def has_peaks(exp: ms.MSExperiment) -> bool:
"""Checks if any spectrum in an experiment has peaks."""
for i in range(exp.getNrSpectra()):
spec = exp.getSpectrum(i)
if spec.size() > 0:
return True
return False
def read_sample(input_file, expt_='ecoli', mode='pos'):
SM = Sample(expt_, mode, input_file)
exp = MSExperiment()
MzMLFile().load(input_file, exp)
print(input_file, exp.getNrSpectra())
scans = []
ii = 0
for sp in exp:
ms_level = sp.getMSLevel()
if ms_level == 1: # ONLY dealig with MS1 here
rt = sp.getRT()
mz, intensity = sp.get_peaks()
# use int and tuple to save space when storage is considered
intensity = [int(x) for x in intensity]
# Scan defined as 'scan_number', 'retention_time', 'mz_values', 'intensity_values'
scans.append(Scan(ii, rt, tuple(mz), tuple(intensity)))
# scans.append(Scan(ii, rt, mz, intensity))
ii += 1
SM.scans = scans
SM.retention_index = tuple([sc.scan_number for sc in scans])
SM.retention_time = tuple([sc.retention_time for sc in scans])
return SM
def store(self, ofname: str, peakMap: pyopenms.MSExperiment):
#sort peakMap if necessary
if not peakMap.isSorted():
peakMap.sortSpectra()
peakMap.updateRanges()
outF = open(ofname, 'w')
firstScan = self._getScan(
peakMap.getSpectrum(0).getNativeID().decode('utf-8'))
dataType = peakMap.getSpectrum(0).getType()
dataType = 'Centroid' if dataType == 1 else 'Profile' if dataType == 2 else 'Unknown'
lastScan = self._getScan(
peakMap.getSpectrum(peakMap.getNrSpectra() -
1).getNativeID().decode('utf-8'))
precursorFile = basename(ofname).replace('ms2', 'ms1')
#print header
outF.write(
self._writeValue(
MS2File._h_tag, 'CreationDate',
datetime.datetime.now().strftime('%m/%d/%Y %I:%M:%S %p')))
outF.write(self._writeValue(MS2File._h_tag, 'Extractor', 'msConvert'))
outF.write(self._writeValue(MS2File._h_tag, 'ExtractorVersion', '0.1'))
outF.write(
self._writeValue(MS2File._h_tag, 'Comments',
'msConvert was written by Aaron Maurais, 2019'))
outF.write(self._writeValue(MS2File._h_tag, 'ExtractorOptions', 'MS2'))
outF.write(
self._writeValue(MS2File._h_tag, 'AcquisitionMethod',
'Data-Dependent'))
outF.write(
self._writeValue(MS2File._h_tag, 'InstrumentType', 'Unknown'))
outF.write(self._writeValue(MS2File._h_tag, 'ScanType', 'MS2'))
outF.write(self._writeValue(MS2File._h_tag, 'DataType', dataType))
outF.write(self._writeValue(MS2File._h_tag, 'FirstScan', firstScan))
outF.write(self._writeValue(MS2File._h_tag, 'LastScan', lastScan))
#iterate through spectra
preScan = 'Unknown'
for i, scan in enumerate(peakMap.getSpectra()):
if scan.getMSLevel() == 1:
preScan = self._getScan(scan.getNativeID().decode('utf-8'))
if scan.getMSLevel() == 2:
#write header info
curScan = self._getScan(scan.getNativeID().decode('utf-8'))
precursors = scan.getPrecursors()
preCharge = int(precursors[0].getCharge())
preMZ = precursors[0].getMZ()
#print scan line
outF.write('{}\t{}\t{}\t{}\n'.format(MS2File._s_tag,
curScan.zfill(6),
curScan.zfill(6), preMZ))
#print scan info
outF.write(
self._writeValue(MS2File._i_tag, 'RetTime', scan.getRT()))
outF.write(
self._writeValue(MS2File._i_tag, 'PrecursorInt',
precursors[0].getIntensity()))
outF.write(
self._writeValue(MS2File._i_tag, 'IonInjectionTime',
'Unknown'))
ameth = list(precursors[0].getActivationMethods())
ameth = ' '.join(
[MS2File._activationMethods[x] for x in ameth])
if not ameth:
ameth = 'Unknown'
outF.write(
self._writeValue(MS2File._i_tag, 'ActivationType', ameth))
outF.write(
self._writeValue(MS2File._i_tag, 'PrecursorFile',
precursorFile))
outF.write(
self._writeValue(MS2File._i_tag, 'PrecursorScan', preScan))
outF.write(
self._writeValue(MS2File._i_tag, 'InstrumentType',
'Unknown'))
#write z line
#after charge, the M+H m/z for the ion is listed, so calculate that here
outF.write(
self._writeValue(
MS2File._z_tag, preCharge, (float(preMZ) * preCharge) -
(preCharge * MS2File._H_mass) + MS2File._H_mass))
#write ions
for ion in scan:
outF.write('{0:.4f} {1:.1f}\n'.format(
round(ion.getMZ(), 4), round(ion.getIntensity(), 1)))
def combine_experiments(exp1: ms.MSExperiment, exp2: ms.MSExperiment) -> None:
"""Merges two experiments (putting the second into the first)."""
for i in range(exp2.getNrSpectra()):
spec = exp2.getSpectrum(i)
exp1.addSpectrum(spec)