def test_getKeys(self):
expectedKeySet = set([
'no compression', 'total ion current', 'filter string', 'scan_id',
'isolation window upper offset', 'collision-induced dissociation',
'scan start time', '64-bit float', 'intensity array',
'isolation window lower offset', 'positive scan', 'peak intensity',
'no combination', 'centroid spectrum', 'base peak m/z',
'm/z array', 'ms level', 'selected ion m/z',
'scan window lower limit', 'highest observed m/z',
'preset scan configuration', 'base peak intensity', '32-bit float',
'mass spectrum', '[thermo trailer extra]monoisotopic m/z:',
'scan window upper limit', 'isolation window target m/z',
'collision energy', 'lowest observed m/z', 'charge state',
'activation energy'
])
peaksMzML = parsePeaksMzML.Reader(
testFolder +
'peaksMzmlTestfile.peaks.mzML') # make a Reader instance
spectra = peaksMzML.getSimpleSpectraInfo()
actualKeySet = set([])
for spectrum in spectra:
for keys in peaksMzML.getKeys():
actualKeySet.add(keys)
self.assertSetEqual(expectedKeySet, actualKeySet)
def test_getPeaks_mzWindow(self): peaks = parsePeaksMzML.Reader(testFolder+'peaksMzmlTestfile.peaks.mzML') peakLocation = getWindow.PeakLocation(peaks) peakList = [] for peak in peakLocation.getPeaks_mzWindow(350,500): peakList.append(peak) self.assertIs(3, len(peakList))
def test_getitems(self):
peaksMzML = parsePeaksMzML.Reader(
testFolder +
'peaksMzmlTestfile.peaks.mzML') # make a Reader instance
spectra = peaksMzML.getSimpleSpectraInfo()
for spectrum in spectra:
for key in peaksMzML.getKeys():
# if this does not give any errors it means it works.
peaksMzML[key]
def test_getAllElements(self):
expectedElementcount = 253
peaksMzML = parsePeaksMzML.Reader(
testFolder +
'peaksMzmlTestfile.peaks.mzML') # make a Reader instance
allElements = peaksMzML.getAllElements()
actualElementCount = 0
for element in allElements:
actualElementCount += 1
self.assertEqual(expectedElementcount, actualElementCount)
def test_getSpectra(self):
expectedMaxId = 52
peaksMzML = parsePeaksMzML.Reader(
testFolder +
'peaksMzmlTestfile.peaks.mzML') # make a Reader instance
spectra = peaksMzML.getSimpleSpectraInfo()
for spectrum in spectra:
actualMaxId = int(
peaksMzML['scan_id']
) # this will hold the last value of the loop, so the max value
self.assertEqual(expectedMaxId, actualMaxId)
def test_Reader(self):
expectedDict = {
'no compression': 'no compression',
'total ion current': '1944280.875',
'32-bit float': '32-bit float',
'64-bit float': '64-bit float',
'[thermo trailer extra]monoisotopic m/z:': '421.760772705078',
'activation energy': '0',
'base peak intensity': '204693.875',
'base peak m/z': '348.990112304688',
'centroid spectrum': 'centroid spectrum',
'charge state': '2',
'collision energy': '35',
'collision-induced dissociation': 'collision-induced dissociation',
'filter string': 'FTMS + p NSI Full ms [335.00-1800.00]',
'highest observed m/z': '1807.22747568909',
'intensity array': 'intensity array',
'isolation window lower offset': '1',
'isolation window target m/z': '421.760772705078',
'isolation window upper offset': '1',
'lowest observed m/z': '334.999113612625',
'm/z array': 'm/z array',
'mass spectrum': 'mass spectrum',
'ms level': '1',
'no combination': 'no combination',
'no compression': 'no compression',
'peak intensity': '567.059326171875',
'positive scan': 'positive scan',
'preset scan configuration': '1',
'scan start time': '49.9378',
'scan window lower limit': '335',
'scan window upper limit': '1800',
'scan_id': '52',
'selected ion m/z': '421.760772705078',
'total ion current': '1944280.875'
}
actualDict = {}
peaksMzML = parsePeaksMzML.Reader(
testFolder +
'peaksMzmlTestfile.peaks.mzML') # make a Reader instance
spectra = peaksMzML.getSimpleSpectraInfo(
) # get all the spectra of the Reader instance
for spectrum in spectra: # loop through all the spectra
for keys in peaksMzML.getKeys(): # get all the keys
actualDict[keys] = peaksMzML[keys]
self.assertDictEqual(expectedDict, actualDict)
def test_getPeaks_rtWindowException(self): peaks = parsePeaksMzML.Reader(testFolder+'peaksMzmlTestfile.peaks.mzML') peakLocation = getWindow.PeakLocation(peaks) self.assertRaises(TypeError, lambda: peakLocation.getPeaks_rtWindow, 'not an int', 1) self.assertRaises(TypeError, lambda: peakLocation.getPeaks_rtWindow , 1, 'not an int')