public void TestFindMassTag()
{
const string testFile = @"\\protoapps\UserData\Kaipo\TopDown\test2\Proteus_Peri_intact_ETD.raw";
const string peaksTestFile = @"\\protoapps\UserData\Kaipo\TopDown\test2\Proteus_Peri_intact_ETD_peaks.txt";
const string massTagFile = @"\\protoapps\UserData\Kaipo\TopDown\test2\Proteus_Peri_intact_ETD_MSAlign_ResultTable.txt";
Run run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
TargetCollection mtc = new TargetCollection();
var mtimporter = new MassTagFromMSAlignFileImporter(massTagFile);
mtc = mtimporter.Import();
const int testMassTagID = 14;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID select n).First();
TargetedWorkflowParameters parameters = new TopDownTargetedWorkflowParameters();
var workflow = new TopDownTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
if (result.FailedResult)
{
Console.WriteLine(result.ErrorDescription);
}
Assert.IsFalse(result.FailedResult);
result.DisplayToConsole();
}
public void problemVladDatasetTest1()
{
var datasetFile =
@"\\protoapps\UserData\Slysz\Data\O16O18\Vlad_O16O18\RawData\test.RAW";
var massTagFile =
@"\\protoapps\UserData\Slysz\Data\O16O18\Vlad_O16O18\Targets\massTags_found_across_all_5_datasets.txt";
var workflowParameterFile =
@"\\protoapps\UserData\Slysz\Data\O16O18\Vlad_O16O18\Workflow_Parameters\TargetedAlignmentWorkflowParameters1.xml";
var run = RunUtilities.CreateAndLoadPeaks(datasetFile, datasetFile.Replace(".RAW", "_peaks.txt"));
var parameters = new TargetedAlignerWorkflowParameters();
parameters.LoadParameters(workflowParameterFile);
parameters.ChromNETTolerance = 0.3;
parameters.ChromGenTolerance = 60;
parameters.MSToleranceInPPM = 60;
Console.WriteLine(parameters.ToStringWithDetails());
var aligner = new TargetedAlignerWorkflow(run, parameters);
aligner.outputToConsole = true;
aligner.SetMassTags(massTagFile);
aligner.Execute();
}
public void standardQCShewDatasetTest1()
{
var datasetFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var massTagFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\MassTags\QCShew_Formic_MassTags_for_alignment.txt";
var workflowParameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\TargetedAlignmentWorkflowParameters1.xml";
var run = RunUtilities.CreateAndLoadPeaks(datasetFile, datasetFile.Replace(".RAW", "_peaks.txt"));
var parameters = new TargetedAlignerWorkflowParameters();
parameters.LoadParameters(workflowParameterFile);
parameters.ChromNETTolerance = 0.3;
parameters.ChromGenTolerance = 60;
parameters.MSToleranceInPPM = 60;
Console.WriteLine(parameters.ToStringWithDetails());
var aligner = new TargetedAlignerWorkflow(run, parameters);
aligner.outputToConsole = true;
aligner.SetMassTags(massTagFile);
aligner.Execute();
}
public void cannotFindMassTag_test1()
{
//
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 26523;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.IsNull(result.IsotopicProfile);
Assert.IsNull(result.ScanSet);
Assert.IsNull(result.ChromPeakSelected);
Assert.IsTrue(result.FailedResult);
Assert.AreEqual(DeconTools.Backend.Globals.TargetedResultFailureType.ChrompeakNotFoundWithinTolerances, result.FailureType);
}
public void Get3DElutionAndExportToFileTest1()
{
var rawFile = @"\\protoapps\UserData\Fujimoto\TopDownPaperData\FINAL_DATA\_004\SBEP_STM_004_02272012_Aragon.raw";
var peaksFile = @"\\protoapps\UserData\Fujimoto\TopDownPaperData\FINAL_DATA\_004\SBEP_STM_004_02272012_Aragon_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(rawFile, peaksFile);
//var run = new RunFactory().CreateRun(rawFile);
var outputFile = @"\\protoapps\UserData\Fujimoto\TopDownPaperData\FINAL_DATA\_004\3D_PLOT\3DelutionProfile.txt";
Assert.IsNotNull(run);
Assert.IsTrue(run.ResultCollection.MSPeakResultList.Count > 0);
var extractor = new IsotopicProfileElutionExtractor();
var minScan = 3270;
var maxScan = 3350;
double minMZ = 700;
double maxMZ = 1700;
int[] scans;
float[] intensities;
double[] mzBinVals;
extractor.Get3DElutionProfileFromPeakLevelData(run, minScan, maxScan, minMZ, maxMZ, out scans, out mzBinVals, out intensities);
var intensities2D = extractor.GetIntensitiesAs2DArray();
extractor.OutputElutionProfileToFile(outputFile);
}
public void getPeakChromatogramTest1()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var targetMZ = 759.4032;
var startScan = 5500;
var stopScan = 6500;
double toleranceInPPM = 20;
var chromGen = new PeakChromatogramGenerator();
var mt = TestUtilities.GetMassTagStandard(1);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new JoshTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
var peakChromGen = new PeakChromatogramGenerator(toleranceInPPM);
peakChromGen.Execute(run.ResultCollection);
run.XYData.Display();
Assert.AreEqual(133, run.XYData.Xvalues.Length);
Assert.AreEqual(5543, (int)run.XYData.Xvalues[35]);
Assert.AreEqual(7319569, (int)run.XYData.Yvalues[35]);
//make sure that the 0's are not trimmed off
Assert.AreEqual(0, run.XYData.Yvalues[1]);
}
public void featuresFoundByTargetedProcessing_thenAligned_test1()
{
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile1;
var run = RunUtilities.CreateAndLoadPeaks(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1, peaksTestFile);
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";
var parameters = new TargetedAlignerWorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.ChromGenTolerance = 25;
parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
parameters.ChromPeakDetectorPeakBR = 2;
parameters.ChromPeakDetectorSigNoise = 2;
parameters.MSToleranceInPPM = 25;
parameters.UpperFitScoreAllowedCriteria = 0.1;
parameters.IScoreAllowedCriteria = 0.15;
var aligner = new TargetedAlignerWorkflow(run, parameters);
aligner.SetMassTags(massTagFile);
aligner.Execute();
Console.WriteLine(aligner.GetAlignmentReport1());
Assert.IsNotNull(run.AlignmentInfo);
Assert.AreEqual(-4.2m, (decimal)(Math.Round(run.AlignmentInfo.GetPPMShiftFromMZ(600.0f), 1)));
}
public void GetPeakChromatogram_IQStyle_Test3()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1, FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var target = TestUtilities.GetIQTargetStandard(1);
var chromGen = new PeakChromatogramGenerator();
chromGen.ChromatogramGeneratorMode = Globals.ChromatogramGeneratorMode.TOP_N_PEAKS;
chromGen.TopNPeaksLowerCutOff = 0.4;
chromGen.Tolerance = 100;
var lowerScan = 6087;
var upperScan = 6418;
var massOfInterest = new List <double>();
massOfInterest.Add(target.TheorIsotopicProfile.Peaklist[0].XValue);
massOfInterest.Add(target.TheorIsotopicProfile.Peaklist[1].XValue);
var chromXYData = chromGen.GenerateChromatogram(run, massOfInterest, lowerScan, upperScan, chromGen.Tolerance, chromGen.ToleranceUnit);
Assert.IsNotNull(chromXYData);
Assert.AreEqual(96, chromXYData.Xvalues.Length);
TestUtilities.DisplayXYValues(chromXYData);
}
public void Get3DElutionTest1()
{
var peaksFile = FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var orbiFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var run = RunUtilities.CreateAndLoadPeaks(orbiFile, peaksFile);
Assert.IsNotNull(run);
Assert.IsTrue(run.ResultCollection.MSPeakResultList.Count > 0);
var extractor = new IsotopicProfileElutionExtractor();
var minScan = 5900;
var maxScan = 6300;
double minMZ = 749;
double maxMZ = 754;
int[] scans;
float[] intensities;
double[] mzBinVals;
extractor.Get3DElutionProfileFromPeakLevelData(run, minScan, maxScan, minMZ, maxMZ, out scans, out mzBinVals, out intensities);
var intensities2D = extractor.GetIntensitiesAs2DArray();
Console.WriteLine(extractor.OutputElutionProfileAsString());
}
public void GetChromatogramsTest1()
{
string testDatasetPath =
@"D:\Data\From_Vlad\Bruker\2013_01_29_ALZ_CTRL_5_0p5_1_01_228.d";
Run run = RunUtilities.CreateAndLoadPeaks(testDatasetPath);
PeakChromatogramGenerator chromGen = new PeakChromatogramGenerator(10);
double targetMZ = 663.3404;
int chargeState = 2;
int peakNum = 4;
targetMZ = targetMZ + peakNum * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS / chargeState;
double toleranceInPPM = 10;
int startScan = 230;
int stopScan = 300;
chromGen.GenerateChromatogram(run, startScan, stopScan, targetMZ, toleranceInPPM);
run.XYData = run.XYData.TrimData(startScan, stopScan);
TestUtilities.DisplayXYValues(run.XYData);
}
public void Get3DElutionAndExportToFileTest1()
{
var peaksFile = FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var orbiFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var run = RunUtilities.CreateAndLoadPeaks(orbiFile, peaksFile);
var outputFile = Path.Combine(run.DataSetPath, run.DatasetName + "_sample3DelutionProfile.txt");
Assert.IsNotNull(run);
Assert.IsTrue(run.ResultCollection.MSPeakResultList.Count > 0);
var extractor = new IsotopicProfileElutionExtractor();
var minScan = 5900;
var maxScan = 6300;
double minMZ = 749;
double maxMZ = 754;
int[] scans;
float[] intensities;
double[] mzBinVals;
extractor.Get3DElutionProfileFromPeakLevelData(run, minScan, maxScan, minMZ, maxMZ, out scans, out mzBinVals, out intensities);
var intensities2D = extractor.GetIntensitiesAs2DArray();
extractor.OutputElutionProfileToFile(outputFile);
}
protected virtual void SetupLogging()
{
string loggingFolder;
if (string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase))
{
loggingFolder = RunUtilities.GetDatasetParentFolder(DatasetPath);
}
else
{
loggingFolder = Path.Combine(ExecutorParameters.OutputFolderBase, "Logs");
}
try
{
if (!Directory.Exists(loggingFolder))
{
Directory.CreateDirectory(loggingFolder);
}
}
catch (Exception ex)
{
throw new System.IO.IOException("Trying to set up logging folder but there was a critical error. Details:\n\n" + ex.Message, ex);
}
_loggingFileName = Path.Combine(loggingFolder, RunUtilities.GetDatasetName(DatasetPath) + "_log.txt");
}
protected void PerformAlignment()
{
if (!string.IsNullOrEmpty(_alignmentFolder))
{
RunUtilities.AlignRunUsingAlignmentInfoInFiles(Run, _alignmentFolder);
}
if (Run.MassIsAligned)
{
ReportGeneralProgress("Run has been mass aligned");
}
else
{
ReportGeneralProgress("FYI - Run has NOT been mass aligned.");
}
if (Run.NETIsAligned)
{
ReportGeneralProgress("Run has been NET aligned using info in either the _NETAlignment.txt file or the _UMCs.txt file");
}
else
{
ReportGeneralProgress("Warning - Run has NOT been NET aligned.");
}
}
public void featuresFoundByTargetedProcessing_thenAligned_test1()
{
string peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile1;
Console.WriteLine("loading peaks.");
Run run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1, peaksTestFile);
Console.WriteLine("done.");
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
DeconToolsTargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.ChromToleranceInPPM = 25;
parameters.ChromGeneratorMode = Backend.ProcessingTasks.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
parameters.ChromPeakDetectorPeakBR = 2;
parameters.ChromPeakDetectorSigNoise = 2;
parameters.MSToleranceInPPM = 25;
TargetedAligner aligner = new TargetedAligner(run, parameters);
aligner.UpperFitScoreAllowedCriteria = 0.1;
aligner.IScoreAllowedCriteria = 0.15;
Console.WriteLine("Loading Mass tags...");
aligner.SetMassTags(massTagFile);
Console.WriteLine("Done.");
aligner.Execute();
}
public void FailureToFindAnyChromatogramDataTest1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromGenTolerance = 1; //very narrow tolerance
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.EmpiricalFormula = DeconTools.Backend.Utilities.IsotopeDistributionCalculation.IsotopicDistributionCalculator.Instance.GetAveragineFormulaAsString(1399);
target.ElutionTimeTheor = 0.3;
target.ChargeState = 1;
target.DoWorkflow();
var result = target.GetResult();
Assert.IsTrue(result.Target.TheorIsotopicProfile != null);
Assert.IsTrue(result != null);
Assert.IsTrue(result.IqResultDetail.Chromatogram == null);
var reportString = result.ToStringWithDetailedReport();
Console.WriteLine(reportString);
}
public void TopDownWorkflowTest1()
{
//see https://jira.pnnl.gov/jira/browse/OMCR-98
string baseFolder =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact";
const string executorParameterFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact\Parameters\topdownExecutorParameters1.xml";
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
executorParameters.ExportChromatogramData = false;
executorParameters.OutputFolderBase =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact";
const string testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact\RawData\Proteus_Peri_intact_ETD.raw";
string testDatasetName = RunUtilities.GetDatasetName(testDatasetPath);
string expectedResultsFilename = executorParameters.OutputFolderBase + "\\IqResults" + "\\" + testDatasetName + "_quant.txt";
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, testDatasetPath);
string proteinSeq =
@"A.VDKTNPYALMEDAAQKTFDKLKTEQPEIRKNPELLREIVQQELLPYVHIKYAGALVLGPYYRNATPAQRDAYFAAFKDYLAQVYGQALAMYEGQEYRIEPAKPFADKSNLTIRVTIIDKNGRPPVRLDFQWRKNSKTGEWQAYDMIAEGVSMITTKQNEWSDILSAKGVDGLTKQLEISAKTPITLDEKK.";
executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.Code == proteinSeq).ToList();
executor.Execute();
Assert.IsNotNull(executor.TargetedWorkflow.Run);
Console.WriteLine("Num targetedResults in Run = " + executor.TargetedWorkflow.Run.ResultCollection.MassTagResultList.Count);
Assert.IsTrue(File.Exists(expectedResultsFilename), "Results file does not exist!");
//TODO: fix _quant.txt output column headers
TopDownTargetedResultFromTextImporter importer = new TopDownTargetedResultFromTextImporter(expectedResultsFilename);
var results = importer.Import();
Assert.IsNotNull(results);
Assert.IsTrue(results.HasResults);
Assert.AreEqual(1, results.Results.Count);
//foreach (var r in results.Results)
//{
// Console.WriteLine(r.TargetID + "\t" + r.ScanLC + "\t" + r.Intensity);
//}
}
public XicAdaptor(string rawPath, string peaksPath)
{
Run run = RunUtilities.CreateAndLoadPeaks(rawPath, peaksPath);
m_run = run;
NetWindow = .02;
MzPpmWindow = 20;
}
private void LoadPeaks(Run run)
{
var sourcePeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt"); //FULL.txt";
RunUtilities.GetPeaks(run, sourcePeaksFile);
//create / load
//TODO: adjust the RunUtilities class so that it can simply take a run and create the _peaks and load them.
}
public void testVladsData()
{
var testFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2_First60.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndAlignRun(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24653;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.MSToleranceInPPM = 10;
parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromatogramCorrelationIsPerformed = true;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as O16O18TargetedResultObject;
Assert.IsTrue(workflow.Success);
Assert.IsFalse(result.FailedResult);
result.DisplayToConsole();
Console.WriteLine("Correlation between 016 and O18(double label)= " + result.ChromCorrO16O18DoubleLabel);
Assert.IsTrue(result.ChromCorrO16O18DoubleLabel > 0);
Console.WriteLine("theor monomass= \t" + result.Target.MonoIsotopicMass);
Console.WriteLine("monomass= \t" + result.IsotopicProfile.MonoIsotopicMass);
Console.WriteLine("ppmError before= \t" + result.MassErrorBeforeAlignment);
Console.WriteLine("ppmError after= \t" + result.MassErrorAfterAlignment);
}
protected string TryFindTargetsForCurrentDataset()
{
var datasetName = RunUtilities.GetDatasetName(DatasetPath);
string[] possibleFileSuffixs = { "_iqTargets.txt", "_targets.txt", "_LCMSFeatures.txt", "_MSGFPlus.tsv", "_msgfdb_fht.txt" };
var possibleTargetFiles = new List <FileInfo>();
var targetsBaseFolder = ExecutorParameters.TargetsBaseFolder;
if (string.IsNullOrEmpty(ExecutorParameters.TargetsBaseFolder))
{
targetsBaseFolder = Path.Combine(ExecutorParameters.OutputFolderBase, "Targets");
}
var dirinfo = new DirectoryInfo(targetsBaseFolder);
foreach (var suffix in possibleFileSuffixs)
{
var fileInfos = dirinfo.GetFiles("*" + suffix);
foreach (var fileInfo in fileInfos)
{
if (fileInfo.Name.StartsWith(datasetName, StringComparison.OrdinalIgnoreCase))
{
possibleTargetFiles.Add(fileInfo);
}
}
}
if (possibleTargetFiles.Count == 0)
{
return(string.Empty);
}
else if (possibleTargetFiles.Count == 1)
{
return(possibleTargetFiles.First().FullName);
}
else
{
var sb = new StringBuilder();
sb.Append("Error in getting IQ target file. Multiple files were found for the dataset: " + datasetName + Environment.NewLine);
sb.Append("Candidate IQ target files: " + Environment.NewLine);
foreach (var possibleTargetFile in possibleTargetFiles)
{
sb.Append(possibleTargetFile.FullName + Environment.NewLine);
}
throw new NotSupportedException(sb.ToString());
}
}
public void TopDownWorkflowFullTargetSet()
{
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = false;
executorParameters.DeleteLocalDatasetAfterProcessing = false;
executorParameters.TargetsFilePath = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Targets\fullTargetSet\Proteus_Peri_intact_ETD_MSAlign_ResultTable.Filtered05FDR.txt";
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
executorParameters.ExportChromatogramData = true;
var workflowParameters = new TopDownTargetedWorkflowParameters();
workflowParameters.AreaOfPeakToSumInDynamicSumming = 2;
workflowParameters.ChromatogramCorrelationIsPerformed = false;
workflowParameters.ChromGeneratorMode = Globals1.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
workflowParameters.ChromGenSourceDataPeakBR = 4;
workflowParameters.ChromGenSourceDataSigNoise = 3;
workflowParameters.ChromNETTolerance = 0.025;
workflowParameters.ChromPeakDetectorPeakBR = 0.1;
workflowParameters.ChromPeakDetectorSigNoise = 0.1;
workflowParameters.ChromPeakSelectorMode = Globals1.PeakSelectorMode.Smart;
workflowParameters.ChromSmootherNumPointsInSmooth = 9;
workflowParameters.MaxScansSummedInDynamicSumming = 100;
workflowParameters.MSPeakDetectorPeakBR = 1.3;
workflowParameters.MSPeakDetectorSigNoise = 2;
workflowParameters.ChromGenTolerance = 15;
workflowParameters.MSToleranceInPPM = 25;
workflowParameters.MultipleHighQualityMatchesAreAllowed = true;
workflowParameters.NumChromPeaksAllowedDuringSelection = 10;
workflowParameters.NumMSScansToSum = 5;
workflowParameters.ResultType = Globals1.ResultType.TOPDOWN_TARGETED_RESULT;
workflowParameters.SummingMode = SummingModeEnum.SUMMINGMODE_STATIC;
const string testDatasetPath =
@"\\protoapps\UserData\Fujimoto\TopDownTesting\RawData\Proteus_Peri_intact_ETD.raw";
string resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "Results");
string testDatasetName = RunUtilities.GetDatasetName(testDatasetPath);
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, workflowParameters, testDatasetPath);
executor.Execute();
Assert.IsNotNull(executor.TargetedWorkflow.Run);
Assert.IsTrue(File.Exists(expectedResultsFilename), "Results file does not exist!");
}
public void findFeatureIn_dataset_with_bad_massCalibration_test1()
{
//mass error in this dataset is typically ~50ppm.
var datasetFile = @"D:\Data\Orbitrap\Subissue01\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24.RAW";
var massTagFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\MassTags\QCShew_Formic_MassTags_Bin10_first10.txt";
var workflowParameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\UnlabelledTargeted_WorkflowParameters_noSum.xml";
var run = RunUtilities.CreateAndLoadPeaks(datasetFile, datasetFile.Replace(".RAW", "_peaks.txt"));
RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
Assert.IsTrue(run.MassIsAligned);
Assert.IsTrue(run.NETIsAligned);
var parameters = new BasicTargetedWorkflowParameters();
parameters.LoadParameters(workflowParameterFile);
var workflow = new BasicTargetedWorkflow(parameters);
workflow.Run = run;
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var mt1 = (from n in mtc.TargetList where n.ID == 24702 && n.ChargeState == 4 select n).First();
run.CurrentMassTag = mt1;
workflow.Execute();
var repo = new TargetedResultRepository();
repo.AddResult(workflow.Result);
Console.WriteLine("theor mono mass = " + mt1.MonoIsotopicMass);
Console.WriteLine("theorMZ = " + mt1.MZ);
Console.WriteLine("theorNET = " + mt1.NormalizedElutionTime);
Console.WriteLine("obsScan = " + repo.Results[0].ScanLC);
Console.WriteLine("obsNET = " + repo.Results[0].NET);
Console.WriteLine("NETError = " + repo.Results[0].NETError);
Console.WriteLine("obsMZ = " + repo.Results[0].MonoMZ);
Console.WriteLine("monoMass = " + repo.Results[0].MonoMass);
Console.WriteLine("obsMonoMassCalibrated = " + repo.Results[0].MonoMassCalibrated);
Console.WriteLine("MassErrorBeforeAlignment = " + (mt1.MZ - repo.Results[0].MonoMZ) / mt1.MZ * 1e6);
Console.WriteLine("MassErrorAfterAlignment = " + repo.Results[0].MassErrorBeforeCalibration);
}
//note: does not actually create peaks. Only loads them. An exception is thrown if it's not there.
private void CreatePeaksIfNeeded()
{
if (_run.ResultCollection.MSPeakResultList.Count == 0)
{
var expectedPeaksfile = Path.Combine(_run.DataSetPath, _run.DatasetName + "_peaks.txt");
if (!File.Exists(expectedPeaksfile))
{
var ex = new Exception("No Peaks file found.");
throw ex;
// CreatePeaksFile();
//ExportPeaks_copied(expectedPeaksfile);
}
RunUtilities.GetPeaks(_run, expectedPeaksfile);
}
}
public void IqWorkflowTest1()
{
//see https://jira.pnnl.gov/jira/browse/OMCS-709
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
var oldStyleTarget = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
parameters.ChromSmootherNumPointsInSmooth = 9;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromPeakDetectorSigNoise = 1;
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.ID = oldStyleTarget.ID;
target.MZTheor = oldStyleTarget.MZ;
target.ElutionTimeTheor = oldStyleTarget.NormalizedElutionTime;
target.MonoMassTheor = oldStyleTarget.MonoIsotopicMass;
target.EmpiricalFormula = oldStyleTarget.EmpiricalFormula;
target.ChargeState = oldStyleTarget.ChargeState;
Console.WriteLine(target.EmpiricalFormula + "\t" + target.ChargeState);
target.DoWorkflow();
var result = target.GetResult();
Assert.IsNotNull(result, "result is null");
var reportString = result.ToStringWithDetailedReport();
Console.WriteLine(reportString);
}
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);
}
}
private void LoadPeaks(string userProvidedOutputFolderPath = null)
{
string outputFolderPath;
if (string.IsNullOrEmpty(userProvidedOutputFolderPath))
{
outputFolderPath = Run.DataSetPath;
}
else
{
outputFolderPath = userProvidedOutputFolderPath;
}
var expectedPeaksFile = Path.Combine(outputFolderPath, Run.DatasetName + "_peaks.txt");
RunUtilities.GetPeaks(Run, expectedPeaksFile);
}
public void GetPeakChromatogram_usePPMTolerance_Test1()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var targetMZ = 759.4032;
var startScan = 5500;
var stopScan = 6500;
double toleranceInPPM = 20;
var chromGen = new PeakChromatogramGenerator();
var xydata = chromGen.GenerateChromatogram(run, startScan, stopScan, targetMZ, toleranceInPPM, Globals.ToleranceUnit.PPM);
Assert.IsNotNull(xydata);
TestUtilities.DisplayXYValues(xydata);
}
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 exporterTest1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";
var exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "UnlabelledTargetedResultsExporterOutput1.txt");
if (File.Exists(exportedResultFile))
{
File.Delete(exportedResultFile);
}
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var selectedMassTags = mtc.TargetList.OrderBy(p => p.ID).Take(10).ToList();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
foreach (var mt in selectedMassTags)
{
run.CurrentMassTag = mt;
workflow.Execute();
}
var repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
var exporter = new UnlabelledTargetedResultToTextExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}
public void findSingleMassTag_checkAlignmentData_test1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.AreEqual(false, result.FailedResult);
result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
Assert.AreEqual(718.41m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2));
Assert.AreEqual(5947m, (decimal)Math.Round(result.ChromPeakSelected.XValue));
Assert.AreEqual(5.91, (decimal)(Math.Round(result.GetMassErrorAfterAlignmentInPPM(), 2)));
Assert.AreEqual(0.0001585m, (decimal)(Math.Round(result.GetNETAlignmentError(), 7)));
RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
//these might change due to unit tests elsewhere. Need a better way of doing this
//Assert.AreEqual(1.99290383722318m, (decimal)result.GetMassErrorAfterAlignmentInPPM());
//Assert.AreEqual(0.00076708197593689m, (decimal)result.GetNETAlignmentError());
}
