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 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 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 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 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 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 LoadParametersForIMSDataprocessingTest2()
{
var parameterFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\IMS\IMS_UIMF_PeakBR4_PeptideBR4_SN3_SumScans3_NoLCSum_Sat90000_newFormat.xml";
Assert.IsTrue(File.Exists(parameterFile));
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(parameterFile);
Assert.IsNotNullOrEmpty(parameters.ThrashParameters.AveragineFormula);
Assert.AreEqual("C4.9384 H7.7583 N1.3577 O1.4773 S0.0417", parameters.ThrashParameters.AveragineFormula);
Assert.AreEqual("AREA", parameters.ThrashParameters.IsotopicProfileFitType.ToString());
Assert.AreEqual(1.00727649, parameters.ThrashParameters.ChargeCarrierMass);
Assert.AreEqual(10, (decimal)parameters.ThrashParameters.MinIntensityForDeletion);
Assert.AreEqual(0.4, parameters.ThrashParameters.MaxFit);
Assert.AreEqual(10, parameters.ThrashParameters.MaxCharge);
Assert.AreEqual(4, parameters.ThrashParameters.MinMSFeatureToBackgroundRatio);
Assert.AreEqual(10000, parameters.ThrashParameters.MaxMass);
Assert.AreEqual(false, parameters.ThrashParameters.IsO16O18Data);
Assert.AreEqual(false, parameters.ThrashParameters.CheckAllPatternsAgainstChargeState1);
Assert.AreEqual(true, parameters.ThrashParameters.IsThrashUsed);
Assert.AreEqual("Text", parameters.ScanBasedWorkflowParameters.ExportFileType.ToString());
Assert.AreEqual("uimf_saturation_repair", parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName.ToLower());
Assert.AreEqual(false, parameters.ScanBasedWorkflowParameters.ExportPeakData);
Assert.AreEqual(500, parameters.MSGeneratorParameters.MinLCScan);
Assert.AreEqual(510, parameters.MSGeneratorParameters.MaxLCScan);
Assert.AreEqual(false, parameters.MSGeneratorParameters.UseMZRange);
Assert.AreEqual(100, parameters.MSGeneratorParameters.MinMZ);
Assert.AreEqual(3000, parameters.MSGeneratorParameters.MaxMZ);
Assert.AreEqual("quadratic", parameters.PeakDetectorParameters.PeakFitType.ToString().ToLower());
Assert.AreEqual(true, parameters.PeakDetectorParameters.IsDataThresholded);
Assert.AreEqual(1, parameters.MSGeneratorParameters.NumLCScansToSum);
Assert.AreEqual(7, parameters.MSGeneratorParameters.NumImsScansToSum);
Assert.AreEqual(true, parameters.MSGeneratorParameters.SumSpectraAcrossIms);
Assert.AreEqual(true, parameters.MSGeneratorParameters.SumSpectraAcrossLC);
}
public void ParameterFileTest1()
{
//see https://jira.pnnl.gov/jira/browse/OMCS-460
var fiParameterFile = new FileInfo(@"..\..\..\TestFiles\SampleParameterFile.xml");
Assert.IsTrue(fiParameterFile.Exists);
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(fiParameterFile.FullName);
Assert.IsNotNullOrEmpty(parameters.ThrashParameters.AveragineFormula);
Assert.AreEqual("C4.9384 H7.7583 N1.3577 O1.4773 S0.0417", parameters.ThrashParameters.AveragineFormula);
Assert.AreEqual("AREA", parameters.ThrashParameters.IsotopicProfileFitType.ToString());
Assert.AreEqual(1.00727649, parameters.ThrashParameters.ChargeCarrierMass);
Assert.AreEqual(1, parameters.ThrashParameters.MinIntensityForDeletion);
Assert.AreEqual(0.3m, (decimal)Math.Round(parameters.ThrashParameters.MaxFit, 1));
Assert.AreEqual(10, parameters.ThrashParameters.MaxCharge);
Assert.AreEqual(1, parameters.ThrashParameters.MinMSFeatureToBackgroundRatio);
Assert.AreEqual(10000, parameters.ThrashParameters.MaxMass);
Assert.AreEqual(false, parameters.ThrashParameters.IsO16O18Data);
Assert.AreEqual(false, parameters.ThrashParameters.CheckAllPatternsAgainstChargeState1);
Assert.AreEqual(true, parameters.ThrashParameters.IsThrashUsed);
Assert.AreEqual("Text", parameters.ScanBasedWorkflowParameters.ExportFileType.ToString());
Assert.AreEqual("standard", parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName.ToLower());
Assert.AreEqual(false, parameters.ScanBasedWorkflowParameters.ExportPeakData);
Assert.AreEqual("ThrashV1", parameters.ScanBasedWorkflowParameters.DeconvolutionType.ToString());
Assert.AreEqual(-2147483648, parameters.MSGeneratorParameters.MinLCScan);
Assert.AreEqual(2147483647, parameters.MSGeneratorParameters.MaxLCScan);
Assert.AreEqual(true, parameters.MSGeneratorParameters.UseMZRange);
Assert.AreEqual(100, parameters.MSGeneratorParameters.MinMZ);
Assert.AreEqual(3000, parameters.MSGeneratorParameters.MaxMZ);
Assert.AreEqual(3, parameters.MSGeneratorParameters.NumLCScansToSum);
Assert.AreEqual(true, parameters.MSGeneratorParameters.SumSpectraAcrossLC);
Assert.AreEqual("quadratic", parameters.PeakDetectorParameters.PeakFitType.ToString().ToLower());
Assert.AreEqual(true, parameters.PeakDetectorParameters.IsDataThresholded);
Assert.AreEqual(false, parameters.PeakDetectorParameters.PeaksAreStored);
}
public static ScanBasedWorkflow CreateWorkflow(string datasetFileName, string parameterFile, string outputFolderPath = null, BackgroundWorker backgroundWorker = null, bool useNewDeconToolsParameterObjects = true)
{
var datasetFile = new FileInfo(datasetFileName);
if (!datasetFile.Exists)
{
var datasetFolder = new DirectoryInfo(datasetFileName);
if (!datasetFolder.Exists)
{
throw new FileNotFoundException("Dataset file (or folder) not found: " + datasetFile);
}
}
var paramFile = new FileInfo(parameterFile);
if (!paramFile.Exists)
{
throw new FileNotFoundException("Parameter file not found: " + parameterFile);
}
// Initialize a new Run
Run run;
try
{
run = new RunFactory().CreateRun(datasetFileName);
}
catch (Exception ex)
{
Logger.Instance.OutputFilename = datasetFileName + "_BAD_ERROR_log.txt";
Logger.Instance.AddEntry("DeconTools.Backend.dll version = " + AssemblyInfoRetriever.GetVersion(typeof(ScanBasedWorkflow)));
Logger.Instance.AddEntry("UIMFLibrary version = " + AssemblyInfoRetriever.GetVersion(typeof(UIMFLibrary.DataReader)), Logger.Instance.OutputFilename); //forces it to write out immediately and clear buffer
Logger.Instance.AddEntry("ERROR message= " + ex.Message, Logger.Instance.OutputFilename);
Logger.Instance.AddEntry("ERROR type= " + ex, Logger.Instance.OutputFilename);
Logger.Instance.AddEntry("STACKTRACE = " + PRISM.clsStackTraceFormatter.GetExceptionStackTraceMultiLine(ex), Logger.Instance.OutputFilename);
throw new ApplicationException(
"A fatal error occured when connecting to the instrument data file. Could not create the Run object. Internal error message: " +
ex.Message + Environment.NewLine + Environment.NewLine + PRISM.clsStackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
}
DeconToolsParameters newParameters;
try
{
newParameters = new DeconToolsParameters();
newParameters.LoadFromOldDeconToolsParameterFile(parameterFile);
}
catch (Exception ex)
{
throw new ApplicationException(
"Error loading the parameter file: " +
ex.Message + Environment.NewLine + Environment.NewLine + PRISM.clsStackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
}
try
{
return(CreateWorkflow(run, newParameters, outputFolderPath, backgroundWorker));
}
catch (Exception ex)
{
throw new ApplicationException(
"Error creating the workflow: " +
ex.Message + Environment.NewLine + Environment.NewLine + PRISM.clsStackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
}
}
public void saturatedFixing_RedmineIssue966()
{
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();
var parameterFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\IMS_UIMF_PeakBR4_PeptideBR4_SN3_SumScans3_NoLCSum_saturationRepair_Frame_1-500.xml";
parameters.LoadFromOldDeconToolsParameterFile(parameterFile);
parameters = new DeconToolsParameters();
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 4;
parameters.PeakDetectorParameters.SignalToNoiseThreshold = 3;
parameters.ThrashParameters.MaxFit = 0.6;
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 320;
parameters.MSGeneratorParameters.MaxLCScan = 328;
parameters.MSGeneratorParameters.SumSpectraAcrossLC = true;
parameters.MSGeneratorParameters.SumSpectraAcrossIms = true;
parameters.MSGeneratorParameters.NumLCScansToSum = 1;
parameters.MSGeneratorParameters.NumImsScansToSum = 3;
parameters.MSGeneratorParameters.UseMZRange = false;
parameters.MiscMSProcessingParameters.UseZeroFilling = true;
parameters.ThrashParameters.MinIntensityForDeletion = 10;
parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "uimf_saturation_repair";
parameters.Save(@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\IMS_UIMF_PeakBR4_PeptideBR4_SN3_SumScans3_NoLCSum_saturationRepair_Frame_1-500_copy.xml");
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();
var minFrame = parameters.MSGeneratorParameters.MinLCScan;
var maxFrame = parameters.MSGeneratorParameters.MaxLCScan;
var minScan = 117;
var maxScan = 131;
var chargestate = 2;
var targetMass = (605.82 - 1.00727649) * chargestate;
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 TraditionalWorkflowTestOrbitrapData1()
{
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.ThrashV1;
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(266185816d, Math.Round(sumIntensities));
var sumPeakIntensities = peaklist.Select(p => p.Height).Sum();
Assert.AreEqual(605170496.0f, sumPeakIntensities);
}
private void btnAutoProcess_Click(object sender, EventArgs e)
{
if (!File.Exists(_parameterFileName))
{
MessageBox.Show("File not found error - Parameter file does not exist.");
return;
}
if (_bw != null && _bw.IsBusy)
{
MessageBox.Show("Already processing... please wait or click 'Abort'");
return;
}
if (this._inputFileList == null || this._parameterFileName == null)
{
MessageBox.Show("Please run the Setup Wizard first");
return;
}
try
{
TrySetOutputFolder();
}
catch (Exception ex)
{
MessageBox.Show(ex.Message);
return;
}
try
{
_parameters = new DeconToolsParameters();
_parameters.LoadFromOldDeconToolsParameterFile(_parameterFileName);
}
catch (Exception ex)
{
MessageBox.Show("Tried to load parameters. Serious error occurred. Error message: " + ex.Message +
"\n\n" + ex.StackTrace);
return;
}
this.txtProcessingStatus.Text = "Working...";
_bw = new BackgroundWorker();
_bw.WorkerReportsProgress = true;
_bw.WorkerSupportsCancellation = true;
_bw.DoWork += bw_DoWork;
_bw.ProgressChanged += bw_ProgressChanged;
_bw.RunWorkerCompleted += bw_RunWorkerCompleted;
_bw.RunWorkerAsync();
//for (int i = 0; i < inputFileList.Length; i++)
//{
// CALL_DeconConsole(inputFileList[i]);
//}
//MessageBox.Show("Processing complete!");
}