public HornDeconvolutor(DeconToolsParameters deconParameters)
{
SetDefaults();
AbsoluteThresholdPeptideIntensity = deconParameters.ThrashParameters.AbsolutePeptideIntensity;
AveragineFormula = deconParameters.ThrashParameters.AveragineFormula;
ChargeCarrierMass = deconParameters.ThrashParameters.ChargeCarrierMass;
CheckPatternsAgainstChargeOne = deconParameters.ThrashParameters.CheckAllPatternsAgainstChargeState1;
DeleteIntensityThreshold = deconParameters.ThrashParameters.MinIntensityForDeletion;
IsAbsolutePepIntensityUsed = deconParameters.ThrashParameters.UseAbsoluteIntensity;
IsActualMonoMZUsed = false;
IsCompleteFit = deconParameters.ThrashParameters.CompleteFit;
IsMercuryCachingUsed = true;
IsMSMSProcessed = deconParameters.ScanBasedWorkflowParameters.ProcessMS2;
IsMZRangeUsed = deconParameters.MSGeneratorParameters.UseMZRange;
IsO16O18Data = deconParameters.ThrashParameters.IsO16O18Data;
IsotopicProfileFitType = deconParameters.ThrashParameters.IsotopicProfileFitType;
IsThrashed = deconParameters.ThrashParameters.IsThrashUsed;
LeftFitStringencyFactor = deconParameters.ThrashParameters.LeftFitStringencyFactor;
MaxChargeAllowed = deconParameters.ThrashParameters.MaxCharge;
MaxFitAllowed = deconParameters.ThrashParameters.MaxFit;
MaxMWAllowed = deconParameters.ThrashParameters.MaxMass;
MaxMZ = deconParameters.MSGeneratorParameters.MaxMZ; //TODO: review this later
MinMZ = deconParameters.MSGeneratorParameters.MinMZ; //TODO: review this later
MinIntensityForScore = deconParameters.ThrashParameters.MinIntensityForScore;
MinPeptideBackgroundRatio = deconParameters.ThrashParameters.MinMSFeatureToBackgroundRatio;
NumAllowedShoulderPeaks = deconParameters.ThrashParameters.NumPeaksForShoulder;
RightFitStringencyFactor = deconParameters.ThrashParameters.RightFitStringencyFactor;
TagFormula = deconParameters.ThrashParameters.TagFormula;
NumPeaksUsedInAbundance = deconParameters.ThrashParameters.NumPeaksUsedInAbundance;
MaxProcessingTimeMinutes = deconParameters.MiscMSProcessingParameters.MaxMinutesPerScan;
SetIsotopeFitScorerOptions();
}
public void ProcessBruker15TSolarixFile1_sumAllScans()
{
var testFile = FileRefs.RawDataMSFiles.Bruker15TFile1;
var dirInfo = new DirectoryInfo(testFile);
var datasetName = dirInfo.Name;
var expectedIsosOutput = Path.Combine(FileRefs.RawDataMSFiles.Bruker15TFile1, datasetName + "_isos.csv");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
var run = new RunFactory().CreateRun(testFile);
var parameters = new DeconToolsParameters();
parameters.MSGeneratorParameters.SumAllSpectra = true;
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 15;
var workflow = new TraditionalScanBasedWorkflow(parameters, run);
workflow.Execute();
Assert.That(File.Exists(expectedIsosOutput));
}
public SaturationIMSScanBasedWorkflow(DeconToolsParameters parameters, Run run, string outputFolderPath = null, BackgroundWorker backgroundWorker = null)
: base(parameters, run, outputFolderPath, backgroundWorker)
{
Check.Require(run is UIMFRun, "Cannot create workflow. Run is required to be a UIMFRun for this type of workflow");
PeakBRSaturatedPeakDetector = parameters.PeakDetectorParameters.PeakToBackgroundRatio * 0.75;
_msGenerator = new UIMF_MSGenerator();
_peakDetector = new DeconToolsPeakDetectorV2(5, 3, Globals.PeakFitType.QUADRATIC, false);
_zeroFiller = new DeconToolsZeroFiller();
//#if Disable_DeconToolsV2
// throw new NotImplementedException("Cannot use class SaturationIMSScanBasedWorkflow since support for C++ based DeconToolsV2 is disabled");
//#else
_deconvolutor = new HornDeconvolutor(parameters)
{
MaxFitAllowed = 0.9,
MinPeptideBackgroundRatio = _peakDetector.PeakToBackgroundRatio
};
//#endif
AdjustMonoIsotopicMasses = true;
Run.PeakList = new List <Peak>();
}
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 static ScanBasedWorkflow CreateWorkflow(Run run, DeconToolsParameters parameters, string outputFolderPath = null, BackgroundWorker backgroundWorker = null)
{
switch (parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName.ToLower())
{
case "uimf_saturation_repair":
return(new SaturationIMSScanBasedWorkflow(parameters, run, outputFolderPath, backgroundWorker));
case "uimf_standard":
return(new StandardIMSScanBasedWorkflow(parameters, run, outputFolderPath, backgroundWorker));
case "standard":
if (run is UIMFRun)
{
return(new StandardIMSScanBasedWorkflow(parameters, run, outputFolderPath, backgroundWorker));
}
return(new TraditionalScanBasedWorkflow(parameters, run, outputFolderPath, backgroundWorker));
case "run_merging_with_peak_export":
return(new RunMergingPeakExportingWorkflow(parameters, null, outputFolderPath, backgroundWorker));
case "deconmsn":
return(new DeconMSnWorkflow(parameters, run, outputFolderPath, backgroundWorker));
default:
throw new Exception("ScanBasedWorkflowName is unknown: " + parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName);
}
}
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();
}
internal IMSScanBasedWorkflow(DeconToolsParameters parameters, Run run, string outputDirectoryPath = null, BackgroundWorker backgroundWorker = null)
: base(parameters, run, outputDirectoryPath, backgroundWorker)
{
DeconTools.Utilities.Check.Require(run is UIMFRun, "Cannot create workflow. Run is required to be a UIMFRun for this type of workflow");
mCachedProgressMessage = string.Empty;
mCachedUserState = new ScanBasedProgressInfo(Run, new ScanSet(), new IMSScanSet(0));
}
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 WorkflowTesting2_SumLC5()
{
var localTestFile =
@"C:\Users\d3x720\Documents\Data\QCShew\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var parameters = new DeconToolsParameters();
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 6012;
parameters.MSGeneratorParameters.MaxLCScan = 6019;
parameters.MSGeneratorParameters.SumSpectraAcrossLC = true;
parameters.MSGeneratorParameters.NumLCScansToSum = 5;
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 1.3;
parameters.PeakDetectorParameters.SignalToNoiseThreshold = 2;
parameters.PeakDetectorParameters.IsDataThresholded = true;
parameters.ThrashParameters.MinIntensityForScore = 1;
parameters.ThrashParameters.MinMSFeatureToBackgroundRatio = 1;
var run = new RunFactory().CreateRun(localTestFile);
var workflow = new DeconMSnWorkflow(parameters, run);
workflow.Execute();
}
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 LowIntensityButGoodFeatureTest1()
{
var rawDataFile = @"D:\Data\DeconMSn_testing\QC_Shew_13_01_pt5_b_23Jan13_Cougar_12-02-27.raw";
var parameters = new DeconToolsParameters();
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 20593;
parameters.MSGeneratorParameters.MaxLCScan = 20598;
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 1.3;
parameters.PeakDetectorParameters.SignalToNoiseThreshold = 2;
parameters.PeakDetectorParameters.IsDataThresholded = true;
parameters.ThrashParameters.MinIntensityForScore = 1;
parameters.ThrashParameters.MinMSFeatureToBackgroundRatio = 1;
var run = new RunFactory().CreateRun(rawDataFile);
var workflow = new DeconMSnWorkflow(parameters, run);
workflow.NumMaxAttemptsAtLowIntensitySpecies = 4;
workflow.Execute();
}
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);
}
protected ScanBasedWorkflow(DeconToolsParameters parameters, Run run, string outputFolderPath = null, BackgroundWorker backgroundWorker = null)
{
NewDeconToolsParameters = parameters;
Run = run;
OutputFolderPath = outputFolderPath; //path is null unless specified
BackgroundWorker = backgroundWorker; //null unless specified
ExportData = true;
}
public DeconMSnWorkflow(DeconToolsParameters parameters, Run run, string outputDirectoryPath = null, BackgroundWorker backgroundWorker = null)
: base(parameters, run, outputDirectoryPath, backgroundWorker)
{
ToleranceInPPM = 30;
NumMaxAttemptsAtLowIntensitySpecies = 4;
parameters.ScanBasedWorkflowParameters.ProcessMS2 = true;
DeconMSnResults = new List <DeconMSnResult>();
IsParentProfileDataExported = true;
}
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 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);
}
public RunMergingPeakExportingWorkflow(DeconToolsParameters parameters, IEnumerable <string> datasetFileNameList, string outputDirectoryPath = null, BackgroundWorker backgroundWorker = null)
: base(null, null)
{
NewDeconToolsParameters = parameters;
NewDeconToolsParameters.ScanBasedWorkflowParameters.ExportPeakData = true;
DatasetFileNameList = datasetFileNameList;
OutputDirectoryPath = outputDirectoryPath;
BackgroundWorker = backgroundWorker;
}
public void fitterOnHornDataTest1()
{
Run run = new XCaliburRun2(xcaliburTestfile);
var results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
var isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1158, isTicRequested);
msGen.Execute(results);
Task peakDetector = new DeconToolsPeakDetectorV2(0.5, 3, Globals.PeakFitType.QUADRATIC, false);
peakDetector.Execute(results);
var deconParameters = new DeconToolsParameters();
deconParameters.ThrashParameters.MinMSFeatureToBackgroundRatio = 2; // PeptideMinBackgroundRatio
Task decon = new HornDeconvolutor(deconParameters);
decon.Execute(results);
var result1 = results.ResultList[0];
var distcreator = new MercuryDistributionCreator();
var resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
var theorXYData = distcreator.Data;
//StringBuilder sb = new StringBuilder();
//TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
//Console.WriteLine(sb.ToString());
var areafitter = new AreaFitter();
var fitval = areafitter.GetFit(theorXYData, run.XYData, 10);
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score);
Assert.AreEqual(0.0207350903681061m, (decimal)fitval); //TODO: fix this test... i'm getting 0.0207350903681061m
}
public void Test1()
{
var parameters = new DeconToolsParameters();
var datasetList = new List <string>();
datasetList.Add(@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\JuliaLaskinRunMergingWorkflow\b-LSOA_HPLC_ESIbox_pos_res60k_RT92-98.raw");
datasetList.Add(@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\JuliaLaskinRunMergingWorkflow\b-LSOA_HPLC_ESIbox_pos_res60k_RT1255-1282.raw");
datasetList.Add(@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\JuliaLaskinRunMergingWorkflow\b-LSOA_HPLC_ESIbox_pos_res60k_RT1400-1500.raw");
var workflow = new RunMergingPeakExportingWorkflow(parameters, datasetList);
workflow.Execute();
}
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 DeconToolsParameters GetDeconToolsParameters()
{
var deconToolsParameters = new DeconToolsParameters();
deconToolsParameters.ThrashParameters.AbsolutePeptideIntensity = HornTransformParameters.AbsolutePeptideIntensity;
deconToolsParameters.ThrashParameters.AveragineFormula = HornTransformParameters.AveragineFormula;
deconToolsParameters.ThrashParameters.ChargeCarrierMass = HornTransformParameters.CCMass;
deconToolsParameters.ThrashParameters.CheckAllPatternsAgainstChargeState1 = HornTransformParameters.CheckAllPatternsAgainstCharge1;
deconToolsParameters.ThrashParameters.MinIntensityForDeletion = HornTransformParameters.DeleteIntensityThreshold;
deconToolsParameters.ThrashParameters.UseAbsoluteIntensity = HornTransformParameters.UseAbsolutePeptideIntensity;
deconToolsParameters.ThrashParameters.CompleteFit = HornTransformParameters.CompleteFit;
deconToolsParameters.ScanBasedWorkflowParameters.ProcessMS2 = HornTransformParameters.ProcessMSMS;
deconToolsParameters.MSGeneratorParameters.UseMZRange = HornTransformParameters.UseMZRange;
deconToolsParameters.ThrashParameters.IsO16O18Data = HornTransformParameters.O16O18Media;
switch (HornTransformParameters.IsotopeFitType)
{
case DeconToolsV2.enmIsotopeFitType.AREA:
deconToolsParameters.ThrashParameters.IsotopicProfileFitType = Globals.IsotopicProfileFitType.AREA;
break;
case DeconToolsV2.enmIsotopeFitType.CHISQ:
deconToolsParameters.ThrashParameters.IsotopicProfileFitType = Globals.IsotopicProfileFitType.CHISQ;
break;
case DeconToolsV2.enmIsotopeFitType.PEAK:
deconToolsParameters.ThrashParameters.IsotopicProfileFitType = Globals.IsotopicProfileFitType.PEAK;
break;
default:
deconToolsParameters.ThrashParameters.IsotopicProfileFitType = Globals.IsotopicProfileFitType.Undefined;
break;
}
deconToolsParameters.ThrashParameters.IsThrashUsed = HornTransformParameters.ThrashOrNot;
deconToolsParameters.ThrashParameters.LeftFitStringencyFactor = HornTransformParameters.LeftFitStringencyFactor;
deconToolsParameters.ThrashParameters.MaxCharge = HornTransformParameters.MaxCharge;
deconToolsParameters.ThrashParameters.MaxFit = HornTransformParameters.MaxFit;
deconToolsParameters.ThrashParameters.MaxMass = HornTransformParameters.MaxMW;
deconToolsParameters.MSGeneratorParameters.MaxMZ = HornTransformParameters.MaxMZ; //TODO: review this later
deconToolsParameters.MSGeneratorParameters.MinMZ = HornTransformParameters.MinMZ; //TODO: review this later
deconToolsParameters.ThrashParameters.MinIntensityForScore = HornTransformParameters.MinIntensityForScore;
deconToolsParameters.ThrashParameters.MinMSFeatureToBackgroundRatio = HornTransformParameters.PeptideMinBackgroundRatio;
deconToolsParameters.ThrashParameters.NumPeaksForShoulder = HornTransformParameters.NumPeaksForShoulder;
deconToolsParameters.ThrashParameters.RightFitStringencyFactor = HornTransformParameters.RightFitStringencyFactor;
deconToolsParameters.ThrashParameters.TagFormula = HornTransformParameters.TagFormula;
deconToolsParameters.ThrashParameters.NumPeaksUsedInAbundance = HornTransformParameters.NumPeaksUsedInAbundance;
return(deconToolsParameters);
}
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 static Deconvolutor CreateDeconvolutor(DeconToolsParameters parameters)
{
Check.Require(parameters != null, "Factory cannot create Deconvolutor class. DeconToolsParameters are null.");
if (parameters == null)
{
return(new NullDeconvolutor());
}
Deconvolutor decon;
switch (parameters.ScanBasedWorkflowParameters.DeconvolutionType)
{
case Globals.DeconvolutionType.None:
return(new NullDeconvolutor());
case Globals.DeconvolutionType.ThrashV1:
// 2016 Port of ThrashV1 in DeconEngineV2 to C#, .NET 4
// This is the preferred deconvoluter as of Fall 2017
decon = new HornDeconvolutor(parameters);
return(decon);
case Globals.DeconvolutionType.ThrashV2:
// 2012 port of DeconEngine to C#
// As of 2016, not used because results do not agree with ThrashV1, C++
#pragma warning disable 618
decon = new InformedThrashDeconvolutor(parameters.ThrashParameters);
#pragma warning restore 618
return(decon);
case Globals.DeconvolutionType.Rapid:
// To include support for Rapid, you must add a reference to DeconEngine.dll, which was compiled with Visual Studio 2003 and uses MSVCP71.dll
// Note that DeconEngine.dll also depends on xerces-c_2_7.dll while DeconEngineV2.dll depends on xerces-c_2_8.dll
#if INCLUDE_RAPID
return(new RapidDeconvolutor(parameters.ThrashParameters.MinMSFeatureToBackgroundRatio,
Deconvolutor.DeconResultComboMode.simplyAddIt));
#else
throw new NotSupportedException("Support for Rapid is not included in this version of the DLL");
#endif
default:
throw new ArgumentOutOfRangeException(nameof(parameters),
"Trying to create the deconvolutor, but an incorrect Deconvolutor type was given. Good example: 'ThrashV1'");
}
}
public void WorkflowTest1()
{
var parameters = new DeconToolsParameters();
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 6005;
parameters.MSGeneratorParameters.MaxLCScan = 6012;
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 1.3;
parameters.PeakDetectorParameters.SignalToNoiseThreshold = 2;
parameters.PeakDetectorParameters.IsDataThresholded = true;
parameters.ThrashParameters.MinIntensityForScore = 1;
parameters.ThrashParameters.MinMSFeatureToBackgroundRatio = 1;
var run = new RunFactory().CreateRun(testFile1);
var expectedResultsFile1 = Path.Combine(run.DataSetPath, run.DatasetName + ".mgf");
var expectedResultsFile2 = Path.Combine(run.DataSetPath, run.DatasetName + "_DeconMSn_log.txt");
var expectedResultsFile3 = Path.Combine(run.DataSetPath, run.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 = new DeconMSnWorkflow(parameters, run);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedResultsFile1));
Assert.IsTrue(File.Exists(expectedResultsFile2));
Assert.IsTrue(File.Exists(expectedResultsFile3));
}
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 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);
}
