def test001(self):
exp = MSExperiment()
basename = "SHORT_MS2_FILE.mzData"
here = os.path.dirname(os.path.abspath(__file__))
FileHandler().loadExperiment(os.path.join(here, "data", basename), exp)
assert exp.size() > 0
pc = Precursor()
pc.setMZ(1.0)
pc.setIntensity(100)
s0 = exp[0]
s0.setPrecursors([pc])
s0.setMSLevel(2)
spec = Spectrum.fromMSSpectrum(s0)
settings = InstrumentSettings()
settings.setPolarity(IonSource.Polarity.POSITIVE)
s0.setInstrumentSettings(settings)
self.compare_specs(spec, s0)
specneu = Spectrum.fromMSSpectrum(spec.toMSSpectrum())
self.compare_specs(specneu, s0)
pm = PeakMap.fromMSExperiment(exp)
assert os.path.basename(pm.meta["source"]) == basename
rtmin, rtmax = pm.rtRange(None)
ms1s = pm.msNPeaks(1, rtmin, rtmax)
assert ms1s.shape == (1797, 2), ms1s.shape
ms1s2 = pm.msNPeaks(1, rtmax=rtmax)
assert np.all(ms1s == ms1s2)
ms1s3 = pm.msNPeaks(1, rtmin=0)
assert np.all(ms1s == ms1s3)
spec = pm.spectra[0]
assert len(list(spec)) == len(spec) # calls iter
allrts = pm.allRts()
assert allrts[0] <= pm.rtRange()[0]
assert allrts[-1] >= pm.rtRange()[1]
assert len(allrts) == 41, len(allrts)
level1 = pm.levelNSpecs(1, 1)
level2 = pm.levelNSpecs(2, 2)
level12 = pm.levelNSpecs(1, 2)
assert len(level1) > 0
assert len(level2) > 0
assert len(level1) + len(level2) == len(level12) == len(pm)
assert level1[0].msLevel == 1
assert level2[0].msLevel == 2
# use default arg: nmax = nmin if not provided:
level1 = pm.levelNSpecs(1)
level2 = pm.levelNSpecs(2)
assert len(level1) > 0
assert len(level2) > 0
assert len(level1) + len(level2) == len(level12) == len(pm)
assert level1[0].msLevel == 1
assert level2[0].msLevel == 2
lone = pm.levelOneRts()
assert len(lone) == len(level1)
self.compare_exp(pm, exp, basename)
pm2 = PeakMap.fromMSExperiment(pm.toMSExperiment())
self.compare_exp(pm2, exp, basename)
pm2 = pm.extract(rtmin=rtmin + .000001)
assert len(pm2) == len(pm) - 1
pm2 = pm2.extract(rtmax=rtmax - 0.000001)
assert len(pm2) == len(pm) - 2
mzmin, mzmax = pm.mzRange(2)
assert mzmin < 250
assert mzmax > 860
mzmin, mzmax = pm.mzRange(1)
assert mzmin >= 700
assert mzmax <= 1050
pm2 = pm.extract(rtmin + 0.00001, mzmin=300)
mzmin2, mzmax2 = pm2.mzRange()
assert mzmin2 >= 300
assert mzmax2 == mzmax
pm2 = pm.extract(rtmin=rtmin + 0.000001, mzmin=300, mzmax=1000)
mzmin2, mzmax2 = pm2.mzRange()
assert mzmin2 >= 300
assert mzmax2 <= 1000
with pytest.raises(Exception):
pm.spectra[0].peaksInRange()
pp1 = pm.spectra[0].peaksInRange(mzmax=10000)
pp2 = pm.spectra[0].peaksInRange(mzmin=0)
assert np.all(pp1 == pp2)
specs0 = list(pm.spectra)
specs1 = pm.specsInRange(0, 99999)
specs2 = pm.specsInRange(0, specs0[0].rt)
specs3 = pm.specsInRange(specs0[-1].rt, 999999)
assert specs0 == specs1
assert specs2 == [specs0[0]]
assert specs3 == [specs0[-1]]
pm.spectra[0].polarity = "+"
pm.spectra[1].polarity = "-"
pm = PeakMap(pm.spectra)
mz = pm.representingMzPeak(0, 99999, 0, 99999)
assert abs(mz - 831.86538) < 0.0001
def test001(self):
exp = MSExperiment()
basename = "SHORT_MS2_FILE.mzData"
here = os.path.dirname(os.path.abspath(__file__))
FileHandler().loadExperiment(os.path.join(here, "data", basename), exp)
assert exp.size()>0
pc = Precursor()
pc.setMZ(1.0)
pc.setIntensity(100)
s0 = exp[0]
s0.setPrecursors([pc])
s0.setMSLevel(2)
spec = Spectrum.fromMSSpectrum(s0)
settings = InstrumentSettings()
settings.setPolarity(IonSource.Polarity.POSITIVE)
s0.setInstrumentSettings(settings)
self.compare_specs(spec, s0)
specneu = Spectrum.fromMSSpectrum(spec.toMSSpectrum())
self.compare_specs(specneu, s0)
pm = PeakMap.fromMSExperiment(exp)
assert os.path.basename(pm.meta["source"]) == basename
rtmin, rtmax = pm.rtRange(None)
ms1s = pm.msNPeaks(1, rtmin, rtmax)
assert ms1s.shape == (1797, 2), ms1s.shape
ms1s2 = pm.msNPeaks(1, rtmax=rtmax)
assert np.all(ms1s == ms1s2)
ms1s3 = pm.msNPeaks(1, rtmin=0)
assert np.all(ms1s == ms1s3)
spec = pm.spectra[0]
assert len(list(spec)) == len(spec) # calls iter
allrts = pm.allRts()
assert allrts[0] <= pm.rtRange()[0]
assert allrts[-1] >= pm.rtRange()[1]
assert len(allrts) == 41, len(allrts)
level1 = pm.levelNSpecs(1, 1)
level2 = pm.levelNSpecs(2, 2)
level12 = pm.levelNSpecs(1, 2)
assert len(level1) > 0
assert len(level2) > 0
assert len(level1) + len(level2) == len(level12) == len(pm)
assert level1[0].msLevel == 1
assert level2[0].msLevel == 2
# use default arg: nmax = nmin if not provided:
level1 = pm.levelNSpecs(1)
level2 = pm.levelNSpecs(2)
assert len(level1) > 0
assert len(level2) > 0
assert len(level1) + len(level2) == len(level12) == len(pm)
assert level1[0].msLevel == 1
assert level2[0].msLevel == 2
lone = pm.levelOneRts()
assert len(lone) == len(level1)
self.compare_exp(pm, exp, basename)
pm2 = PeakMap.fromMSExperiment(pm.toMSExperiment())
self.compare_exp(pm2, exp, basename)
pm2 = pm.extract(rtmin=rtmin + .000001)
assert len(pm2) == len(pm) - 1
pm2 = pm2.extract(rtmax=rtmax - 0.000001)
assert len(pm2) == len(pm) - 2
mzmin, mzmax = pm.mzRange(2)
assert mzmin < 250
assert mzmax > 860
mzmin, mzmax = pm.mzRange(1)
assert mzmin >= 700
assert mzmax <= 1050
pm2 = pm.extract(rtmin+0.00001, mzmin=300)
mzmin2, mzmax2 = pm2.mzRange()
assert mzmin2 >= 300
assert mzmax2 == mzmax
pm2 = pm.extract(rtmin = rtmin+0.000001, mzmin=300, mzmax=1000)
mzmin2, mzmax2 = pm2.mzRange()
assert mzmin2 >= 300
assert mzmax2 <= 1000
with pytest.raises(Exception):
pm.spectra[0].peaksInRange()
pp1 = pm.spectra[0].peaksInRange(mzmax = 10000)
pp2 = pm.spectra[0].peaksInRange(mzmin = 0)
assert np.all(pp1 == pp2)
specs0 = list(pm.spectra)
specs1 = pm.specsInRange(0, 99999)
specs2 = pm.specsInRange(0, specs0[0].rt)
specs3 = pm.specsInRange(specs0[-1].rt, 999999)
assert specs0 == specs1
assert specs2 == [ specs0[0] ]
assert specs3 == [ specs0[-1] ]
pm.spectra[0].polarity = "+"
pm.spectra[1].polarity = "-"
pm = PeakMap(pm.spectra)
mz = pm.representingMzPeak(0, 99999, 0, 99999)
assert abs(mz-831.86538) < 0.0001
