/// <summary>
/// Process the given file or folder
/// </summary>
/// <returns>0 if success, otherwise an error code</returns>
/// <remarks>Folder could either be a supported mass spec data folder, or a normal directory with several supported data files</remarks>
public int Run()
{
// Normalize the input path. Only affects paths to a file/folder in a folder-type dataset
Parameters.InputPath = MassSpecDataReaderFactory.NormalizeDatasetPath(Parameters.InputPath);
var attr = File.GetAttributes(Parameters.InputPath);
int errorCode;
if ((attr & FileAttributes.Directory) == FileAttributes.Directory &&
!MassSpecDataReaderFactory.IsADirectoryDataset(Parameters.InputPath))
{
errorCode = ProcessDirectory(Parameters.InputPath);
}
else
{
if (!MsRawFile(Parameters.InputPath) && !MsPbfFile(Parameters.InputPath))
{
ShowErrorMessage(@"File extension not supported, " + Parameters.InputPath);
return(-1);
}
errorCode = ProcessFile(Parameters.InputPath);
}
return(errorCode);
}
/// <summary>
/// Initialize this data set by reading the raw file asynchronously and initializing child view models
/// </summary>
/// <param name="filePath">The raw File Path.</param>
/// <returns>
/// The <see cref="Task"/>.
/// </returns>
public async Task InitializeAsync(string filePath)
{
filePath = MassSpecDataReaderFactory.NormalizeDatasetPath(filePath);
this.IsLoading = true; // Show animated loading screen
this.Title = Path.GetFileNameWithoutExtension(Path.GetFileNameWithoutExtension(filePath));
this.rawFilePath = filePath;
this.LoadProgressPercent = 0.0;
this.LoadProgressStatus = "Loading...";
var progress = new Progress <ProgressData>(progressData =>
{
progressData.UpdateFrequencySeconds = 2;
if (progressData.ShouldUpdate())
{
this.LoadProgressPercent = progressData.Percent;
this.LoadProgressStatus = progressData.Status;
}
});
// load raw file
this.LcMs = await Task.Run(() => PbfLcMsRun.GetLcMsRun(filePath, 0, 0, progress));
// Now that we have an LcMsRun, initialize viewmodels that require it
this.XicViewModel = new XicViewModel(this.dialogService, this.LcMs);
this.SpectrumViewModel = new SpectrumViewModel(this.dialogService, this.LcMs);
this.FeatureMapViewModel = new FeatureViewerViewModel((LcMsRun)this.LcMs, this.dialogService);
// When the selected scan changes in the xic plots, the selected scan for the prsm should update
this.XicViewModel.SelectedScanUpdated().Subscribe(scan => this.SelectedPrSm.Scan = scan);
// When an ID is selected on FeatureMap, update selectedPrSm
this.FeatureMapViewModel.FeatureMapViewModel.WhenAnyValue(x => x.SelectedPrSm).Where(prsm => prsm != null).Subscribe(prsm => this.SelectedPrSm = prsm);
// Create prsms for scan numbers (unidentified)
await this.LoadScans();
////await this.ScanViewModel.ToggleShowInstrumentDataAsync(IcParameters.Instance.ShowInstrumentData, (PbfLcMsRun)this.LcMs);
this.SelectedPrSm.LcMs = this.LcMs; // For the selected PrSm, we should always use the LcMsRun for this dataset.
this.IsLoading = false; // Hide animated loading screen
}
public bool RunSearch(double corrThreshold = 0.7, CancellationToken?cancellationToken = null, IProgress <ProgressData> progress = null)
{
// Get the Normalized spec file/folder path
SpecFilePath = MassSpecDataReaderFactory.NormalizeDatasetPath(SpecFilePath);
var prog = new Progress <ProgressData>();
var progData = new ProgressData(progress);
if (progress != null)
{
prog = new Progress <ProgressData>(p =>
{
progData.Status = p.Status;
progData.StatusInternal = p.StatusInternal;
progData.Report(p.Percent);
});
}
var sw = new Stopwatch();
var swAll = new Stopwatch();
swAll.Start();
ErrorMessage = string.Empty;
Console.Write(@"Reading raw file...");
progData.Status = "Reading spectra file";
progData.StepRange(10.0);
sw.Start();
_run = PbfLcMsRun.GetLcMsRun(SpecFilePath, 0, 0, prog);
_ms2ScanNums = _run.GetScanNumbers(2).ToArray();
_isolationWindowTargetMz = new double[_run.MaxLcScan + 1];
foreach (var ms2Scan in _ms2ScanNums)
{
var ms2Spec = _run.GetSpectrum(ms2Scan) as ProductSpectrum;
if (ms2Spec == null)
{
continue;
}
_isolationWindowTargetMz[ms2Scan] = ms2Spec.IsolationWindow.IsolationWindowTargetMz;
}
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
progData.StepRange(20.0);
ISequenceFilter ms1Filter;
if (this.ScanNumbers != null && this.ScanNumbers.Any())
{
ms1Filter = new SelectedMsMsFilter(this.ScanNumbers);
}
else if (string.IsNullOrWhiteSpace(FeatureFilePath))
{
// Checks whether SpecFileName.ms1ft exists
var ms1FtFilePath = MassSpecDataReaderFactory.ChangeExtension(SpecFilePath, LcMsFeatureFinderLauncher.FileExtension);
if (!File.Exists(ms1FtFilePath))
{
Console.WriteLine(@"Running ProMex...");
sw.Start();
var param = new LcMsFeatureFinderInputParameter
{
InputPath = SpecFilePath,
MinSearchMass = MinSequenceMass,
MaxSearchMass = MaxSequenceMass,
MinSearchCharge = MinPrecursorIonCharge,
MaxSearchCharge = MaxPrecursorIonCharge,
CsvOutput = false,
ScoreReport = false,
LikelihoodScoreThreshold = -10
};
var featureFinder = new LcMsFeatureFinderLauncher(param);
featureFinder.Run();
}
sw.Reset();
sw.Start();
Console.Write(@"Reading ProMex results...");
ms1Filter = new Ms1FtFilter(_run, PrecursorIonTolerance, ms1FtFilePath, -10);
}
else
{
sw.Reset();
sw.Start();
var extension = Path.GetExtension(FeatureFilePath);
if (extension.ToLower().Equals(".csv"))
{
Console.Write(@"Reading ICR2LS/Decon2LS results...");
ms1Filter = new IsosFilter(_run, PrecursorIonTolerance, FeatureFilePath);
}
else if (extension.ToLower().Equals(".ms1ft"))
{
Console.Write(@"Reading ProMex results...");
ms1Filter = new Ms1FtFilter(_run, PrecursorIonTolerance, FeatureFilePath, -10);
}
else if (extension.ToLower().Equals(".msalign"))
{
Console.Write(@"Reading MS-Align+ results...");
ms1Filter = new MsDeconvFilter(_run, PrecursorIonTolerance, FeatureFilePath);
}
else
{
ms1Filter = null; //new Ms1FeatureMatrix(_run);
}
}
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
// pre-generate deconvoluted spectra for scoring
_massBinComparer = new FilteredProteinMassBinning(AminoAcidSet, MaxSequenceMass + 1000);
_ms2ScorerFactory2 = new CompositeScorerFactory(_run, _massBinComparer, AminoAcidSet,
MinProductIonCharge, MaxProductIonCharge, ProductIonTolerance);
sw.Reset();
Console.WriteLine(@"Generating deconvoluted spectra for MS/MS spectra...");
sw.Start();
var pfeOptions = new ParallelOptions
{
MaxDegreeOfParallelism = MaxNumThreads,
CancellationToken = cancellationToken ?? CancellationToken.None
};
Parallel.ForEach(_ms2ScanNums, pfeOptions, ms2ScanNum =>
{
_ms2ScorerFactory2.DeconvonluteProductSpectrum(ms2ScanNum);
});
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
progData.StepRange(10.0);
progData.Status = "Reading Fasta File";
// Target database
var targetDb = new FastaDatabase(DatabaseFilePath);
targetDb.Read();
// Generate sequence tags for all MS/MS spectra
if (TagBasedSearch)
{
progData.StepRange(25.0);
progData.Status = "Generating Sequence Tags";
sw.Reset();
Console.WriteLine(@"Generating sequence tags for MS/MS spectra...");
sw.Start();
var seqTagGen = GetSequenceTagGenerator();
_tagMs2ScanNum = seqTagGen.GetMs2ScanNumsContainingTags().ToArray();
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
_tagSearchEngine = new ScanBasedTagSearchEngine(_run, seqTagGen, new LcMsPeakMatrix(_run, ms1Filter), targetDb, ProductIonTolerance, AminoAcidSet,
_ms2ScorerFactory2,
ScanBasedTagSearchEngine.DefaultMinMatchedTagLength,
MaxSequenceMass, MinProductIonCharge, MaxProductIonCharge);
}
var specFileName = MassSpecDataReaderFactory.RemoveExtension(Path.GetFileName(SpecFilePath));
var targetOutputFilePath = Path.Combine(OutputDir, specFileName + TargetFileNameEnding);
var decoyOutputFilePath = Path.Combine(OutputDir, specFileName + DecoyFileNameEnding);
var tdaOutputFilePath = Path.Combine(OutputDir, specFileName + TdaFileNameEnding);
progData.StepRange(60.0);
progData.Status = "Running Target search";
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Target))
{
sw.Reset();
Console.Write(@"Reading the target database...");
sw.Start();
targetDb.Read();
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
var targetMatches = new SortedSet <DatabaseSequenceSpectrumMatch> [_run.MaxLcScan + 1];
progData.MaxPercentage = 42.5;
if (TagBasedSearch)
{
sw.Reset();
Console.WriteLine(@"Tag-based searching the target database");
sw.Start();
RunTagBasedSearch(targetMatches, targetDb, null, prog);
Console.WriteLine(@"Target database tag-based search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.MaxPercentage = 60.0;
sw.Reset();
Console.WriteLine(@"Searching the target database");
sw.Start();
RunSearch(targetMatches, targetDb, ms1Filter, null, prog);
Console.WriteLine(@"Target database search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
// calculate spectral e-value usign generating function
sw.Reset();
Console.WriteLine(@"Calculating spectral E-values for target-spectrum matches");
sw.Start();
var bestTargetMatches = RunGeneratingFunction(targetMatches);
WriteResultsToFile(bestTargetMatches, targetOutputFilePath, targetDb);
sw.Stop();
Console.WriteLine(@"Target-spectrum match E-value calculation elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.StepRange(95.0); // total to 95%
progData.Status = "Running Decoy search";
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Decoy))
{
// Decoy database
sw.Reset();
sw.Start();
var decoyDb = targetDb.Decoy(null, true);
Console.Write(@"Reading the decoy database...");
decoyDb.Read();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
progData.MaxPercentage = 77.5;
var decoyMatches = new SortedSet <DatabaseSequenceSpectrumMatch> [_run.MaxLcScan + 1];
if (TagBasedSearch)
{
sw.Reset();
Console.WriteLine(@"Tag-based searching the decoy database");
sw.Start();
RunTagBasedSearch(decoyMatches, decoyDb, null, prog);
Console.WriteLine(@"Decoy database tag-based search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.MaxPercentage = 95.0;
sw.Reset();
Console.WriteLine(@"Searching the decoy database");
sw.Start();
RunSearch(decoyMatches, decoyDb, ms1Filter, null, prog);
Console.WriteLine(@"Decoy database search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
// calculate spectral e-value usign generating function
sw.Reset();
Console.WriteLine(@"Calculating spectral E-values for decoy-spectrum matches");
sw.Start();
var bestDecoyMatches = RunGeneratingFunction(decoyMatches);
WriteResultsToFile(bestDecoyMatches, decoyOutputFilePath, decoyDb);
sw.Stop();
Console.WriteLine(@"Decoy-spectrum match E-value calculation elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.StepRange(100.0);
progData.Status = "Writing combined results file";
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Both))
{
// Add "Qvalue" and "PepQValue"
var fdrCalculator = new FdrCalculator(targetOutputFilePath, decoyOutputFilePath);
if (fdrCalculator.HasError())
{
ErrorMessage = fdrCalculator.ErrorMessage;
Console.WriteLine(@"Error computing FDR: " + fdrCalculator.ErrorMessage);
return(false);
}
fdrCalculator.WriteTo(tdaOutputFilePath);
}
progData.Report(100.0);
Console.WriteLine(@"Done.");
swAll.Stop();
Console.WriteLine(@"Total elapsed time for search: {0:f1} sec ({1:f2} min)", swAll.Elapsed.TotalSeconds, swAll.Elapsed.TotalMinutes);
return(true);
}
