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 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(); }