public void constructor_noRun_test1()
{
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(parameters);
//workflow.Execute();
}
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 cannotFindMassTag_test1()
{
//
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 26523;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.IsNull(result.IsotopicProfile);
Assert.IsNull(result.ScanSet);
Assert.IsNull(result.ChromPeakSelected);
Assert.IsTrue(result.FailedResult);
Assert.AreEqual(DeconTools.Backend.Globals.TargetedResultFailureType.ChrompeakNotFoundWithinTolerances, result.FailureType);
}
public void 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 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 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 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 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 TargetedAligner(Run run, DeconToolsTargetedWorkflowParameters workflowParameters)
{
_run = run;
_parameters = workflowParameters;
_netGroupings = createNETGroupings();
_workflow = new BasicTargetedWorkflow(_run, workflowParameters);
IsAlignmentInfoExported = true;
NumberOfDesiredMassTagsFoundPerNETGrouping = 25;
NumberOfChromPeaksWithinToleranceAllowed = 1;
NumberOfMaxAttemptsPerNETGrouping = 200;
this.UpperFitScoreAllowedCriteria = 0.1;
this.MinimumChromPeakIntensityCriteria = 2.5e5f;
this.IScoreAllowedCriteria = 0.15;
this.AreFeaturesSavedToTextFile = true;
}
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 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 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 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
}
