public void Test1()
{
var run =
new RunFactory().CreateRun(
@"\\proto-7\VOrbiETD01\2012_3\Click_chemistry_labelfree_4Jul12_Lynx_12-2-32\Click_chemistry_labelfree_4Jul12_Lynx_12-2-32.raw");
Assert.IsNotNull(run);
var msGen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentScanSet = new ScanSet(20000);
msGen.Execute(run.ResultCollection);
}
public void MSGeneratorOnOrbiTest1()
{
var testfile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var run = new RunFactory().CreateRun(testfile);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var testLCScan = 6005;
var scanSet = new ScanSetFactory().CreateScanSet(run, testLCScan, 1);
var xydata = msgen.GenerateMS(run, scanSet);
Assert.IsNotNull(xydata);
Assert.IsTrue(xydata.Xvalues.Length > 1000);
}
public void CreateScanSetBasedOnRangeOfScansTest1()
{
var startScan = 5970;
var stopScan = 6035;
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var ssf = new ScanSetFactory();
var scan = ssf.CreateScanSet(run, 6005, startScan, stopScan);
Assert.AreEqual("6005 {5970, 5977, 5984, 5991, 5998, 6005, 6012, 6019, 6026, 6033}", scan.ToString());
}
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);
}
/// <summary>
/// summerizes test steps after test has run
/// </summary>
/// <param name="test"></param>
/// <returns>a string containing descriptions of step states and messags</returns>
string GetTestStepsDescFromQc(ITSTest test)
{
StringBuilder sb = new StringBuilder();
try
{
//get runs for the test
RunFactory rfactory = test.RunFactory;
List runs = rfactory.NewList("");
if (runs.Count == 0)
{
return("");
}
//get steps from run
StepFactory stepFact = runs[runs.Count].StepFactory;
List steps = stepFact.NewList("");
if (steps.Count == 0)
{
return("");
}
//go over steps and format a string
foreach (IStep step in steps)
{
sb.Append("Step: " + step.Name);
if (!string.IsNullOrWhiteSpace(step.Status))
{
sb.Append(", Status: " + step.Status);
}
string desc = step["ST_DESCRIPTION"] as string;
if (!string.IsNullOrEmpty(desc))
{
desc = "\n\t" + desc.Trim().Replace("\n", "\t").Replace("\r", "");
if (!string.IsNullOrWhiteSpace(desc))
{
sb.AppendLine(desc);
}
}
}
}
catch (Exception ex)
{
sb.AppendLine("Exception while reading step data: " + ex.Message);
}
return(sb.ToString().TrimEnd());
}
public void EasyDecision()
{
var fileName =
@"\\Protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
//Run run = RunUtilities.CreateAndLoadPeaks(fileName);
var run = new RunFactory().CreateRun(fileName);
List <IsotopicProfile> potentialFeatures;
EasyDecisionSetUp(out potentialFeatures);
ChargeStateDecider chargestatedecider = new ChromCorrelatingChargeDecider(run);
var msFeature = chargestatedecider.DetermineCorrectIsotopicProfile(potentialFeatures);
Assert.AreEqual(msFeature.ChargeState, 2);
}
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 Test1()
{
var rawfilename = @"D:\Data\O16O18\GlueGrant\GG_MO_Trauma_374020_20May11_Sphinx_11-03-28.RAW";
var exportedIsos = Path.Combine(Path.GetDirectoryName(rawfilename), Path.GetFileName(rawfilename).Replace(".RAW", "_test_isos.csv"));
if (File.Exists(exportedIsos))
{
File.Delete(exportedIsos);
}
var run = new RunFactory().CreateRun(rawfilename);
run.ResultCollection.ResultType = Backend.Globals.ResultType.O16O18_TRADITIONAL_RESULT;
run.ScanSetCollection.Create(run, 5000, 5000, 1, 1);
run.CurrentScanSet = run.ScanSetCollection.ScanSetList[0];
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2();
peakDet.PeakToBackgroundRatio = 1.3;
peakDet.SignalToNoiseThreshold = 2;
var decon = new HornDeconvolutor();
decon.IsO16O18Data = true;
var appender = new O16O18PeakDataAppender();
var exporter = IsosExporterFactory.CreateIsosExporter(run.ResultCollection.ResultType, Backend.Globals.ExporterType.Text, exportedIsos);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
appender.Execute(run.ResultCollection);
var testResult = (O16O18IsosResult)run.ResultCollection.ResultList[1];
Assert.AreEqual(DeconTools.Backend.Globals.ResultType.O16O18_TRADITIONAL_RESULT, run.ResultCollection.ResultType);
Assert.AreEqual(5905390, testResult.IsotopicProfile.GetMonoAbundance());
Assert.AreEqual(3017899, testResult.MonoPlus2Abundance);
Assert.AreEqual(162389, testResult.MonoPlus4Abundance);
exporter.Execute(run.ResultCollection);
run.Close();
}
public void JoinTargetsTest1()
{
var targetsFileName =
@"\\proto-7\VOrbi05\2013_2\mhp_plat_test_1_14April13_Frodo_12-12-04\MSG201305011339_Auto939903\mhp_plat_test_1_14April13_Frodo_12-12-04_msgfdb_fht.txt";
var massTagFilename =
@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set1_P890_targets.txt";
var rawFile = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw";
IqTargetImporter massTagImporter = new BasicIqTargetImporter(massTagFilename);
var massTagRefs = massTagImporter.Import().OrderBy(p => p.Code).ToList();
WorkflowExecutorBaseParameters parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.TargetsFilePath = targetsFileName;
var run = new RunFactory().CreateRun(rawFile);
var massAndNetAligner = new IqMassAndNetAligner(parameters, run);
massAndNetAligner.LoadAndInitializeTargets();
var testNET = massAndNetAligner.Targets.First().ElutionTimeTheor;
var query = (from massTag in massTagRefs
join target in massAndNetAligner.Targets on massTag.Code equals target.Code
select new
{
MassTag = massTag,
MSGFTarget = target
}).ToList();
foreach (var thing in query)
{
thing.MSGFTarget.ID = thing.MassTag.ID;
thing.MSGFTarget.ElutionTimeTheor = thing.MassTag.ElutionTimeTheor;
}
var targets = query.Select(p => p.MSGFTarget).ToList();
var testNETAfter = massAndNetAligner.Targets.First().ElutionTimeTheor;
Console.WriteLine("NET before= " + testNET);
Console.WriteLine("NET before= " + testNETAfter);
}
public void test2()
{
string testFile = @"D:\Data\UIMF\Problem_datasets\FPGA\QCSHEW_FPGA_99min_0003.UIMF";
RunFactory rf = new RunFactory();
UIMFRun run = (UIMFRun)rf.CreateRun(testFile);
UIMFRunTester tester = new UIMFRunTester();
tester.DisplayBasicRunInfo(run);
//UIMFLibrary.DataReader dr = new UIMFLibrary.DataReader();
//dr.OpenUIMF(testFile);
tester.DisplayFrameParameters(run, run.MinLCScan, run.MaxLCScan);
}
private Run setupRun(string runFile, string peaksFile)
{
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(runFile);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(peaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
return(run);
}
public void createScanSets_MS1_test1()
{
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var startScan = 6000;
var stopScan = 6020;
var processMSMS = false;
run.ScanSetCollection.Create(run, startScan, stopScan, 1, 1, processMSMS);
Assert.AreEqual(3, run.ScanSetCollection.ScanSetList.Count);
Assert.AreEqual(6005, run.ScanSetCollection.ScanSetList[0].PrimaryScanNumber);
}
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 LoadAndApplyMassAlignmentFromViperDataTest1()
{
var testFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var run = new RunFactory().CreateRun(testFile);
var viperMassAlignmentFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MassAndGANETErrors_BeforeRefinement.txt";
var loader = new ViperMassCalibrationLoader(viperMassAlignmentFile);
/*
* From unit test: targetedWorkflow_alignUsingDataFromFiles
* TargetID = 24702
* ChargeState = 3
* theor monomass= 2920.5319802
* theor m/z= 974.517936556667
* obs monomass= 2920.49120230408
* obs m/z= 974.504343924692
* ppmError before= 13.9597398284934
* ppmError after= 10.8899784905986
* calibrated mass= 2920.50017566955
* calibrated mass2= 2920.50017566955
* Database NET= 0.4197696
* Result NET= 0.42916464805603
* Result NET Error= -0.00934833288192749
* NumChromPeaksWithinTol= 3
*
*
*/
var calibrationData = loader.ImportMassCalibrationData();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(calibrationData);
run.MassAlignmentInfo = massAlignmentInfo;
var testMZ = 974.504343924692;
var alignedMZ = run.GetAlignedMZ(testMZ);
var ppmDiff = (testMZ - alignedMZ) / testMZ * 1e6;
Console.WriteLine("input m/z= " + testMZ);
Console.WriteLine("aligned m/z= " + alignedMZ);
Console.WriteLine("ppmDiff= " + ppmDiff);
Assert.AreEqual(-3.6, (decimal)Math.Round(ppmDiff, 1));
}
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 CreateFrameSetCollectionProcessMS1_Only()
{
var rf = new RunFactory();
var run = rf.CreateRun(FileRefs.RawDataMSFiles.UIMFFileContainingMSMSLevelData);
var numFramesToSum = 3;
var uimfRun = (UIMFRun)run;
uimfRun.ScanSetCollection.Create(uimfRun, numFramesToSum, 1, false);
Assert.AreEqual(3, uimfRun.ScanSetCollection.ScanSetList.Count);
Assert.AreEqual("1 {1, 6}", uimfRun.ScanSetCollection.ScanSetList[0].ToString());
Assert.AreEqual("6 {1, 6, 11}", uimfRun.ScanSetCollection.ScanSetList[1].ToString());
Assert.AreEqual("11 {6, 11}", uimfRun.ScanSetCollection.ScanSetList[2].ToString());
}
public void ImportNET_and_Try_Alignment_Test1()
{
string importFilename = Path.Combine(FileRefs.OutputFolderPath, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ScanNetAlignment.txt");
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
NETAlignmentFromTextImporter importer = new NETAlignmentFromTextImporter(importFilename);
run.AlignmentInfo = importer.Import();
float testScan = 6005;
float testNET1 = run.AlignmentInfo.GetNETFromTime(testScan);
Assert.AreEqual(0.3253423m, (decimal)testNET1);
}
public void ValidateDataTest1() //purpose is to compare
{
var testMz5File = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\mzXML\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.mz5";
var testThermoFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var mz5run = new RunFactory().CreateRun(testMz5File);
var thermoRun = new RunFactory().CreateRun(testThermoFile);
var testScanMz5 = 6004;
var testScanThermo = 6005;
var testScanSet1 = new ScanSet(testScanMz5);
var testScanSetThermo = new ScanSet(testScanThermo);
mz5run.CurrentScanSet = testScanSet1;
thermoRun.CurrentScanSet = testScanSetThermo;
mz5run.XYData = mz5run.GetMassSpectrum(testScanSet1);
thermoRun.XYData = thermoRun.GetMassSpectrum(testScanSetThermo);
Assert.AreEqual(mz5run.XYData.Xvalues.Length, thermoRun.XYData.Xvalues.Length);
for (var i = 0; i < mz5run.XYData.Xvalues.Length; i++)
{
Assert.AreEqual(mz5run.XYData.Xvalues[i], thermoRun.XYData.Xvalues[i]);
}
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeakToBackgroundRatio = 3;
peakDetector.SignalToNoiseThreshold = 2;
//peakDetector.Execute(mz5run.ResultCollection);
peakDetector.Execute(thermoRun.ResultCollection);
//TestUtilities.DisplayPeaks(mz5run.PeakList);
Console.WriteLine();
Console.WriteLine();
TestUtilities.DisplayPeaks(thermoRun.PeakList);
}
public void InvestigateIQFailures()
{
var executorParamFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Parameters\ExecutorParameters1 - Copy.xml";
var executorParameters =
new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParamFile);
var testFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Testing\LNA_A_Expo_Sample_SC_9_LNA_ExpA_Expo_Stat_SeattleBioMed_15Feb13_Cougar_12-12-35.raw";
var run = new RunFactory().CreateRun(testFile);
var iqparameterFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Testing\IQWorkflowParameters1.xml";
var workflowParameters = new BasicTargetedWorkflowParameters();
workflowParameters.LoadParameters(iqparameterFile);
workflowParameters.MSToleranceInPPM = 10;
workflowParameters.ChromPeakDetectorPeakBR = 0.25;
workflowParameters.ChromPeakDetectorSigNoise = 2;
var targetedWorkflow = new BasicTargetedWorkflow(run, workflowParameters);
var executor = new BasicTargetedWorkflowExecutor(executorParameters, targetedWorkflow, testFile);
//int[] testTargets = {349959971, 349951038,349954483 };
//int[] testTargets = { 349951038 };
//int[] testTargets = { 349954483 };
//int[] testTargets = { 2911730 };
int[] testTargets = { 349946881 };
var chargeState = 3;
executor.Targets.TargetList = (from n in executor.Targets.TargetList where testTargets.Contains(n.ID) select n).ToList();
executor.Targets.TargetList = (from n in executor.Targets.TargetList where n.ChargeState == chargeState select n).ToList();
executor.Execute();
//Results of investiga tion! - 349959971 was being missed because the MSTolerance was too narrow. When changed from 5 to 6, it was found. I think we can safely set this at 10.
//Results of investigation! - 349951038 was being missed because it was being flagged (peak to the left) problem.
TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
}
public void ExecutorCreatingTargetsTest1()
{
var util = new IqTargetUtilities();
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_scans5500-6500_peaks.txt";
var targetsFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var resultsFolder = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Results";
var expectedResultsFilename = Path.Combine(resultsFolder, RunUtilities.GetDatasetName(testFile) + "_iqResults.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
executorBaseParameters.ChromGenSourceDataPeakBR = 3;
executorBaseParameters.ChromGenSourceDataSigNoise = 2;
executorBaseParameters.TargetsFilePath = targetsFile;
//create no more than two charge state targets per peptide
executorBaseParameters.MaxNumberOfChargeStateTargetsToCreate = 2;
var run = new RunFactory().CreateRun(testFile);
var executor = new IqExecutor(executorBaseParameters, run);
executor.ChromSourceDataFilePath = peaksTestFile;
executor.LoadAndInitializeTargets(targetsFile);
executor.Targets = (from n in executor.Targets where n.ElutionTimeTheor > 0.305 && n.ElutionTimeTheor < 0.325 select n).Take(10).ToList();
foreach (var iqTarget in executor.Targets)
{
var numChildTargets = iqTarget.GetChildCount();
Assert.IsTrue(numChildTargets <= 2); //MaxNumberOfChargeStateTargetsToCreate = 2;
Console.WriteLine(iqTarget + "\t" + numChildTargets);
}
}
public void getVeryLowN15ProfileWithIterativeTFFTest1()
{
var n14n15Util = new N14N15TestingUtilities();
//get sample MS from Test Data
var rf = new RunFactory();
var run = rf.CreateRun(N14N15TestingUtilities.MS_AMTTag23085904_z2_sum1_lowN15);
run.XYData = N14N15TestingUtilities.GetTestSpectrum(N14N15TestingUtilities.MS_AMTTag23085904_z2_sum1_lowN15);
var mt23140708 = n14n15Util.CreateMT23085904_Z2();
run.CurrentMassTag = mt23140708;
run.ResultCollection.ResultType = Globals.ResultType.N14N15_TARGETED_RESULT;
var theorN14FeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
theorN14FeatureGen.GenerateTheorFeature(mt23140708);
var theorN15FeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.N15, 0.005);
theorN15FeatureGen.GenerateTheorFeature(mt23140708);
var parameters = new IterativeTFFParameters();
parameters.IsotopicProfileType = Globals.IsotopicProfileType.LABELLED;
parameters.ToleranceInPPM = 30;
var itff = new IterativeTFF(parameters);
itff.Execute(run.ResultCollection);
// IsotopicProfile iso = itff.iterativelyFindMSFeature(run, mt23140708.IsotopicProfileLabelled);
var result = (N14N15_TResult)run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Assert.IsNotNull(result.IsotopicProfileLabeled);
Assert.AreEqual(82280, (int)result.IntensityAggregate);
Assert.AreEqual(3, result.IsotopicProfileLabeled.MonoIsotopicPeakIndex);
TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfileLabeled);
}
public void featuresLoadedFromFile_test1()
{
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt";
DeconToolsTargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
TargetedAligner aligner = new TargetedAligner(run, parameters);
aligner.SetMassTags(massTagFile);
aligner.ImportedFeaturesFilename = deconToolsResultFile;
aligner.Execute();
}
public void check_alignment_of_MZ()
{
var mzAlignmentInfoFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MZAlignment.txt");
var NETAlignmentInfoFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ScanNetAlignment.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var importer = new MassAlignmentInfoFromTextImporter(mzAlignmentInfoFilename);
var massAlignmentData = importer.Import();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
run.MassAlignmentInfo = massAlignmentInfo;
var netAlignmentInfoImporter = new NETAlignmentFromTextImporter(NETAlignmentInfoFilename);
var scanNETdata = netAlignmentInfoImporter.Import();
run.NetAlignmentInfo.SetScanToNETAlignmentData(scanNETdata);
float testScan = 6439;
var theorMZ = 698.875137f; //QCSHEW massTag 37003; m/z 698.875137 (2+) See Redmine issue 627: http://redmine.pnl.gov/issues/627
var ppmshift = run.MassAlignmentInfo.GetPpmShift(theorMZ, (int)testScan);
Console.WriteLine("ppm shift = " + ppmshift);
var observedMZ = 698.8721;
var alignedTargetMZ = run.GetTargetMZAligned(theorMZ);
var differenceInMZ = Math.Abs(observedMZ - alignedTargetMZ);
Console.WriteLine("theor m/z of monoisotopic peak = " + theorMZ.ToString("0.0000"));
Console.WriteLine("observed m/z of monoisotopic peak = " + observedMZ.ToString("0.0000"));
Console.WriteLine("aligned theor m/z = " + alignedTargetMZ.ToString("0.00000"));
Assert.IsTrue(differenceInMZ < 0.001);
}
public void ensureAlignment_was_executed()
{
var run = new RunFactory().CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_READONLY_alignedFeatures.txt";
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_Formic_MassTags_Bin10_all.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var parameters = new NETAndMassAlignerParameters();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
var scan = 7835;
var theorMZ = 780.08485; //massTagID = 24701 (+3)
var obsMZ = 780.0824;
var netBeforeAlignment = run.NetAlignmentInfo.GetNETValueForScan(scan);
var mzBeforeAlignment = run.GetAlignedMZ(obsMZ);
aligner.Execute(run);
var netAfterAlignment = run.NetAlignmentInfo.GetNETValueForScan(scan);
var mzAfterAlignment = run.GetAlignedMZ(obsMZ);
Console.WriteLine("NET before alignment = " + netBeforeAlignment);
Console.WriteLine("NET after alignment = " + netAfterAlignment);
Console.WriteLine("Theor MZ = " + theorMZ);
Console.WriteLine("MZ before alignment = " + mzBeforeAlignment);
Console.WriteLine("MZ after alignment = " + mzAfterAlignment);
Console.WriteLine("PPMDiff before alignment = " + (theorMZ - mzBeforeAlignment) / theorMZ * 1e6);
Console.WriteLine("PPMDiff after alignment = " + (theorMZ - mzAfterAlignment) / theorMZ * 1e6);
}
public void Test1()
{
var rawdataFile = @"D:\Data\Orbitrap\QC_Shew_09_05-pt5-6_4Jan10_Doc_09-11-08.RAW";
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var parameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\UnlabelledTargeted_WorkflowParameters_noSum.xml";
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
var mtc = new TargetCollection();
mtc = mtimporter.Import();
var run = new RunFactory().CreateRun(rawdataFile);
//RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
var expectedPeaksFilename = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(expectedPeaksFilename, null);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var testMassTagID = 3513677;
var massTagChargeState = 2;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == massTagChargeState select n).First();
var parameters = WorkflowParameters.CreateParameters(parameterFile);
var workflow = TargetedWorkflow.CreateWorkflow(parameters);
workflow.Run = run;
workflow.Execute();
workflow.Result.DisplayToConsole();
RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
workflow.Execute();
workflow.Result.DisplayToConsole();
}
public void ProblemTesting_correlationProb1()
{
//see JIRA https://jira.pnnl.gov/jira/browse/OMCS-628
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
var testDatasetPath =
@"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1B_8Apr13_Cougar_13-03-25.raw";
executorParameters.IsMassAlignmentPerformed = true;
executorParameters.IsNetAlignmentPerformed = true;
executorParameters.ReferenceTargetsFilePath =
@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set3_P892_targets.txt";
var run = new RunFactory().CreateRun(testDatasetPath);
var executor = new IqExecutor(executorParameters, run);
var targetsFile =
@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set3_P892_targets.txt";
executor.LoadAndInitializeTargets(targetsFile);
executor.SetupMassAndNetAlignment();
var testTarget = 6955012;
executor.Targets = (from n in executor.Targets where n.ID == testTarget select n).ToList();
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.LoadParameters(@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Parameters\O16O18WorkflowParameters_2011_08_23_sum5.xml");
//define workflows for parentTarget and childTargets
var parentWorkflow = new O16O18ParentIqWorkflow(run, targetedWorkflowParameters);
var childWorkflow = new O16O18IqWorkflow(run, targetedWorkflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);
executor.DoAlignment();
executor.Execute();
}
public void featuresLoadedFromFile_test1()
{
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt");
var parameters = new TargetedAlignerWorkflowParameters();
parameters.ImportedFeaturesFilename = deconToolsResultFile;
var aligner = new TargetedAlignerWorkflow(run, parameters);
aligner.SetMassTags(massTagFile);
aligner.Execute();
}
public void ImportNET_and_Try_Alignment_Test2()
{
var importFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ScanNetAlignment.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var importer = new NETAlignmentFromTextImporter(importFilename);
importer.Execute(run);
var testScan = 6005;
var testNET1 = run.NetAlignmentInfo.GetNETValueForScan(testScan);
Assert.AreEqual(0.3252918m, (decimal)Math.Round(testNET1, 7));
Assert.IsTrue(run.NETIsAligned);
}
public void FileFromZaiaTest1()
{
string testfile = @"D:\Data\From_Joe_Zaia\RNaseB20_2_nocal.d\RNaseB20_2_nocal.d";
Run run = new RunFactory().CreateRun(testfile);
Console.WriteLine(TestUtilities.DisplayRunInformation(run));
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
ScanSet scanSet = new ScanSet(1000);
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
TestUtilities.DisplayXYValues(run.XYData);
}
public void createIMSScanSets1()
{
var factory = new RunFactory();
var run = factory.CreateRun(FileRefs.RawDataMSFiles.UIMFStdFile3);
var startScan = 120;
var stopScan = 200;
var numScansSummed = 7;
run.ScanSetCollection.Create(run, startScan, stopScan, numScansSummed, 1);
Assert.IsNotNull(run.ScanSetCollection);
Assert.AreEqual(81, run.ScanSetCollection.ScanSetList.Count);
Assert.AreEqual(7, run.ScanSetCollection.ScanSetList[0].IndexValues.Count);
Assert.AreEqual(117, run.ScanSetCollection.ScanSetList[0].IndexValues[0]);
Assert.AreEqual(123, run.ScanSetCollection.ScanSetList[0].IndexValues[6]);
}
private void InitializeRun(string datasetName)
{
//Datasets have to all be in the same folder
//currently works for datasets that have a File reference as
//opposed to datasets having a Folder reference (Agilent/Bruker)
DirectoryInfo dirInfo = new DirectoryInfo(_fileInputs.DatasetDirectory);
var fileInfo = dirInfo.GetFiles(datasetName + ".*");
if (!fileInfo.Any())
{
throw new FileNotFoundException("Run could not be initialized. File not found");
}
RunFactory rf = new RunFactory();
Run = rf.CreateRun(fileInfo.First().FullName);
bool peaksFileExists = checkForPeaksFile();
if (!peaksFileExists)
{
ReportGeneralProgress("Creating extracted ion chromatogram (XIC) source data... takes 1-5 minutes.. only needs to be done once.");
CreatePeaksForChromSourceData();
ReportGeneralProgress("Done creating XIC source data.");
}
string baseFileName;
baseFileName = this.Run.DataSetPath + "\\" + this.Run.DatasetName;
string expectedPeaksFilename = baseFileName + "_peaks.txt";
if (File.Exists(expectedPeaksFilename))
{
PeakImporterFromText peakImporter = new PeakImporterFromText(expectedPeaksFilename, _backgroundWorker);
peakImporter.ImportPeaks(this.Run.ResultCollection.MSPeakResultList);
}
else
{
ReportGeneralProgress(DateTime.Now + "\tCRITICAL FAILURE. Chrom source data (_peaks.txt) file not loaded.");
return;
}
ReportGeneralProgress(DateTime.Now + "\tPeak Loading complete.");
return;
}
public void LoadRun(string fileOrFolderPath)
{
if (Run != null)
{
Run.Close();
Run = null;
GC.Collect();
}
try
{
Run = new RunFactory().CreateRun(fileOrFolderPath);
}
catch (Exception ex)
{
GeneralStatusMessage = ex.Message;
}
OnPropertyChanged("RunStatusText");
OnPropertyChanged("DatasetFilePath");
if (Run != null)
{
LoadPeaksUsingBackgroundWorker();
FileInputs.DatasetParentFolder = Run.DataSetPath;
}
}
public void LoadRun(string fileOrFolderPath)
{
if (Run != null)
{
Run.Close();
Run = null;
GC.Collect();
}
try
{
Run = new RunFactory().CreateRun(fileOrFolderPath);
}
catch (Exception ex)
{
GeneralStatusMessage = ex.Message;
}
if (Run != null)
{
LoadPeaksUsingBackgroundWorker();
}
if (Run != null)
{
NavigateToNextMS1MassSpectrum();
}
OnPropertyChanged("DatasetName");
}
