public void DemoParameterTest1()
{
var outputFileName = baseFolder + @"\BasicTargetedWorkflowExecutorParameters_autoGenerated.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.SaveParametersToXML(outputFileName);
}
public void ExecuteSipperOnMSGFOutputTest1()
{
var paramFile =
@"\\protoapps\DataPkgs\Public\2013\788_Sipper_C13_Analysis_Hot_Lake_SNC_Ana_preliminary\Parameters\ExecutorParameters1.xml";
var parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.LoadParameters(paramFile);
parameters.CopyRawFileLocal = false;
parameters.FolderPathForCopiedRawDataset = @"D:\Data\Sipper\HLP_Ana";
var testDataset =
@"D:\Data\Sipper\HLP_Ana\HLP_Ana_SIP_02_19APR13_Frodo_12-12-04.raw";
var outputParameterFile = Path.Combine(Path.GetDirectoryName(paramFile),
Path.GetFileNameWithoutExtension(paramFile) + " - copy.xml");
parameters.SaveParametersToXML(outputParameterFile);
var executor = new BasicTargetedWorkflowExecutor(parameters, testDataset);
executor.Targets.TargetList = executor.Targets.TargetList.Take(10).ToList();
executor.Execute();
var workflow = executor.TargetedWorkflow as SipperTargetedWorkflow;
var result = workflow.Result as SipperLcmsTargetedResult;
Assert.IsNotNull(result);
Assert.IsNotNull(result.ChromCorrelationData);
Assert.IsNotNull(result.ChromCorrelationData.CorrelationDataItems);
Assert.IsTrue(result.ChromCorrelationData.CorrelationDataItems.Count > 0);
//foreach (var dataItem in result.ChromCorrelationData.CorrelationDataItems)
//{
// Console.WriteLine(dataItem.CorrelationRSquaredVal);
//}
//foreach (var fitScoreDataItem in workflow.FitScoreData)
//{
// Console.WriteLine(fitScoreDataItem.Key + "\t" + fitScoreDataItem.Value);
//}
}
public void O16O18Workflow_ProblemCaseTesting1()
{
//This is a nice case where the O16 is quite low and can be missed. In the current settings
//the O16Chrom is null (by itself), so the chrom correlation fails.
//Thus quant based on chrom corr fails, but quant based on O16O18 feature finding succeeds.
//7673789
var executorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParametersFile);
var testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var autoSavedExecutorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1_autosaved.xml";
executorParameters.SaveParametersToXML(autoSavedExecutorParametersFile);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
var testTarget = 7415;
executor.Targets.TargetList =
executor.Targets.TargetList.Where(p => p.ID == testTarget).ToList();
executor.Execute();
var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase,
"Results",
executor.TargetedWorkflow.Run.DatasetName + "_results.txt");
var importer = new O16O18TargetedResultFromTextImporter(expectedResultsFilename);
var results = importer.Import().Results;
var result1 = results.First();
Console.WriteLine(result1.ToStringWithDetailsAsRow());
}
public void saveExecutorParameterFileTest1()
{
var targetsFilePath = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Targets\POnly_MassTagsMatchingInHalfOfDatasets_Filtered0.45-0.47NET_first18.txt";
var workflowFilePath = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Parameters\N14N15WorkflowParameters1.xml";
var targetedAlignmentParameterFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Parameters\TargetedAlignmentWorkflowParameters1.xml";
var exportedExecutorParametersFilePath = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Parameters\ExecutorParameters1.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = false;
executorParameters.DeleteLocalDatasetAfterProcessing = false;
executorParameters.TargetType = Globals.TargetType.DatabaseTarget;
executorParameters.TargetedAlignmentIsPerformed = true;
executorParameters.TargetedAlignmentWorkflowParameterFile = targetedAlignmentParameterFile;
executorParameters.TargetsFilePath = targetsFilePath;
executorParameters.WorkflowParameterFile = workflowFilePath;
executorParameters.SaveParametersToXML(exportedExecutorParametersFilePath);
}
public void ParameterTest1()
{
var outputFileName = @"\\protoapps\UserData\Slysz\IQDemo\Parameters" + @"\IQExecutorParameters.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = false;
executorParameters.DeleteLocalDatasetAfterProcessing = true;
executorParameters.FolderPathForCopiedRawDataset = @"\\protoapps\UserData\Slysz\IQ_Demo\RawData";
executorParameters.TargetType = Globals.TargetType.DatabaseTarget;
executorParameters.TargetsBaseFolder = "";
executorParameters.TargetedAlignmentIsPerformed = false;
executorParameters.TargetedAlignmentWorkflowParameterFile =
@"\\protoapps\UserData\Slysz\IQ_Demo\Parameters\TargetedAlignmentWorkflowParameters1.xml";
executorParameters.TargetsFilePath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_Formic_MassTags_Bin10_first10.txt";
executorParameters.WorkflowParameterFile = @"\\protoapps\UserData\Slysz\IQ_Demo\Parameters\IQParameters1.xml";
executorParameters.SaveParametersToXML(outputFileName);
}
public void exportParametersTest1()
{
var exportedParametersFile = Path.Combine(FileRefs.OutputFolderPath, "exportedBasicTargetedWorkflowExecutorParameters.xml");
var parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.CopyRawFileLocal = true;
parameters.DeleteLocalDatasetAfterProcessing = true;
parameters.FolderPathForCopiedRawDataset = @"d:\temp\rawdata";
parameters.TargetsFilePath = @"d:\temp\MassTags\massTagsToBeTargeted.txt";
parameters.TargetsBaseFolder = @"d:\temp";
parameters.TargetedAlignmentWorkflowParameterFile = @"d:\temp\Parameters\targetedAlignmentParameters.xml";
parameters.WorkflowParameterFile = @"d:\temp\Parameters\WorkflowParameters.xml";
parameters.TargetsBaseFolder = @"d:\temp";
parameters.SaveParametersToXML(exportedParametersFile);
}
public void TargetedWorkflowUsingMsgfInputsTest1()
{
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.TargetsFilePath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\Yellow_C13_070_23Mar10_Griffin_10-01-28_msgfplus.tsv";
executorParameters.TargetedAlignmentIsPerformed = false;
executorParameters.SaveParametersToXML(
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\IQConsoleDemo\IqExecutorParameters.xml");
var workflowParameters = new BasicTargetedWorkflowParameters();
workflowParameters.ChromSmootherNumPointsInSmooth = 9;
workflowParameters.ChromPeakDetectorPeakBR = 1;
workflowParameters.ChromPeakDetectorSigNoise = 3;
workflowParameters.ChromGenTolerance = 20;
workflowParameters.ChromNETTolerance = 0.025;
workflowParameters.MSToleranceInPPM = 20;
workflowParameters.SaveParametersToXML(
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\IQConsoleDemo\IqWorkflowParameters.xml");
var workflow = new BasicTargetedWorkflow(workflowParameters);
var testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw";
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, workflow, testDatasetPath);
executor.Targets.TargetList = executor.Targets.TargetList.Take(10).ToList();
executor.Execute();
}
public void LocalQCShewProcessingTest1()
{
var parameterFileName = @"C:\Users\d3x720\Documents\Data\QCShew\IQ\IQExecutorParameterFile1.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.TargetsFilePath =
@"C:\Users\d3x720\Documents\Data\QCShew\IQ\QCShew_Formic_MassTags_Bin10_first10.txt";
executorParameters.SaveParametersToXML(parameterFileName);
var workflowParameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(workflowParameters);
var testDatasetPath =
@"C:\Users\d3x720\Documents\Data\QCShew\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, workflow,
testDatasetPath);
var testTargetID = 24749;
var testTargetZ = 3;
executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.ID == testTargetID &&
p.ChargeState == testTargetZ).ToList();
executor.Execute();
//TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
foreach (var chrompeak in executor.TargetedWorkflow.ChromPeaksDetected)
{
Console.WriteLine(chrompeak.XValue.ToString("0.0000") + "\t" + chrompeak.Height.ToString("0") + "\t" + chrompeak.Width.ToString("0.000") + "\n");
}
}
public void O16O18Workflow_ProblemCaseTesting2()
{
var executorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParametersFile);
executorParameters.TargetsFilePath =
@"\\protoapps\DataPkgs\Public\2012\641_Alz_O16O18_dataprocessing2\Targets\MT_Human_ALZ_O18_P852\MassTags_PMT2.txt";
var testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var autoSavedExecutorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1_autosaved.xml";
executorParameters.SaveParametersToXML(autoSavedExecutorParametersFile);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
//int testTarget = 7673789;
//executor.Targets.TargetList =executor.Targets.TargetList.Where(p => p.ID == testTarget && p.ChargeState==3).ToList();
executor.Execute();
var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase, "Results",
executor.TargetedWorkflow.Run.DatasetName + "_results.txt");
var importer = new O16O18TargetedResultFromTextImporter(expectedResultsFilename);
var results = importer.Import().Results;
var result1 = results.First();
Console.WriteLine(result1.ToStringWithDetailsAsRow());
}
public void Test1()
{
var testDatasetPath = uimfTestfile1;
var executorParameterFilename =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\UIMF_O16O18Testing\Parameters\WorkflowExecutorParameters.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFilename);
var outputExecutorParameterFilename = executorParameterFilename.Replace(".xml", "_autoGen.xml");
executorParameters.SaveParametersToXML(outputExecutorParameterFilename);
var testTarget = 7563580;
var executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.ID == testTarget).ToList();
executor.Execute();
}
public void IqExecutor_StandardO16O18Testing_VladAlz()
{
//see JIRA https://jira.pnnl.gov/jira/browse/OMCS-628
var executorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParametersFile);
executorParameters.OutputFolderBase =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz";
var testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
executorParameters.IsMassAlignmentPerformed = true;
executorParameters.IsNetAlignmentPerformed = true;
executorParameters.ReferenceTargetsFilePath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2.txt";
var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase, "IqResults", RunUtilities.GetDatasetName(testDatasetPath) + "_iqResults.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var autoSavedExecutorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1_autosaved.xml";
executorParameters.SaveParametersToXML(autoSavedExecutorParametersFile);
var run = new RunFactory().CreateRun(testDatasetPath);
var executor = new IqExecutor(executorParameters, run);
var targetsFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2_First60.txt";
targetsFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2.txt";
executor.LoadAndInitializeTargets(targetsFile);
executor.SetupMassAndNetAlignment();
var testTarget = 9282;
executor.Targets = (from n in executor.Targets where n.ID == testTarget select n).ToList();
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.ChromNETTolerance = 0.025;
targetedWorkflowParameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
//define workflows for parentTarget and childTargets
var parentWorkflow = new O16O18ParentIqWorkflow(run, targetedWorkflowParameters);
var childWorkflow = new O16O18IqWorkflow(run, targetedWorkflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);
executor.DoAlignment();
executor.Execute();
IqResultImporter importer = new IqResultImporterBasic(expectedResultsFilename);
var allResults = importer.Import();
var result1 = allResults.First(p => p.Target.ID == 9282 && p.Target.ChargeState == 2);
Assert.AreEqual(9282, result1.Target.ID);
Assert.AreEqual(0.32678m, (decimal)result1.ElutionTimeObs);
Assert.AreEqual(4545, result1.LcScanObs);
Assert.AreEqual(0.02, (decimal)result1.FitScore);
}
public void StandardO16O18Testing_VladAlz()
{
//see JIRA https://jira.pnnl.gov/jira/browse/OMCS-628
var executorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParametersFile);
var testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var autoSavedExecutorParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Parameters\ExecutorParameters1_autosaved.xml";
executorParameters.SaveParametersToXML(autoSavedExecutorParametersFile);
executorParameters.OutputFolderBase =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz";
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
var testTarget = 9282;
executor.Targets.TargetList =
executor.Targets.TargetList.Where(p => p.ID == testTarget).ToList();
//executor.InitializeRun(testDatasetPath);
//executor.TargetedWorkflow.Run = executor.Run;
//foreach (var targetBase in executor.Targets.TargetList)
//{
// executor.Run.CurrentMassTag = targetBase;
// var workflow = (O16O18Workflow)executor.TargetedWorkflow;
// workflow.Execute();
// var result = workflow.Result as DeconTools.Backend.Core.Results.LcmsFeatureTargetedResult;
//}
executor.Execute();
var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase,
"Results",
executor.TargetedWorkflow.Run.DatasetName + "_Results.txt");
var importer = new O16O18TargetedResultFromTextImporter(expectedResultsFilename);
var repository = importer.Import();
Assert.AreEqual(3, repository.Results.Count);
var result1 = repository.Results[1] as O16O18TargetedResultDTO;
Assert.AreEqual(9282, result1.TargetID);
Assert.AreEqual(2, result1.ChargeState);
Assert.AreEqual(4537, result1.ScanLC);
Assert.AreEqual(0.32514m, (decimal)Math.Round(result1.NET, 5));
Assert.AreEqual(-0.001662m, (decimal)Math.Round(result1.NETError, 6));
Assert.AreEqual(0.274m, (decimal)Math.Round(result1.Ratio, 3));
Assert.IsTrue(result1.ChromCorrO16O18DoubleLabel > 0);
Console.WriteLine(result1.ToStringWithDetailsAsRow());
}
public void ExecuteSipperUsingStandardExecutorClass1()
{
var paramFile =
@"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\Parameters\ExecutorParameters1.xml";
var parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.LoadParameters(paramFile);
parameters.CopyRawFileLocal = false;
//parameters.FolderPathForCopiedRawDataset = @"D:\data\temp";
var testDataset =
@"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\RawData\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw";
var outputParameterFile = Path.Combine(Path.GetDirectoryName(paramFile),
Path.GetFileNameWithoutExtension(paramFile) + " - copy.xml");
parameters.SaveParametersToXML(outputParameterFile);
parameters.TargetType = Globals.TargetType.LcmsFeature;
var executor = new BasicTargetedWorkflowExecutor(parameters, testDataset);
var targetsOfInterest = new int[] { 5555 };
//targetsOfInterest = new int[] { 5905 }; //throwing error in Chromcorr
//targetsOfInterest = new int[]{6110};
//targetsOfInterest = new int[]
// {
// 5555, 5677, 5746, 5905, 6110, 6496, 7039, 7116, 7220, 7229, 7370, 7585, 8338, 8491, 8517, 8616, 8618,
// 8715, 8947, 8958, 8968, 9024, 9159, 9240, 9242, 9261, 9328, 9441, 9474, 9506, 9519, 9583, 9792, 9944,
// 9965, 10223, 10251, 10329, 10649, 10673, 11249, 11367, 11523, 11677, 11912, 12178, 12304, 12383, 12395,
// 12492, 12517, 12692, 12700, 12828, 13443, 13590, 13740, 14090, 14256
// };
executor.Targets.TargetList =
(executor.Targets.TargetList.Where(n => targetsOfInterest.Contains(n.ID))).ToList();
executor.Execute();
var workflow = executor.TargetedWorkflow as SipperTargetedWorkflow;
workflow.WorkflowParameters.SaveParametersToXML(
@"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\Parameters\SipperTargetedWorkflowParameters_Sum5 - copy.xml");
var result = workflow.Result as SipperLcmsTargetedResult;
Assert.IsNotNull(result);
Assert.IsNotNull(result.ChromCorrelationData);
Assert.IsNotNull(result.ChromCorrelationData.CorrelationDataItems);
Assert.IsTrue(result.ChromCorrelationData.CorrelationDataItems.Count > 0);
//foreach (var dataItem in result.ChromCorrelationData.CorrelationDataItems)
//{
// Console.WriteLine(dataItem.CorrelationRSquaredVal);
//}
//foreach (var fitScoreDataItem in workflow.FitScoreData)
//{
// Console.WriteLine(fitScoreDataItem.Key + "\t" + fitScoreDataItem.Value);
//}
}