public void doAlignmentTest1()
{
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt";
UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
TargetedResultRepository repo = importer.Import();
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
MassTagCollection mtc = new MassTagCollection();
MassTagFromTextFileImporter mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
NETAndMassAligner aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.MassTagList);
aligner.Execute(run);
Assert.IsNotNull(run.AlignmentInfo);
Assert.IsNotNull(run.AlignmentInfo.marrNETFncTimeInput);
Assert.AreEqual(2273.0f, run.AlignmentInfo.marrNETFncTimeInput[0]);
float testScan = 6005;
float testNET1 = run.AlignmentInfo.GetNETFromTime(testScan);
Assert.AreEqual(0.3253423m, (decimal)testNET1);
}
public void ExportNET_andMass_AlignmentDataTest1()
{
string exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt");
string exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt");
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt";
UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
TargetedResultRepository repo = importer.Import();
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
MassTagCollection mtc = new MassTagCollection();
MassTagFromTextFileImporter mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
NETAndMassAligner aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.MassTagList);
aligner.Execute(run);
NETAlignmentInfoToTextExporter exporter = new NETAlignmentInfoToTextExporter(exportNETFilename);
exporter.ExportAlignmentInfo(run.AlignmentInfo);
MassAlignmentInfoToTextExporter massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename);
massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo);
}
public void doAlignmentTest1()
{
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
aligner.Execute(run);
float testScan = 6005;
var testNET1 = run.NetAlignmentInfo.GetNETValueForScan((int)testScan);
//note - this is Multialign's
Assert.AreEqual(0.3253423m, (decimal)testNET1);
}
public void ExportNET_andMass_AlignmentDataTest1()
{
var exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt");
var exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
aligner.Execute(run);
var exporter = new NETAlignmentInfoToTextExporter(exportNETFilename);
exporter.ExportAlignmentInfo(run.AlignmentInfo);
var massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename);
massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo);
}
public void importerTest1()
{
var importedResultFile = Path.Combine(FileRefs.OutputFolderPath, "UnlabelledTargetedResultsExporterOutput1.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(importedResultFile);
var repo = importer.Import();
Assert.IsNotNull(repo);
Assert.IsTrue(repo.Results.Count > 0);
var testResult1 = repo.Results[0];
Assert.AreEqual("QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18", testResult1.DatasetName);
Assert.AreEqual(24698, testResult1.TargetID);
Assert.AreEqual(3, testResult1.ChargeState);
Assert.AreEqual(5880, testResult1.ScanLC);
Assert.AreEqual(5876, testResult1.ScanLCStart);
Assert.AreEqual(5888, testResult1.ScanLCEnd);
Assert.AreEqual(0.3160, (decimal)testResult1.NET);
Assert.AreEqual(1, testResult1.NumChromPeaksWithinTol);
Assert.AreEqual(2311.07759, (decimal)testResult1.MonoMass);
Assert.AreEqual(771.36647, (decimal)testResult1.MonoMZ);
Assert.AreEqual(8247913, (decimal)testResult1.Intensity);
Assert.AreEqual(0.0119, (decimal)testResult1.FitScore);
Assert.AreEqual(0, (decimal)testResult1.IScore);
}
public void TestTargetedWorkflowExecutorMod()
{
const string executorParameterFile = @"\\protoapps\UserData\Kaipo\TopDown\test2paramsmod.xml";
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
string resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "Results");
const string testDatasetPath = @"\\protoapps\UserData\Kaipo\TopDown\test2\Proteus_Peri_intact_ETD.raw";
const string testDatasetName = "Proteus_Peri_intact_ETD";
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
// Output chrom data
var wf = executor.TargetedWorkflow as TopDownTargetedWorkflow;
Console.Write("***** chrom data *****\n");
foreach (var resultData in wf.TargetResults)
{
int id = resultData.Key;
TargetedResultBase result = resultData.Value;
double chromPeakSelected = (result.ChromPeakSelected != null) ? result.ChromPeakSelected.XValue : -1;
Console.Write("TargetID=" + id + "; ChromPeakSelected=" + chromPeakSelected + "\n");
for (int i = 0; i < result.ChromValues.Xvalues.Length; i++)
{
Console.Write(result.ChromValues.Xvalues[i] + "\t" + result.ChromValues.Yvalues[i] + "\n");
}
Console.Write("\n");
}
Console.Write("**********************\n");
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new UnlabelledTargetedResultFromTextImporter(expectedResultsFilename);
TargetedResultRepository repository = importer.Import();
Assert.AreEqual(9, repository.Results.Count);
}
public void copyToLocalTest1()
{
var executorParameterFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\basicTargetedWorkflowExecutorParameters_CopyToLocalTestCase2.xml";
var datasetPath = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var testDatasetName = "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase, "Results", testDatasetName + "_results.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath);
executor.Execute();
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new UnlabelledTargetedResultFromTextImporter(expectedResultsFilename);
var repository = importer.Import();
Assert.AreEqual(10, repository.Results.Count);
var result1 = repository.Results[2];
Assert.AreEqual(24702, result1.TargetID);
Assert.AreEqual(3, result1.ChargeState);
Assert.AreEqual(8112, result1.ScanLC);
//Dataset MassTagID ChargeState Scan ScanStart ScanEnd NET NumChromPeaksWithinTol NumQualityChromPeaksWithinTol MonoisotopicMass MonoMZ IntensityRep FitScore IScore FailureType
//QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18 24702 3 8119 8112 8124 0.4172 2 1 2920.53082 974.51755 1379489 0.1136 0.0000
}
public void ensureAlignment_was_executed()
{
var run = new RunFactory().CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_READONLY_alignedFeatures.txt";
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_Formic_MassTags_Bin10_all.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var parameters = new NETAndMassAlignerParameters();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
var scan = 7835;
var theorMZ = 780.08485; //massTagID = 24701 (+3)
var obsMZ = 780.0824;
var netBeforeAlignment = run.NetAlignmentInfo.GetNETValueForScan(scan);
var mzBeforeAlignment = run.GetAlignedMZ(obsMZ);
aligner.Execute(run);
var netAfterAlignment = run.NetAlignmentInfo.GetNETValueForScan(scan);
var mzAfterAlignment = run.GetAlignedMZ(obsMZ);
Console.WriteLine("NET before alignment = " + netBeforeAlignment);
Console.WriteLine("NET after alignment = " + netAfterAlignment);
Console.WriteLine("Theor MZ = " + theorMZ);
Console.WriteLine("MZ before alignment = " + mzBeforeAlignment);
Console.WriteLine("MZ after alignment = " + mzAfterAlignment);
Console.WriteLine("PPMDiff before alignment = " + (theorMZ - mzBeforeAlignment) / theorMZ * 1e6);
Console.WriteLine("PPMDiff after alignment = " + (theorMZ - mzAfterAlignment) / theorMZ * 1e6);
}
public void TestTargetedWorkflowExecutor()
{
const string executorParameterFile = @"\\protoapps\UserData\Kaipo\TopDown\test2params.xml";
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
string resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "IqResults");
const string testDatasetPath = @"\\protoapps\UserData\Kaipo\TopDown\test2\Proteus_Peri_intact_ETD.raw";
const string testDatasetName = "Proteus_Peri_intact_ETD";
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, testDatasetPath);
string proteinSeq =
@"A.VDKTNPYALMEDAAQKTFDKLKTEQPEIRKNPELLREIVQQELLPYVHIKYAGALVLGPYYRNATPAQRDAYFAAFKDYLAQVYGQALAMYEGQEYRIEPAKPFADKSNLTIRVTIIDKNGRPPVRLDFQWRKNSKTGEWQAYDMIAEGVSMITTKQNEWSDILSAKGVDGLTKQLEISAKTPITLDEKK.";
executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.Code == proteinSeq).ToList();
executor.Execute();
// Output chrom data
//var wf = executor.TargetedWorkflow as TopDownTargetedWorkflow;
//Console.Write("***** chrom data *****\n");
//foreach (var resultData in wf.TargetResults)
//{
// int id = resultData.Key;
// TargetedResultBase result = resultData.Value;
// double chromPeakSelected = (result.ChromPeakSelected != null) ? result.ChromPeakSelected.XValue : -1;
// Console.Write("TargetID=" + id + "; ChromPeakSelected=" + chromPeakSelected + "\n");
// for (int i = 0; i < result.ChromValues.Xvalues.Length; i++)
// {
// //Console.Write(result.ChromValues.Xvalues[i] + "\t" + result.ChromValues.Yvalues[i] + "\n");
// }
// //Console.Write("\n");
//}
Console.Write("**********************\n");
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new UnlabelledTargetedResultFromTextImporter(expectedResultsFilename);
TargetedResultRepository repository = importer.Import();
Assert.AreEqual(1, repository.Results.Count);
//// expected results as tuples in format: <target id, charge state, scan lc>
//var expectedResults = new HashSet<Tuple<long, int, int>>
//{
// new Tuple<long, int, int>(1, 8, 1583),
// new Tuple<long, int, int>(2, 23, 2643),
// new Tuple<long, int, int>(3, 21, 1853),
// new Tuple<long, int, int>(4, 14, 2303),
// new Tuple<long, int, int>(5, 17, 2339),
// new Tuple<long, int, int>(6, 26, 4630),
// new Tuple<long, int, int>(7, 26, 3583),
// new Tuple<long, int, int>(8, 7, 3709),
// new Tuple<long, int, int>(9, 42, 3439),
//};
//foreach (TargetedResultDTO result in repository.Results)
//{
// expectedResults.Remove(new Tuple<long, int, int>(result.TargetID, result.ChargeState, result.ScanLC));
//}
//Assert.IsEmpty(expectedResults);
}
public override void Execute()
{
if (string.IsNullOrEmpty(ExecutorParameters.TargetsFilePath))
{
throw new ApplicationException("Processing failed. TargetsFilePath is empty. Check your parameter file.");
}
if (!File.Exists(ExecutorParameters.TargetsFilePath))
{
throw new FileNotFoundException("File not found error for the TargetsFilePath. Check your parameter file for " + ExecutorParameters.TargetsFilePath);
}
TargetedResultFromTextImporter resultImporter = new UnlabelledTargetedResultFromTextImporter(ExecutorParameters.TargetsFilePath);
var allresults = resultImporter.Import();
var resultsSortedByDataset = allresults.Results.OrderBy(p => p.DatasetName);
var totalResults = resultsSortedByDataset.Count();
ResultRepository.Clear();
//iterate over results
var resultCounter = 0;
foreach (var result in resultsSortedByDataset)
{
resultCounter++;
_currentResult = result;
if (result.DatasetName != _currentDatasetName)
{
if (Run != null)
{
Run.Close();
}
InitializeRun(result.DatasetName);
if (Run == null)
{
throw new ApplicationException("Error initializing dataset. (Run is null)");
}
_currentDatasetName = Run.DatasetName;
}
SetCurrentWorkflowTarget(result);
try
{
this.TargetedWorkflow.Execute();
ResultRepository.AddResult(this.TargetedWorkflow.Result);
}
catch (Exception ex)
{
var errorString = "Error on MT\t" + result.TargetID + "\tchargeState\t" + result.ChargeState + "\t" + ex.Message + "\t" + ex.StackTrace;
ReportProcessingProgress(errorString, resultCounter);
throw;
}
var progressString = "Processed " + resultCounter + " of " + totalResults;
if (_backgroundWorker != null)
{
if (_backgroundWorker.CancellationPending)
{
return;
}
}
ReportProcessingProgress(progressString, resultCounter);
}
}
public void Issue0725_AlignmentProblemsTest1()
{
var run = new RunFactory().CreateRun(@"D:\Data\Orbitrap\Issue0725_badAlignment\QC_Shew_10_03-2_100min_06May10_Tiger_10-04-08.RAW");
var alignmentFeaturesFile = run.Filename.Replace(".RAW", "_alignedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\MassTags\QCShew_Formic_MassTags_for_alignment.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var parameters = new NETAndMassAlignerParameters();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
var sb = new StringBuilder();
sb.Append("mtid\tscanLC\ttheorMZ\tobsMZ\talignedMZ\tppmErrorBefore\tppmErrorAfter\n");
parameters.MassCalibrationWindow = 50;
parameters.MassCalibrationNumMassDeltaBins = 100;
int[] massCalXSliceValues = { 3, 6, 9, 10, 12, 15,18,20 };
//int[] massCalXSliceValues = { 6 };
foreach (var xsliceVal in massCalXSliceValues)
{
var ppmErrorsBefore = new List<double>();
var ppmErrorsAfter = new List<double>();
parameters.MassCalibrationNumXSlices = (short)xsliceVal;
aligner.AlignerParameters = parameters;
aligner.Execute(run);
foreach (var result in repo.Results)
{
var mt = mtc.TargetList.Where(p => p.ID == result.TargetID).Where(p => p.ChargeState == result.ChargeState).First();
var theorMZ = mt.MZ;
var obsMZ = result.MonoMZ;
double scan = result.ScanLC;
var alignedMZ = run.GetAlignedMZ(obsMZ, scan);
var ppmErrorBefore = (theorMZ - obsMZ) / theorMZ * 1e6;
var ppmErrorAfter = (theorMZ - alignedMZ) / theorMZ * 1e6;
double theorNET = mt.NormalizedElutionTime;
double obsNET = result.NET;
var alignedNET = run.NetAlignmentInfo.GetNETValueForScan((int) scan);
sb.Append(result.TargetID + "\t" + result.ScanLC + "\t" + theorMZ.ToString("0.00000") + "\t" + obsMZ.ToString("0.00000") + "\t" + alignedMZ.ToString("0.00000") + "\t" + ppmErrorBefore.ToString("0.0") + "\t" + ppmErrorAfter.ToString("0.0") + "\t" + theorNET.ToString("0.0000") + "\t" + obsNET.ToString("0.0000") + "\t" + alignedNET.ToString("0.0000"));
//sb.Append(result.MassTagID + "\t" + result.ScanLC + "\t" + theo
sb.Append(Environment.NewLine);
ppmErrorsAfter.Add(ppmErrorAfter);
ppmErrorsBefore.Add(ppmErrorBefore);
}
// Console.WriteLine(sb.ToString());
//Console.WriteLine();
//Console.WriteLine();
//Console.WriteLine("Average ppm error before alignment = " + filterWithGrubbsApplied(ppmErrorsBefore).Average().ToString("0.00"));
//Console.WriteLine("Average ppm error after alignment = " + filterWithGrubbsApplied(ppmErrorsAfter).Average().ToString("0.00"));
//Console.WriteLine();
//Console.WriteLine();
Console.WriteLine(xsliceVal + "\t" + filterWithGrubbsApplied(ppmErrorsBefore).Average().ToString("0.00") + "\t" + filterWithGrubbsApplied(ppmErrorsAfter).Average().ToString("0.00"));
}
}
public void AlignmentParameterTesting1()
{
var run = new RunFactory().CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_READONLY_alignedFeatures.txt";
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_Formic_MassTags_Bin10_all.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var parameters = new NETAndMassAlignerParameters();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
var sb = new StringBuilder();
sb.Append("theorMZ\tobsMZ\talignedMZ\tppmErrorBefore\tppmErrorAfter\n");
parameters.MassCalibrationWindow = 50;
parameters.MassCalibrationNumMassDeltaBins = 100;
int[]massCalXSliceValues = {3,6,9,12,15,20,30,50};
foreach (var xsliceVal in massCalXSliceValues)
{
var ppmErrorsBefore = new List<double>();
var ppmErrorsAfter = new List<double>();
parameters.MassCalibrationNumXSlices =(short)xsliceVal;
aligner.AlignerParameters = parameters;
aligner.Execute(run);
foreach (var result in repo.Results)
{
var mt = mtc.TargetList.Where(p => p.ID == result.TargetID).Where(p => p.ChargeState == result.ChargeState).First();
var theorMZ = mt.MZ;
var obsMZ = result.MonoMZ;
double scan = result.ScanLC;
var alignedMZ = run.GetAlignedMZ(obsMZ, scan);
var ppmErrorBefore = (theorMZ - obsMZ) / theorMZ * 1e6;
var ppmErrorAfter = (theorMZ - alignedMZ) / theorMZ * 1e6;
sb.Append(result.TargetID + "\t" + result.ScanLC + "\t" + theorMZ.ToString("0.00000") + "\t" + obsMZ.ToString("0.00000") + "\t" + alignedMZ.ToString("0.00000") + "\t" + ppmErrorBefore.ToString("0.0") + "\t" + ppmErrorAfter.ToString("0.0"));
sb.Append(Environment.NewLine);
ppmErrorsAfter.Add(ppmErrorAfter);
ppmErrorsBefore.Add(ppmErrorBefore);
}
Console.WriteLine(xsliceVal + "\t" + ppmErrorsBefore.Average().ToString("0.00") + "\t"+ ppmErrorsAfter.Average().ToString("0.00"));
//Console.WriteLine(sb.ToString());
//Console.WriteLine();
//Console.WriteLine();
//Console.WriteLine("Average ppm error before alignment = " + ppmErrorsBefore.Average().ToString("0.00"));
//Console.WriteLine("Average ppm error after alignment = " + ppmErrorsAfter.Average().ToString("0.00"));
}
}
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 targetedWorkflow_withTargetedAlignment_test()
{
var executorParameterFile = baseFolder + @"\Parameters\QCShew_OrbiStandard_workflowExecutorParameters.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
var resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "Results");
var testDatasetPath = baseFolder + @"\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var testDatasetName = "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18";
var expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_results.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var rawFileInfo = new FileInfo(testDatasetPath);
var mzalignmentFile = Path.Combine(rawFileInfo.DirectoryName, testDatasetName + "_mzAlignment.txt");
var netAlignmentFile = Path.Combine(rawFileInfo.DirectoryName, testDatasetName + "_netAlignment.txt");
if (File.Exists(mzalignmentFile))
{
File.Delete(mzalignmentFile);
}
if (File.Exists(netAlignmentFile))
{
File.Delete(netAlignmentFile);
}
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new UnlabelledTargetedResultFromTextImporter(expectedResultsFilename);
var repository = importer.Import();
Assert.AreEqual(10, repository.Results.Count);
var result1 = repository.Results[0];
Assert.AreEqual(24702, result1.TargetID);
Assert.AreEqual(3, result1.ChargeState);
Assert.AreEqual(8627, result1.ScanLC);
//Assert.AreEqual(0.41724m, (decimal)Math.Round(result1.NET, 5));
//Assert.AreEqual(0.002534m, (decimal)Math.Round(result1.NETError, 6));
//Assert.AreEqual(2920.53082m, (decimal)Math.Round(result1.MonoMass, 5));
//Assert.AreEqual(2920.53879m, (decimal)Math.Round(result1.MonoMassCalibrated, 5));
//Assert.AreEqual(-2.33m, (decimal)Math.Round(result1.MassErrorInPPM, 2));
//Dataset MassTagID ChargeState Scan ScanStart ScanEnd NET NumChromPeaksWithinTol NumQualityChromPeaksWithinTol MonoisotopicMass MonoMZ IntensityRep FitScore IScore FailureType
//QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18 24702 3 8119 8112 8124 0.4172 2 1 2920.53082 974.51755 1379489 0.1136 0.0000
}
public void targetedWorkflow_noAlignment()
{
//TODO: fix test - it is using previous data for alignment
//TODO: make JIRA issue so we can see chromatogram, etc.
var executorParameterFile = baseFolder + @"\Parameters\QCShew_OrbiStandard_workflowExecutorParameters.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
var resultsFolderLocation = executorParameters.OutputFolderBase + "\\Results";
var testDatasetPath = baseFolder + @"\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var testDatasetName = "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18";
var expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_results.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var rawFileInfo = new FileInfo(testDatasetPath);
//delete alignment files
var mzalignmentFile = Path.Combine(rawFileInfo.DirectoryName, testDatasetName + "_mzAlignment.txt");
var netAlignmentFile = Path.Combine(rawFileInfo.DirectoryName, testDatasetName + "_netAlignment.txt");
if (File.Exists(mzalignmentFile))
{
File.Delete(mzalignmentFile);
}
if (File.Exists(netAlignmentFile))
{
File.Delete(netAlignmentFile);
}
executorParameters.TargetedAlignmentIsPerformed = false; //no targeted alignment
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new UnlabelledTargetedResultFromTextImporter(expectedResultsFilename);
var repository = importer.Import();
Assert.AreEqual(10, repository.Results.Count);
var result1 = repository.Results[0];
Assert.AreEqual(24702, result1.TargetID);
Assert.AreEqual(3, result1.ChargeState);
Assert.AreEqual(8637, result1.ScanLC);
//TODO: confirm/fix this NET value
//Assert.AreEqual(0.41724m, (decimal)Math.Round(result1.NET, 5));
// Assert.AreEqual(0.002534m, (decimal)Math.Round(result1.NETError, 6));
//Assert.AreEqual(974.52068m, (decimal)Math.Round(result1.MonoMZ, 5));
//Assert.AreEqual(2920.53082m, (decimal)Math.Round(result1.MonoMass, 5));
//Assert.AreEqual(2920.53733m, (decimal)Math.Round(result1.MonoMassCalibrated, 5));
//Assert.AreEqual(-1.83m, (decimal)Math.Round(result1.MassErrorInPPM, 2));
}
public void AlignmentParameterTesting2()
{
var run = new RunFactory().CreateRun(@"D:\Data\Orbitrap\Subissue01\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24.RAW");
var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\AlignmentInfo\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24_alignedFeatures.txt";
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_Formic_MassTags_Bin10_all.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var parameters = new NETAndMassAlignerParameters();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
var sb = new StringBuilder();
sb.Append("mtid\tscanLC\ttheorMZ\tobsMZ\talignedMZ\tppmErrorBefore\tppmErrorAfter\n");
parameters.MassCalibrationWindow = 20;
parameters.MassCalibrationNumMassDeltaBins = 100;
// int[] massCalXSliceValues = { 3, 6, 9, 12, 15 };
int[] massCalXSliceValues = { 15 };
foreach (var xsliceVal in massCalXSliceValues)
{
var ppmErrorsBefore = new List<double>();
var ppmErrorsAfter = new List<double>();
parameters.MassCalibrationNumXSlices = (short)xsliceVal;
aligner.AlignerParameters = parameters;
aligner.Execute(run);
foreach (var result in repo.Results)
{
var mt = mtc.TargetList.Where(p => p.ID == result.TargetID).Where(p => p.ChargeState == result.ChargeState).First();
var theorMZ = mt.MZ;
var obsMZ = result.MonoMZ;
double scan = result.ScanLC;
var alignedMZ = run.GetAlignedMZ(obsMZ, scan);
var ppmErrorBefore = (theorMZ - obsMZ) / theorMZ * 1e6;
var ppmErrorAfter = (theorMZ - alignedMZ) / theorMZ * 1e6;
sb.Append(result.TargetID + "\t" + result.ScanLC + "\t" + theorMZ.ToString("0.00000") + "\t" + obsMZ.ToString("0.00000") + "\t" + alignedMZ.ToString("0.00000") + "\t" + ppmErrorBefore.ToString("0.0") + "\t" + ppmErrorAfter.ToString("0.0"));
sb.Append(Environment.NewLine);
ppmErrorsAfter.Add(ppmErrorAfter);
ppmErrorsBefore.Add(ppmErrorBefore);
}
Console.WriteLine(sb.ToString());
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("Average ppm error before alignment = " + ppmErrorsBefore.Average().ToString("0.00"));
Console.WriteLine("Average ppm error after alignment = " + ppmErrorsAfter.Average().ToString("0.00"));
Console.WriteLine();
Console.WriteLine();
Console.WriteLine(xsliceVal + "\t" + ppmErrorsBefore.Average().ToString("0.00") + "\t" + ppmErrorsAfter.Average().ToString("0.00"));
}
}
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();
}
}
