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();
        }
コード例 #2
0
        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 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();
        }
コード例 #4
0
        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();
        }