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 importParameterTests1()
{
var importedParametersFile = Path.Combine(FileRefs.OutputFolderPath, "exportedTargetedAlignmentWorkflowParameters.xml");
var parameters = new TargetedAlignerWorkflowParameters();
parameters.LoadParameters(importedParametersFile);
}
public void ChaoChaoPeptidomicsTesting1()
{
var executorParameters =
@"\\protoapps\DataPkgs\Public\2013\727_IQ_analysis_of_Peptidomics_data_First_attempts\Parameters\ExecutorParameters1.xml";
var alignmentParametersFile =
@"\\protoapps\DataPkgs\Public\2013\727_IQ_analysis_of_Peptidomics_data_First_attempts\Parameters\TargetedAlignmentWorkflowParameters1.xml";
var rawDatafile = @"D:\Data\From_ChaoChao\CPTAC_OT_Pep_JB_5439_60min_4May12_Legolas_11-07-64.raw";
var parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.LoadParameters(executorParameters);
parameters.TargetedAlignmentIsPerformed = true;
var targetedAlignerWorkflowParameters = new TargetedAlignerWorkflowParameters();
targetedAlignerWorkflowParameters.LoadParameters(alignmentParametersFile);
var alignmentParametersOutputfile = alignmentParametersFile.Replace(".xml", "_autoGenerated.xml");
targetedAlignerWorkflowParameters.SaveParametersToXML(alignmentParametersOutputfile);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(parameters, rawDatafile);
executor.Execute();
}
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 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 highMassError_DatasetTest1()
{
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_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();
}
