def test_add_precursor_mz_no_precursor_mz(key, value, expected):
"""Test if precursor_mz is correctly derived if "precursor_mz" is str."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {key: value}
spectrum_in = SpectrumBuilder().with_metadata(
metadata).with_mz(mz).with_intensities(intensities).build()
spectrum = add_precursor_mz(spectrum_in)
assert spectrum.get("precursor_mz") == expected, "Expected different precursor_mz."
def test_add_precursor_mz_logging(key, value, expected_log, caplog):
"""Test if precursor_mz is correctly derived if "precursor_mz" is str."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {key: value}
spectrum_in = SpectrumBuilder().with_metadata(
metadata).with_mz(mz).with_intensities(intensities).build()
_ = add_precursor_mz(spectrum_in)
assert expected_log in caplog.text, "Expected different logging message."
def spectrum_processing(s):
"""This is how one would typically design a desired pre- and post-
processing pipeline."""
s = default_filters(s)
s = add_precursor_mz(s)
s = normalize_intensities(s)
s = reduce_to_number_of_peaks(s, n_required=5, ratio_desired=0.5, n_max=500)
s = select_by_mz(s, mz_from=0, mz_to=1000)
s = add_losses(s, loss_mz_from=10.0, loss_mz_to=200.0)
s = require_minimum_number_of_peaks(s, n_required=5)
return s
def test_add_precursor_mz():
"""Test if precursor_mz is correctly derived. Here nothing should change."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {"precursor_mz": 444.0}
spectrum_in = Spectrum(mz=mz,
intensities=intensities,
metadata=metadata)
spectrum = add_precursor_mz(spectrum_in)
assert spectrum.get("precursor_mz") == 444.0, "Expected different precursor_mz."
def test_add_precursor_mz_no_precursor_mz():
"""Test if precursor_mz is correctly derived if "precursor_mz" is str."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {"precursor_mz": "444.0"}
spectrum_in = Spectrum(mz=mz,
intensities=intensities,
metadata=metadata)
spectrum = add_precursor_mz(spectrum_in)
assert spectrum.get("precursor_mz") == 444.0, "Expected different precursor_mz."
def test_add_precursor_mz_only_pepmass_present():
"""Test if precursor_mz is correctly derived if only pepmass is present."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {"pepmass": (444.0, 10)}
spectrum_in = Spectrum(mz=mz,
intensities=intensities,
metadata=metadata)
spectrum = add_precursor_mz(spectrum_in)
assert spectrum.get("precursor_mz") == 444.0, "Expected different precursor_mz."
def test_add_precursor_mz_no_masses():
"""Test if no precursor_mz is handled correctly. Here nothing should change."""
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {}
spectrum_in = Spectrum(mz=mz,
intensities=intensities,
metadata=metadata)
spectrum = add_precursor_mz(spectrum_in)
assert spectrum.get("precursor_mz") is None, "Outcome should be None."
def test_add_precursor_mz_only_pepmass_present(caplog):
"""Test if precursor_mz is correctly derived if only pepmass is present."""
set_matchms_logger_level("INFO")
mz = numpy.array([], dtype='float')
intensities = numpy.array([], dtype='float')
metadata = {"pepmass": (444.0, 10)}
spectrum_in = SpectrumBuilder().with_metadata(
metadata).with_mz(mz).with_intensities(intensities).build()
spectrum = add_precursor_mz(spectrum_in)
assert spectrum.get("precursor_mz") == 444.0, "Expected different precursor_mz."
assert "Added precursor_mz entry based on field 'pepmass'" in caplog.text, \
"Expected different log message"
reset_matchms_logger()
def test_empty_spectrum():
spectrum_in = None
spectrum = add_precursor_mz(spectrum_in)
assert spectrum is None, "Expected different handling of None spectrum."
def test_add_precursor_mz(metadata, expected):
spectrum_in = SpectrumBuilder().with_metadata(metadata).build()
spectrum = add_precursor_mz(spectrum_in)
assert spectrum.get("precursor_mz") == expected, "Expected different precursor_mz."
