Package: pymsfilereader
Thermo MSFileReader Python bindingsThermo MSFileReader is a C++ dynamic-link library (.dll) made available by ThermoFisher Scientific (onhttps://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 theXRawfile2_x64.dll. As a consequence, to make it work:Install MSFileReader 3.1 SP4,backup the 3.1 SP4XRawfile2_x64.dllfile atC:\Program Files\Thermo\MSFileReader\somewhere,uninstall MSFileReader 3.1 SP4, then install MSFileReader 3.1 SP2,override the 3.1 SP2XRawfile2_x64.dllfile atC:\Program Files\Thermo\MSFileReader\with the 3.1 SP4XRawfile2_x64.dllbacked 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...RequirementsPython 2.7 or 3.x, MSFileReader 3.1 is 64-bits only, MSFileReader 3.0 is 32 and 64-bits.The comtypes librarypip install comtypesor available athttp://www.lfd.uci.edu/~gohlke/pythonlibs/and thenpip install comtype-package.whlThermo MSFileReader fromhttps://thermo.flexnetoperations.com/control/thmo/product?plneID=632401or fromhttps://github.com/frallain/pymsfilereader/tree/master/MSFileReader.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 testsUnit tests are done with pytest. Justpip install pytestand runpytestat the root of the project.ExampleFor convenience, the example below can be run on any rawfile by runningpython MSFileReader.py myfile.raw.frompymsfilereaderimportMSFileReaderrawfile=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 3.0.29.0print('############################################## INSTRUMENT END')scan_number=1print('############################################## XCALIBUR INTERFACE BEGIN')print('GetScanHeaderInfoForScanNum',rawfile.GetScanHeaderInfoForScanNum(scan_number))# "View/Scan header", upper partprint('GetTrailerExtraForScanNum',rawfile.GetTrailerExtraForScanNum(scan_number))# "View/Scan header", lower partprint('GetNumTuneData',rawfile.GetNumTuneData())print('GetTuneData(0)',rawfile.GetTuneData(0))# "View/Report/Tune Method"print('GetNumInstMethods',rawfile.GetNumInstMethods())print('GetInstMethodNames',rawfile.GetInstMethodNames())foriinrange(rawfile.GetNumInstMethods()):print('-------------------------------------------------------------------------------')print(rawfile.GetInstMethod(i))# "View/Report/Instrument Method"print('-------------------------------------------------------------------------------')print('rawfile.ExtractInstMethodFromRaw',rawfile.ExtractInstMethodFromRaw(rawfile.filename+'.meth'))# # # # # # "View/Report/Sample Information" BEGINprint('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" ENDprint('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())foriinrange(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))withopen('test.tsv','wt')asf: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)foriinrange(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()