public void Test1() { string testFile = @"\\proto-10\IMS_TOF_4\2012_3\Sarc_P22_B06_2034_23Jul12_Cheetah_11-12-23\Sarc_P22_B06_2034_23Jul12_Cheetah_11-12-23.uimf"; testFile = @"D:\Data\UIMF\Problem_datasets\Sarc_P22_B06_2034_23Jul12_Cheetah_11-12-23.uimf"; string parameterFile = @"\\gigasax\DMS_Parameter_Files\Decon2LS\IMS_UIMF_PeakBR2_PeptideBR3_SN3_SumScans3_NoLCSum_Sat50000_2012-02-27.xml"; string expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv"); string expectedScansOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_scans.csv"); if (File.Exists(expectedIsosOutput)) { File.Delete(expectedIsosOutput); } if (File.Exists(expectedScansOutput)) { File.Delete(expectedScansOutput); } var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile); workflow.Execute(); }
public void Test1() { Run run = new RunFactory().CreateRun( @"\\pnl\projects\MSSHARE\Webb_Ian\no cid.UIMF"); DeconToolsParameters parameters = new DeconToolsParameters(); parameters.LoadFromOldDeconToolsParameterFile( @"\\pnl\projects\MSSHARE\Webb_Ian\IMS_UIMF_PeakBR2_PeptideBR3_SN3_SumScans3_NoLCSum_Sat50000_2012-02-27.xml"); string expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv"); string expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv"); string expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt"); if (File.Exists(expectedIsosFile)) { File.Delete(expectedIsosFile); } if (File.Exists(expectedScansFile)) { File.Delete(expectedScansFile); } if (File.Exists(expectedPeaksFile)) { File.Delete(expectedPeaksFile); } var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.Execute(); }
public void scanBasedWorkflowTest1() { string testFile = @"D:\Data\JIRA_issues\OMCS-149_MS2_not_in_Scans\DsrC_Black_02_6Feb12_Cougar_11-10-11.raw"; string parameterFile = @"D:\Data\JIRA_issues\OMCS-149_MS2_not_in_Scans\LTQ_Orb_USTags_MS2_THRASH_WithPeaks_Relaxed.xml"; Run run = new RunFactory().CreateRun(testFile); var parameters = new OldDecon2LSParameters(); parameters.Load(parameterFile); var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.OldDecon2LsParameters.HornTransformParameters.UseScanRange = true; workflow.OldDecon2LsParameters.HornTransformParameters.MinScan = 25; workflow.OldDecon2LsParameters.HornTransformParameters.MaxScan = 35; workflow.ExportData = true; workflow.Execute(); // foreach (var isosResult in run.ResultCollection.ResultList) // { // isosResult.Display(); // } }
public void saturatedFixingTest2() { string uimfFile = @"D:\Data\UIMF\Sarc_Main_Study_Controls\Sarc_P08_A01_0673_21Nov11_Cheetah_11-09-03.uimf"; Run run = new RunFactory().CreateRun(uimfFile); var parameters = new DeconToolsParameters(); parameters.LoadFromOldDeconToolsParameterFile(@"\\gigasax\DMS_Parameter_Files\Decon2LS\IMS_UIMF_PeakBR4_PeptideBR4_SN3_SumScans3_NoLCSum_Sat50000_2012-01-30.xml"); parameters.MSGeneratorParameters.UseLCScanRange = true; parameters.MSGeneratorParameters.MinLCScan = 397; parameters.MSGeneratorParameters.MaxLCScan = 408; parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "uimf_saturation_repair"; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.ExportData = true; var sw = new Stopwatch(); sw.Start(); workflow.Execute(); return; sw.Stop(); var distinctItems = run.ResultCollection.ResultList.GroupBy(x => x.MSFeatureID).Select(y => y.First()).ToList(); int minFrame = parameters.MSGeneratorParameters.MinLCScan; int maxFrame = parameters.MSGeneratorParameters.MaxLCScan; int minScan = 102; int maxScan = 125; double targetMass = 1642.85958; int chargestate = 4; double tolerance = 0.3; var featureData = (from n in distinctItems where (Math.Abs(n.IsotopicProfile.MonoIsotopicMass - targetMass)) < tolerance && n.IsotopicProfile.ChargeState == chargestate select n).Select <IsosResult, UIMFIsosResult>(r => (UIMFIsosResult)r).ToList(); OutputFeatureIntensityData(featureData, minFrame, maxFrame, maxScan, minScan); MathUtils mathUtils = new MathUtils(); var monoMasses = (from n in featureData select n.IsotopicProfile.MonoIsotopicMass).ToList(); var massVariance = MathUtils.GetStDev(monoMasses); Console.WriteLine("Mass variance = " + massVariance); Console.WriteLine("Time taken = " + sw.ElapsedMilliseconds); }
public void TempSaturationFixingTestOnYehiaBSAData() { var uimfFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\BSA_30N2_30ms_gate_10tof_Padjust_0000.UIMF"; var run = new RunFactory().CreateRun(uimfFile); var parameters = new DeconToolsParameters(); parameters.PeakDetectorParameters.PeakToBackgroundRatio = 4; parameters.PeakDetectorParameters.SignalToNoiseThreshold = 3; parameters.ThrashParameters.MaxFit = 0.6; parameters.MSGeneratorParameters.UseLCScanRange = true; parameters.MSGeneratorParameters.MinLCScan = 2; parameters.MSGeneratorParameters.MaxLCScan = 2; parameters.MSGeneratorParameters.UseMZRange = true; parameters.MSGeneratorParameters.MinMZ = 652; parameters.MSGeneratorParameters.MaxMZ = 657; parameters.MSGeneratorParameters.SumSpectraAcrossLC = true; parameters.MSGeneratorParameters.SumSpectraAcrossIms = true; parameters.MSGeneratorParameters.NumLCScansToSum = 1; parameters.MSGeneratorParameters.NumImsScansToSum = 7; parameters.MiscMSProcessingParameters.UseZeroFilling = true; parameters.ThrashParameters.MinIntensityForDeletion = 10; parameters.MiscMSProcessingParameters.SaturationThreshold = 6000; parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "uimf_saturation_repair"; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); //workflow.ExportData = false; workflow.Execute(); }
public void scanBasedWorkflowTest1() { string testFile = @"D:\Data\UIMF\Problem_datasets\DsrC_Black_02_6Feb12_Cougar_11-10-11.raw"; string parameterFile = @"D:\Data\UIMF\Problem_datasets\LTQ_Orb_USTags_MS2_THRASH_WithPeaks_Relaxed.xml"; Run run = new RunFactory().CreateRun(testFile); var parameters = new DeconToolsParameters(); parameters.LoadFromOldDeconToolsParameterFile(parameterFile); var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.NewDeconToolsParameters.MSGeneratorParameters.UseLCScanRange = true; workflow.NewDeconToolsParameters.MSGeneratorParameters.MinLCScan = 1; workflow.NewDeconToolsParameters.MSGeneratorParameters.MaxLCScan = 5; workflow.ExportData = true; workflow.Execute(); // foreach (var isosResult in run.ResultCollection.ResultList) // { // isosResult.Display(); // } }
public void saturatedFixingTest3() { var uimfFile = @"D:\Data\UIMF\Sarc_Main_Study_Controls\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf"; var run = new RunFactory().CreateRun(uimfFile); var parameters = new DeconToolsParameters(); parameters.LoadFromOldDeconToolsParameterFile( @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\IMS_UIMF_PeakBR2_PeptideBR3_SN3_SumScans3_NoLCSum_Sat50000_2012-02-27_frames_180_195.xml"); parameters.MSGeneratorParameters.UseLCScanRange = true; parameters.MSGeneratorParameters.MinLCScan = 394; parameters.MSGeneratorParameters.MaxLCScan = 404; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.ExportData = false; var sw = new Stopwatch(); sw.Start(); workflow.Execute(); //return; sw.Stop(); var distinctItems = run.ResultCollection.ResultList.GroupBy(x => x.MSFeatureID).Select(y => y.First()).ToList(); var minFrame = parameters.MSGeneratorParameters.MinLCScan; var maxFrame = parameters.MSGeneratorParameters.MaxLCScan; var minScan = 102; var maxScan = 127; var targetMass = 1059.55169; var chargestate = 2; var tolerance = 0.3; var featureData = (from n in distinctItems where (Math.Abs(n.IsotopicProfile.MonoIsotopicMass - targetMass)) < tolerance && n.IsotopicProfile.ChargeState == chargestate select n).Select <IsosResult, UIMFIsosResult>(r => (UIMFIsosResult)r).ToList(); OutputFeatureIntensityData(featureData, minFrame, maxFrame, maxScan, minScan); var mathUtils = new MathUtils(); var monoMasses = (from n in featureData select n.IsotopicProfile.MonoIsotopicMass).ToList(); var massVariance = MathUtils.GetStDev(monoMasses); Console.WriteLine("Mass variance = " + massVariance); Console.WriteLine("Time taken = " + sw.ElapsedMilliseconds); }
public void TraditionalWorkflowTestOrbitrapData_useThrashV1_test2() { var parameterFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\LTQ_Orb\LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_Thrash_scan6000_9000 - oldThrash.xml"; var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1); var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv"); var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv"); var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt"); if (File.Exists(expectedIsosFile)) { File.Delete(expectedIsosFile); } if (File.Exists(expectedScansFile)) { File.Delete(expectedScansFile); } if (File.Exists(expectedPeaksFile)) { File.Delete(expectedPeaksFile); } var parameters = new DeconToolsParameters(); parameters.LoadFromOldDeconToolsParameterFile(parameterFile); //parameters.MSGeneratorParameters.MinLCScan = 6005; //parameters.MSGeneratorParameters.MaxLCScan = 6005; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.Execute(); Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created."); Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created."); Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created."); var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType); var isos = isosImporter.Import(); Assert.AreEqual(186, isos.Count); var peakImporter = new PeakImporterFromText(expectedPeaksFile); var peaklist = new List <MSPeakResult>(); peakImporter.ImportPeaks(peaklist); Assert.AreEqual(809, peaklist.Count); var sumIntensities = isos.Select(p => p.IntensityAggregate).Sum(); //Assert.AreEqual(263499300d, Math.Round(sumIntensities)); var sumPeakIntensities = peaklist.Select(p => p.Height).Sum(); //Assert.AreEqual(605170496.0f, sumPeakIntensities); }
public void ProcessOrbitrapData1() { var testFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1; var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile; var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv"); var expectedPeaksFileOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_peaks.txt"); if (File.Exists(expectedIsosOutput)) { File.Delete(expectedIsosOutput); } if (File.Exists(expectedPeaksFileOutput)) { File.Delete(expectedPeaksFileOutput); } var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile); var stopwatch = new Stopwatch(); stopwatch.Start(); workflow.Execute(); stopwatch.Stop(); var typicalTimeInSeconds = 11.0; var currentTimeInSeconds = Math.Round(stopwatch.ElapsedMilliseconds / (double)1000, 1); Console.WriteLine("Typical processing time (sec)= " + typicalTimeInSeconds); Console.WriteLine("Current Processing time (sec) = " + currentTimeInSeconds); var percentDiff = (currentTimeInSeconds - typicalTimeInSeconds) / typicalTimeInSeconds * 100; Assert.IsTrue(percentDiff < 20, "Processing failed time test. Too slow."); Assert.That(File.Exists(expectedIsosOutput)); Assert.That(File.Exists(expectedPeaksFileOutput)); Console.WriteLine(percentDiff); var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.Finnigan); var results = new List <IsosResult>(); results = importer.Import(); //TestUtilities.DisplayMSFeatures(results); //Assert.AreEqual(1340, results.Count); //Assert.AreEqual(2006580356, results.Sum(p => p.IntensityAggregate)); }
public void NegativeIonModeDeisotoping_useThrashV1() { var parameterFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\LTQ_Orb\LTQ_Orb_SN2_PeakBR2_PeptideBR1_NegIon_Thrash_Sum3.xml"; var testFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\NegativeIonMode\AC2_Neg_highpH_14Apr13_Sauron_13-04-03.raw"; var run = new RunFactory().CreateRun(testFile); var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv"); var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv"); var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt"); if (File.Exists(expectedIsosFile)) { File.Delete(expectedIsosFile); } if (File.Exists(expectedScansFile)) { File.Delete(expectedScansFile); } if (File.Exists(expectedPeaksFile)) { File.Delete(expectedPeaksFile); } var parameters = new DeconToolsParameters(); parameters.LoadFromOldDeconToolsParameterFile(parameterFile); parameters.ScanBasedWorkflowParameters.DeconvolutionType = Globals.DeconvolutionType.ThrashV1; parameters.MSGeneratorParameters.MinLCScan = 4100; parameters.MSGeneratorParameters.MaxLCScan = 4100; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.Execute(); Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created."); Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created."); Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created."); var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType); var isos = isosImporter.Import(); var testIso = (from n in isos where n.IsotopicProfile.MonoPeakMZ > 744 && n.IsotopicProfile.MonoPeakMZ < 749 select n).FirstOrDefault(); Assert.IsNotNull(testIso, "Test iso not found."); Console.WriteLine("monomass= " + testIso.IsotopicProfile.MonoIsotopicMass); Assert.AreEqual(1491.32852m, (decimal)Math.Round(testIso.IsotopicProfile.MonoIsotopicMass, 5)); }
public void TraditionalWorkflowTestOrbitrapData_usingNewThrash() { var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile; var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1); var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv"); var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv"); var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt"); if (File.Exists(expectedIsosFile)) { File.Delete(expectedIsosFile); } if (File.Exists(expectedScansFile)) { File.Delete(expectedScansFile); } if (File.Exists(expectedPeaksFile)) { File.Delete(expectedPeaksFile); } var allPeaksFilepath = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_peaksFULL.txt"; File.Copy(allPeaksFilepath, allPeaksFilepath.Replace("FULL", "")); var parameters = new DeconToolsParameters(); parameters.LoadFromOldDeconToolsParameterFile(parameterFile); parameters.ScanBasedWorkflowParameters.DeconvolutionType = Globals.DeconvolutionType.ThrashV2; parameters.MSGeneratorParameters.UseLCScanRange = true; parameters.MSGeneratorParameters.MinLCScan = 6000; // run.GetMinPossibleLCScanNum(); parameters.MSGeneratorParameters.MaxLCScan = 6050; // run.GetMaxPossibleLCScanNum(); var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.Execute(); Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created."); Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created."); Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created."); var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType); var isos = isosImporter.Import(); //Assert.AreEqual(186, isos.Count); //TODO: still report Console.WriteLine("Num MSfeatures = " + isos.Count); var sumIntensities = isos.Select(p => p.IntensityAggregate).Sum(); // Assert.AreEqual(266185816d, Math.Round(sumIntensities)); }
public void ProblemTesting() { var parameterFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\DeconMSn\ParameterFiles\DeconMSn_LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_scans6000_6050.xml"; var rawdataFile = @"D:\Data\DeconMSn_testing\CPTAC_CompRef_test_iTRAQ_NiNTA_08_17Jan13_Frodo_12-12-50.raw"; var workflow = ScanBasedWorkflow.CreateWorkflow(rawdataFile, parameterFile); workflow.Execute(); }
public void WorkflowTypeIsWrongTest1() { var uimfFile = @"D:\Data\UIMF\Sarc_Main_Study_Controls\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf"; var run = new RunFactory().CreateRun(uimfFile); var parameters = new DeconToolsParameters(); parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "incorrectTextProblem"; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); }
void bw_DoWork(object sender, DoWorkEventArgs e) { var bw = (BackgroundWorker)sender; try { //This mode was requested by Julia Laskin. //This mode detects peaks in each dataset and merges the output if (_parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName.ToLower() == "run_merging_with_peak_export") { var workflow = new RunMergingPeakExportingWorkflow(_parameters, _inputFileList, _outputPath, bw); workflow.Execute(); } else { foreach (var file in _inputFileList) { _currentFile = file; var workflow = ScanBasedWorkflow.CreateWorkflow(file, _parameterFileName, _outputPath, bw); workflow.Execute(); } } } catch (COMException ex) { // bool isFile = RunUtilities.RunIsFileOrFolder(_currentFile); var errorMessage = "A 'COMException' has occurred. This can happen when the vendor library has not been installed.\n\n"; errorMessage += "If you are trying to read Thermo .raw files, please install Thermo's MSFileReader library. "; errorMessage += "To do so, Google 'thermo msfilereader' and you should find it. If not, contact us.\n\n"; errorMessage += "Full error details below:\n"; errorMessage += ex.Message; MessageBox.Show(errorMessage, "COMError occurred"); } catch (Exception ex) { MessageBox.Show(ex.Message + Environment.NewLine + Environment.NewLine + "**NOTE: see log file for additional details."); } if (bw.CancellationPending) { e.Cancel = true; } }
public void TraditionalWorkflowTestOrbitrapData_DetectPeaksOnly() { var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile; var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1); var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv"); var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv"); var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt"); if (File.Exists(expectedIsosFile)) { File.Delete(expectedIsosFile); } if (File.Exists(expectedScansFile)) { File.Delete(expectedScansFile); } if (File.Exists(expectedPeaksFile)) { File.Delete(expectedPeaksFile); } var parameters = new DeconToolsParameters(); parameters.LoadFromOldDeconToolsParameterFile(parameterFile); parameters.ScanBasedWorkflowParameters.DeconvolutionType = Globals.DeconvolutionType.None; parameters.MSGeneratorParameters.MinLCScan = 6005; parameters.MSGeneratorParameters.MaxLCScan = 6005; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.Execute(); Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created."); Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created."); Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created."); var peakImporter = new PeakImporterFromText(expectedPeaksFile); var peaklist = new List <MSPeakResult>(); peakImporter.ImportPeaks(peaklist); Assert.AreEqual(809, peaklist.Count); var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType); var isos = isosImporter.Import(); Assert.AreEqual(0, isos.Count); }
public void createScanSetTests() { int testScan1 = 6005; var run = new RunFactory().CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1); ScanBasedWorkflow workflow = new ScanBasedWorkflow(run); workflow.NumScansSummed = 3; workflow.SetScanSet(testScan1); Assert.AreEqual(3, workflow.scanSetSelected.IndexValues.Count); }
public void getRunInfoTest1() { var run = new RunFactory().CreateRun(_testdatafile); Console.WriteLine(TestUtilities.DisplayRunInformation(run)); OldDecon2LSParameters parameters = new OldDecon2LSParameters(); parameters.PeakProcessorParameters.WritePeaksToTextFile = true; ScanBasedWorkflow workflow = ScanBasedWorkflow.CreateWorkflow(run, new OldDecon2LSParameters()); workflow.Execute(); }
public void processOrbitrapData_outputMS2_and_peaks_test1() { var testFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1; var parameterFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\LTQ_Orb\LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_Thrash_scans6000_6050_MS2.xml"; var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv"); var expectedScansOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_scans.csv"); var expectedPeaksFileOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_peaks.txt"); if (File.Exists(expectedIsosOutput)) { File.Delete(expectedIsosOutput); } if (File.Exists(expectedScansOutput)) { File.Delete(expectedScansOutput); } if (File.Exists(expectedPeaksFileOutput)) { File.Delete(expectedPeaksFileOutput); } var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile); workflow.Execute(); Assert.That(File.Exists(expectedIsosOutput)); Assert.That(File.Exists(expectedScansOutput)); Assert.That(File.Exists(expectedPeaksFileOutput)); var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.Finnigan); var results = new List <IsosResult>(); results = importer.Import(); // TestUtilities.DisplayMSFeatures(results); //Assert.AreEqual(1340, results.Count); //Assert.AreEqual(2006580356, results.Sum(p => p.IntensityAggregate)); }
public void TraditionalWorkflowTestOrbitrapData_InformedThrash() { var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile; var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1); var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv"); var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv"); var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt"); if (File.Exists(expectedIsosFile)) { File.Delete(expectedIsosFile); } if (File.Exists(expectedScansFile)) { File.Delete(expectedScansFile); } //if (File.Exists(expectedPeaksFile)) File.Delete(expectedPeaksFile); var parameters = new DeconToolsParameters(); parameters.LoadFromOldDeconToolsParameterFile(parameterFile); parameters.ScanBasedWorkflowParameters.DeconvolutionType = Globals.DeconvolutionType.ThrashV2; parameters.MSGeneratorParameters.MinLCScan = 6005; parameters.MSGeneratorParameters.MaxLCScan = 6050; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.Execute(); Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created."); Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created."); Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created."); var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType); var isos = isosImporter.Import(); Assert.AreEqual(1287, isos.Count); var sumIntensities = isos.Select(p => p.IntensityAggregate).Sum(); Assert.AreEqual(1974438598m, (decimal)Math.Round(sumIntensities)); // Expected: 1973657234m // But was: 1974438598m }
public void WorkflowTypeIsCorrectTest1() { var uimfFile = @"D:\Data\UIMF\Sarc_Main_Study_Controls\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf"; var run = new RunFactory().CreateRun(uimfFile); var parameters = new DeconToolsParameters(); parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "standard"; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); Assert.IsTrue(workflow is IMSScanBasedWorkflow); parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "uimf_saturation_repair"; workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); Assert.IsTrue(workflow is SaturationIMSScanBasedWorkflow); }
public void WorkflowTestUsingParameterFile_Sum5_Test1() { var parameterFile = @"C:\Users\d3x720\Documents\Data\QCShew\DeconMSn_LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_LCSum5.xml"; var localTestFile = @"C:\Users\d3x720\Documents\Data\QCShew\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW"; var outputFolder = @"C:\Users\d3x720\Documents\Data\QCShew\Output"; var workflow = ScanBasedWorkflow.CreateWorkflow(localTestFile, parameterFile, outputFolder); workflow.Execute(); }
public void processUIMFContainingMSMS() { var testFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\MSMS_Testing\PepMix_MSMS_4msSA.UIMF"; var run = new RunFactory().CreateRun(testFile); var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv"); if (File.Exists(expectedIsosOutput)) { File.Delete(expectedIsosOutput); } var parameters = new DeconToolsParameters(); parameters.MSGeneratorParameters.NumLCScansToSum = 3; parameters.MSGeneratorParameters.NumImsScansToSum = 9; parameters.PeakDetectorParameters.PeakToBackgroundRatio = 4; parameters.MiscMSProcessingParameters.UseZeroFilling = true; parameters.ScanBasedWorkflowParameters.ProcessMS2 = true; parameters.MSGeneratorParameters.UseLCScanRange = true; parameters.MSGeneratorParameters.SumSpectraAcrossLC = true; parameters.MSGeneratorParameters.MinLCScan = 1; //min frame parameters.MSGeneratorParameters.MaxLCScan = 15; //max frame var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.Execute(); var results = new List <IsosResult>(); Assert.That(File.Exists(expectedIsosOutput)); var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.PNNL_UIMF); results = importer.Import(); //TestUtilities.DisplayMSFeatures(results); //Assert.AreEqual(36078, results.Count); //Assert.AreEqual(1224247916, (int)results.Sum(p => p.IntensityAggregate)); }
public void ProcessMZ5File() { var testFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\mzXML\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.mz5"; var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile; var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv"); var expectedPeaksFileOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_peaks.txt"); if (File.Exists(expectedIsosOutput)) { File.Delete(expectedIsosOutput); } if (File.Exists(expectedPeaksFileOutput)) { File.Delete(expectedPeaksFileOutput); } var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile); workflow.Execute(); Assert.That(File.Exists(expectedIsosOutput)); Assert.That(File.Exists(expectedPeaksFileOutput)); var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.Finnigan); var results = new List <IsosResult>(); results = importer.Import(); TestUtilities.DisplayMSFeatures(results); Assert.AreEqual(1340, results.Count); Assert.AreEqual(2006580356, results.Sum(p => p.IntensityAggregate)); }
public void ProcessBruker9T() { var testFile = FileRefs.RawDataMSFiles.Bruker9TStandardFile2; var dirInfo = new DirectoryInfo(testFile); var datasetName = dirInfo.Name; var expectedIsosOutput = Path.Combine(testFile, datasetName + "_isos.csv"); if (File.Exists(expectedIsosOutput)) { File.Delete(expectedIsosOutput); } var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, FileRefs.ParameterFiles.Bruker9T_Scans1000_1010ParamFile); workflow.Execute(); Assert.That(File.Exists(expectedIsosOutput)); }
public void processYAFMSFile1() { var testFile = FileRefs.RawDataMSFiles.YAFMSStandardFile2; var parameterFile = FileRefs.ParameterFiles.YAFMSParameterFileScans4000_4050; var dirInfo = new DirectoryInfo(testFile); var datasetName = dirInfo.Name; var expectedIsosOutput = Path.Combine(testFile, datasetName + "_isos.csv"); if (File.Exists(expectedIsosOutput)) { File.Delete(expectedIsosOutput); } var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile); workflow.Execute(); //Assert.That(File.Exists(expectedIsosOutput)); }
public void processUIMF_Frames800_802_SumAllIMSScansPerFrame() { var testFile = FileRefs.RawDataMSFiles.UIMFStdFile3; var parameterFile = Path.Combine(FileRefs.RawDataBasePath, "ParameterFiles", "UIMF_frames_peakBR7_800-802_OneSpectrumPerFrame.xml"); var run = new RunFactory().CreateRun(testFile); var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv"); if (File.Exists(expectedIsosOutput)) { File.Delete(expectedIsosOutput); } var parameters = new DeconToolsParameters(); parameters.MSGeneratorParameters.MinLCScan = 800; parameters.MSGeneratorParameters.MaxLCScan = 802; parameters.MSGeneratorParameters.UseLCScanRange = true; parameters.MSGeneratorParameters.SumAllSpectra = true; parameters.MiscMSProcessingParameters.UseZeroFilling = true; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.Execute(); var results = new List <IsosResult>(); Assert.That(File.Exists(expectedIsosOutput)); var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.PNNL_UIMF); results = importer.Import(); //TestUtilities.DisplayMSFeatures(results); //Assert.AreEqual(189, results.Count); //Assert.AreEqual(62294623, (int)results.Sum(p => p.IntensityAggregate)); }
public void ProcessBruker12TSolarixFile1() { var testFile = FileRefs.RawDataMSFiles.BrukerSolarix12TFile1; var dirInfo = new DirectoryInfo(testFile); var datasetName = dirInfo.Name; var expectedIsosOutput = Path.Combine(FileRefs.RawDataMSFiles.BrukerSolarix12TFile1, datasetName + "_isos.csv"); if (File.Exists(expectedIsosOutput)) { File.Delete(expectedIsosOutput); } var run = new RunFactory().CreateRun(testFile); var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, FileRefs.ParameterFiles.Bruker12TSolarixScans4_8ParamFile); workflow.Execute(); Assert.That(File.Exists(expectedIsosOutput)); }
public void noFixingTest1() { var uimfFile = @"D:\Data\UIMF\Sarc_Main_Study_Controls\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf"; var run = new RunFactory().CreateRun(uimfFile); var parameters = new DeconToolsParameters(); parameters.PeakDetectorParameters.PeakToBackgroundRatio = 4; parameters.PeakDetectorParameters.SignalToNoiseThreshold = 3; parameters.MSGeneratorParameters.UseLCScanRange = true; parameters.MSGeneratorParameters.MinLCScan = 180; parameters.MSGeneratorParameters.MaxLCScan = 180; parameters.MSGeneratorParameters.SumSpectraAcrossLC = true; parameters.MSGeneratorParameters.SumSpectraAcrossIms = true; parameters.MSGeneratorParameters.NumLCScansToSum = 1; parameters.MSGeneratorParameters.NumImsScansToSum = 3; var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters); workflow.Execute(); }
public void WorkflowTestUsingParameterFile1() { var parameterFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\DeconMSn\ParameterFiles\DeconMSn_LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_scans6000_6050.xml"; var rawdataFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1; var outputFolder = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\DeconMSn\Output"; var datasetName = RunUtilities.GetDatasetName(rawdataFile); var expectedResultsFile1 = Path.Combine(outputFolder, datasetName + ".mgf"); var expectedResultsFile2 = Path.Combine(outputFolder, datasetName + "_DeconMSn_log.txt"); var expectedResultsFile3 = Path.Combine(outputFolder, datasetName + "_profile.txt"); if (File.Exists(expectedResultsFile1)) { File.Delete(expectedResultsFile1); } if (File.Exists(expectedResultsFile2)) { File.Delete(expectedResultsFile2); } if (File.Exists(expectedResultsFile3)) { File.Delete(expectedResultsFile3); } var workflow = ScanBasedWorkflow.CreateWorkflow(rawdataFile, parameterFile, outputFolder); workflow.Execute(); Assert.IsTrue(File.Exists(expectedResultsFile1)); Assert.IsTrue(File.Exists(expectedResultsFile2)); Assert.IsTrue(File.Exists(expectedResultsFile3)); }
public void ProcessAgilentCentroidedFile() { var testFile = @"\\protoapps\UserData\Nikola\DDD_Milk\D6.1.forExpRepAnal_3.14.2012.d"; var parameterFile = @"\\protoapps\UserData\Nikola\DDD_Milk\agilTOF_Normal_SavGolSmooth_2007-08-16_DEFAULT.xml"; var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile); workflow.Execute(); //return; string expectedIsosOutput = null; var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.Finnigan); var results = new List <IsosResult>(); results = importer.Import(); TestUtilities.DisplayMSFeatures(results); Assert.AreEqual(1340, results.Count); Assert.AreEqual(2006580356, results.Sum(p => p.IsotopicProfile.IntensityMostAbundant)); }