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());
}
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
}
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);
}
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();
}
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 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());
}
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);
}
}
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");
}
}
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);
}
}
public void executeWorkflowTest1()
{
var testFile = FileRefs.SipperRawDataFile;
var exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "ExportedSipperResults1.txt");
var peaksFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksFile);
var lcmsfeaturesFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_LCMSFeatures.txt";
// load LCMSFeatures as targets
var importer =
new LcmsTargetFromFeaturesFileImporter(lcmsfeaturesFile);
var lcmsTargetCollection = importer.Import();
// load MassTags
var massTagFile1 =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_MassTags.txt";
var massTagImporter = new MassTagFromTextFileImporter(massTagFile1);
var massTagCollection = massTagImporter.Import();
//enriched
var testMassTags = new int[] { 355116553, 355129038, 355160150, 355162540, 355163371 };
var filteredLcmsFeatureTargets = (from n in lcmsTargetCollection.TargetList
where testMassTags.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
select n).ToList();
TargetCollection.UpdateTargetsWithMassTagInfo(filteredLcmsFeatureTargets, massTagCollection.TargetList);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
var workflow = new SipperTargetedWorkflow(run, parameters);
foreach (var target in filteredLcmsFeatureTargets)
{
run.CurrentMassTag = target;
workflow.Execute();
}
var results = run.ResultCollection.GetMassTagResults();
var repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
var exporter = new SipperResultToLcmsFeatureExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}
public 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);
}
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);
}
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);
}
}
}
}
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);
}
}
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
}
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);
}
public AutoprocessorViewModel()
{
ExecutorParameters = new BasicTargetedWorkflowExecutorParameters();
TargetedWorkflowParameters = new BasicTargetedWorkflowParameters();
}