public static void ParseDIA(IRawFileThreadManager rawFile, WorkflowParameters parameters)
{
var staticRawFile = rawFile.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
staticRawFile.CheckIfBoxcar();
ScanIndex Index = Extract.ScanIndices(rawFile.CreateThreadAccessor());
TrailerExtraCollection trailerExtras = Extract.TrailerExtras(rawFile.CreateThreadAccessor(), Index);
MethodDataContainer methodData = Extract.MethodData(rawFile.CreateThreadAccessor(), Index);
PrecursorScanCollection precursorScans = Extract.PrecursorScansByMasterScanMs2Only(rawFile.CreateThreadAccessor(), trailerExtras, Index);
(CentroidStreamCollection centroidStreams, SegmentScanCollection segmentScans) =
Extract.MsData(rawFile: rawFile.CreateThreadAccessor(), index: Index);
RetentionTimeCollection retentionTimes = Extract.RetentionTimes(rawFile.CreateThreadAccessor(), Index);
ScanMetaDataCollectionDIA metaData = MetaDataProcessingDIA.AggregateMetaDataDIA(centroidStreams, segmentScans, methodData,
trailerExtras, retentionTimes, Index);
RawMetricsDataDIA metrics = null;
if (parameters.ParseParams.Metrics)
{
metrics = MetaDataProcessingDIA.GetMetricsDataDIA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index);
MetricsWriter.WriteMatrix(metrics, staticRawFile.FileName, parameters.ParseParams.OutputDirectory);
}
if (parameters.ParseParams.Parse)
{
string matrixFileName = ReadWrite.GetPathToFile(parameters.ParseParams.OutputDirectory, staticRawFile.FileName, "._parse.txt");
//MatrixWriter.ParseQuantDIA()
//ParseWriter writerDIA = new ParseWriter(matrixFileName, centroidStreams, segmentScans, metaData,
// retentionTimes, trailerExtras, precursorScans, Index);
//writerDIA.WriteMatrixDIA();
}
// I'm not sure what goes into a DIA mgf file, so we aren't making one yet
//if (parameters.ParseParams.WriteMgf)
//{
// ParseWriter writerMGF = new ParseWriter(centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
// writerMGF.WriteMGF(staticRawFile.FileName);
//}
}
public static void UniversalDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters, QcDataCollection qcDataCollection)
{
MethodDataContainer methodData;
CentroidStreamCollection centroidStreams;
SegmentScanCollection segmentScans;
TrailerExtraCollection trailerExtras;
PrecursorMassCollection precursorMasses;
RetentionTimeCollection retentionTimes;
ScanEventReactionCollection reactions;
ScanMetaDataCollectionDDA metaData = null;
PrecursorPeakCollection peakData = null;
int nScans;
var staticRawFile = rawFileThreadManager.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
var err = staticRawFile.FileError;
if (err.HasError)
{
Console.WriteLine("ERROR: {0} reports error code: {1}. The associated message is: {2}",
Path.GetFileName(staticRawFile.FileName), err.ErrorCode, err.ErrorMessage);
Console.WriteLine("Skipping this file");
Log.Error("{FILE} reports error code: {ERRORCODE}. The associated message is: {ERRORMESSAGE}",
Path.GetFileName(staticRawFile.FileName), err.ErrorCode, err.ErrorMessage);
return;
}
//staticRawFile.CheckIfBoxcar();
(ScanIndex Index, PrecursorScanCollection precursorScans, ScanDependentsCollections scanDependents) =
Extract.ScanIndicesPrecursorsDependents(rawFileThreadManager, MaxProcesses: parameters.MaxProcesses);
nScans = Index.ScanEnumerators[MSOrderType.Ms2].Length;
using (var rawFile = rawFileThreadManager.CreateThreadAccessor())
{
reactions = Extract.ScanEvents(rawFile, Index);
methodData = Extract.MethodData(rawFile, Index);
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
trailerExtras = Extract.TrailerExtras(rawFile, Index);
precursorMasses = Extract.PrecursorMasses(rawFile, precursorScans, trailerExtras, Index);
retentionTimes = Extract.RetentionTimes(rawFile, Index);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant | parameters.ParseParams.Metrics | parameters.RefineMassCharge | parameters.QcParams.QcDirectory != null)
{
peakData = AnalyzePeaks.AnalyzeAllPeaks(centroidStreams, retentionTimes, precursorMasses, precursorScans, Index, parameters.MaxProcesses);
if (parameters.RefineMassCharge)
{
MonoIsoPredictor.RefineMonoIsoMassChargeValues(parameters, centroidStreams, precursorMasses, trailerExtras, peakData, precursorScans);
}
metaData = MetaDataProcessingDDA.AggregateMetaDataDDA(centroidStreams, segmentScans, methodData, precursorScans,
trailerExtras, precursorMasses, retentionTimes, scanDependents, reactions, Index, parameters.MaxProcesses);
}
QuantDataCollection quantData = null;
if (parameters.ParseParams.Quant)
{
quantData = Quantification.Quantify(centroidStreams, segmentScans, parameters, methodData, Index);
}
RawMetricsDataDDA rawMetrics = null;
if (parameters.ParseParams.Metrics | parameters.QcParams.QcDirectory != null)
{
rawMetrics = MetaDataProcessingDDA.GetMetricsDataDDA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index, peakData, precursorScans, quantData);
}
if (parameters.ParseParams.Metrics)
{
MetricsWriter.WriteMatrix(rawMetrics, null, staticRawFile.FileName, parameters.ParseParams.OutputDirectory);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant)
{
string matrixFileName = ReadWrite.GetPathToFile(parameters.ParseParams.OutputDirectory, staticRawFile.FileName, "_Matrix.txt");
/*
* ParseWriter writerDDA = new ParseWriter(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
* precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
* writerDDA.WriteMatrixDDA(methodData.AnalysisOrder);
*/
MatrixWriter.ParseQuantDDA(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
}
if (parameters.ParseParams.WriteMgf)
{
//ParseWriter writerMGF = new ParseWriter(centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
//writerMGF.WriteMGF(staticRawFile.FileName);
MgfWriter.WriteMGF(staticRawFile.FileName, centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
}
if (parameters.ParseParams.Chromatogram != null)
{
ChromatogramWriter.WriteChromatogram(centroidStreams, segmentScans, retentionTimes, methodData, Index, parameters, staticRawFile.FileName);
}
if (parameters.QcParams.QcDirectory != null)
{
qcDataCollection = QC.QcWorkflow.LoadOrCreateQcCollection(parameters);
SearchMetricsContainer searchMetrics = new SearchMetricsContainer(staticRawFile.FileName, staticRawFile.CreationDate, methodData);
// check if the raw file already exists in the QC data with a different name
if (QcWorkflow.CheckIfFilePresentInQcCollection(staticRawFile.FileName, qcDataCollection))
{
Log.Information("A file with the same creation date and time as {File} already exists in the QC data", staticRawFile.FileName);
Console.WriteLine("A file with the same creation date and time as {File} already exists in the QC data. Skipping to next file.",
staticRawFile.FileName);
}
else
{
if (parameters.QcParams.PerformSearch)
{
Search.WriteSearchMGF(parameters, centroidStreams, segmentScans, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData,
Index, staticRawFile.FileName, parameters.QcParams.FixedScans);
Search.RunSearch(parameters, methodData, staticRawFile.FileName);
searchMetrics = SearchQC.ParseSearchResults(searchMetrics, parameters, staticRawFile.FileName, nScans);
}
QcDataContainer qcData = new QcDataContainer();
qcData.DDA = rawMetrics;
qcData.SearchMetrics = searchMetrics;
QC.QcWorkflow.UpdateQcCollection(qcDataCollection, qcData, methodData, staticRawFile.FileName);
}
}
}
public static void ParseDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters)
{
MethodDataContainer methodData;
CentroidStreamCollection centroidStreams;
SegmentScanCollection segmentScans;
TrailerExtraCollection trailerExtras;
PrecursorMassCollection precursorMasses;
RetentionTimeCollection retentionTimes;
ScanEventReactionCollection reactions;
ScanMetaDataCollectionDDA metaData = null;
PrecursorPeakCollection peakData = null;
RawMetricsDataDDA rawMetrics = null;
QuantDataCollection quantData = null;
var staticRawFile = rawFileThreadManager.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
//staticRawFile.CheckIfBoxcar();
(ScanIndex Index, PrecursorScanCollection precursorScans, ScanDependentsCollections scanDependents) =
Extract.ScanIndicesPrecursorsDependents(rawFileThreadManager);
using (var rawFile = rawFileThreadManager.CreateThreadAccessor())
{
reactions = Extract.ScanEvents(rawFile, Index);
methodData = Extract.MethodData(rawFile, Index);
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
trailerExtras = Extract.TrailerExtras(rawFile, Index);
precursorMasses = Extract.PrecursorMasses(rawFile, precursorScans, trailerExtras, Index);
retentionTimes = Extract.RetentionTimes(rawFile, Index);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant | parameters.ParseParams.Metrics | parameters.RefineMassCharge)
{
peakData = AnalyzePeaks.AnalyzeAllPeaks(centroidStreams, retentionTimes, precursorMasses, precursorScans, Index);
if (parameters.RefineMassCharge)
{
MonoIsoPredictor.RefineMonoIsoMassChargeValues(centroidStreams, precursorMasses, trailerExtras, peakData, precursorScans);
}
metaData = MetaDataProcessingDDA.AggregateMetaDataDDA(centroidStreams, segmentScans, methodData, precursorScans,
trailerExtras, precursorMasses, retentionTimes, scanDependents, reactions, Index);
}
if (parameters.ParseParams.Quant)
{
quantData = Quantification.Quantify(centroidStreams, segmentScans, parameters, methodData, Index);
}
if (parameters.ParseParams.Metrics)
{
rawMetrics = MetaDataProcessingDDA.GetMetricsDataDDA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index, peakData, precursorScans, quantData);
MetricsWriter.WriteMatrix(rawMetrics, null, staticRawFile.FileName, parameters.ParseParams.OutputDirectory);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant)
{
string matrixFileName = ReadWrite.GetPathToFile(parameters.ParseParams.OutputDirectory, staticRawFile.FileName, "_Matrix.txt");
/*
* ParseWriter writerDDA = new ParseWriter(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
* precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
* writerDDA.WriteMatrixDDA(methodData.AnalysisOrder);
*/
MatrixWriter.ParseQuantDDA(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
}
if (parameters.ParseParams.WriteMgf)
{
//ParseWriter writerMGF = new ParseWriter(centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
//writerMGF.WriteMGF(staticRawFile.FileName);
MgfWriter.WriteMGF(staticRawFile.FileName, centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
}
if (parameters.ParseParams.Chromatogram != null)
{
ChromatogramWriter.WriteChromatogram(centroidStreams, segmentScans, retentionTimes, methodData, Index, parameters, staticRawFile.FileName);
}
}