public void doAlignmentTest1() { RunFactory rf = new RunFactory(); Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1); string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt"; UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile); TargetedResultRepository repo = importer.Import(); string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt"; MassTagCollection mtc = new MassTagCollection(); MassTagFromTextFileImporter mtimporter = new MassTagFromTextFileImporter(massTagFile); mtc = mtimporter.Import(); NETAndMassAligner aligner = new NETAndMassAligner(); aligner.SetFeaturesToBeAligned(repo.Results); aligner.SetReferenceMassTags(mtc.MassTagList); aligner.Execute(run); Assert.IsNotNull(run.AlignmentInfo); Assert.IsNotNull(run.AlignmentInfo.marrNETFncTimeInput); Assert.AreEqual(2273.0f, run.AlignmentInfo.marrNETFncTimeInput[0]); float testScan = 6005; float testNET1 = run.AlignmentInfo.GetNETFromTime(testScan); Assert.AreEqual(0.3253423m, (decimal)testNET1); }
public void ExportNET_andMass_AlignmentDataTest1() { var exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt"); var exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt"); var rf = new RunFactory(); var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1); var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt"); var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile); var repo = importer.Import(); var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt"; var mtc = new TargetCollection(); var mtimporter = new MassTagFromTextFileImporter(massTagFile); mtc = mtimporter.Import(); var aligner = new NETAndMassAligner(); aligner.SetFeaturesToBeAligned(repo.Results); aligner.SetReferenceMassTags(mtc.TargetList); aligner.Execute(run); var exporter = new NETAlignmentInfoToTextExporter(exportNETFilename); exporter.ExportAlignmentInfo(run.AlignmentInfo); var massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename); massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo); }
public void test1() { var mtc = new TargetCollection(); var massTagImporter = new MassTagFromTextFileImporter(massTagTestFile1); mtc = massTagImporter.Import(); Assert.AreNotEqual(null, mtc.TargetList); Assert.AreEqual(101, mtc.TargetList.Count); var testMassTag = (PeptideTarget)mtc.TargetList[0]; Assert.AreEqual("AVAFGEALRPEFK", testMassTag.Code); Assert.AreEqual(2, testMassTag.ChargeState); Assert.AreEqual(0.3649905m, (decimal)testMassTag.NormalizedElutionTime); Assert.AreEqual("C67H103N17O18", testMassTag.EmpiricalFormula); Assert.AreEqual(872, testMassTag.RefID); Assert.AreEqual("ABA80002 SHMT serine hydroxymethyltransferase", testMassTag.ProteinDescription); Assert.AreEqual(1433.766629m, (decimal)testMassTag.MonoIsotopicMass); Assert.AreEqual(717.8905912m, (decimal)testMassTag.MZ); Assert.AreEqual(75, testMassTag.ObsCount); Assert.AreEqual(4225609, testMassTag.ID); }
public void SetMassTags(string massTagFilename) { var importer = new MassTagFromTextFileImporter(massTagFilename); var mtc = importer.Import(); MassTagList = mtc.TargetList; }
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 ExportNET_andMass_AlignmentDataTest1() { string exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt"); string exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt"); RunFactory rf = new RunFactory(); Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1); string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt"; UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile); TargetedResultRepository repo = importer.Import(); string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt"; MassTagCollection mtc = new MassTagCollection(); MassTagFromTextFileImporter mtimporter = new MassTagFromTextFileImporter(massTagFile); mtc = mtimporter.Import(); NETAndMassAligner aligner = new NETAndMassAligner(); aligner.SetFeaturesToBeAligned(repo.Results); aligner.SetReferenceMassTags(mtc.MassTagList); aligner.Execute(run); NETAlignmentInfoToTextExporter exporter = new NETAlignmentInfoToTextExporter(exportNETFilename); exporter.ExportAlignmentInfo(run.AlignmentInfo); MassAlignmentInfoToTextExporter massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename); massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo); }
public void doAlignmentTest1() { var rf = new RunFactory(); var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1); var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt"); var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile); var repo = importer.Import(); var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt"; var mtc = new TargetCollection(); var mtimporter = new MassTagFromTextFileImporter(massTagFile); mtc = mtimporter.Import(); var aligner = new NETAndMassAligner(); aligner.SetFeaturesToBeAligned(repo.Results); aligner.SetReferenceMassTags(mtc.TargetList); aligner.Execute(run); float testScan = 6005; var testNET1 = run.NetAlignmentInfo.GetNETValueForScan((int)testScan); //note - this is Multialign's Assert.AreEqual(0.3253423m, (decimal)testNET1); }
public void exportMassTagsToTextFile_Test1() { //first, import some data var mtc = new TargetCollection(); var massTagTestFile1 = "..\\..\\..\\TestFiles\\FileIOTests\\top40MassTags.txt"; var massTagImporter = new MassTagFromTextFileImporter(massTagTestFile1); mtc = massTagImporter.Import(); //second, export it //but first delete any existing output file if (File.Exists(testOutput1)) { File.Delete(testOutput1); } var exporter = new MassTagTextFileExporter(testOutput1); exporter.ExportResults(mtc.TargetList); var fi = new FileInfo(testOutput1); Assert.IsTrue(fi.Exists); //Assert.AreEqual(13716, fi.Length); }
public void SetMassTags(string massTagFilename) { MassTagFromTextFileImporter importer = new MassTagFromTextFileImporter(massTagFilename); MassTagCollection mtc = importer.Import(); MassTagList = mtc.MassTagList; }
public void tempUpdateLCMSFeaturesWithEmpiricalFormulaTest1() { var testLCMSFile1 = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_allWithIDs_LCMSFeatures.txt"; var massTagFileName = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_MassTags.txt"; var importer = new LcmsTargetFromFeaturesFileImporter(testLCMSFile1); var features = importer.Import(); var mtImporter = new MassTagFromTextFileImporter(massTagFileName); var massTags = mtImporter.Import(); massTags.TargetList = (from n in massTags.TargetList group n by new { n.ID, n.ChargeState } into grp select grp.First()).ToList(); var massTagIDList = features.TargetList.Select(p => (long)((LcmsFeatureTarget)p).FeatureToMassTagID).ToList(); var outputLCMSFeaturesFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_withEmpFormulas_LCMSFeatures.txt"; using (var writer = new StreamWriter(outputLCMSFeaturesFile)) { var headerLine = "TargetID\tScan\tMonoIsotopicMass\tChargeState\tMatchedMassTagID\tEmpiricalFormula"; writer.WriteLine(headerLine); foreach (var targetBase in features.TargetList) { UpdateTargetsUsingMassTagInfo(massTagIDList, features, massTags); var stringBuilder = new StringBuilder(); stringBuilder.Append(targetBase.ID); stringBuilder.Append("\t"); stringBuilder.Append(targetBase.ScanLCTarget); stringBuilder.Append("\t"); stringBuilder.Append(targetBase.MonoIsotopicMass); stringBuilder.Append("\t"); stringBuilder.Append(targetBase.ChargeState); stringBuilder.Append("\t"); stringBuilder.Append(((LcmsFeatureTarget)targetBase).FeatureToMassTagID); stringBuilder.Append("\t"); stringBuilder.Append(targetBase.EmpiricalFormula); writer.WriteLine(stringBuilder.ToString()); } } }
public void unlabelled_data_TFFTest1() { var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_first10.txt"; var masstagImporter = new MassTagFromTextFileImporter(massTagFile); var massTagColl = masstagImporter.Import(); var mt24702_charge3 = (from n in massTagColl.TargetList where n.ID == 24702 && n.ChargeState == 3 select n).First(); var mt24702_charge4 = (from n in massTagColl.TargetList where n.ID == 24702 && n.ChargeState == 4 select n).First(); }
public void testVladsData() { var testFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW"; var massTagFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2_First60.txt"; var peakTestFile = testFile.Replace(".RAW", "_peaks.txt"); var run = RunUtilities.CreateAndAlignRun(testFile, peakTestFile); var mtc = new TargetCollection(); var mtimporter = new MassTagFromTextFileImporter(massTagFile); mtc = mtimporter.Import(); var testMassTagID = 24653; run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First(); TargetedWorkflowParameters parameters = new O16O18WorkflowParameters(); parameters.ChromNETTolerance = 0.2; parameters.MSToleranceInPPM = 10; parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS; parameters.ChromPeakDetectorPeakBR = 1; parameters.ChromatogramCorrelationIsPerformed = true; var workflow = new O16O18Workflow(run, parameters); workflow.Execute(); var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as O16O18TargetedResultObject; Assert.IsTrue(workflow.Success); Assert.IsFalse(result.FailedResult); result.DisplayToConsole(); Console.WriteLine("Correlation between 016 and O18(double label)= " + result.ChromCorrO16O18DoubleLabel); Assert.IsTrue(result.ChromCorrO16O18DoubleLabel > 0); Console.WriteLine("theor monomass= \t" + result.Target.MonoIsotopicMass); Console.WriteLine("monomass= \t" + result.IsotopicProfile.MonoIsotopicMass); Console.WriteLine("ppmError before= \t" + result.MassErrorBeforeAlignment); Console.WriteLine("ppmError after= \t" + result.MassErrorAfterAlignment); }
public void 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 ComparePeakFitterVsAreaFitter() { var massTagFile1 = Path.Combine(FileRefs.RawDataBasePath, "TargetedWorkflowStandards", "QCShew_peptidesWithObsCountGreaterThan1000.txt"); //load target var masstagImporter = new MassTagFromTextFileImporter(massTagFile1); var targets = masstagImporter.Import().TargetList; var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1); var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType); var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true); var scanSet = new ScanSet(9575); run.CurrentScanSet = scanSet; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); var selectedTarget = targets.First(p => p.ID == 635428 && p.ChargeState == 3); var theorFeatureGen = new JoshTheorFeatureGenerator(Backend.Globals.LabellingType.NONE, 0.005); theorFeatureGen.GenerateTheorFeature(selectedTarget); var peakForFWHM = run.PeakList.First(p => p.XValue > 768.38 && p.XValue < 768.39); var theorXYdata = TheorXYDataCalculationUtilities.GetTheoreticalIsotopicProfileXYData(selectedTarget.IsotopicProfile, peakForFWHM.Width); theorXYdata.NormalizeYData(); var areaFitter = new AreaFitter(); var areaFitScore = areaFitter.GetFit(theorXYdata, run.XYData, 0.1); var peakLeastSquaresFitter = new PeakLeastSquaresFitter(); var peakBasedFitScore = peakLeastSquaresFitter.GetFit(new List <Peak>(selectedTarget.IsotopicProfile.Peaklist), run.PeakList, 0.1, 25); Console.WriteLine("fit score based on XYData = " + areaFitScore); Console.WriteLine("fit score based on Peaks= " + peakBasedFitScore); Assert.IsTrue(peakBasedFitScore < 0.1); }
public void loadLCMSFeatures_and_massTags() { var lcmsfeaturesFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2012\C12C13YellowStone\2011_02_20_SIPPER_workflow_standards\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 = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2012\C12C13YellowStone\2011_02_20_SIPPER_workflow_standards\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 foreach (LcmsFeatureTarget target in lcmsTargetCollection.TargetList) { if (masstagIDlist.Contains(target.ID)) { var mt = massTagCollection.TargetList.Where(p => p.ID == target.FeatureToMassTagID).First(); target.Code = mt.Code; target.EmpiricalFormula = mt.EmpiricalFormula; } else { } } int[] testMassTags = { 344540889, 344540889, 344972415, 354881152, 355157363, 355162540, 355315129 }; var filteredLcmsFeatureTargets = (from n in lcmsTargetCollection.TargetList where testMassTags.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID) select n).ToList(); foreach (LcmsFeatureTarget filteredLcmsFeatureTarget in filteredLcmsFeatureTargets) { Console.WriteLine(filteredLcmsFeatureTarget); } }
public void test2() { MassTagCollection mtc = new MassTagCollection(); MassTagFromTextFileImporter massTagImporter = new MassTagFromTextFileImporter(massTagTestFile2); massTagImporter.Import(mtc); Assert.AreEqual(3, mtc.MassTagList.Count); //Assert.AreEqual("SAMPLER", mtc.MassTagList[0].PeptideSequence); //Assert.AreEqual(2, mtc.MassTagList[0].ChargeState); //Assert.AreEqual(0.34m, (decimal)mtc.MassTagList[0].NETVal); //Assert.AreEqual("C33H58N10O11S1", mtc.MassTagList[0].Peptide.GetEmpiricalFormula()); }
protected TargetCollection GetMassTagTargets(string massTagFileName, List <int> targetIDsToFilterOn) { if (String.IsNullOrEmpty(massTagFileName) || !File.Exists(massTagFileName)) { return(new TargetCollection()); } if (massTagFileName.ToLower().Contains("_msgfplus.tsv")) { var iqTargetImporter = new BasicIqTargetImporter(massTagFileName); var iqTargets = iqTargetImporter.Import(); var targetUtilities = new IqTargetUtilities(); var targetCollection = new TargetCollection { TargetList = new List <TargetBase>() }; foreach (var iqTarget in iqTargets) { if (iqTarget.QualityScore > MsgfFdrScoreCutoff) { continue; } targetUtilities.UpdateTargetMissingInfo(iqTarget); TargetBase oldStyleTarget = new PeptideTarget(); oldStyleTarget.ChargeState = (short)iqTarget.ChargeState; oldStyleTarget.Code = iqTarget.Code; oldStyleTarget.EmpiricalFormula = iqTarget.EmpiricalFormula; oldStyleTarget.ID = iqTarget.ID; oldStyleTarget.MZ = iqTarget.MZTheor; oldStyleTarget.MonoIsotopicMass = iqTarget.MonoMassTheor; oldStyleTarget.ScanLCTarget = iqTarget.ScanLC; oldStyleTarget.NormalizedElutionTime = (float)iqTarget.ElutionTimeTheor; oldStyleTarget.ElutionTimeUnit = DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum; targetCollection.TargetList.Add(oldStyleTarget); } return(targetCollection); } var importer = new MassTagFromTextFileImporter(massTagFileName); return(importer.Import(targetIDsToFilterOn)); }
public void ImportTargetsContainingEmpiricalFormulaAndScanNumber() { var testfile = @"..\\..\\..\\TestFiles\\FileIOTests\\BSAmassTags_EmpiricalFormula_and_scans.txt"; var mtc = new TargetCollection(); var massTagImporter = new MassTagFromTextFileImporter(testfile); mtc = massTagImporter.Import(); Assert.AreNotEqual(null, mtc.TargetList); foreach (PeptideTarget peptideTarget in mtc.TargetList) { Console.WriteLine(peptideTarget); } }
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 ImportTargetsContainingOnlyEmpiricalFormula() { var testfile = @"..\\..\\..\\TestFiles\\FileIOTests\\QCShew_Bin10_Top10_empiricalFormula_NET_only.txt"; var mtc = new TargetCollection(); var massTagImporter = new MassTagFromTextFileImporter(testfile); mtc = massTagImporter.Import(); Assert.AreNotEqual(null, mtc.TargetList); foreach (PeptideTarget peptideTarget in mtc.TargetList) { Console.WriteLine(peptideTarget); } }
public void ensureAlignment_was_executed() { var run = new RunFactory().CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1); var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_READONLY_alignedFeatures.txt"; var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile); var repo = importer.Import(); var massTagFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_Formic_MassTags_Bin10_all.txt"; var mtc = new TargetCollection(); var mtimporter = new MassTagFromTextFileImporter(massTagFile); mtc = mtimporter.Import(); var parameters = new NETAndMassAlignerParameters(); var aligner = new NETAndMassAligner(); aligner.SetFeaturesToBeAligned(repo.Results); aligner.SetReferenceMassTags(mtc.TargetList); var scan = 7835; var theorMZ = 780.08485; //massTagID = 24701 (+3) var obsMZ = 780.0824; var netBeforeAlignment = run.NetAlignmentInfo.GetNETValueForScan(scan); var mzBeforeAlignment = run.GetAlignedMZ(obsMZ); aligner.Execute(run); var netAfterAlignment = run.NetAlignmentInfo.GetNETValueForScan(scan); var mzAfterAlignment = run.GetAlignedMZ(obsMZ); Console.WriteLine("NET before alignment = " + netBeforeAlignment); Console.WriteLine("NET after alignment = " + netAfterAlignment); Console.WriteLine("Theor MZ = " + theorMZ); Console.WriteLine("MZ before alignment = " + mzBeforeAlignment); Console.WriteLine("MZ after alignment = " + mzAfterAlignment); Console.WriteLine("PPMDiff before alignment = " + (theorMZ - mzBeforeAlignment) / theorMZ * 1e6); Console.WriteLine("PPMDiff after alignment = " + (theorMZ - mzAfterAlignment) / theorMZ * 1e6); }
public void Test1() { var rawdataFile = @"D:\Data\Orbitrap\QC_Shew_09_05-pt5-6_4Jan10_Doc_09-11-08.RAW"; var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt"; var parameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\UnlabelledTargeted_WorkflowParameters_noSum.xml"; var mtimporter = new MassTagFromTextFileImporter(massTagFile); var mtc = new TargetCollection(); mtc = mtimporter.Import(); var run = new RunFactory().CreateRun(rawdataFile); //RunUtilities.AlignRunUsingAlignmentInfoInFiles(run); var expectedPeaksFilename = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt"); var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(expectedPeaksFilename, null); peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList); var testMassTagID = 3513677; var massTagChargeState = 2; run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == massTagChargeState select n).First(); var parameters = WorkflowParameters.CreateParameters(parameterFile); var workflow = TargetedWorkflow.CreateWorkflow(parameters); workflow.Run = run; workflow.Execute(); workflow.Result.DisplayToConsole(); RunUtilities.AlignRunUsingAlignmentInfoInFiles(run); workflow.Execute(); workflow.Result.DisplayToConsole(); }
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 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 ImportPeptidesWithModsTest1() { var mtc = new TargetCollection(); var massTagImporter = new MassTagFromTextFileImporter(massTagsWithModsFile1); mtc = massTagImporter.Import(); Assert.AreNotEqual(null, mtc.TargetList); Assert.AreEqual(1868, mtc.TargetList.Count); var testMassTag = (PeptideTarget)mtc.TargetList[1021]; Assert.AreEqual(testMassTag.EmpiricalFormula, "C56H82N10O13"); Assert.AreEqual(1, testMassTag.ModCount); Assert.AreEqual(testMassTag.ModDescription, "NH3_Loss:1"); //250663994 1102.60623 QFPILLDFK 2 C56H82N10O13 1 NH3_Loss:1 }
public void findSingleMassTag_test1() { var testFile = @"D:\Data\O16O18\Weijun\TechTest_O18_02\TechTest_O18_02_RunA_10Dec09_Doc_09-11-08.RAW"; var massTagFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2011\O16O18_TargetedProcessing\Targets\MassTags_MousePlasma_1709_allChargeStates_nonRedundant.txt"; var peakTestFile = testFile.Replace(".RAW", "_peaks.txt"); var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile); var mtc = new TargetCollection(); var mtimporter = new MassTagFromTextFileImporter(massTagFile); mtc = mtimporter.Import(); var testMassTagID = 6643962; run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First(); TargetedWorkflowParameters parameters = new O16O18WorkflowParameters(); parameters.ChromNETTolerance = 0.1; parameters.MSToleranceInPPM = 10; var workflow = new O16O18Workflow(run, parameters); workflow.Execute(); var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag); Assert.IsNotNull(result); result.DisplayToConsole(); Assert.IsNotNull(result.IsotopicProfile); Assert.IsNotNull(result.ScanSet); Assert.IsNotNull(result.ChromPeakSelected); Assert.AreEqual(2, result.IsotopicProfile.ChargeState); Assert.AreEqual(6865, result.ScanSet.PrimaryScanNumber); }
public void Test1() { var testFile = @"\\protoapps\UserData\Slysz\Data\O16O18\BSA\BSA_18O_99_8Jan11_Falcon_10-12-09.RAW"; var massTagFile = @"\\protoapps\UserData\Slysz\Data\O16O18\BSA\Targets\BSAmassTags_MinimalInfo_withScans.txt"; var peakTestFile = testFile.Replace(".RAW", "_peaks.txt"); var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile); var mtc = new TargetCollection(); var mtimporter = new MassTagFromTextFileImporter(massTagFile); mtc = mtimporter.Import(); var testMassTagID = 3; run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First(); TargetedWorkflowParameters parameters = new O16O18WorkflowParameters(); parameters.ChromNETTolerance = 0.2; parameters.MSToleranceInPPM = 10; parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.MostIntense; parameters.ChromGeneratorMode = DeconTools.Backend.Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS; parameters.ChromSmootherNumPointsInSmooth = 31; var workflow = new O16O18Workflow(run, parameters); workflow.Execute(); Assert.IsTrue(workflow.Result.Target.ScanLCTarget > 0); Assert.IsNotNull(workflow.ChromPeakSelected); Assert.AreEqual(10622, (int)workflow.ChromPeakSelected.XValue); Console.WriteLine("ChromPeak scan value = " + workflow.ChromPeakSelected.XValue); }
public void importFromSQLManagmentStyleTextFile_test1() { var mtc = new TargetCollection(); var massTagImporter = new MassTagFromTextFileImporter(massTagTestFile2); mtc = massTagImporter.Import(); Assert.AreNotEqual(null, mtc.TargetList); Assert.AreEqual(33, mtc.TargetList.Count); var testMassTag = mtc.TargetList[0] as PeptideTarget; Assert.AreEqual("AVTTADQVQQEVER", testMassTag.Code); Assert.AreEqual(2, testMassTag.ChargeState); Assert.AreEqual(0.2365603m, (decimal)testMassTag.NormalizedElutionTime); Assert.AreEqual("C64H108N20O26", testMassTag.EmpiricalFormula); Assert.AreEqual(137, testMassTag.RefID); Assert.AreEqual(1572.774283m, (decimal)testMassTag.MonoIsotopicMass); Assert.AreEqual(787.39441799m, (decimal)testMassTag.MZ); Assert.AreEqual(6, testMassTag.ObsCount); Assert.AreEqual(354885422, testMassTag.ID); }
public void ImportPeptidesContainingOnlySequenceInfo() { var testfile = @"..\\..\\..\\TestFiles\\FileIOTests\\BSAmassTags_MinimalInfo1.txt"; var mtc = new TargetCollection(); var massTagImporter = new MassTagFromTextFileImporter(testfile); mtc = massTagImporter.Import(); Assert.AreNotEqual(null, mtc.TargetList); foreach (PeptideTarget peptideTarget in mtc.TargetList) { Console.WriteLine(peptideTarget); } Assert.AreEqual(111, mtc.TargetList.Count); var testMassTag = (PeptideTarget)mtc.TargetList[0]; Assert.AreEqual("LFTFHADICTLPDTEK", testMassTag.Code); Assert.AreEqual("C84H127N19O26S", testMassTag.EmpiricalFormula); Assert.IsTrue(testMassTag.MonoIsotopicMass > 0); }