Thermo MSFileReader Python 绑定，用于与 Thermo 串联质谱仪生成的 .raw 文件进行交互。
项目描述
Thermo MSFileReader Python 绑定
Thermo MSFileReader 是 ThermoFisher Scientific（在https://thermo.flexnetoperations.com/control/thmo/product?plneID=632401上）提供的 C++ 动态链接库 (.dll)，可与由其范围生成的 .raw 文件进行交互串联质谱仪。
在这里，我提供了一些 Python 绑定，使 Thermo MSFileReader C++ 动态链接库可在 Python 中使用。
在 3.0SP2（2014 年 8 月）和 3.0SP3（2015 年 4 月）版本上进行了测试。150 / 171 个函数已绑定，21 / 171 个已被认为与已绑定函数冗余（参见 REDUNDANT 标志）。
注意：3.1 SP4 安装程序无法正确注册XRawfile2_x64.dll. 因此，要使其工作：
- 安装 MSFileReader 3.1 SP4，
- 在某处备份 3.1 SP4
XRawfile2_x64.dll文件，C:\Program Files\Thermo\MSFileReader\ - 卸载 MSFileReader 3.1 SP4，然后安装 MSFileReader 3.1 SP2，
- 用之前备份的 3.1 SP4覆盖 3.1 SP2
XRawfile2_x64.dll文件。C:\Program Files\Thermo\MSFileReader\XRawfile2_x64.dll
注意：函数 IsQExactive 仅适用于 3.0SP3 及更高版本。
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
- Python 2.7 或 3.x，MSFileReader 3.1 只有 64 位，MSFileReader 3.0 是 32 和 64 位。
- comtypes 库
pip install comtypes- 或可在http://www.lfd.uci.edu/~gohlke/pythonlibs/获得，然后
pip install comtype-package.whl
- 来自https://thermo.flexnetoperations.com/control/thmo/product?plneID=632401或来自https://github.com/frallain/pymsfilereader/tree/master/MSFileReader的 Thermo MSFileReader 。
请注意，这些绑定要求您根据您的 Python 架构（32 位或 64 位）安装适当的 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
单元测试是用 pytest 完成的。只需在项目的根目录下pip install pytest运行即可。pytest
例子
为方便起见，下面的示例可以通过运行在任何原始文件上运行python MSFileReader.py myfile.raw.
从 pymsfilereader 导入 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' ,
原始文件。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 卡' ))
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()' ， 原始文件。GetErrorFlag ())
print ( 'GetFlags()' , rawfile .GetFlags ()) print ( 'GetAcquisitionFileName()' , rawfile .GetAcquisitionFileName ( ) ) print ( ' GetOperator ()' , rawfile .GetOperator ( ) ) print ( 'GetComment1 ()' , rawfile .GetComment1 ()) print ( 'GetComment2( ) ' , rawfile .GetComment2
())
打印( 'GetFilters()' , rawfile .GetFilters ( ))打印( ' 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 ( ))打印( ' GetAcquisitionDate ' , rawfile .GetAcquisitionDate ())打印
( 'GetUniqueCompoundNames' , rawfile.GetUniqueCompoundNames ( ) )
print ( '############################################# 仪器BEGIN' ）
打印（'GetInstrumentDescription' ， rawfile.GetInstrumentDescription （））打印（'GetInstrumentID' ，rawfile.GetInstrumentID （））打印（' GetInstSerialNumber ' ，rawfile.GetInstSerialNumber （））打印（' GetInstName ' ，rawfile.GetInstName （）)打印( 'GetInstModel' , 原始文件
. 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'
， 原始文件。IsQExactive ()) # 在 MSFileReader 3.0.29.0 中未实现
print ( '################################## ########### 仪器结束' )
scan_number = 1
打印( '########################################### ## XCALIBUR INTERFACE BEGIN' )
print ( 'GetScanHeaderInfoForScanNum' ,
rawfile . GetScanHeaderInfoForScanNum ( scan_number )) # "View/Scan header", 上半部分
print ( 'GetTrailerExtraForScanNum' , rawfile . GetTrailerExtraForScanNum ( scan_number )) # "View/Scan header" , 下部
打印( ' GetNumTuneData ' , rawfile .GetNumTuneData ())
print ( 'GetTuneData(0)' , rawfile . GetTuneData ( 0 )) # "View/Report/Tune Method"
print ( 'GetNumInstMethods' , rawfile . GetNumInstMethods ())
print ( 'GetInstMethodNames' , rawfile . GetInstMethodNames ())
for 我 在 范围内( rawfile . GetNumInstMethods ()):
print ( '------------------------------------ --------------------------------------------' )
打印( rawfile . GetInstMethod ( i )) # "View/Report/Instrument Method"
print ( '----------------------------- --------------------------------------------------' )
print ( 'rawfile.ExtractInstMethodFromRaw ' , rawfile.ExtractInstMethodFromRaw ( rawfile.filename + ' .meth ' ) )
###### “查看/报告/样品信息” 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 ( ) ）打印（'GetSeqRowDataPath' ，原始文件。GetSeqRowDataPath （ ））打印（
'GetSeqRowRawFileName' ，原始文件 。GetSeqRowRawFileName ()) print ( 'GetSeqRowSampleName' , rawfile . GetSeqRowSampleName ()) print ( 'GetSeqRowSampleID' , rawfile . GetSeqRowSampleID ()) print ( 'GetSeqRowComment' , rawfile . GetSeqRowComment ()) print ( ' GetSeqRowLevelName ' ( Level ) ))打印( 'GetSeqRowUserText' ,
原始文件。GetSeqRowUserText ( index = 0 ))
print ( 'GetSeqRowUserText' , rawfile.GetSeqRowUserText ( index = 1 ) ) print ( ' GetSeqRowUserText ' , rawfile.GetSeqRowUserText ( index = 2 ) ) print ( ' GetSeqRowUserText ' , rawfile.GetSeqRowUserText ( index = 3 ) ))打印( 'GetSeqRowUserText'
， 原始文件。GetSeqRowUserText ( index = 4 ))
print ( 'GetSeqRowInstrumentMethod' , rawfile . GetSeqRowInstrumentMethod ())
print ( 'GetSeqRowProcessingMethod' , rawfile . GetSeqRowProcessingMethod ())
print ( 'GetSeqRowCalibrationFile' , rawfile . GetSeqRowCalibrationFile ())
print ( 'GetSeqRowVial' , rawfile .GetSeqRowVial ( ))
打印('GetSeqRowInjectionVolume' ，原始文件 。GetSeqRowInjectionVolume ()) print ( 'GetSeqRowSampleWeight' , rawfile.GetSeqRowSampleWeight ( )) print ( 'GetSeqRowSampleVolume ' , rawfile.GetSeqRowSampleVolume ( ) ) print ( ' GetSeqRowISTDAmount ' , rawfile.GetSeqRowISTDAmount ( ) ) print ( ' GetSeqRowDilutionFactorDilution . , ))打印(
'GetSeqRowUserLabel' ，原始文件 。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 ））
打印（'GetSeqRowUserTextEx' ，rawfile.GetSeqRowUserTextEx （ 索引= 3 ））打印（' GetSeqRowUserTextEx' ，rawfile.GetSeqRowUserTextEx （索引= 4 ））打印（' GetSeqRowBarcode ' ，rawfile.GetSeqRowBarcode （））打印（' GetSeqRowBarcodeStatus ' , rawfile .GetSeqRowBarcodeStatus ( )) # # # # # # # "查看/报告/样品信息" END
print ( 'GetNumStatusLog' , rawfile . GetNumStatusLog ())
print ( 'GetStatusLogForScanNum' ) # "查看/报告/状态日志"
pprint ( rawfile . GetStatusLogForScanNum ( scan_number ))
print ( 'GetStatusLogForPos(position=0)' , rawfile . GetStatusLogForPos ( position = 0 ))
print ( 'GetStatusLogForPos(position=1)' , rawfile . GetStatusLogForPos ( position= 1 ))
打印( ' 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 接口结束' )
打印（'GetMassListFromScanNum ' ， rawfile.GetMassListFromScanNum （scan_number ））打印（' GetMassListRangeFromScanNum ' ，rawfile.GetMassListRangeFromScanNum （scan_number ））打印（' GetSegmentedMassListFromScanNum ' ，rawfile.GetSegmentedMassListFromScanNum （scan_number ））打印（扫描_编号GetAverageMassList 。,
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 ]) )
打印( '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 ,
结束时间=原始文件。结束时间，massRange1 = “ {} - {} ” 。格式( 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 ))
用 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)' ,