public void cannotFindMassTag_test1()
{
//
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 26523;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.IsNull(result.IsotopicProfile);
Assert.IsNull(result.ScanSet);
Assert.IsNull(result.ChromPeakSelected);
Assert.IsTrue(result.FailedResult);
Assert.AreEqual(DeconTools.Backend.Globals.TargetedResultFailureType.ChrompeakNotFoundWithinTolerances, result.FailureType);
}
public void testVladsData()
{
var testFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2_First60.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndAlignRun(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24653;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.MSToleranceInPPM = 10;
parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromatogramCorrelationIsPerformed = true;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as O16O18TargetedResultObject;
Assert.IsTrue(workflow.Success);
Assert.IsFalse(result.FailedResult);
result.DisplayToConsole();
Console.WriteLine("Correlation between 016 and O18(double label)= " + result.ChromCorrO16O18DoubleLabel);
Assert.IsTrue(result.ChromCorrO16O18DoubleLabel > 0);
Console.WriteLine("theor monomass= \t" + result.Target.MonoIsotopicMass);
Console.WriteLine("monomass= \t" + result.IsotopicProfile.MonoIsotopicMass);
Console.WriteLine("ppmError before= \t" + result.MassErrorBeforeAlignment);
Console.WriteLine("ppmError after= \t" + result.MassErrorAfterAlignment);
}
public void IqWorkflowTest1()
{
//see https://jira.pnnl.gov/jira/browse/OMCS-709
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
var oldStyleTarget = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
parameters.ChromSmootherNumPointsInSmooth = 9;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromPeakDetectorSigNoise = 1;
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.ID = oldStyleTarget.ID;
target.MZTheor = oldStyleTarget.MZ;
target.ElutionTimeTheor = oldStyleTarget.NormalizedElutionTime;
target.MonoMassTheor = oldStyleTarget.MonoIsotopicMass;
target.EmpiricalFormula = oldStyleTarget.EmpiricalFormula;
target.ChargeState = oldStyleTarget.ChargeState;
Console.WriteLine(target.EmpiricalFormula + "\t" + target.ChargeState);
target.DoWorkflow();
var result = target.GetResult();
Assert.IsNotNull(result, "result is null");
var reportString = result.ToStringWithDetailedReport();
Console.WriteLine(reportString);
}
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 WorkflowTest1()
{
//GORD: 3/18/2013 - this test is broken. We need to fix the N14N15 workflow and get this to pass
// See: https://jira.pnnl.gov/jira/browse/OMCS-409
var run = RunUtilities.CreateAndAlignRun(bruker9t_samplefile1, bruker9t_peaksfile1);
var targetsFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Targets\POnly_MassTagsMatchingInHalfOfDatasets_Filtered0.45-0.47NET_first18.txt";
var importer = new MassTagFromTextFileImporter(targetsFile);
var targetCollection = importer.Import();
run.CurrentMassTag = targetCollection.TargetList.FirstOrDefault(p => p.ChargeState == 1);
var parameters = new N14N15Workflow2Parameters();
parameters.LoadParameters(Path.Combine(FileRefs.ImportedData, "importedN14N15WorkflowParameters.xml"));
parameters.ChromGenTolerance = 25;
parameters.MSToleranceInPPM = 25;
parameters.TargetedFeatureFinderToleranceInPPM = 25;
parameters.MultipleHighQualityMatchesAreAllowed = true;
parameters.NumMSScansToSum = 5;
parameters.SaveParametersToXML(
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Parameters\N14N15WorkflowParameters1_test.xml");
Console.WriteLine(parameters.ToStringWithDetails());
var workflow = new N14N15Workflow2(run, parameters);
workflow.Execute();
Assert.IsTrue(run.ResultCollection.ResultType == Globals.ResultType.N14N15_TARGETED_RESULT);
//TestUtilities.DisplayXYValues(workflow.ChromatogramXYData);
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as N14N15_TResult;
result.DisplayToConsole();
Assert.AreEqual(23085448, result.Target.ID);
Assert.AreEqual(1, result.IsotopicProfile.ChargeState);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.IsNotNull(result.ChromPeakSelectedN15);
return;
Assert.AreEqual(1639.3m, (decimal)Math.Round(result.ChromPeakSelected.XValue, 1));
Assert.AreEqual(1638.5m, (decimal)Math.Round(result.ChromPeakSelectedN15.XValue, 1));
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.IsotopicProfileLabeled);
Console.WriteLine("theor monomass= \t" + result.Target.MonoIsotopicMass);
Console.WriteLine("monomass= \t" + result.IsotopicProfile.MonoIsotopicMass);
Console.WriteLine("monomassN15= \t" + result.IsotopicProfileLabeled.MonoIsotopicMass);
Console.WriteLine("monoMZ= \t" + result.IsotopicProfile.MonoPeakMZ);
Console.WriteLine("monoMZN15= \t" + result.IsotopicProfileLabeled.MonoPeakMZ);
Console.WriteLine("ppmError= \t" + result.MassErrorAfterAlignment);
Console.WriteLine("Database NET= " + result.Target.NormalizedElutionTime);
Console.WriteLine("Result NET= " + result.GetNET());
Console.WriteLine("Result NET Error= " + result.GetNETAlignmentError());
Console.WriteLine("NumChromPeaksWithinTol= " + result.NumChromPeaksWithinTolerance);
Console.WriteLine("NumChromPeaksWithinTolN15= " + result.NumChromPeaksWithinToleranceForN15Profile);
}
public void findSingleMassTag_test1()
{
//see https://jira.pnnl.gov/jira/browse/OMCS-709
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
parameters.ChromSmootherNumPointsInSmooth = 9;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromPeakDetectorSigNoise = 1;
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
Assert.IsNotNull(workflow.ChromatogramXYData, "Chrom XY data is empty");
Assert.IsNotEmpty(workflow.ChromPeaksDetected, "Chrom peaks are empty");
Console.WriteLine("Chrom peaks detected");
foreach (var chromPeak in workflow.ChromPeaksDetected)
{
Console.WriteLine(chromPeak.XValue.ToString("0.0") + "\t" + chromPeak.Height.ToString("0") + "\t" +
chromPeak.Width.ToString("0.0"));
}
Assert.AreEqual(3, workflow.ChromPeaksDetected.Count);
Assert.IsNotNull(workflow.ChromPeakSelected, "No chrom peak was selected");
Assert.IsNotNull(workflow.MassSpectrumXYData, "Mass spectrum for selected chrom peak was not generated");
//TestUtilities.DisplayXYValues(workflow.MassSpectrumXYData);
//TestUtilities.DisplayXYValues(workflow.ChromatogramXYData);
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
if (result.FailedResult)
{
Console.WriteLine(result.ErrorDescription);
}
Assert.IsFalse(result.FailedResult);
// result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
Assert.AreEqual(718.41m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2));
Assert.AreEqual(5939, (decimal)Math.Round(result.ChromPeakSelected.XValue));
Assert.IsNotNull(result.ChromCorrelationData);
foreach (var dataItem in result.ChromCorrelationData.CorrelationDataItems)
{
Console.WriteLine(dataItem);
}
}
public void IqExportResultsTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-832
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
var oldStyleTarget = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
parameters.ChromSmootherNumPointsInSmooth = 9;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromPeakDetectorSigNoise = 1;
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.ID = oldStyleTarget.ID;
target.MZTheor = oldStyleTarget.MZ;
target.ElutionTimeTheor = oldStyleTarget.NormalizedElutionTime;
target.MonoMassTheor = oldStyleTarget.MonoIsotopicMass;
target.EmpiricalFormula = oldStyleTarget.EmpiricalFormula;
target.ChargeState = oldStyleTarget.ChargeState;
var targets = new List <IqTarget>(1);
targets.Add(target);
var executor = new IqExecutor(executorBaseParameters, run);
//executor.ChromSourceDataFilePath = peaksTestFile;
executor.Execute(targets);
Assert.IsTrue(File.Exists(@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Results\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_iqResults.txt"));
using (var reader = new StreamReader(@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Results\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_iqResults.txt"))
{
var temp = reader.ReadLine();
Assert.AreEqual(
"TargetID\tCode\tEmpiricalFormula\tChargeState\tMonomassTheor\tMZTheor\tElutionTimeTheor\tMonoMassObs\tMZObs\tElutionTimeObs\tChromPeaksWithinTolerance\tScan\tAbundance\tIsoFitScore\tInterferenceScore",
temp);
temp = reader.ReadLine();
Console.WriteLine(temp);
Assert.AreEqual(
"24800\t\tC64H110N18O19\t2\t1434.8193888\t718.41697089\t0.321639209985733\t1434.81096195126\t718.412757465632\t0.318046778440475\t0\t5942\t1352176\t0.0850492709063084\t0.0942918054560866",
temp);
}
}