public static void QcDIA(IRawDataPlus rawFile, WorkflowParameters parameters)
{
rawFile.SelectInstrument(Device.MS, 1);
rawFile.CheckIfBoxcar();
ScanIndex Index = Extract.ScanIndices(rawFile);
MethodDataContainer methodData = Extract.MethodData(rawFile, Index);
CentroidStreamCollection centroidStreams = new CentroidStreamCollection();
SegmentScanCollection segmentScans = new SegmentScanCollection();
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
TrailerExtraCollection trailerExtras = Extract.TrailerExtras(rawFile, Index);
RetentionTimeCollection retentionTimes = Extract.RetentionTimes(rawFile, Index);
ScanMetaDataCollectionDIA metaData = MetaDataProcessingDIA.AggregateMetaDataDIA(centroidStreams, segmentScans, methodData,
trailerExtras, retentionTimes, Index);
RawMetricsDataDIA metrics = MetaDataProcessingDIA.GetMetricsDataDIA(metaData, methodData, rawFile.FileName, retentionTimes, Index);
QcDataContainer qcData = new QcDataContainer();
qcData.DIA = metrics;
QcDataCollection qcDataCollection = QC.QcWorkflow.LoadOrCreateQcCollection(parameters);
QC.QcWorkflow.UpdateQcCollection(qcDataCollection, qcData, methodData, rawFile.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);
}
}
}
static int Run(Dictionary <string, object> opts)
{
if ((bool)opts["ExampleCommands"] == true)
{
Examples.CommandLineUsage();
Environment.Exit(0);
}
if ((bool)opts["ExampleModifications"] == true)
{
Examples.ExampleMods();
Environment.Exit(0);
}
List <string> files = new List <string>();
QcDataCollection qcDataCollection = new QcDataCollection();
WorkflowParameters parameters = new WorkflowParameters(opts);
if (parameters.InputFiles != null) // did the user give us a list of files?
{
List <string> problems = new List <string>();
files = parameters.InputFiles.ToList();
// check if the list provided contains only .raw files
foreach (string file in files)
{
if (!file.EndsWith(".raw", StringComparison.OrdinalIgnoreCase))
{
problems.Add(file);
}
}
if (problems.Count() == 1)
{
Console.WriteLine("\nERROR: {0} does not appear to be a .raw file. Invoke '>RawTools --help' if you need help.", problems.ElementAt(0));
Log.Error("Invalid file provided: {0}", problems.ElementAt(0));
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
if (problems.Count() > 1)
{
Console.WriteLine("\nERROR: The following {0} files do not appear to be .raw files. Invoke '>RawTools --help' if you need help." +
"\n\n{1}", problems.Count(), String.Join("\n", problems));
Log.Error("Invalid files provided: {0}", String.Join(" ", problems));
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
files = RawFileInfo.RemoveInAcquistionFiles(files);
// if the file location(s) are relative, we need to get the absolute path to them
files.EnsureAbsolutePaths();
Log.Information("Files to be processed, provided as list: {0}", String.Join(" ", files));
}
else if (!String.IsNullOrEmpty(parameters.RawFileDirectory)) // did the user give us a directory?
{
// if QC is being done, use the QC method snf get the qc data collection at the same time
if (parameters.QcParams.QcDirectory != null)
{
(files, qcDataCollection) = QcWorkflow.GetFileListAndQcFile(parameters, parameters.IncludeSubdirectories);
}
// if not, the parse method
else if (Directory.Exists(parameters.RawFileDirectory))
{
files = Directory.GetFiles(parameters.RawFileDirectory, "*.*", SearchOption.TopDirectoryOnly)
.Where(s => s.EndsWith(".raw", StringComparison.OrdinalIgnoreCase)).ToList();
}
else
{
Console.WriteLine("ERROR: The provided directory does not appear to be valid.");
Log.Error("Invalid directory provided: {0}", parameters.RawFileDirectory);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
files = RawFileInfo.RemoveInAcquistionFiles(files);
// if the file location(s) are relative, we need to get the absolute path to them
files.EnsureAbsolutePaths();
Log.Information("Files to be processed, provided as directory: {0}", String.Join(" ", files));
}
else
{
Console.WriteLine("ERROR: At least one of the following arguments is required: -f, -d");
Log.Error("No raw files or directory specified.");
return(1);
}
if (parameters.ParseParams.Quant)
{
List <string> possible = new List <string>()
{
"TMT0", "TMT2", "TMT6", "TMT10", "TMT11", "iTRAQ4", "iTRAQ8"
};
if (!possible.Contains(parameters.ParseParams.LabelingReagents))
{
Console.WriteLine("ERROR: For quantification, the labeling reagent must be one of {TMT0, TMT2, TMT6, TMT10, TMT11, iTRAQ4, iTRAQ8}");
Log.Error("Invalid labeling reagent provided: {0}", parameters.ParseParams.LabelingReagents);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
}
if (parameters.ParseParams.Chromatogram != null)
{
List <string> possible = new List <string>()
{
"1", "2", "3", "T", "B"
};
foreach (var x in parameters.ParseParams.Chromatogram)
{
if (!possible.Contains(x.ToString()))
{
Console.WriteLine("ERROR: Incorrect format for -chro. See help.");
Log.Error("Invalid chromatogram argument provided: {Chro}", parameters.ParseParams.Chromatogram);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
}
}
System.Diagnostics.Stopwatch singleFileTime = new System.Diagnostics.Stopwatch();
System.Diagnostics.Stopwatch totalTime = new System.Diagnostics.Stopwatch();
totalTime.Start();
foreach (string file in files)
{
singleFileTime.Start();
Console.WriteLine("\nProcessing: {0}\n", file);
//using (IRawDataPlus rawFile = RawFileReaderFactory.ReadFile(fileName:file))
using (IRawFileThreadManager rawFile = RawFileReaderFactory.CreateThreadManager(file))
{
if (parameters.ParseParams.OutputDirectory == null)
{
parameters.ParseParams.OutputDirectory = Path.GetDirectoryName(file);
}
WorkFlowsDDA.UniversalDDA(rawFile, parameters, qcDataCollection);
}
singleFileTime.Stop();
Console.WriteLine("\nElapsed time: {0} s", Math.Round(Convert.ToDouble(singleFileTime.ElapsedMilliseconds) / 1000.0, 2));
singleFileTime.Reset();
}
if (parameters.LogDump)
{
Write.LogDump.WriteToDisk(parameters);
}
totalTime.Stop();
Console.WriteLine("\nTime to process all {0} files: {1}", files.Count(), totalTime.Elapsed);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(0);
}
public static void QcDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters)
{
MethodDataContainer methodData;
CentroidStreamCollection centroidStreams;
SegmentScanCollection segmentScans;
TrailerExtraCollection trailerExtras;
PrecursorMassCollection precursorMasses;
RetentionTimeCollection retentionTimes;
ScanEventReactionCollection reactions;
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())
{
methodData = Extract.MethodData(rawFile, Index);
reactions = Extract.ScanEvents(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);
}
PrecursorPeakCollection peakData = AnalyzePeaks.AnalyzeAllPeaks(centroidStreams, retentionTimes, precursorMasses, precursorScans, Index);
if (parameters.RefineMassCharge)
{
MonoIsoPredictor.RefineMonoIsoMassChargeValues(centroidStreams, precursorMasses, trailerExtras, peakData, precursorScans);
}
ScanMetaDataCollectionDDA metaData = MetaDataProcessingDDA.AggregateMetaDataDDA(centroidStreams, segmentScans, methodData, precursorScans,
trailerExtras, precursorMasses, retentionTimes, scanDependents, reactions, Index);
RawMetricsDataDDA rawMetrics = MetaDataProcessingDDA.GetMetricsDataDDA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index, peakData, precursorScans);
QcDataCollection qcDataCollection = QC.QcWorkflow.LoadOrCreateQcCollection(parameters);
SearchMetricsContainer searchMetrics = new SearchMetricsContainer(staticRawFile.FileName, staticRawFile.CreationDate, methodData);
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);
}
QcDataContainer qcData = new QcDataContainer();
qcData.DDA = rawMetrics;
qcData.SearchMetrics = searchMetrics;
QC.QcWorkflow.UpdateQcCollection(qcDataCollection, qcData, methodData, staticRawFile.FileName);
staticRawFile.Dispose();
}
public static void WriteQcToTable(this QcDataCollection qcData)
{
if (File.Exists(Path.Combine(qcData.QcDirectory, "QcDataTable.csv")))
{
while (Utilities.ReadWrite.IsFileLocked(Path.Combine(qcData.QcDirectory, "QcDataTable.csv")))
{
Console.WriteLine("{0} is in use. Please close the file and press any key to continue.", Path.Combine(qcData.QcDirectory, "QcDataTable.csv"));
Console.ReadKey();
}
}
using (StreamWriter f = new StreamWriter(Path.Combine(qcData.QcDirectory, "QcDataTable.csv"), append: false))
{
f.WriteLine("DateAcquired,FileName,Instrument,ExperimentMsOrder,Ms1Analyzer,Ms2Analyzer,Ms3Analyzer,TotalAnalysisTime,TotalScans,NumMs1Scans,NumMs2Scans," +
"NumMs3Scans,Ms1ScanRate(/s),Ms2ScanRate(/s),Ms3ScanRate(/s),MeanDutyCycle(s),MeanMs2TriggerRate(/Ms1Scan),Ms1MedianSummedIntensity,Ms2MedianSummedIntensity," +
"MedianPrecursorIntensity,MedianMs1IsolationInterence,MedianMs2PeakFractionConsumingTop80PercentTotalIntensity,EsiInstabilityFlags(count),MedianMassDrift(ppm)," +
"IdentificationRate(IDs/Ms2Scan),DigestionEfficiency,MissedCleavageRate(/PSM),ModificationFrequencyAtNTerm,ModificationFrequencyAtK,ModificationFrequencyAtX," +
"MedianMsFillTime(ms),MedianMs2FillTime(ms),MedianMs3FillTime(ms),WidthAt10%H(s),WidthAt50%H(s),AsymmetryAt10%H,AsymmetryAt50%H," +
"PeakCapacity,TimeBeforeFirstExceedanceOf10%MaxIntensity,TimeAfterLastExceedanceOf10%MaxIntensity,FractionOfRunAbove10%MaxIntensity,IdChargeRatio3to2,IdChargeRatio4to2,IdentipyParameters");
}
List <DateTime> keys = qcData.QcData.Keys.ToList();
keys.Sort();
using (StreamWriter f = new StreamWriter(Path.Combine(qcData.QcDirectory, "QcDataTable.csv"), append: true))
{
foreach (DateTime key in keys)
{
f.Write(qcData.QcData[key].DateAcquired + ",");
f.Write(qcData.QcData[key].RawFile + ",");
f.Write(qcData.QcData[key].Instrument + ",");
f.Write(qcData.QcData[key].ExperimentMsOrder + ",");
f.Write(qcData.QcData[key].Ms1Analyzer + ",");
f.Write(qcData.QcData[key].Ms2Analyzer + ",");
f.Write(qcData.QcData[key].Ms3Analyzer + ",");
f.Write(qcData.QcData[key].GradientTime + ",");
f.Write(qcData.QcData[key].TotalScans + ",");
f.Write(qcData.QcData[key].NumMs1Scans + ",");
f.Write(qcData.QcData[key].NumMs2Scans + ",");
f.Write(qcData.QcData[key].NumMs3Scans + ",");
f.Write(qcData.QcData[key].Ms1ScanRate / 60 + ",");
f.Write(qcData.QcData[key].Ms2ScanRate / 60 + ",");
f.Write(qcData.QcData[key].Ms3ScanRate / 60 + ",");
f.Write(qcData.QcData[key].MeanDutyCycle + ",");
f.Write(qcData.QcData[key].MeanTopN + ",");
f.Write(qcData.QcData[key].MedianSummedMs1Intensity + ",");
f.Write(qcData.QcData[key].MedianSummedMs2Intensity + ",");
f.Write(qcData.QcData[key].MedianPrecursorIntensity + ",");
f.Write(qcData.QcData[key].MedianMs1IsolationInterference + ",");
f.Write(qcData.QcData[key].MedianMs2FractionConsumingTop80PercentTotalIntensity + ",");
f.Write(qcData.QcData[key].NumEsiStabilityFlags + ",");
f.Write(qcData.QcData[key].MedianMassDrift + ",");
//f.Write(qcData.QcData[key].QuantMeta.medianReporterIntensity + ",");
f.Write(qcData.QcData[key].IdentificationRate + ",");
f.Write(qcData.QcData[key].DigestionEfficiency + ",");
f.Write(qcData.QcData[key].MissedCleavageRate + ",");
f.Write(qcData.QcData[key].LabelingEfficiencyAtNTerm + ",");
f.Write(qcData.QcData[key].LabelingEfficiencyAtK + ",");
f.Write(qcData.QcData[key].LabelingEfficiencyAtX + ",");
f.Write(qcData.QcData[key].Ms1FillTime.P50 + ",");
f.Write(qcData.QcData[key].Ms2FillTime.P50 + ",");
f.Write(qcData.QcData[key].Ms3FillTime.P50 + ",");
f.Write(qcData.QcData[key].PeakShape.Width.P10 * 60 + ",");
f.Write(qcData.QcData[key].PeakShape.Width.P50 * 60 + ",");
f.Write(qcData.QcData[key].PeakShape.Asymmetry.P10 + ",");
f.Write(qcData.QcData[key].PeakShape.Asymmetry.P50 + ",");
f.Write(qcData.QcData[key].ColumnPeakCapacity + ",");
f.Write(qcData.QcData[key].TimeBeforeFirstScanToExceedPoint1MaxIntensity + ",");
f.Write(qcData.QcData[key].TimeAfterLastScanToExceedPoint1MaxIntensity + ",");
f.Write(qcData.QcData[key].FractionOfRunAbovePoint1MaxIntensity + ",");
f.Write(qcData.QcData[key].ChargeRatio3to2 + ",");
f.Write(qcData.QcData[key].ChargeRatio4to2 + ",");
f.Write(qcData.QcData[key].IdentipyParameters + "\n");
}
}
Console.WriteLine("Finished writing QC data to csv\n");
}
