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."