public void findFeatureIn_dataset_with_bad_massCalibration_test1()
        {
            //mass error in this dataset is typically ~50ppm.

            var datasetFile = @"D:\Data\Orbitrap\Subissue01\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24.RAW";

            var massTagFile           = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\MassTags\QCShew_Formic_MassTags_Bin10_first10.txt";
            var workflowParameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\UnlabelledTargeted_WorkflowParameters_noSum.xml";


            var run = RunUtilities.CreateAndLoadPeaks(datasetFile, datasetFile.Replace(".RAW", "_peaks.txt"));

            RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);

            Assert.IsTrue(run.MassIsAligned);
            Assert.IsTrue(run.NETIsAligned);


            var parameters = new BasicTargetedWorkflowParameters();

            parameters.LoadParameters(workflowParameterFile);
            var workflow = new BasicTargetedWorkflow(parameters);


            workflow.Run = run;

            var mtc        = new TargetCollection();
            var mtimporter = new MassTagFromTextFileImporter(massTagFile);

            mtc = mtimporter.Import();

            var mt1 = (from n in mtc.TargetList where n.ID == 24702 && n.ChargeState == 4 select n).First();

            run.CurrentMassTag = mt1;

            workflow.Execute();

            var repo = new TargetedResultRepository();

            repo.AddResult(workflow.Result);


            Console.WriteLine("theor mono mass = " + mt1.MonoIsotopicMass);
            Console.WriteLine("theorMZ = " + mt1.MZ);
            Console.WriteLine("theorNET = " + mt1.NormalizedElutionTime);
            Console.WriteLine("obsScan = " + repo.Results[0].ScanLC);
            Console.WriteLine("obsNET = " + repo.Results[0].NET);
            Console.WriteLine("NETError = " + repo.Results[0].NETError);
            Console.WriteLine("obsMZ = " + repo.Results[0].MonoMZ);
            Console.WriteLine("monoMass = " + repo.Results[0].MonoMass);
            Console.WriteLine("obsMonoMassCalibrated = " + repo.Results[0].MonoMassCalibrated);

            Console.WriteLine("MassErrorBeforeAlignment = " + (mt1.MZ - repo.Results[0].MonoMZ) / mt1.MZ * 1e6);
            Console.WriteLine("MassErrorAfterAlignment = " + repo.Results[0].MassErrorBeforeCalibration);
        }
        public void importParametersTest2()
        {
            var importedParametersFile = Path.Combine(FileRefs.ImportedData, "importedParameters_MostIntenseChromPeakSelection.xml");

            var parameters = new BasicTargetedWorkflowParameters();

            parameters.LoadParameters(importedParametersFile);

            Assert.AreEqual("BASIC_TARGETED_RESULT", parameters.ResultType.ToString());
            Assert.AreEqual("MostIntense", parameters.ChromPeakSelectorMode.ToString());
        }
Ejemplo n.º 3
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        public void ChromPeakAnalyzerWorkflowWrongTargetTest()
        {
            //Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884

            var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
            var run      = new RunFactory().CreateRun(testFile);
            TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
            IqTarget testTarget = new IqChargeStateTarget();

            testTarget.SetWorkflow(new ChromPeakAnalyzerIqWorkflow(run, parameters));
            testTarget.DoWorkflow();
        }
        public void parameterFileImportTest1()
        {
            var parameters = new BasicTargetedWorkflowParameters();

            var importTestFile =
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Parameters\BasicTargetedWorkflowParameters1_forImportTesting.xml";

            parameters.LoadParameters(importTestFile);

            //TODO: complete testing of other values
            Assert.AreEqual(parameters.ChromGenToleranceUnit, Globals.ToleranceUnit.MZ);
            Assert.AreEqual(0.01, parameters.ChromGenTolerance);
        }
        public void targetedWorkflow_alignUsingDataFromFiles_localVersion()
        {
            //TODO: figure out result is correct
            //TODO: get MS and Chrom in Jira
            var executorParameters = new BasicTargetedWorkflowExecutorParameters();

            executorParameters.TargetsFilePath =
                @"C:\Users\d3x720\Documents\Data\QCShew\IQ\QCShew_Formic_MassTags_Bin10_MT24702_Z3.txt";
            executorParameters.TargetedAlignmentIsPerformed = true;

            var workflowParameters = new BasicTargetedWorkflowParameters();

            workflowParameters.ChromSmootherNumPointsInSmooth = 9;
            workflowParameters.ChromPeakDetectorPeakBR        = 1;
            workflowParameters.ChromPeakDetectorSigNoise      = 1;
            workflowParameters.ChromGenTolerance = 20;
            workflowParameters.ChromNETTolerance = 0.025;
            workflowParameters.MSToleranceInPPM  = 20;

            var workflow = new BasicTargetedWorkflow(workflowParameters);

            var testDatasetPath =
                @"C:\Users\d3x720\Documents\Data\QCShew\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";

            TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, workflow, testDatasetPath);

            executor.Execute();

            var expectedResultsFilename =
                @"C:\Users\d3x720\Documents\Data\QCShew\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_results.txt";


            var result = executor.TargetedWorkflow.Result;

            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);

            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);

            //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
        }
Ejemplo n.º 6
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        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 exportParametersTest1()
        {
            var exportedParametersFile = Path.Combine(FileRefs.OutputFolderPath, "exportedBasicTargetedWorkflowParameters.xml");

            if (File.Exists(exportedParametersFile))
            {
                File.Delete(exportedParametersFile);
            }


            var parameters = new BasicTargetedWorkflowParameters();

            parameters.SaveParametersToXML(exportedParametersFile);

            Assert.That(File.Exists(exportedParametersFile), "Parameter file doesn't exist: " + exportedParametersFile);
        }
        public void InvestigateIQFailures()
        {
            var executorParamFile =
                @"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Parameters\ExecutorParameters1 - Copy.xml";

            var executorParameters =
                new BasicTargetedWorkflowExecutorParameters();

            executorParameters.LoadParameters(executorParamFile);

            var testFile =
                @"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Testing\LNA_A_Expo_Sample_SC_9_LNA_ExpA_Expo_Stat_SeattleBioMed_15Feb13_Cougar_12-12-35.raw";
            var run = new RunFactory().CreateRun(testFile);


            var iqparameterFile =
                @"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Testing\IQWorkflowParameters1.xml";

            var workflowParameters = new BasicTargetedWorkflowParameters();

            workflowParameters.LoadParameters(iqparameterFile);
            workflowParameters.MSToleranceInPPM          = 10;
            workflowParameters.ChromPeakDetectorPeakBR   = 0.25;
            workflowParameters.ChromPeakDetectorSigNoise = 2;

            var targetedWorkflow = new BasicTargetedWorkflow(run, workflowParameters);
            var executor         = new BasicTargetedWorkflowExecutor(executorParameters, targetedWorkflow, testFile);

            //int[] testTargets = {349959971, 349951038,349954483 };
            //int[] testTargets = { 349951038 };

            //int[] testTargets = { 349954483 };
            //int[] testTargets = { 2911730 };

            int[] testTargets = { 349946881 };
            var   chargeState = 3;

            executor.Targets.TargetList = (from n in executor.Targets.TargetList where testTargets.Contains(n.ID) select n).ToList();
            executor.Targets.TargetList = (from n in executor.Targets.TargetList where n.ChargeState == chargeState select n).ToList();

            executor.Execute();

            //Results of investiga  tion!  -  349959971 was being missed because the MSTolerance was too narrow. When changed from 5 to 6, it was found. I think we can safely set this at 10.
            //Results of investigation!  -  349951038 was being missed because it was being flagged (peak to the left) problem.

            TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
        }
Ejemplo n.º 9
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        public void featuresLoadedFromFile_test1()
        {
            RunFactory rf  = new RunFactory();
            Run        run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);

            string massTagFile          = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
            string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt";

            DeconToolsTargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();

            TargetedAligner aligner = new TargetedAligner(run, parameters);

            aligner.SetMassTags(massTagFile);
            aligner.ImportedFeaturesFilename = deconToolsResultFile;

            aligner.Execute();
        }
Ejemplo n.º 10
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        public void ProblemTesting_correlationProb1()
        {
            //see JIRA https://jira.pnnl.gov/jira/browse/OMCS-628


            var executorParameters = new BasicTargetedWorkflowExecutorParameters();

            var testDatasetPath =
                @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1B_8Apr13_Cougar_13-03-25.raw";

            executorParameters.IsMassAlignmentPerformed = true;
            executorParameters.IsNetAlignmentPerformed  = true;

            executorParameters.ReferenceTargetsFilePath =
                @"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set3_P892_targets.txt";

            var run      = new RunFactory().CreateRun(testDatasetPath);
            var executor = new IqExecutor(executorParameters, run);

            var targetsFile =
                @"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set3_P892_targets.txt";

            executor.LoadAndInitializeTargets(targetsFile);
            executor.SetupMassAndNetAlignment();

            var testTarget = 6955012;

            executor.Targets = (from n in executor.Targets where n.ID == testTarget select n).ToList();

            var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();

            targetedWorkflowParameters.LoadParameters(@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Parameters\O16O18WorkflowParameters_2011_08_23_sum5.xml");

            //define workflows for parentTarget and childTargets
            var parentWorkflow = new O16O18ParentIqWorkflow(run, targetedWorkflowParameters);
            var childWorkflow  = new O16O18IqWorkflow(run, targetedWorkflowParameters);

            var workflowAssigner = new IqWorkflowAssigner();

            workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
            workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);

            executor.DoAlignment();
            executor.Execute();
        }
Ejemplo n.º 11
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        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 findSingleMassTag_checkAlignmentData_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.CreateAndLoadPeaks(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();
            var workflow = new BasicTargetedWorkflow(run, parameters);

            workflow.Execute();

            var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;

            Assert.AreEqual(false, 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(5947m, (decimal)Math.Round(result.ChromPeakSelected.XValue));


            Assert.AreEqual(5.91, (decimal)(Math.Round(result.GetMassErrorAfterAlignmentInPPM(), 2)));
            Assert.AreEqual(0.0001585m, (decimal)(Math.Round(result.GetNETAlignmentError(), 7)));

            RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);

            //these might change due to unit tests elsewhere. Need a better way of doing this
            //Assert.AreEqual(1.99290383722318m, (decimal)result.GetMassErrorAfterAlignmentInPPM());
            //Assert.AreEqual(0.00076708197593689m, (decimal)result.GetNETAlignmentError());
        }
Ejemplo n.º 13
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        public void ChromPeakAnalyzerWorkflowTest()
        {
            //Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884

            var testFile      = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
            var peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
            var run           = new RunFactory().CreateRun(testFile);
            TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
            var testTarget = new ChromPeakIqTarget();
            ITheorFeatureGenerator TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);

            var testPeak = new ChromPeak(5184, 840963, 50, 0);

            var executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
            var executor = new TopDownMSAlignExecutor(executorBaseParameters, run);

            executor.ChromSourceDataFilePath = peaksTestFile;

            var workflow = new ChromPeakAnalyzerIqWorkflow(run, parameters);

            testTarget.SetWorkflow(workflow);

            testTarget.ID                   = 1;
            testTarget.Code                 = "NGIIMMENR";
            testTarget.EmpiricalFormula     = "C43H76N14O14S2";
            testTarget.MonoMassTheor        = 1076.510631;
            testTarget.ChromPeak            = testPeak;
            testTarget.ChargeState          = 1;
            testTarget.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(testTarget.EmpiricalFormula, testTarget.ChargeState);

            var      testTargetList = new List <IqTarget>();
            IqTarget testParent     = new IqChargeStateTarget();

            testParent.AddTarget(testTarget);
            testTargetList.Add(testTarget);

            executor.Execute(testTargetList);

            var result = testTarget.GetResult();

            Assert.NotNull(result.LCScanSetSelected);
            Assert.AreNotEqual(1, result.FitScore);
            Assert.AreEqual(true, result.IsotopicProfileFound);
        }
        public void findSingleModifiedMassTagTest1()
        {
            var testFile      = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
            var peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
            var massTagFile   = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";

            var run        = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
            var mtc        = new TargetCollection();
            var mtimporter = new MassTagFromTextFileImporter(massTagFile);

            mtc = mtimporter.Import();

            var testMassTagID = 189685150;

            run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();

            Assert.AreEqual(true, run.CurrentMassTag.ContainsMods);

            TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();

            parameters.ChromatogramCorrelationIsPerformed = true;

            var workflow = new BasicTargetedWorkflow(run, parameters);

            workflow.Execute();

            var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;

            Assert.AreEqual(false, result.FailedResult);

            result.DisplayToConsole();

            Assert.IsNotNull(result.IsotopicProfile);
            Assert.IsNotNull(result.ScanSet);
            Assert.IsNotNull(result.ChromPeakSelected);
            Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
            Assert.AreEqual(959.48m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2));
            //Assert.AreEqual(6070, (decimal)Math.Round(result.ChromPeakSelected.XValue));

            foreach (var dataItem in result.ChromCorrelationData.CorrelationDataItems)
            {
                Console.WriteLine(dataItem);
            }
        }
Ejemplo n.º 15
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        public void createPeaksTest1()
        {
            var testFile =
                @"D:\Data\Orbitrap\BrianIQTesting\QC_Shew_11_02_pt5-b_6Jun11_Sphinx_11-03-27.RAW";
            var run = new RunFactory().CreateRun(testFile);

            var parameters = new PeakDetectAndExportWorkflowParameters();
            TargetedWorkflowParameters deconParam = new BasicTargetedWorkflowParameters();

            deconParam.ChromGenSourceDataPeakBR = 3;


            parameters.PeakBR            = deconParam.ChromGenSourceDataPeakBR;
            parameters.PeakFitType       = DeconTools.Backend.Globals.PeakFitType.QUADRATIC;
            parameters.SigNoiseThreshold = deconParam.ChromGenSourceDataSigNoise;
            var peakCreator = new PeakDetectAndExportWorkflow(run, parameters);

            peakCreator.Execute();
        }
        public void TargetedWorkflowUsingMsgfInputsTest1()
        {
            var executorParameters = new BasicTargetedWorkflowExecutorParameters();

            executorParameters.TargetsFilePath =
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\Yellow_C13_070_23Mar10_Griffin_10-01-28_msgfplus.tsv";

            executorParameters.TargetedAlignmentIsPerformed = false;


            executorParameters.SaveParametersToXML(
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\IQConsoleDemo\IqExecutorParameters.xml");



            var workflowParameters = new BasicTargetedWorkflowParameters();

            workflowParameters.ChromSmootherNumPointsInSmooth = 9;
            workflowParameters.ChromPeakDetectorPeakBR        = 1;
            workflowParameters.ChromPeakDetectorSigNoise      = 3;
            workflowParameters.ChromGenTolerance = 20;
            workflowParameters.ChromNETTolerance = 0.025;
            workflowParameters.MSToleranceInPPM  = 20;

            workflowParameters.SaveParametersToXML(
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\IQConsoleDemo\IqWorkflowParameters.xml");


            var workflow = new BasicTargetedWorkflow(workflowParameters);



            var testDatasetPath =
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw";

            TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, workflow, testDatasetPath);

            executor.Targets.TargetList = executor.Targets.TargetList.Take(10).ToList();

            executor.Execute();
        }
        public void LocalQCShewProcessingTest1()
        {
            var parameterFileName = @"C:\Users\d3x720\Documents\Data\QCShew\IQ\IQExecutorParameterFile1.xml";

            var executorParameters = new BasicTargetedWorkflowExecutorParameters();

            executorParameters.TargetsFilePath =
                @"C:\Users\d3x720\Documents\Data\QCShew\IQ\QCShew_Formic_MassTags_Bin10_first10.txt";

            executorParameters.SaveParametersToXML(parameterFileName);


            var workflowParameters = new BasicTargetedWorkflowParameters();


            var workflow = new BasicTargetedWorkflow(workflowParameters);

            var testDatasetPath =
                @"C:\Users\d3x720\Documents\Data\QCShew\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
            TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, workflow,
                                                                                  testDatasetPath);
            var testTargetID = 24749;
            var testTargetZ  = 3;



            executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.ID == testTargetID &&
                                                                            p.ChargeState == testTargetZ).ToList();

            executor.Execute();


            //TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);

            foreach (var chrompeak in executor.TargetedWorkflow.ChromPeaksDetected)
            {
                Console.WriteLine(chrompeak.XValue.ToString("0.0000") + "\t" + chrompeak.Height.ToString("0") + "\t" + chrompeak.Width.ToString("0.000") + "\n");
            }
        }
Ejemplo n.º 18
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        public void ensure_alignmentIsBeingUsed_duringProcessing_test2()
        {
            var massTagFile              = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
            var mzAlignmentInfoFilename  = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16_MZAlignment.txt";
            var NETAlignmentInfoFilename = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16_NETAlignment.txt";
            var rawDataFile              = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16.RAW";
            var peaksDataFile            = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16_peaks.txt";

            var run = DeconTools.Backend.Utilities.RunUtilities.CreateAndLoadPeaks(rawDataFile, peaksDataFile);


            var importer          = new MassAlignmentInfoFromTextImporter(mzAlignmentInfoFilename);
            var massAlignmentData = importer.Import();

            var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();

            massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
            run.MassAlignmentInfo = massAlignmentInfo;

            var mtc        = new TargetCollection();
            var mtimporter = new MassTagFromTextFileImporter(massTagFile);

            mtc = mtimporter.Import();

            var testMassTagID = 24730;

            run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();

            //first will execute workflow on a dataset that was NOT aligned

            TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();

            parameters.ChromNETTolerance = 0.2;   //use a very wide tolerance
            parameters.ChromGenTolerance = 5;
            parameters.MSToleranceInPPM  = 15;

            var workflow = new BasicTargetedWorkflow(run, parameters);

            workflow.Execute();

            var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);

            Assert.IsTrue(result.ChromPeakSelected != null);
            Assert.AreEqual(9367, (int)result.ChromPeakSelected.XValue);


            var netDiff = result.Target.NormalizedElutionTime - result.GetNET();

            Console.WriteLine("NET diff before alignment = " + netDiff);

            var expectedNETDiff = 0.071m;

            Assert.AreEqual(expectedNETDiff, (decimal)Math.Round(netDiff, 3));


            //import NET alignment information
            var netAlignmentInfoImporter = new NETAlignmentFromTextImporter(NETAlignmentInfoFilename);
            var scanNETdata = netAlignmentInfoImporter.Import();

            run.NetAlignmentInfo.SetScanToNETAlignmentData(scanNETdata);

            parameters = new BasicTargetedWorkflowParameters();
            parameters.ChromNETTolerance = 0.01;   //use a more narrow tolerance
            parameters.ChromGenTolerance = 5;
            parameters.MSToleranceInPPM  = 15;

            workflow = new BasicTargetedWorkflow(run, parameters);
            workflow.Execute();


            netDiff = result.Target.NormalizedElutionTime - result.GetNET();
            Console.WriteLine("NET diff after alignment = " + netDiff);


            Assert.IsTrue(result.ChromPeakSelected != null);

            var expectedNETDiffMaximum = 0.01;

            Assert.IsTrue(netDiff < expectedNETDiffMaximum);
        }
        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 findSingleMassTag_alternateQCShew()
        {
            var testFile      = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16.RAW";
            var peaksTestFile = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16_peaks.txt";
            var massTagFile   = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16_peakMatchedFeatures.txt";


            var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);


            var mtc        = new TargetCollection();
            var mtimporter = new MassTagFromTextFileImporter(massTagFile);

            mtc = mtimporter.Import();

            var testMassTagID = 24709;

            run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 4 select n).First();


            TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();

            parameters.ChromNETTolerance = 0.2;
            parameters.MSToleranceInPPM  = 25;
            parameters.ChromatogramCorrelationIsPerformed = true;

            var workflow = new BasicTargetedWorkflow(run, parameters);

            workflow.Execute();

            var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;

            result.DisplayToConsole();

            Assert.IsNotNull(result.IsotopicProfile);
            Assert.IsNotNull(result.ScanSet);
            Assert.IsNotNull(result.ChromPeakSelected);
            Assert.AreEqual(4, result.IsotopicProfile.ChargeState);



            // Assert.AreEqual(610.81m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2));
            //Assert.AreEqual(6483, (decimal)Math.Round(result.ChromPeakSelected.XValue));


            double maxIntensity = result.IsotopicProfile.Peaklist.Max(p => p.Height);

            for (var i = 0; i < result.IsotopicProfile.Peaklist.Count; i++)
            {
                double correctedRatio = 0;
                if (i < result.ChromCorrelationData.CorrelationDataItems.Count)
                {
                    var correlationSlope = result.ChromCorrelationData.CorrelationDataItems[i].CorrelationSlope;
                    if (correlationSlope != null)
                    {
                        correctedRatio = (double)correlationSlope;
                    }
                }
                else
                {
                    correctedRatio = 0;
                }

                var observedRelIntensity = result.IsotopicProfile.Peaklist[i].Height / maxIntensity;

                Console.WriteLine(i + "\t" + observedRelIntensity + "\t" + correctedRatio);
            }
        }
Ejemplo n.º 21
0
        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);
        }
Ejemplo n.º 22
0
        public override void LoadAndInitializeTargets(string targetsFilePath)
        {
            if (string.IsNullOrEmpty(targetsFilePath))
            {
                IqLogger.Log.Info("IqMassAndNetAligner - no alignment targets were loaded. The inputted targets file path is NULL.");
                return;
            }

            if (!File.Exists(targetsFilePath))
            {
                IqLogger.Log.Info("IqMassAndNetAligner - no alignment targets were loaded. The inputted targets file path is does not exist.");
                return;
            }

            var importer = new IqTargetsFromFirstHitsFileImporter(targetsFilePath);

            Targets = importer.Import().Where(p => p.QualityScore < 0.01).OrderBy(p => p.ID).ToList();

            //Targets = Targets.Where(p => p.Code.Contains("FEQDGENYTGTIDGNMGAYAR")).ToList();

            var filteredList = new List <IqTarget>();

            //calculate empirical formula for targets using Code and then monoisotopic mass

            foreach (var iqTarget in Targets)
            {
                iqTarget.Code = _peptideUtils.CleanUpPeptideSequence(iqTarget.Code);

                if (_peptideUtils.ValidateSequence(iqTarget.Code))
                {
                    iqTarget.EmpiricalFormula = _peptideUtils.GetEmpiricalFormulaForPeptideSequence(iqTarget.Code, true, true);
                    var calcMonoMass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(iqTarget.EmpiricalFormula);
                    var monoMassFromFirstHitsFile = iqTarget.MonoMassTheor;

                    var massCalculationsAgree = Math.Abs(monoMassFromFirstHitsFile - calcMonoMass) < 0.02;
                    if (massCalculationsAgree)
                    {
                        iqTarget.MonoMassTheor    = calcMonoMass;
                        iqTarget.ElutionTimeTheor = iqTarget.ScanLC / (double)Run.MaxLCScan;

                        filteredList.Add(iqTarget);
                        _targetUtilities.UpdateTargetMissingInfo(iqTarget, true);

                        var chargeStateTarget = new IqTargetMsgfFirstHit();

                        _targetUtilities.CopyTargetProperties(iqTarget, chargeStateTarget);

                        iqTarget.AddTarget(chargeStateTarget);
                    }
                }
            }

            filteredList = (from n in filteredList
                            group n by new
            {
                n.Code,
                n.ChargeState
            }
                            into grp
                            select grp.OrderBy(p => p.QualityScore).First()
                            ).ToList();


            Targets = filteredList;

            TargetedWorkflowParameters workflowParameters = new BasicTargetedWorkflowParameters();

            workflowParameters.ChromNETTolerance = 0.005;
            workflowParameters.ChromGenTolerance = 50;

            //define workflows for parentTarget and childTargets
            var parentWorkflow = new ChromPeakDeciderIqWorkflow(Run, workflowParameters);
            var childWorkflow  = new ChargeStateChildIqWorkflow(Run, workflowParameters);

            var workflowAssigner = new IqWorkflowAssigner();

            workflowAssigner.AssignWorkflowToParent(parentWorkflow, Targets);
            workflowAssigner.AssignWorkflowToChildren(childWorkflow, Targets);


            if (Targets.Count > 0)
            {
                IqLogger.Log.Info("IqMassAndNetAligner - Loaded " + Targets.Count + " targets for use in mass and net alignment");
            }
            else
            {
                IqLogger.Log.Info("IqMassAndNetAligner - NOTE - no targets have been loaded.");
            }



            //IqWorkflowAssigner workflowAssigner = new IqWorkflowAssigner();
            //workflowAssigner.AssignWorkflowToParent(workflow, Targets);
        }
        public void HemePeptidesProcessingTest1()
        {
            var executorParameters = new BasicTargetedWorkflowExecutorParameters();

            executorParameters.TargetsFilePath =
                @"\\protoapps\DataPkgs\Public\2013\686_IQ_analysis_of_heme_peptides\Targets\SL-MtoA_peptides_formulas.txt";


            var testDatasetPath = @"D:\Data\From_EricMerkley\HisHemeSL-MtrA_002_2Feb11_Sphinx_10-12-01.RAW";



            var workflowParameters = new BasicTargetedWorkflowParameters();

            workflowParameters.ChromNETTolerance = 0.5;
            workflowParameters.ChromSmootherNumPointsInSmooth = 9;

            var workflow = new BasicTargetedWorkflow(workflowParameters);



            TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, workflow, testDatasetPath);


            var testTargetID = 1950;
            var testTargetZ  = 3;

            testTargetID = 240;
            testTargetZ  = 4;

            testTargetID = 359;
            testTargetZ  = 3;

            testTargetID = 750;
            testTargetZ  = 5;


            executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.ID == testTargetID &&
                                                                            p.ChargeState == testTargetZ).ToList();

            //executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.ID == testTargetID).ToList();

            executor.InitializeRun(testDatasetPath);
            executor.Run.CurrentMassTag = executor.Targets.TargetList.First();
            double[] chromParamValues = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 25 };

            //chromPeakBRValues =new double[] {10,15,25};

            foreach (var value in chromParamValues)
            {
                var parameters = executor.TargetedWorkflow.WorkflowParameters as BasicTargetedWorkflowParameters;
                parameters.ChromPeakDetectorPeakBR   = 5;
                parameters.ChromPeakDetectorSigNoise = value;

                executor.TargetedWorkflow = new BasicTargetedWorkflow(executor.Run, parameters);

                executor.TargetedWorkflow.Execute();

                Console.WriteLine("PeakBR=" + value + " num chrom peaks= " + executor.TargetedWorkflow.ChromPeaksDetected.Count);
                foreach (var chrompeak in executor.TargetedWorkflow.ChromPeaksDetected)
                {
                    Console.WriteLine(chrompeak.XValue.ToString("0.0000") + "\t" + chrompeak.Height.ToString("0") + "\t" + chrompeak.Width.ToString("0.000"));
                }
            }



            foreach (var chrompeak in executor.TargetedWorkflow.ChromPeaksDetected)
            {
                Console.WriteLine(chrompeak.XValue.ToString("0.0000") + "\t" + chrompeak.Height.ToString("0") + "\t" + chrompeak.Width.ToString("0.000"));
            }

            Console.WriteLine();
            Console.WriteLine();

            //TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
            //TestUtilities.DisplayIsotopicProfileData(executor.TargetedWorkflow.Result.Target.IsotopicProfile);

            // Console.WriteLine(executor.TargetedWorkflow.Result.Target.EmpiricalFormula);
        }
Ejemplo n.º 24
0
        public void IqExecutor_StandardO16O18Testing_VladAlz()
        {
            //see JIRA https://jira.pnnl.gov/jira/browse/OMCS-628

            var executorParametersFile =
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1.xml";

            var executorParameters = new BasicTargetedWorkflowExecutorParameters();

            executorParameters.LoadParameters(executorParametersFile);

            executorParameters.OutputFolderBase =
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz";

            var testDatasetPath =
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";

            executorParameters.IsMassAlignmentPerformed = true;
            executorParameters.IsNetAlignmentPerformed  = true;

            executorParameters.ReferenceTargetsFilePath =
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2.txt";


            var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase, "IqResults", RunUtilities.GetDatasetName(testDatasetPath) + "_iqResults.txt");

            if (File.Exists(expectedResultsFilename))
            {
                File.Delete(expectedResultsFilename);
            }



            var autoSavedExecutorParametersFile =
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1_autosaved.xml";

            executorParameters.SaveParametersToXML(autoSavedExecutorParametersFile);

            var run      = new RunFactory().CreateRun(testDatasetPath);
            var executor = new IqExecutor(executorParameters, run);

            var targetsFile =
                @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2_First60.txt";

            targetsFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2.txt";


            executor.LoadAndInitializeTargets(targetsFile);
            executor.SetupMassAndNetAlignment();

            var testTarget = 9282;

            executor.Targets = (from n in executor.Targets where n.ID == testTarget select n).ToList();

            var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();

            targetedWorkflowParameters.ChromNETTolerance  = 0.025;
            targetedWorkflowParameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;

            //define workflows for parentTarget and childTargets
            var parentWorkflow = new O16O18ParentIqWorkflow(run, targetedWorkflowParameters);
            var childWorkflow  = new O16O18IqWorkflow(run, targetedWorkflowParameters);

            var workflowAssigner = new IqWorkflowAssigner();

            workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
            workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);

            executor.DoAlignment();
            executor.Execute();

            IqResultImporter importer = new IqResultImporterBasic(expectedResultsFilename);
            var allResults            = importer.Import();

            var result1 = allResults.First(p => p.Target.ID == 9282 && p.Target.ChargeState == 2);

            Assert.AreEqual(9282, result1.Target.ID);
            Assert.AreEqual(0.32678m, (decimal)result1.ElutionTimeObs);
            Assert.AreEqual(4545, result1.LcScanObs);
            Assert.AreEqual(0.02, (decimal)result1.FitScore);
        }
Ejemplo n.º 25
0
        public void ExecutorTest1()
        {
            Console.WriteLine(Environment.CurrentDirectory);
            var util     = new IqTargetUtilities();
            var testFile = @"\\proto-5\External_Waters_TOF_Xfer\MzML_Files\130716_iPRG14_004.mzML";
            //string peaksTestFile =
            //@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_scans5500-6500_peaks.txt";
            var targetsFile = @"\\protoapps\UserData\Fujimoto\SangtaeBottomUp\msgfPlus\C~~data~iPRG 2014~130716_iPRG14_004.raw.-1_Filtered.tsv";

            WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();

            executorBaseParameters.ChromGenSourceDataPeakBR   = 3;
            executorBaseParameters.ChromGenSourceDataSigNoise = 2;
            executorBaseParameters.TargetsFilePath            = targetsFile;
            executorBaseParameters.OutputFolderBase           =
                @"\\protoapps\UserData\Fujimoto\SangtaeBottomUp\Results";


            var expectedResultsFilename = Path.Combine(executorBaseParameters.OutputFolderBase,
                                                       "IqResults",
                                                       RunUtilities.GetDatasetName(testFile) + "_iqResults.txt");

            if (File.Exists(expectedResultsFilename))
            {
                File.Delete(expectedResultsFilename);
            }


            var run = new RunFactory().CreateRun(testFile);

            var executor = new IqExecutor(executorBaseParameters, run);

            //executor.ChromSourceDataFilePath = peaksTestFile;

            executor.LoadAndInitializeTargets(targetsFile);

            var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();

            targetedWorkflowParameters.ChromNETTolerance = 0.05;

            //define workflows for parentTarget and childTargets
            var parentWorkflow = new ChromPeakDeciderIqWorkflow(run, targetedWorkflowParameters);
            var childWorkflow  = new ChargeStateChildIqWorkflow(run, targetedWorkflowParameters);

            var workflowAssigner = new IqWorkflowAssigner();

            workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
            workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);

            //SipperDataDump.DataDumpSetup(@"\\pnl\projects\MSSHARE\Merkley_Eric\For_Grant\IqResults\EXP6B_F1_CSCL_LIGHT_130520020056\EXP6B_F1_CSCL_LIGHT_FULLRESULTS.txt");

            //Main line for executing IQ:
            executor.Execute();

            //Test the results...
            var numResultsInResultsFile = 0;
            var outputToConsole         = true;

            using (var reader = new StreamReader(expectedResultsFilename))
            {
                while (reader.Peek() != -1)
                {
                    var line = reader.ReadLine();
                    numResultsInResultsFile++;

                    if (outputToConsole)
                    {
                        Console.WriteLine(line);
                    }
                }
            }
        }
Ejemplo n.º 26
0
        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);
            }
        }
Ejemplo n.º 27
0
        public void ExecuteMultipleTargetsTest1()
        {
            var util          = new IqTargetUtilities();
            var testFile      = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
            var peaksTestFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_scans5500-6500_peaks.txt";

            var targetsFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";

            WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();

            executorBaseParameters.ChromGenSourceDataPeakBR   = 3;
            executorBaseParameters.ChromGenSourceDataSigNoise = 2;
            executorBaseParameters.TargetsFilePath            = targetsFile;
            executorBaseParameters.OutputFolderBase           = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled";

            var expectedResultsFilename = Path.Combine(executorBaseParameters.OutputFolderBase,
                                                       "IqResults",
                                                       RunUtilities.GetDatasetName(testFile) + "_iqResults.txt");

            if (File.Exists(expectedResultsFilename))
            {
                File.Delete(expectedResultsFilename);
            }

            var run = new RunFactory().CreateRun(testFile);

            var executor = new IqExecutor(executorBaseParameters, run);

            executor.ChromSourceDataFilePath = peaksTestFile;

            executor.LoadAndInitializeTargets(targetsFile);
            executor.Targets = (from n in executor.Targets where n.ElutionTimeTheor > 0.305 && n.ElutionTimeTheor < 0.325 select n).Take(10).ToList();

            var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();

            targetedWorkflowParameters.ChromNETTolerance = 0.5;

            //define workflows for parentTarget and childTargets
            var parentWorkflow = new BasicIqWorkflow(run, targetedWorkflowParameters);
            var childWorkflow  = new BasicIqWorkflow(run, targetedWorkflowParameters);

            var workflowAssigner = new IqWorkflowAssigner();

            workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
            workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);


            //Main line for executing IQ:
            executor.Execute();

            //Test the results...
            Assert.IsTrue(File.Exists(expectedResultsFilename), "results file doesn't exist");
            var numResultsInResultsFile = 0;
            var outputToConsole         = true;

            using (var reader = new StreamReader(expectedResultsFilename))
            {
                while (reader.Peek() != -1)
                {
                    var line = reader.ReadLine();
                    numResultsInResultsFile++;

                    if (outputToConsole)
                    {
                        Console.WriteLine(line);
                    }
                }
            }

            Assert.IsTrue(numResultsInResultsFile > 1, "No results in output file");

            //the Result Tree is flattened out in the results file.
            Assert.IsTrue(numResultsInResultsFile == 11);

            //the results in the Executor are in the a Result tree. So there should be just 10.
            Assert.AreEqual(10, executor.Results.Count);
        }
        public void targetedWorkflow_alignUsingDataFromFiles()
        {
            // https://jira.pnnl.gov/jira/browse/OMCS-714

            var executorParameters = new BasicTargetedWorkflowExecutorParameters();

            executorParameters.TargetsFilePath =
                baseFolder + @"\Targets\QCShew_Formic_MassTags_Bin10_MT24702_Z3.txt";
            executorParameters.TargetedAlignmentIsPerformed           = true;
            executorParameters.TargetedAlignmentWorkflowParameterFile =
                baseFolder + @"\Parameters\TargetedAlignmentWorkflowParameters1.xml";

            var workflowParameters = new BasicTargetedWorkflowParameters();

            workflowParameters.ChromSmootherNumPointsInSmooth = 9;
            workflowParameters.ChromPeakDetectorPeakBR        = 1;
            workflowParameters.ChromPeakDetectorSigNoise      = 3;
            workflowParameters.ChromGenTolerance = 20;
            workflowParameters.ChromNETTolerance = 0.025;
            workflowParameters.MSToleranceInPPM  = 20;

            var workflow = new BasicTargetedWorkflow(workflowParameters);

            var testDatasetPath =
                baseFolder + @"\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";

            TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, workflow, testDatasetPath);

            executor.Execute();

            var expectedResultsFilename =
                @"C:\Users\d3x720\Documents\Data\QCShew\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_results.txt";

            var result = executor.TargetedWorkflow.Result;

            Assert.IsTrue(workflow.Success);
            Assert.IsFalse(result.FailedResult);
            Assert.IsNotNull(result.ScanSet);
            Assert.IsNotNull(result.ChromPeakSelected);

            Assert.IsTrue(result.Score < 0.1);



            Assert.AreEqual(3, result.NumChromPeaksWithinTolerance);
            Assert.AreEqual(8627, (decimal)Math.Round(result.ChromPeakSelected.XValue, 0));

            //non-calibrated mass directly from mass spectrum
            Assert.AreEqual(2920.49120m, (decimal)Math.Round(result.IsotopicProfile.MonoIsotopicMass, 5));

            //calibrated mass
            Assert.AreEqual(2920.50017m, (decimal)Math.Round(result.MonoIsotopicMassCalibrated, 5));

            Console.WriteLine("theor monomass= \t" + result.Target.MonoIsotopicMass);
            Console.WriteLine("monomass= \t" + result.IsotopicProfile.MonoIsotopicMass);
            Console.WriteLine("calibrated monomass= \t" + result.MonoIsotopicMassCalibrated);

            Console.WriteLine("ppmError before= \t" + result.MassErrorBeforeAlignment);
            Console.WriteLine("ppmError after= \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);

            //Dataset	TargetID	Code	EmpiricalFormula	ChargeState	Scan	ScanStart	ScanEnd	NumMSSummed	NET	NETError	NumChromPeaksWithinTol	NumQualityChromPeaksWithinTol	MonoisotopicMass	MonoisotopicMassCalibrated	MassErrorInPPM	MonoMZ	IntensityRep	FitScore	IScore	FailureType	ErrorDescription
            //QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18	24702	LLKEEGYIADYAVADEAKPELEITLK	C133H213N29O44	3	8624	8596	8659	0	0.42916	-0.009395	3	1	2920.49120	2920.50018	13.96	974.50434	7529645	0.0193	0.0000
        }
Ejemplo n.º 29
0
        public void executeWorkflowTest1()
        {
            var testFile  = FileRefs.SipperRawDataFile;
            var peaksFile =
                @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2012\C12C13YellowStone\2011_02_20_SIPPER_workflow_standards\Yellow_C13_070_23Mar10_Griffin_10-01-28_peaks.txt";

            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();


            var masstagIDlist = (from n in massTagCollection.TargetList select n.ID).ToList();


            // Update LCMSFeatures using MassTag info

            int[] testMassTags = { 344540889, 344972415, 354881152, 355157363, 355162540, 355315129, 355054192, 355160150 };

            //testMassTags = new[] {344540889};

            //testMassTags = new int[]
            //                   {
            //                       354942933, 355066611, 354882356, 354928525, 17440471, 355046165, 355008036, 354977066,
            //                       355166304, 354879605, 344965520, 354870998, 355084057, 355034961, 354963652, 344969970,
            //                       355157492, 355176429, 355162540, 355244316, 355139611, 355036935, 355044786, 355139579,
            //                       355163558, 355065622, 355167968, 355033793, 354879421, 355090391, 355034165, 354880925,
            //                       344747857, 354879494, 355315129, 344968376, 355022502, 354879347, 354881152, 354879406,
            //                       344968302, 355037491, 355033717, 355034652, 354879414, 344972415, 355039789, 355025762,
            //                       355129038, 355355053, 354879164, 355037247, 355033862, 355034180, 355033668, 344540889,
            //                       355160123, 345073233, 354880183, 354879165, 354879192, 354879842, 355046211, 355033627,
            //                       355030074, 355033620, 354879142, 354879360, 355034183, 354879174, 354879150
            //                   };

            //no enrichment peptides:
            //testMassTags = new int[] { 355057553, 355058671, 355084418 };

            //enriched
            //testMassTags = new int[] { 355116553, 355129038, 355160150, 355162540, 355163371 };


            //testMassTags = new int[] { 355008295 };

            //co-elution peptides
            //testMassTags = new int[] {355034154, 355033668, 355154211, 355035781};

            //testMassTags = new int[] { 355033668 };


            //testMassTags = new int[]{355157492};

            testMassTags = new int[] { 355033977 };

            var filteredLcmsFeatureTargets = (from n in lcmsTargetCollection.TargetList
                                              where testMassTags.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
                                              select n).ToList();


            foreach (LcmsFeatureTarget target in filteredLcmsFeatureTargets)
            {
                if (masstagIDlist.Contains(target.FeatureToMassTagID))
                {
                    var mt = massTagCollection.TargetList.Where(p => p.ID == target.FeatureToMassTagID).First();
                    target.Code             = mt.Code;
                    target.EmpiricalFormula = mt.EmpiricalFormula;
                }
                else
                {
                    //get target's code + empirical formula based on averagine model
                }
            }



            TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();

            parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;

            var workflow = new SipperTargetedWorkflow(run, parameters);


            var outputFolder = @"C:\data\temp\SipperOutput";

            if (!Directory.Exists(outputFolder))
            {
                Directory.CreateDirectory(outputFolder);
            }


            var stopwatch = new Stopwatch();

            stopwatch.Start();
            foreach (var target in filteredLcmsFeatureTargets)
            {
                run.CurrentMassTag = target;

                workflow.Execute();

                OutputMassSpectrum(outputFolder, workflow.MassSpectrumXYData, target, workflow.Result as SipperLcmsTargetedResult);
            }
            stopwatch.Stop();

            foreach (var targetedResultBase in (run.ResultCollection.MassTagResultList))
            {
                var result = (SipperLcmsTargetedResult)targetedResultBase.Value;



                Console.WriteLine(result + "\t" + result.Target.IsotopicProfile.Peaklist.Count);
            }

            Console.WriteLine("Total workflow time (ms) = " + stopwatch.ElapsedMilliseconds);
            Console.WriteLine("Time per target (ms) = " + stopwatch.ElapsedMilliseconds / (double)filteredLcmsFeatureTargets.Count);
        }
Ejemplo n.º 30
0
 public AutoprocessorViewModel()
 {
     ExecutorParameters         = new BasicTargetedWorkflowExecutorParameters();
     TargetedWorkflowParameters = new BasicTargetedWorkflowParameters();
 }