum = remove_peaks_around_precursor_mz(spectrum_in)
assert spectrum == spectrum_in, "Expected no changes."
def test_remove_peaks_around_precursor_with_wrong_precursor_mz():
"""Test if correct assert error is raised for precursor-mz as string."""
spectrum_in = Spectrum(mz=numpy.array([10, 20, 30, 40], dtype="float"),
intensities=numpy.array([0, 1, 10, 100],
dtype="float"),
metadata={"precursor_mz": "445.0"})
with pytest.raises(AssertionError) as msg:
_ = remove_peaks_around_precursor_mz(spectrum_in)
assert "Expected 'precursor_mz' to be a scalar number." in str(msg.value)
def test_remove_peaks_around_precursor_without_precursor_mz():
"""Test if correct assert error is raised for missing precursor-mz."""
spectrum_in = Spectrum(mz=numpy.array([10, 20, 30, 40], dtype="float"),
intensities=numpy.array([0, 1, 10, 100],
dtype="float"),
metadata={})
with pytest.raises(AssertionError) as msg:
_ = remove_peaks_around_precursor_mz(spectrum_in)
assert str(msg.value
) == "Precursor mz absent.", "Expected different error message."
def test_if_spectrum_is_cloned():
"""Test if filter is correctly cloning the input spectrum."""
mz = numpy.array([], dtype="float")
intensities = numpy.array([], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum_in.set("precursor_mz", 1.)
spectrum = remove_peaks_around_precursor_mz(spectrum_in)
spectrum.set("testfield", "test")
assert not spectrum_in.get(
"testfield"), "Expected input spectrum to remain unchanged."
def test_remove_peaks_around_precursor_mz_tolerance_20():
"""Set mz_tolerance to 20."""
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([0, 1, 10, 100], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum_in.set("precursor_mz", 60.)
spectrum = remove_peaks_around_precursor_mz(spectrum_in, mz_tolerance=20)
assert len(spectrum.peaks) == 3, "Expected 3 peaks to remain."
assert spectrum.peaks.mz.tolist() == [
10., 20., 30.
], "Expected different peaks to remain."
def test_with_input_none():
"""Test if input spectrum is None."""
spectrum_in = None
spectrum = remove_peaks_around_precursor_mz(spectrum_in)
assert spectrum is None
def test_remove_peaks_around_precursor_mz_no_params(spectrum_in):
"""Using defaults with precursor mz present."""
spectrum = remove_peaks_around_precursor_mz(spectrum_in)
assert spectrum == spectrum_in, "Expected no changes."