Thermo MSFileReader python绑定以与由Thermo串联质谱仪生成的.raw文件交互。

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pymsfilereader的Python项目详细描述


Thermo MSFileReader Python绑定

热MsFieleRADER是一个C++动态链接库（.DLL），由TealFuffisher Sealon（关于{A1}）提供，以与它们的串联质谱仪产生的原始文件交互。

这里，我提供了一些Python绑定，使TythMsFieleRead C++动态链接库可以在Python中使用。

测试版本3.0SP2（2014年8月）和3.0SP3（2015年4月）。 150/171函数已绑定，21/171已被认为与已绑定的函数冗余（参见冗余标志）。

注意：3.1sp4安装程序没有正确注册XRawfile2_x64.dll。因此，要使其工作：

  1. 安装msfilereader 3.1 sp4，
  2. 在C:\Program Files\Thermo\MSFileReader\某处备份3.1sp4 XRawfile2_x64.dll文件，
  3. 卸载msfilereader 3.1 sp4，然后安装msfilereader 3.1 sp2，
  4. 用之前备份的3.1 sp4XRawfile2_x64.dll覆盖位于C:\Program Files\Thermo\MSFileReader\的3.1 sp2XRawfile2_x64.dll文件。

注意：函数isqexactive仅适用于3.0sp3及以上版本。

注意：官方文档在3.0sp2版本中似乎比在3.0sp3版本中更新…

要求

请注意，这些绑定要求您根据python体系结构（32位或64位）安装了相应的thermo msfilereader版本，以便将.dll注册到正确的windows com服务器（32位或64位）。

单元测试

单元测试使用pytest完成。只需pip install pytest并在项目的根目录下运行pytest。

示例

为了方便起见，下面的示例可以通过运行python MSFileReader.py myfile.raw在任何rawfile上运行。

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()

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