public void AlternateConstructor_targetedWorkflowNoAlignment() { 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 basicTargetedWorkflowParameters = new BasicTargetedWorkflowParameters(); var workflow = new BasicTargetedWorkflow(basicTargetedWorkflowParameters); TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, workflow, testDatasetPath); executor.Execute(); Assert.IsTrue(File.Exists(expectedResultsFilename)); }
public void TestErnestosData1() { string baseFolder = @"\\protoapps\DataPkgs\Public\2012\573_O16O18_Data_analysis_of_ubiquintated_peptides"; string outputFolder = @"D:\Temp\TargetedTesting"; BasicTargetedWorkflowExecutorParameters executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.TargetsBaseFolder = Path.Combine(baseFolder, "Targets"); executorParameters.WorkflowParameterFile = Path.Combine(baseFolder, "Parameters", "O16O18WorkflowParameters_2011_08_23_sum5.xml"); executorParameters.OutputFolderBase = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowTesting\Output"; executorParameters.TargetType = Globals.TargetType.LcmsFeature; string testDatasetPath = @"\\protoapps\UserData\Slysz\Data\O16O18\Ernesto\PSI_LRW_18O_02A_18Jun12_Falcon_12-03-34.RAW"; testDatasetPath = @"D:\Data\O16O18\Ernesto\PSI_LRW_1to1_03A_6Jul12_Falcon_12-06-04.raw"; string outputtedParameterFile = @"\\protoapps\DataPkgs\Public\2012\573_O16O18_Data_analysis_of_ubiquintated_peptides\Parameters\ExecutorParameters1.xml"; //executorParameters.SaveParametersToXML(outputtedParameterFile); TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath); executor.Execute(); }
public void DemoParameterTest1() { var outputFileName = baseFolder + @"\BasicTargetedWorkflowExecutorParameters_autoGenerated.xml"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.SaveParametersToXML(outputFileName); }
public void ChaoChaoPeptidomicsTesting1() { var executorParameters = @"\\protoapps\DataPkgs\Public\2013\727_IQ_analysis_of_Peptidomics_data_First_attempts\Parameters\ExecutorParameters1.xml"; var alignmentParametersFile = @"\\protoapps\DataPkgs\Public\2013\727_IQ_analysis_of_Peptidomics_data_First_attempts\Parameters\TargetedAlignmentWorkflowParameters1.xml"; var rawDatafile = @"D:\Data\From_ChaoChao\CPTAC_OT_Pep_JB_5439_60min_4May12_Legolas_11-07-64.raw"; var parameters = new BasicTargetedWorkflowExecutorParameters(); parameters.LoadParameters(executorParameters); parameters.TargetedAlignmentIsPerformed = true; var targetedAlignerWorkflowParameters = new TargetedAlignerWorkflowParameters(); targetedAlignerWorkflowParameters.LoadParameters(alignmentParametersFile); var alignmentParametersOutputfile = alignmentParametersFile.Replace(".xml", "_autoGenerated.xml"); targetedAlignerWorkflowParameters.SaveParametersToXML(alignmentParametersOutputfile); TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(parameters, rawDatafile); executor.Execute(); }
public void ProcessSangTaeStuff() { string executorParametersFile = @"\\protoapps\UserData\Sangtae\ToSlysz\IQ\ExecutorParameters1.xml"; BasicTargetedWorkflowExecutorParameters executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParametersFile); executorParameters.TargetType = Globals.TargetType.LcmsFeature; executorParameters.TargetsFilePath = @"\\protoapps\UserData\Sangtae\ToSlysz\IQ\Target_TD.txt"; string testDatasetPath = @"\\protoapps\UserData\Sangtae\ToSlysz\IQ\QC_Shew_12_02_2_1Aug12_Cougar_12-06-11.raw"; TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath); int testTarget = 7673789; //executor.Targets.TargetList =executor.Targets.TargetList.Where(p => p.ID == testTarget && p.ChargeState==3).ToList(); string testTargetSeq = "SEVIAVVSSDTFVRPIYAGNALATVQSHDAVK"; testTargetSeq = "ILQGYGAGHQFAAGGDGTAINQGGIAEQVTSAALNYR"; executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.Code == testTargetSeq).ToList(); //executor.Targets.TargetList = executor.Targets.TargetList.Take(50).ToList(); executor.Execute(); TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData); }
public void O16O18_onBruker15T() { string executorParametersFile = @"\\protoapps\DataPkgs\Public\2012\641_Alz_O16O18_dataprocessing2\Parameters\ExecutorParameters1 - Copy.xml"; BasicTargetedWorkflowExecutorParameters executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParametersFile); executorParameters.TargetsFilePath = @"\\protoapps\DataPkgs\Public\2012\641_Alz_O16O18_dataprocessing2\Targets\MT_Human_ALZ_O18_P852\MassTags_PMT2.txt"; string testDatasetPath = @"D:\Data\From_Vlad\2013_01_29_ALZ_CTRL_5_0p05_1_01_224.d"; TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath); int testTarget = 7673789; //executor.Targets.TargetList =executor.Targets.TargetList.Where(p => p.ID == testTarget && p.ChargeState==3).ToList(); executor.Targets.TargetList = executor.Targets.TargetList.Take(50).ToList(); executor.Execute(); }
public void Test1() { string executorParametersFile = @"D:\Data\From_Vlad\Bruker\Parameters\ExecutorParameters1 - Copy.xml"; BasicTargetedWorkflowExecutorParameters executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParametersFile); string testDatasetPath = @"D:\Data\From_Vlad\Bruker\2013_01_29_ALZ_CTRL_5_0p5_1_01_228.d"; Run run = new RunFactory().CreateRun(testDatasetPath); int numScans = run.GetNumMSScans(); TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath); int testTarget = 206675561; //beta amyloid executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.ID == testTarget && p.ChargeState == 2).ToList(); executor.Execute(); //TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData); executor.TargetedWorkflow.Result.DisplayToConsole(); Console.WriteLine("expected mz= " + executor.TargetedWorkflow.Result.Target.MZ); double expectedNET = executor.TargetedWorkflow.Result.Target.NormalizedElutionTime; double expectedScan = expectedNET * numScans; Console.WriteLine("Expected NET= " + expectedNET + "; Corresponds to scan: " + expectedScan); }
public void TestUIMFTargetedMSMSWorkflow() { var datasetPath = uimfMsMsFile; var executorParameterFilename = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\UIMF_Targeted_MSMS_Testing\Parameters\UIMFTargetedMSMSWorkflowExecutorParametersMostConfidentMassTags.xml"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParameterFilename); var executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath); executor.Execute(); //List<TargetedResultBase> resultList = executor.TargetedWorkflow.Run.ResultCollection.GetMassTagResults(); //foreach (var targetedResultBase in resultList) //{ // Console.WriteLine("*******************************************************"); // Console.WriteLine(targetedResultBase.Target.Code + "\t" + targetedResultBase.Target.ChargeState); // foreach (var peakQualityData in targetedResultBase.ChromPeakQualityList) // { // peakQualityData.Display(); // } //} //TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData); }
public void MSAlignTargetDataTest() { var testFile = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\SBEP_STM_001_02222012_Aragon.raw"; var targetsFile = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\salmonella_top_target.txt"; var resultsFolder = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\Results"; //Backend.Utilities.SipperDataDump.DataDumpSetup(@"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\Results\detailed_results.txt"); WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters(); executorBaseParameters.ChromGenSourceDataPeakBR = 3; executorBaseParameters.ChromGenSourceDataSigNoise = 2; executorBaseParameters.TargetsFilePath = targetsFile; executorBaseParameters.OutputFolderBase = resultsFolder; var run = new RunFactory().CreateRun(testFile); var executor = new TopDownMSAlignExecutor(executorBaseParameters, run); var s = Stopwatch.StartNew(); executor.LoadAndInitializeTargets(targetsFile); s.Stop(); var rt = s.Elapsed; Console.WriteLine("import: " + rt); var targetedWorkflowParameters = new BasicTargetedWorkflowParameters(); targetedWorkflowParameters.ChromNETTolerance = 0.05; targetedWorkflowParameters.ChromatogramCorrelationIsPerformed = true; targetedWorkflowParameters.ChromSmootherNumPointsInSmooth = 15; targetedWorkflowParameters.MSToleranceInPPM = 15; targetedWorkflowParameters.NumMSScansToSum = 5; //define workflows for parentTarget and childTargets var parentWorkflow = new ChromPeakDeciderTopDownIqWorkflow(run, targetedWorkflowParameters); var childWorkflow = new ChargeStateChildTopDownIqWorkflow(run, targetedWorkflowParameters); var workflowAssigner = new IqWorkflowAssigner(); workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets); workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets); var stopwatch = Stopwatch.StartNew(); //Main line for executing IQ: executor.Execute(); stopwatch.Stop(); var runtime = stopwatch.Elapsed; Console.WriteLine("Runtime: " + runtime); }
public void LoadExecutorParametersTest1() { var inputFilename = baseFolder + @"\Parameters\BasicTargetedWorkflowExecutorParameters_forImport.xml"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(inputFilename); Assert.AreEqual(1500, (int)executorParameters.MaxMzForDefiningChargeStateTargets); Assert.AreEqual(100, executorParameters.MaxNumberOfChargeStateTargetsToCreate); }
public void ChromCorrelatorTest1() { var rawFilename = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw"; var run = new RunFactory().CreateRun(rawFilename); WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters(); var executor = new IqExecutor(executorBaseParameters, run); executor.LoadChromData(run); var workflowAssigner = new IqWorkflowAssigner(); TargetedWorkflowParameters workflowParameters = new O16O18WorkflowParameters(); IqWorkflow workflow = new O16O18IqWorkflow(run, workflowParameters); IqTarget iqTarget = new IqChargeStateTarget(); iqTarget.EmpiricalFormula = "C58H100N18O20"; iqTarget.Code = "GAAQNIIPASTGAAK"; iqTarget.ID = 1093; iqTarget.ChargeState = 0; var iqTargetList = new List <IqTarget>(); iqTargetList.Add(iqTarget); var utilities = new IqTargetUtilities(); utilities.CreateChildTargets(iqTargetList); workflowAssigner.AssignWorkflowToParent(workflow, iqTargetList); workflowAssigner.AssignWorkflowToChildren(workflow, iqTargetList); var theorFeatureGenerator = new JoshTheorFeatureGenerator(); foreach (var target in iqTarget.ChildTargets()) { utilities.UpdateTargetMissingInfo(target); target.TheorIsotopicProfile = theorFeatureGenerator.GenerateTheorProfile(target.EmpiricalFormula, target.ChargeState); } foreach (var childTarget in iqTarget.ChildTargets()) { var result = childTarget.CreateResult(); var correlator = new O16O18ChromCorrelator(7, 0.1, 20, Globals.ToleranceUnit.PPM); var corrData = correlator.CorrelateData(run, result, 5700, 6500); var corrDataItem1 = corrData.CorrelationDataItems.First(); Console.WriteLine("z= \t" + childTarget.ChargeState + "\tCorrelationData (slope,intercept,rsquared)= \t" + corrDataItem1); } }
public void issue0725_targetedAlignmentProblems() { var executorParameterFile = @"D:\Data\Orbitrap\Issue0725_badAlignment\Issue0725_executorWorkflow.xml"; var datasetPath = @"D:\Data\Orbitrap\Issue0725_badAlignment\QC_Shew_10_03-2_100min_06May10_Tiger_10-04-08.RAW"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParameterFile); TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath); executor.Execute(); }
public void issue0705_completelyFailedAlignment_multialignErrors() { var executorParameterFile = @"\\protoapps\UserData\Slysz\Data\Redmine_Issues\Issue0705_failedAlignment\workflowExecutorParameters.xml"; var datasetPath = @"\\proto-3\LTQ_Orb_3\2010_1\QC_Shew_10_01-pt5-4_12Feb10_Doc_09-12-26\QC_Shew_10_01-pt5-4_12Feb10_Doc_09-12-26.raw"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParameterFile); TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath); executor.Execute(); }
public void ExecutorTest2() { var executorParamFile = baseFolder + @"\Parameters" + "\\" + @"QCShew_OrbiStandard_workflowExecutorParameters.xml"; var testDatasetPath = baseFolder + "\\" + "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParamFile); TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath); executor.Execute(); }
public void ExecuteSipperOnMSGFOutputTest1() { var paramFile = @"\\protoapps\DataPkgs\Public\2013\788_Sipper_C13_Analysis_Hot_Lake_SNC_Ana_preliminary\Parameters\ExecutorParameters1.xml"; var parameters = new BasicTargetedWorkflowExecutorParameters(); parameters.LoadParameters(paramFile); parameters.CopyRawFileLocal = false; parameters.FolderPathForCopiedRawDataset = @"D:\Data\Sipper\HLP_Ana"; var testDataset = @"D:\Data\Sipper\HLP_Ana\HLP_Ana_SIP_02_19APR13_Frodo_12-12-04.raw"; var outputParameterFile = Path.Combine(Path.GetDirectoryName(paramFile), Path.GetFileNameWithoutExtension(paramFile) + " - copy.xml"); parameters.SaveParametersToXML(outputParameterFile); var executor = new BasicTargetedWorkflowExecutor(parameters, testDataset); executor.Targets.TargetList = executor.Targets.TargetList.Take(10).ToList(); executor.Execute(); var workflow = executor.TargetedWorkflow as SipperTargetedWorkflow; var result = workflow.Result as SipperLcmsTargetedResult; Assert.IsNotNull(result); Assert.IsNotNull(result.ChromCorrelationData); Assert.IsNotNull(result.ChromCorrelationData.CorrelationDataItems); Assert.IsTrue(result.ChromCorrelationData.CorrelationDataItems.Count > 0); //foreach (var dataItem in result.ChromCorrelationData.CorrelationDataItems) //{ // Console.WriteLine(dataItem.CorrelationRSquaredVal); //} //foreach (var fitScoreDataItem in workflow.FitScoreData) //{ // Console.WriteLine(fitScoreDataItem.Key + "\t" + fitScoreDataItem.Value); //} }
public void JoinTargetsTest1() { var targetsFileName = @"\\proto-7\VOrbi05\2013_2\mhp_plat_test_1_14April13_Frodo_12-12-04\MSG201305011339_Auto939903\mhp_plat_test_1_14April13_Frodo_12-12-04_msgfdb_fht.txt"; var massTagFilename = @"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set1_P890_targets.txt"; var rawFile = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw"; IqTargetImporter massTagImporter = new BasicIqTargetImporter(massTagFilename); var massTagRefs = massTagImporter.Import().OrderBy(p => p.Code).ToList(); WorkflowExecutorBaseParameters parameters = new BasicTargetedWorkflowExecutorParameters(); parameters.TargetsFilePath = targetsFileName; var run = new RunFactory().CreateRun(rawFile); var massAndNetAligner = new IqMassAndNetAligner(parameters, run); massAndNetAligner.LoadAndInitializeTargets(); var testNET = massAndNetAligner.Targets.First().ElutionTimeTheor; var query = (from massTag in massTagRefs join target in massAndNetAligner.Targets on massTag.Code equals target.Code select new { MassTag = massTag, MSGFTarget = target }).ToList(); foreach (var thing in query) { thing.MSGFTarget.ID = thing.MassTag.ID; thing.MSGFTarget.ElutionTimeTheor = thing.MassTag.ElutionTimeTheor; } var targets = query.Select(p => p.MSGFTarget).ToList(); var testNETAfter = massAndNetAligner.Targets.First().ElutionTimeTheor; Console.WriteLine("NET before= " + testNET); Console.WriteLine("NET before= " + testNETAfter); }
public void TestUIMFTargetedMSMSWorkflowLotsOfTargets() { var datasetPath = uimfMsMsFile; var executorParameterFilename = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\UIMF_Targeted_MSMS_Testing\Parameters\UIMFTargetedMSMSWorkflowExecutorParametersLotsOfMassTags.xml"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParameterFilename); var executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath); executor.Execute(); }
public void Bruker9T_N14N15_executorTest1() { var testfile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\RawData\RSPH_PtoA_L_28_rep1_28Feb08_Raptor_08-01-01"; var parameterFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Parameters\ExecutorParameters1 - forTesting.xml"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(parameterFile); executorParameters.CopyRawFileLocal = false; var executor = new BasicTargetedWorkflowExecutor(executorParameters, testfile); executor.Execute(); }
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 }
public void Test1() { string executorParameterFileName = @"D:\Data\IQ_testing\From_SangTae\ExecutorParameters1.xml"; BasicTargetedWorkflowExecutorParameters executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParameterFileName); string testDataFile = @"D:\Data\IQ_testing\From_SangTae\QC_Shew_12_02_2_1Aug12_Cougar_12-06-11.raw"; TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDataFile); executor.Targets.TargetList = executor.Targets.TargetList.Take(10).ToList(); executor.Execute(); }
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); }
public void TestUIMFTargetedMSMSWorkflowSingleTarget() { var datasetPath = uimfMsMsFile; var executorParameterFilename = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\UIMF_Targeted_MSMS_Testing\Parameters\UIMFTargetedMSMSWorkflowExecutorParameters.xml"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParameterFilename); var executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath); executor.Execute(); //TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData); }
public void ExecutorCreatingTargetsTest1() { 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"; var resultsFolder = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Results"; var expectedResultsFilename = Path.Combine(resultsFolder, RunUtilities.GetDatasetName(testFile) + "_iqResults.txt"); if (File.Exists(expectedResultsFilename)) { File.Delete(expectedResultsFilename); } WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters(); executorBaseParameters.ChromGenSourceDataPeakBR = 3; executorBaseParameters.ChromGenSourceDataSigNoise = 2; executorBaseParameters.TargetsFilePath = targetsFile; //create no more than two charge state targets per peptide executorBaseParameters.MaxNumberOfChargeStateTargetsToCreate = 2; 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(); foreach (var iqTarget in executor.Targets) { var numChildTargets = iqTarget.GetChildCount(); Assert.IsTrue(numChildTargets <= 2); //MaxNumberOfChargeStateTargetsToCreate = 2; Console.WriteLine(iqTarget + "\t" + numChildTargets); } }
public void importParametersTest1() { var importedParametersFile = Path.Combine(FileRefs.ImportedData, "importedBasicTargetedWorkflowExecutorParameters_defaults.xml"); var parameters = new BasicTargetedWorkflowExecutorParameters(); parameters.LoadParameters(importedParametersFile); Assert.AreEqual(true, parameters.CopyRawFileLocal); Assert.AreEqual(true, parameters.DeleteLocalDatasetAfterProcessing); Assert.AreEqual(@"d:\temp\rawdata", parameters.FolderPathForCopiedRawDataset); Assert.AreEqual(@"d:\temp\MassTags\massTagsToBeTargeted.txt", parameters.TargetsFilePath); Assert.AreEqual(@"d:\temp\Parameters\targetedAlignmentParameters.xml", parameters.TargetedAlignmentWorkflowParameterFile); Assert.AreEqual(@"d:\temp\Parameters\WorkflowParameters.xml", parameters.WorkflowParameterFile); Assert.AreEqual(@"d:\temp", parameters.TargetsBaseFolder); }
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 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(); }
public void GlycanProcessingTest1() { var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.WorkflowParameterFile = @"D:\Data\From_Scott\BasicTargetedWorkflowParameters1.xml"; executorParameters.TargetsFilePath = @"D:\Data\From_Scott\Glycan_targets.txt"; //executorParameters.TargetType = Globals.TargetType.LcmsFeature; var testDatasetPath = @"D:\Data\From_Scott\Gly08_Velos4_Jaguar_200nL_Sp01_3X_7uL_1000A_31Aug12.raw"; TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath); //executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.ID == 18).ToList(); executor.Execute(); }
public void ExecutorTest3Temp() { var executorParamFile = @"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\Parameters\ExecutorParameters1 - Copy.xml"; var testDatasetPath = @"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\RawData\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParamFile); executorParameters.TargetType = Globals.TargetType.LcmsFeature; TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath); executor.Execute(); }
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 O16O18Workflow_ProblemCaseTesting1() { //This is a nice case where the O16 is quite low and can be missed. In the current settings //the O16Chrom is null (by itself), so the chrom correlation fails. //Thus quant based on chrom corr fails, but quant based on O16O18 feature finding succeeds. //7673789 var executorParametersFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1.xml"; var executorParameters = new BasicTargetedWorkflowExecutorParameters(); executorParameters.LoadParameters(executorParametersFile); 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"; var autoSavedExecutorParametersFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1_autosaved.xml"; executorParameters.SaveParametersToXML(autoSavedExecutorParametersFile); TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath); var testTarget = 7415; executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.ID == testTarget).ToList(); executor.Execute(); var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase, "Results", executor.TargetedWorkflow.Run.DatasetName + "_results.txt"); var importer = new O16O18TargetedResultFromTextImporter(expectedResultsFilename); var results = importer.Import().Results; var result1 = results.First(); Console.WriteLine(result1.ToStringWithDetailsAsRow()); }