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Thermo MSFileReader Python bindings to interact with .raw files generated by Thermo tandem mass spectrometers.

Project description

Thermo MSFileReader Python bindings

Thermo MSFileReader is a C++ dynamic-link library (.dll) made available by ThermoFisher Scientific (on https://thermo.flexnetoperations.com/control/thmo/product?plneID=632401) to interact with .raw files generated by their range of tandem mass spectrometers.

Here I make available some Python bindings that make the Thermo MSFileReader C++ dynamic-link library usable in Python.

tested on versions 3.0SP2 (August 2014) and 3.0SP3 (April 2015). 150 / 171 functions have been binded, 21 / 171 have been considered redundant with already binded functions (cf. REDUNDANT flag).

NOTE: The 3.1 SP4 installer does not register properly the XRawfile2_x64.dll. As a consequence, to make it work:

  1. Install MSFileReader 3.1 SP4,
  2. backup the 3.1 SP4 XRawfile2_x64.dll file at C:\Program Files\Thermo\MSFileReader\ somewhere,
  3. uninstall MSFileReader 3.1 SP4, then install MSFileReader 3.1 SP2,
  4. override the 3.1 SP2 XRawfile2_x64.dll file at C:\Program Files\Thermo\MSFileReader\ with the 3.1 SP4 XRawfile2_x64.dll backed up previously.

NOTE: The function IsQExactive only works in version 3.0SP3 and upwards.

NOTE: The official documentation seems more up-to-date in the 3.0SP2 version than in the 3.0SP3 version...

Requirements

Note that these bindings require that you have installed the appropriate Thermo MSFileReader version depending on your Python architecture (32bits or 64bits) so that the .dll is registered with the right Windows COM server (32bits or 64bits).

Unit tests

Unit tests are done with pytest. Just pip install pytest and run pytest at the root of the project.

Example

For convenience, the example below can be run on any rawfile by running python MSFileReader.py myfile.raw.

from pymsfilereader import MSFileReader

rawfile = MSFileReader("myfile.raw")

print('Version', rawfile.Version())
print('GetFileName', rawfile.GetFileName())
print('GetCreatorID', rawfile.GetCreatorID())
print('GetVersionNumber', rawfile.GetVersionNumber())
print('GetCreationDate', rawfile.GetCreationDate())
print('IsError', rawfile.IsError())
print('IsNewFile', rawfile.IsNewFile())
print('IsThereMSData', rawfile.IsThereMSData())
print('HasExpMethod', rawfile.HasExpMethod())
print('InAcquisition', rawfile.InAcquisition())
print('GetErrorCode', rawfile.GetErrorCode())
print('GetErrorMessage', rawfile.GetErrorMessage())
print('GetWarningMessage', rawfile.GetWarningMessage())
print('RefreshViewOfFile', rawfile.RefreshViewOfFile())
print('GetNumberOfControllers', rawfile.GetNumberOfControllers())

print("GetNumberOfControllersOfType('No device')", rawfile.GetNumberOfControllersOfType('No device'))
print("GetNumberOfControllersOfType('MS')", rawfile.GetNumberOfControllersOfType('MS'))
print("GetNumberOfControllersOfType('Analog')", rawfile.GetNumberOfControllersOfType('Analog'))
print("GetNumberOfControllersOfType('A/D card')", rawfile.GetNumberOfControllersOfType('A/D card'))
print("GetNumberOfControllersOfType('PDA')", rawfile.GetNumberOfControllersOfType('PDA'))
print("GetNumberOfControllersOfType('UV')", rawfile.GetNumberOfControllersOfType('UV'))
print("GetControllerType('MS')", rawfile.GetControllerType('MS'))
# print( 'GetControllerType(1)',  rawfile.GetControllerType(1) )

# print( 'GetControllerType(2)',  rawfile.GetControllerType(2) )
# print( 'GetControllerType(3)',  rawfile.GetControllerType(3) )
# print( 'GetControllerType(4)',  rawfile.GetControllerType(4) )
print('GetCurrentController()', rawfile.GetCurrentController())
# print( 'SetCurrentController(4,1)',  rawfile.SetCurrentController(4,1) )

print('GetCurrentController()', rawfile.GetCurrentController())
# print( 'SetCurrentController(0,1)',  rawfile.SetCurrentController(0,1) )

print('GetCurrentController()', rawfile.GetCurrentController())
print('GetExpectedRunTime()', rawfile.GetExpectedRunTime())
print('GetMaxIntegratedIntensity()', rawfile.GetMaxIntegratedIntensity())
print('GetMaxIntensity()', rawfile.GetMaxIntensity())
print('GetInletID()', rawfile.GetInletID())
print('GetErrorFlag()', rawfile.GetErrorFlag())
print('GetFlags()', rawfile.GetFlags())
print('GetAcquisitionFileName()', rawfile.GetAcquisitionFileName())
print('GetOperator()', rawfile.GetOperator())
print('GetComment1()', rawfile.GetComment1())
print('GetComment2()', rawfile.GetComment2())
print('GetFilters()', rawfile.GetFilters())
print('GetMassTolerance()', rawfile.GetMassTolerance())

print('rawfile.SetMassTolerance(userDefined=True, massTolerance=555.0, units=2)',
        rawfile.SetMassTolerance(userDefined=True, massTolerance=555.0, units=2))
print('GetMassTolerance()', rawfile.GetMassTolerance())
print('rawfile.SetMassTolerance(userDefined=False, massTolerance=500.0, units=0)',
        rawfile.SetMassTolerance(userDefined=False, massTolerance=500.0, units=0))
print('GetMassResolution', rawfile.GetMassResolution())
print('GetNumTrailerExtra', rawfile.GetNumTrailerExtra())
print('GetLowMass', rawfile.GetLowMass())
print('GetHighMass', rawfile.GetHighMass())
print('GetStartTime', rawfile.GetStartTime())
print('GetEndTime', rawfile.GetEndTime())
print('GetNumSpectra', rawfile.GetNumSpectra())
print('GetFirstSpectrumNumber', rawfile.GetFirstSpectrumNumber())
print('GetLastSpectrumNumber', rawfile.GetLastSpectrumNumber())
print('GetAcquisitionDate', rawfile.GetAcquisitionDate())
print('GetUniqueCompoundNames', rawfile.GetUniqueCompoundNames())

print('############################################## INSTRUMENT BEGIN')
print('GetInstrumentDescription', rawfile.GetInstrumentDescription())
print('GetInstrumentID', rawfile.GetInstrumentID())
print('GetInstSerialNumber', rawfile.GetInstSerialNumber())
print('GetInstName', rawfile.GetInstName())
print('GetInstModel', rawfile.GetInstModel())
print('GetInstSoftwareVersion', rawfile.GetInstSoftwareVersion())
print('GetInstHardwareVersion', rawfile.GetInstHardwareVersion())
print('GetInstFlags', rawfile.GetInstFlags())
print('GetInstNumChannelLabels', rawfile.GetInstNumChannelLabels())
# print( 'GetInstChannelLabel(0)', rawfile.GetInstChannelLabel(0) )
print('IsQExactive', rawfile.IsQExactive())  # Not implemented in MSFileReader 3.0.29.0
print('############################################## INSTRUMENT END')

scan_number = 1
print('############################################## XCALIBUR INTERFACE BEGIN')
print('GetScanHeaderInfoForScanNum',
        rawfile.GetScanHeaderInfoForScanNum(scan_number))  # "View/Scan header", upper part
print('GetTrailerExtraForScanNum', rawfile.GetTrailerExtraForScanNum(scan_number))  # "View/Scan header", lower part
print('GetNumTuneData', rawfile.GetNumTuneData())
print('GetTuneData(0)', rawfile.GetTuneData(0))  # "View/Report/Tune Method"
print('GetNumInstMethods', rawfile.GetNumInstMethods())
print('GetInstMethodNames', rawfile.GetInstMethodNames())
for i in range(rawfile.GetNumInstMethods()):
    print('-------------------------------------------------------------------------------')
    print(rawfile.GetInstMethod(i))  # "View/Report/Instrument Method"
    print('-------------------------------------------------------------------------------')
print('rawfile.ExtractInstMethodFromRaw', rawfile.ExtractInstMethodFromRaw(rawfile.filename + '.meth'))

# # # # # # "View/Report/Sample Information" BEGIN
print('GetVialNumber', rawfile.GetVialNumber())
print('GetInjectionVolume', rawfile.GetInjectionVolume())
print('GetInjectionAmountUnits', rawfile.GetInjectionAmountUnits())
print('GetSampleVolume', rawfile.GetSampleVolume())
print('GetSampleVolumeUnits', rawfile.GetSampleVolumeUnits())
print('GetSampleWeight', rawfile.GetSampleWeight())
print('GetSampleAmountUnits', rawfile.GetSampleAmountUnits())
print('GetSeqRowNumber', rawfile.GetSeqRowNumber())
print('GetSeqRowSampleType', rawfile.GetSeqRowSampleType())
print('GetSeqRowDataPath', rawfile.GetSeqRowDataPath())
print('GetSeqRowRawFileName', rawfile.GetSeqRowRawFileName())
print('GetSeqRowSampleName', rawfile.GetSeqRowSampleName())
print('GetSeqRowSampleID', rawfile.GetSeqRowSampleID())
print('GetSeqRowComment', rawfile.GetSeqRowComment())
print('GetSeqRowLevelName', rawfile.GetSeqRowLevelName())
print('GetSeqRowUserText', rawfile.GetSeqRowUserText(index=0))
print('GetSeqRowUserText', rawfile.GetSeqRowUserText(index=1))
print('GetSeqRowUserText', rawfile.GetSeqRowUserText(index=2))
print('GetSeqRowUserText', rawfile.GetSeqRowUserText(index=3))
print('GetSeqRowUserText', rawfile.GetSeqRowUserText(index=4))
print('GetSeqRowInstrumentMethod', rawfile.GetSeqRowInstrumentMethod())
print('GetSeqRowProcessingMethod', rawfile.GetSeqRowProcessingMethod())
print('GetSeqRowCalibrationFile', rawfile.GetSeqRowCalibrationFile())
print('GetSeqRowVial', rawfile.GetSeqRowVial())
print('GetSeqRowInjectionVolume', rawfile.GetSeqRowInjectionVolume())
print('GetSeqRowSampleWeight', rawfile.GetSeqRowSampleWeight())
print('GetSeqRowSampleVolume', rawfile.GetSeqRowSampleVolume())
print('GetSeqRowISTDAmount', rawfile.GetSeqRowISTDAmount())
print('GetSeqRowDilutionFactor', rawfile.GetSeqRowDilutionFactor())
print('GetSeqRowUserLabel', rawfile.GetSeqRowUserLabel(index=0))
print('GetSeqRowUserLabel', rawfile.GetSeqRowUserLabel(index=1))
print('GetSeqRowUserLabel', rawfile.GetSeqRowUserLabel(index=2))
print('GetSeqRowUserLabel', rawfile.GetSeqRowUserLabel(index=3))
print('GetSeqRowUserLabel', rawfile.GetSeqRowUserLabel(index=4))
print('GetSeqRowUserTextEx', rawfile.GetSeqRowUserTextEx(index=0))
print('GetSeqRowUserTextEx', rawfile.GetSeqRowUserTextEx(index=1))
print('GetSeqRowUserTextEx', rawfile.GetSeqRowUserTextEx(index=2))
print('GetSeqRowUserTextEx', rawfile.GetSeqRowUserTextEx(index=3))
print('GetSeqRowUserTextEx', rawfile.GetSeqRowUserTextEx(index=4))
print('GetSeqRowBarcode', rawfile.GetSeqRowBarcode())
print('GetSeqRowBarcodeStatus', rawfile.GetSeqRowBarcodeStatus())
# # # # # # # "View/Report/Sample Information" END
print('GetNumStatusLog', rawfile.GetNumStatusLog())
print('GetStatusLogForScanNum')  # "View/Report/Status Log"
pprint(rawfile.GetStatusLogForScanNum(scan_number))
print('GetStatusLogForPos(position=0)', rawfile.GetStatusLogForPos(position=0))
print('GetStatusLogForPos(position=1)', rawfile.GetStatusLogForPos(position=1))
print('GetStatusLogPlottableIndex()', rawfile.GetStatusLogPlottableIndex())

print('GetNumErrorLog', rawfile.GetNumErrorLog())
for i in range(rawfile.GetNumErrorLog()):
    print('GetErrorLogItem', i, rawfile.GetErrorLogItem(i))  # "View/Report/Error Log"
print('############################################## XCALIBUR INTERFACE END')

print('GetMassListFromScanNum', rawfile.GetMassListFromScanNum(scan_number))
print('GetMassListRangeFromScanNum', rawfile.GetMassListRangeFromScanNum(scan_number))
print('GetSegmentedMassListFromScanNum', rawfile.GetSegmentedMassListFromScanNum(scan_number))
print('GetAverageMassList', rawfile.GetAverageMassList(scan_number, scan_number + 10))
print('GetAveragedMassSpectrum', rawfile.GetAveragedMassSpectrum([scan_number, scan_number + 5, scan_number + 10]))
print('GetSummedMassSpectrum', rawfile.GetSummedMassSpectrum([scan_number, scan_number + 5, scan_number + 10]))
print('GetLabelData', rawfile.GetLabelData(scan_number))
print('GetAveragedLabelData', rawfile.GetAveragedLabelData([scan_number, scan_number + 5, scan_number + 10]))
print('GetAllMSOrderData', rawfile.GetAllMSOrderData(scan_number))
print('GetChroData', rawfile.GetChroData(startTime=rawfile.StartTime,
                                            endTime=rawfile.EndTime,
                                            massRange1="{}-{}".format(rawfile.LowMass, rawfile.HighMass),
                                            scanFilter="Full ms "))
# print( 'GetChroByCompoundName', rawfile.GetChroByCompoundName(["methyltestosterone"]) )

# print( 'GetMassPrecisionEstimate', rawfile.GetMassPrecisionEstimate(scan_number) )

print('GetFullMSOrderPrecursorDataFromScanNum(scan_number,0)',
        rawfile.GetFullMSOrderPrecursorDataFromScanNum(scan_number, 0))
print('GetFullMSOrderPrecursorDataFromScanNum(scan_number,1)',
        rawfile.GetFullMSOrderPrecursorDataFromScanNum(scan_number, 1))

print('GetPrecursorInfoFromScanNum(scan_number,1)', rawfile.GetPrecursorInfoFromScanNum(scan_number))

with open('test.tsv', 'wt') as f:
    print('\t'.join(map(str, ('scan_number',
                                'RetentionTime',
                                'scan_number',
                                'GetFilterForScanNum(i)',
                                'GetMSOrderForScanNum(i)',
                                'GetNumberOfMSOrdersFromScanNum(i)',
                                'GetScanTypeForScanNum(i)',
                                'GetDetectorTypeForScanNum(i)',
                                'GetMassAnalyzerTypeForScanNum(i)',
                                'GetActivationTypeForScanNum(i,MSOrder=2)',
                                'IsProfileScanForScanNum(i)',
                                'IsCentroidScanForScanNum(i)',
                                'GetIsolationWidthForScanNum(i,MSOrder=1)',
                                'GetCollisionEnergyForScanNum(i,MSOrder=1)',
                                'GetPrecursorInfoFromScanNum(i)',
                                'GetMassCalibrationValueFromScanNum(i,massCalibrationIndex=0)',
                                'GetScanEventForScanNum(i)',
                                'GetSegmentAndEventForScanNum(i)',
                                'GetCycleNumberFromScanNumber(i)',
                                'GetAValueFromScanNum(i)',
                                'GetBValueFromScanNum(i)',
                                'GetKValueFromScanNum(i)',
                                'GetRValueFromScanNum(i)',
                                'GetVValueFromScanNum(i)',
                                'GetMSXMultiplexValueFromScanNum(i)',
                                'GetCompoundNameFromScanNum(i)',
                                'GetNumberOfMassRangesFromScanNum(i)',
                                'GetMassRangeFromScanNum(i,0)',
                                'GetMassRangeFromScanNum(i,1)',
                                'GetNumberOfSourceFragmentsFromScanNum(i)',
                                'GetSourceFragmentValueFromScanNum(i,0)',
                                'GetNumberOfSourceFragmentationMassRangesFromScanNum(i)'
                                ))), file=f)

    for i in range(rawfile.FirstSpectrumNumber, rawfile.LastSpectrumNumber + 1):
        print('\t'.join(map(str, (i,
                                    rawfile.RTFromScanNum(i),
                                    rawfile.ScanNumFromRT(rawfile.RTFromScanNum(i)),
                                    rawfile.GetFilterForScanNum(i),
                                    rawfile.GetMSOrderForScanNum(i),
                                    rawfile.GetNumberOfMSOrdersFromScanNum(i),
                                    rawfile.GetScanTypeForScanNum(i),
                                    rawfile.GetDetectorTypeForScanNum(i),
                                    rawfile.GetMassAnalyzerTypeForScanNum(i),
                                    rawfile.GetActivationTypeForScanNum(i, MSOrder=2),
                                    rawfile.IsProfileScanForScanNum(i),
                                    rawfile.IsCentroidScanForScanNum(i),
                                    rawfile.GetIsolationWidthForScanNum(i, MSOrder=1),
                                    rawfile.GetCollisionEnergyForScanNum(i, MSOrder=1),
                                    rawfile.GetPrecursorInfoFromScanNum(i),
                                    rawfile.GetMassCalibrationValueFromScanNum(i, massCalibrationIndex=0),
                                    rawfile.GetScanEventForScanNum(i),
                                    rawfile.GetSegmentAndEventForScanNum(i),
                                    rawfile.GetCycleNumberFromScanNumber(i),
                                    rawfile.GetAValueFromScanNum(i),
                                    rawfile.GetBValueFromScanNum(i),
                                    rawfile.GetKValueFromScanNum(i),
                                    rawfile.GetRValueFromScanNum(i),
                                    rawfile.GetVValueFromScanNum(i),
                                    rawfile.GetMSXMultiplexValueFromScanNum(i),
                                    rawfile.GetCompoundNameFromScanNum(i),
                                    rawfile.GetNumberOfMassRangesFromScanNum(i),
                                    rawfile.GetMassRangeFromScanNum(i, 0),
                                    rawfile.GetMassRangeFromScanNum(i, 1),
                                    rawfile.GetNumberOfSourceFragmentsFromScanNum(i),
                                    rawfile.GetSourceFragmentValueFromScanNum(i, 0),
                                    rawfile.GetNumberOfSourceFragmentationMassRangesFromScanNum(i)
                                    ))), file=f)

rawfile.Close()

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