def MZMLtoSpectrum(filename, rtOnly=False):
spectra = []
import pyopenms
# need to use OnDiscMSExperiment to sequentially read
# spectra without loading whole file into memory
experiment = pyopenms.OnDiscMSExperiment()
pyopenms.IndexedMzMLFileLoader().load(filename, experiment)
for i in range(experiment.getNrSpectra()):
spectrum = experiment.getSpectrum(i)
try:
time = spectrum.getRT()
except KeyError, e:
time_prev = time
if delta_time > 0:
time += delta_time
else:
time += 1.0
if rtOnly:
mzData, intData, spectrum = None, None, None
else:
(mzData, intData) = spectrum.get_peaks()
if mzData.shape[0] == 0:
mzData = np.empty(0, dtype='float32')
intData = np.empty(0, dtype='float32')
yield Spectrum(time, mzData, intData, spectrum)
def test_readfile_content(self):
e = pyopenms.OnDiscMSExperiment()
pyopenms.IndexedMzMLFileLoader().load(self.filename, e)
self.assertEqual(e.getNrSpectra(), 2)
self.assertEqual(e.getNrChromatograms(), 1)
s = e.getSpectrum(0)
data_mz, data_int = s.get_peaks()
self.assertEqual(len(data_mz), 19914)
self.assertEqual(len(data_int), 19914)
self.assertEqual(len(e.getSpectrum(1).get_peaks()[0]), 19800)
self.assertEqual(len(e.getSpectrum(1).get_peaks()[1]), 19800)
self.assertEqual(len(e.getChromatogram(0).get_peaks()[0]), 48)
self.assertEqual(len(e.getChromatogram(0).get_peaks()[1]), 48)
if False:
# Currently we don't deal with exceptions properly
raised = False
try:
e.getChromatogram(2).get_peaks()
except Exception as e:
raised = True
self.assertTrue(raised)
def test_readfile_content(self):
e = pyopenms.OnDiscMSExperiment()
pyopenms.IndexedMzMLFileLoader().load(self.filename, e)
self.assertEqual(e.getNrSpectra(), 2)
self.assertEqual(e.getNrChromatograms(), 1)
s = e.getSpectrum(0)
data = s.get_peaks()
self.assertEqual(len(data), 19914)
self.assertEqual(len(e.getSpectrum(1).get_peaks()), 19800)
self.assertEqual(len(e.getChromatogram(0).get_peaks()), 48)
raised = False
try:
e.getChromatogram(2).get_peaks()
except Exception, e:
raised = True
def test_readfile(self):
e = pyopenms.OnDiscMSExperiment()
success = pyopenms.IndexedMzMLFileLoader().load(self.filename, e)
self.assertTrue(success)