public void exporterTest1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";
var exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "UnlabelledTargetedResultsExporterOutput1.txt");
if (File.Exists(exportedResultFile))
{
File.Delete(exportedResultFile);
}
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var selectedMassTags = mtc.TargetList.OrderBy(p => p.ID).Take(10).ToList();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
foreach (var mt in selectedMassTags)
{
run.CurrentMassTag = mt;
workflow.Execute();
}
var repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
var exporter = new UnlabelledTargetedResultToTextExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}
public void Execute()
{
Check.Require(_run != null, "Run has not been defined.");
//Use Features file if it exists; if not, find the quality Features
List <MassTagResultBase> resultsPassingCriteria;
_targetedResultRepository = new TargetedResultRepository();
if (ImportedFeaturesFilename == null || ImportedFeaturesFilename.Length == 0)
{
Check.Require(_run.ResultCollection.MSPeakResultList != null && _run.ResultCollection.MSPeakResultList.Count > 0, "Dataset's Peak-level data is empty. This is needed for chromatogram generation.");
resultsPassingCriteria = FindTargetsThatPassCriteria();
_targetedResultRepository.AddResults(resultsPassingCriteria);
if (AreFeaturesSavedToTextFile)
{
string outputfolder;
if (ExportAlignmentFolder == null || ExportAlignmentFolder.Length == 0)
{
outputfolder = _run.DataSetPath;
}
else
{
outputfolder = ExportAlignmentFolder;
}
string exportTargetedFeaturesFile = Path.Combine(outputfolder, _run.DatasetName + "_alignedFeatures.txt");
UnlabelledTargetedResultToTextExporter exporter = new UnlabelledTargetedResultToTextExporter(exportTargetedFeaturesFile);
exporter.ExportResults(_targetedResultRepository.Results);
}
}
else
{
//load them from the Features file
UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(ImportedFeaturesFilename);
TargetedResultRepository repo = importer.Import();
_targetedResultRepository.Results = repo.Results;
}
//do alignment
NETAndMassAligner aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(_targetedResultRepository.Results);
aligner.SetReferenceMassTags(this.MassTagList);
aligner.Execute(this._run);
//save the alignment data
if (IsAlignmentInfoExported)
{
string outputfolder;
if (ExportAlignmentFolder == null || ExportAlignmentFolder.Length == 0)
{
outputfolder = _run.DataSetPath;
}
else
{
outputfolder = ExportAlignmentFolder;
}
string exportNETAlignmentFilename = Path.Combine(outputfolder, _run.DatasetName + "_NETAlignment.txt");
string exportMZAlignmentFilename = Path.Combine(outputfolder, _run.DatasetName + "_MZAlignment.txt");
MassAlignmentInfoToTextExporter mzAlignmentExporter = new MassAlignmentInfoToTextExporter(exportMZAlignmentFilename);
mzAlignmentExporter.ExportAlignmentInfo(_run.AlignmentInfo);
NETAlignmentInfoToTextExporter netAlignmentExporter = new NETAlignmentInfoToTextExporter(exportNETAlignmentFilename);
netAlignmentExporter.ExportAlignmentInfo(_run.AlignmentInfo);
}
}
public void executeWorkflowTest1()
{
var testFile = FileRefs.SipperRawDataFile;
var exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "ExportedSipperResults1.txt");
var peaksFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksFile);
var lcmsfeaturesFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_LCMSFeatures.txt";
// load LCMSFeatures as targets
var importer =
new LcmsTargetFromFeaturesFileImporter(lcmsfeaturesFile);
var lcmsTargetCollection = importer.Import();
// load MassTags
var massTagFile1 =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_MassTags.txt";
var massTagImporter = new MassTagFromTextFileImporter(massTagFile1);
var massTagCollection = massTagImporter.Import();
//enriched
var testMassTags = new int[] { 355116553, 355129038, 355160150, 355162540, 355163371 };
var filteredLcmsFeatureTargets = (from n in lcmsTargetCollection.TargetList
where testMassTags.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
select n).ToList();
TargetCollection.UpdateTargetsWithMassTagInfo(filteredLcmsFeatureTargets, massTagCollection.TargetList);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
var workflow = new SipperTargetedWorkflow(run, parameters);
foreach (var target in filteredLcmsFeatureTargets)
{
run.CurrentMassTag = target;
workflow.Execute();
}
var results = run.ResultCollection.GetMassTagResults();
var repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
var exporter = new SipperResultToLcmsFeatureExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}
public void SetFeaturesToBeAligned(List <TargetedResultBase> featuresToAlign)
{
_featuresToBeAligned.Clear();
_featuresToBeAligned.AddResults(featuresToAlign);
}
public override void Execute()
{
List <TargetedResultBase> resultsPassingCriteria;
_targetedResultRepository = new TargetedResultRepository();
var featuresAreImportedFromFile = !string.IsNullOrEmpty(AlignerParameters.ImportedFeaturesFilename);
if (featuresAreImportedFromFile)
{
//load them from the Features file
var importer = new UnlabelledTargetedResultFromTextImporter(AlignerParameters.ImportedFeaturesFilename);
var repo = importer.Import();
_targetedResultRepository.Results = repo.Results;
}
else
{
Check.Require(Run.ResultCollection.MSPeakResultList != null && Run.ResultCollection.MSPeakResultList.Count > 0, "Dataset's Peak-level data is empty. This is needed for chromatogram generation.");
//execute targeted feature finding to find the massTags in the raw data
_workflow = new BasicTargetedWorkflow(Run, AlignerParameters);
var netGrouping = 0.2;
double chromTolerance = 5; //in ppm
var progressString = "First trying to find alignment targets using narrow mass tolerances.... ";
ReportProgress(0, progressString);
var firstPassResults = FindTargetsThatPassSpecifiedMassTolerance(netGrouping, chromTolerance);
if (firstPassResults.Count < 10)
{
//try another netGrouping
netGrouping = 0.3;
chromTolerance = 20;
progressString = "Couldn't find enough. Now trying wider mass tolerance = " + chromTolerance;
ReportProgress(0, progressString);
var secondPassResults = FindTargetsThatPassSpecifiedMassTolerance(netGrouping, chromTolerance);
firstPassResults.AddRange(secondPassResults);
}
if (firstPassResults.Count < 10)
{
netGrouping = 0.4;
chromTolerance = 50;
progressString = "Ok this is a tough one. Now going even wider. Mass tolerance = " + chromTolerance;
ReportProgress(0, progressString);
var thirdPassResults = FindTargetsThatPassSpecifiedMassTolerance(netGrouping, chromTolerance);
firstPassResults.AddRange(thirdPassResults);
}
var ppmErrors = getMassErrors(firstPassResults);
var filteredUsingGrubbsPPMErrors = MathUtilities.filterWithGrubbsApplied(ppmErrors);
var canUseNarrowTolerances = executeDecisionOnUsingTightTolerances(filteredUsingGrubbsPPMErrors);
if (canUseNarrowTolerances)
{
var avgPPMError = filteredUsingGrubbsPPMErrors.Average();
var stdev = MathUtilities.GetStDev(filteredUsingGrubbsPPMErrors);
var tolerance = Math.Abs(avgPPMError) + 2 * stdev;
this.AlignerParameters.ChromGenTolerance = (int)Math.Ceiling(tolerance);
this.AlignerParameters.MSToleranceInPPM = (int)Math.Ceiling(tolerance);
progressString = "STRICT_Matches_AveragePPMError = \t" + avgPPMError.ToString("0.00") + "; Stdev = \t" + stdev.ToString("0.00000");
ReportProgress(0, progressString);
progressString = "NOTE: using the new PPMTolerance= " + this.AlignerParameters.ChromGenTolerance;
ReportProgress(0, progressString);
_workflow = new BasicTargetedWorkflow(Run, AlignerParameters);
}
else
{
double avgPPMError = 0;
double stdev = 0;
if (filteredUsingGrubbsPPMErrors.Count != 0)
{
avgPPMError = filteredUsingGrubbsPPMErrors.Average();
stdev = MathUtilities.GetStDev(filteredUsingGrubbsPPMErrors);
}
progressString = "STRICT_Matches_AveragePPMError = \t" + avgPPMError.ToString("0.00") + "; Stdev = \t" + stdev.ToString("0.00000");
ReportProgress(0, progressString);
progressString = "Cannot use narrow ppm tolerances during NET/Mass alignment. Either the massError was too high or couldn't find enough strict matches.";
ReportProgress(0, progressString);
// find a way to work with datasets with masses way off but low stdev
}
resultsPassingCriteria = FindTargetsThatPassCriteria();
_targetedResultRepository.AddResults(resultsPassingCriteria);
}
var canDoAlignment = _targetedResultRepository.Results.Count > 0;
if (canDoAlignment)
{
doAlignment();
}
}