public void test01_mt230140708_z3()
{
double featureFinderTol = 15;
var featureFinderRequiresMonoPeak = false;
var numPeaksUsedInQuant = 3;
var n14n15Util = new N14N15TestingUtilities();
//get MS
var massSpectrum = n14n15Util.GetSpectrumAMTTag23140708_Z3_Sum3(); //this is the diff b/w previous test and this one
var smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(3, 2);
massSpectrum = smoother.Smooth(massSpectrum);
//get target MT
var mt23140708 = n14n15Util.CreateMT23140708_Z3();
//get ms peaks
var peakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, false);
var msPeakList = peakDet.FindPeaks(massSpectrum, 0, 0);
//TestUtilities.DisplayPeaks(msPeakList);
var featureGen = new TomTheorFeatureGenerator();
featureGen.GenerateTheorFeature(mt23140708);
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
var featureGen2 = new JoshTheorFeatureGenerator();
featureGen2.GenerateTheorFeature(mt23140708);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
var gen = new N15IsotopeProfileGenerator();
var theorN15Profile = gen.GetN15IsotopicProfile(mt23140708, 0.005);
var bff = new BasicTFF(featureFinderTol, featureFinderRequiresMonoPeak);
var n14Profile = bff.FindMSFeature(msPeakList, mt23140708.IsotopicProfile);
var n15Profile = bff.FindMSFeature(msPeakList, theorN15Profile);
Console.WriteLine(mt23140708.GetEmpiricalFormulaFromTargetCode());
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(theorN15Profile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n14Profile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n15Profile);
var quant = new BasicN14N15Quantifier(featureFinderTol);
double ratioContribIso1;
double ratioContribIso2;
double ratio;
quant.GetRatioBasedOnTopPeaks(n14Profile, n15Profile, mt23140708.IsotopicProfile, theorN15Profile, peakDet.BackgroundIntensity,
numPeaksUsedInQuant, out ratio, out ratioContribIso1, out ratioContribIso2);
Console.WriteLine("--------------------------------");
Console.WriteLine("Background intensity = " + peakDet.BackgroundIntensity);
Console.WriteLine("--------------------------------");
Console.WriteLine("Ratio = " + ratio);
Console.WriteLine("Ratio contrib Iso1 = " + ratioContribIso1);
Console.WriteLine("Ratio contrib Iso2 = " + ratioContribIso2);
Console.WriteLine("--------------------------------");
Assert.AreEqual(1.458267m, (decimal)Math.Round(ratio, 6)); //see 'N14N15Quantification_manualValidation_of_algorithm.xls' for manual validation
}
public void find_targetMassTag_131959Test1()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
var massTagColl = masstagImporter.Import();
Assert.AreEqual(2719, massTagColl.TargetList.Count);
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
//int mtID = 635428;
var mtID = 131959;
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(23, 2);
Task zeroFill = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 1);
Task msPeakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var basicChromPeakSelParam = new ChromPeakSelectorParameters();
basicChromPeakSelParam.NETTolerance = 0.1f;
basicChromPeakSelParam.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
Task chromPeakSel = new BasicChromPeakSelector(basicChromPeakSelParam);
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentMassTag = massTagColl.TargetList.Find(p => p.ID == mtID);
var mt = run.CurrentMassTag;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Task theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
Task targetedFeatureFinder = new BasicTFF();
Task fitScoreCalc = new IsotopicProfileFitScoreCalculator();
theorFeatureGen.Execute(run.ResultCollection);
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NormalizedElutionTime.ToString("0.000") + "; Sequence = " + mt.Code + "; EmpiricalFormula= " + mt.EmpiricalFormula + "\n");
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
msPeakDet.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
var massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
//Console.WriteLine("------------------------------ end --------------------------");
}
public void ChromAnalysisForAllSelectedPrecursors()
{
var isDataSmoothed = true;
var numPointsInSmoothing = 9;
var smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(numPointsInSmoothing, 2);
var graphGenerator = new BasicGraphControl();
var thermoFile1 = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var run = new RunFactory().CreateRun(thermoFile1);
var outputFolderForChromGraphs = @"\\protoapps\DataPkgs\Public\2012\684_DeconMSn_research1\ChromatogramImages";
if (!Directory.Exists(outputFolderForChromGraphs))
{
Directory.CreateDirectory(outputFolderForChromGraphs);
}
var scanSetCollection = new ScanSetCollection();
var scanStart = run.MinLCScan;
var scanStop = run.MaxLCScan;
scanSetCollection.Create(run, scanStart, scanStop, 1, 1, true);
var sb = new StringBuilder();
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (!File.Exists(expectedPeaksFile))
{
var peakCreatorParams = new PeakDetectAndExportWorkflowParameters();
peakCreatorParams.PeakBR = 1.75;
var peakCreator = new PeakDetectAndExportWorkflow(run, peakCreatorParams);
peakCreator.Execute();
}
var peakImporter = new PeakImporterFromText(expectedPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
double ppmTol = 50;
var peakChromatogramGenerator = new PeakChromatogramGenerator(ppmTol, Globals.ChromatogramGeneratorMode.MZ_BASED);
var scansetList = scanSetCollection.ScanSetList;
var scanCounter = 0;
var currentBin = 0;
foreach (var scanSet in scansetList)
{
run.CurrentScanSet = scanSet;
var currentScanLevel = run.GetMSLevel(scanSet.PrimaryScanNumber);
if (currentScanLevel > 1)
{
scanCounter++;
var precursorInfo = run.GetPrecursorInfo(scanSet.PrimaryScanNumber);
var scanInfo = run.GetScanInfo(scanSet.PrimaryScanNumber);
var scanWindowSize = 400;
var startScan = scanSet.PrimaryScanNumber - scanWindowSize / 2;
var stopScan = scanSet.PrimaryScanNumber + scanWindowSize / 2;
run.XYData = peakChromatogramGenerator.GenerateChromatogram(run, startScan, stopScan, precursorInfo.PrecursorMZ, ppmTol);
if (run.XYData == null)
{
run.XYData = new XYData();
run.XYData.Xvalues = new double[] { 0, 1, 2 };
run.XYData.Yvalues = new double[] { 0, 1, 2 };
Console.WriteLine(scanSet.PrimaryScanNumber + "\t" + precursorInfo.MSLevel + "\t" + precursorInfo.PrecursorMZ +
"\t" + precursorInfo.PrecursorScan + "--------- NO XYData!!! -------------");
}
else
{
if (isDataSmoothed)
{
run.XYData = smoother.Smooth(run.XYData);
}
}
Console.WriteLine(scanSet.PrimaryScanNumber + "\t" + precursorInfo.MSLevel + "\t" + precursorInfo.PrecursorMZ +
"\t" + precursorInfo.PrecursorScan);
graphGenerator.GenerateGraph(run.XYData.Xvalues, run.XYData.Yvalues);
var line = graphGenerator.GraphPane.CurveList[0] as LineItem;
line.Line.IsVisible = true;
line.Symbol.Size = 2;
line.Symbol.Type = SymbolType.Circle;
graphGenerator.GraphPane.XAxis.Title.Text = "scan";
graphGenerator.GraphPane.YAxis.Title.Text = "intensity";
graphGenerator.GraphPane.XAxis.Scale.MinAuto = true;
graphGenerator.GraphPane.YAxis.Scale.MinAuto = false;
graphGenerator.GraphPane.YAxis.Scale.Min = 0;
graphGenerator.GraphPane.XAxis.Scale.FontSpec.Size = 12;
graphGenerator.AddVerticalLineToGraph(scanSet.PrimaryScanNumber, 3);
graphGenerator.AddAnnotationRelativeAxis(scanInfo, 0.3, 0.1);
if (scanCounter > 500)
{
currentBin++;
scanCounter = 0;
}
var currentOutputFolder = Path.Combine(outputFolderForChromGraphs, "bin" + currentBin);
if (!Directory.Exists(currentOutputFolder))
{
Directory.CreateDirectory(currentOutputFolder);
}
var baseFilename = Path.Combine(currentOutputFolder,
scanSet.PrimaryScanNumber.ToString().PadLeft(5, '0') + "_mz" + precursorInfo.PrecursorMZ);
string outputGraphFilename;
string outputXYData;
if (isDataSmoothed)
{
outputGraphFilename = baseFilename + "_smoothed_chrom.png";
outputXYData = baseFilename + "_smoothed_xydata.txt";
}
else
{
outputXYData = baseFilename + "_xydata.txt";
outputGraphFilename = baseFilename + "_chrom.png";
}
graphGenerator.SaveGraph(outputGraphFilename);
TestUtilities.WriteToFile(run.XYData, outputXYData);
}
}
Console.WriteLine(sb.ToString());
}
