public void O16O18_onBruker15T()
{
string executorParametersFile =
@"\\protoapps\DataPkgs\Public\2012\641_Alz_O16O18_dataprocessing2\Parameters\ExecutorParameters1 - Copy.xml";
BasicTargetedWorkflowExecutorParameters 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";
string testDatasetPath = @"D:\Data\From_Vlad\2013_01_29_ALZ_CTRL_5_0p05_1_01_224.d";
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.Targets.TargetList = executor.Targets.TargetList.Take(50).ToList();
executor.Execute();
}
public void AlternateConstructor_targetedWorkflowNoAlignment()
{
var executorParameterFile = baseFolder + @"\Parameters\QCShew_OrbiStandard_workflowExecutorParameters.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
var resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "Results");
var testDatasetPath = baseFolder + @"\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var testDatasetName = "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18";
var expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_results.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var basicTargetedWorkflowParameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(basicTargetedWorkflowParameters);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters,
workflow, testDatasetPath);
executor.Execute();
Assert.IsTrue(File.Exists(expectedResultsFilename));
}
public void TestUIMFTargetedMSMSWorkflow()
{
var datasetPath = uimfMsMsFile;
var executorParameterFilename =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\UIMF_Targeted_MSMS_Testing\Parameters\UIMFTargetedMSMSWorkflowExecutorParametersMostConfidentMassTags.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFilename);
var executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath);
executor.Execute();
//List<TargetedResultBase> resultList = executor.TargetedWorkflow.Run.ResultCollection.GetMassTagResults();
//foreach (var targetedResultBase in resultList)
//{
// Console.WriteLine("*******************************************************");
// Console.WriteLine(targetedResultBase.Target.Code + "\t" + targetedResultBase.Target.ChargeState);
// foreach (var peakQualityData in targetedResultBase.ChromPeakQualityList)
// {
// peakQualityData.Display();
// }
//}
//TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
}
public void ProcessSangTaeStuff()
{
string executorParametersFile =
@"\\protoapps\UserData\Sangtae\ToSlysz\IQ\ExecutorParameters1.xml";
BasicTargetedWorkflowExecutorParameters executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParametersFile);
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
executorParameters.TargetsFilePath = @"\\protoapps\UserData\Sangtae\ToSlysz\IQ\Target_TD.txt";
string testDatasetPath = @"\\protoapps\UserData\Sangtae\ToSlysz\IQ\QC_Shew_12_02_2_1Aug12_Cougar_12-06-11.raw";
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
int testTarget = 7673789;
//executor.Targets.TargetList =executor.Targets.TargetList.Where(p => p.ID == testTarget && p.ChargeState==3).ToList();
string testTargetSeq = "SEVIAVVSSDTFVRPIYAGNALATVQSHDAVK";
testTargetSeq = "ILQGYGAGHQFAAGGDGTAINQGGIAEQVTSAALNYR";
executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.Code == testTargetSeq).ToList();
//executor.Targets.TargetList = executor.Targets.TargetList.Take(50).ToList();
executor.Execute();
TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
}
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 Test1()
{
string executorParametersFile =
@"D:\Data\From_Vlad\Bruker\Parameters\ExecutorParameters1 - Copy.xml";
BasicTargetedWorkflowExecutorParameters executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParametersFile);
string testDatasetPath =
@"D:\Data\From_Vlad\Bruker\2013_01_29_ALZ_CTRL_5_0p5_1_01_228.d";
Run run = new RunFactory().CreateRun(testDatasetPath);
int numScans = run.GetNumMSScans();
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
int testTarget = 206675561; //beta amyloid
executor.Targets.TargetList =
executor.Targets.TargetList.Where(p => p.ID == testTarget && p.ChargeState == 2).ToList();
executor.Execute();
//TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
executor.TargetedWorkflow.Result.DisplayToConsole();
Console.WriteLine("expected mz= " + executor.TargetedWorkflow.Result.Target.MZ);
double expectedNET = executor.TargetedWorkflow.Result.Target.NormalizedElutionTime;
double expectedScan = expectedNET * numScans;
Console.WriteLine("Expected NET= " + expectedNET + "; Corresponds to scan: " + expectedScan);
}
public void LoadExecutorParametersTest1()
{
var inputFilename = baseFolder + @"\Parameters\BasicTargetedWorkflowExecutorParameters_forImport.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(inputFilename);
Assert.AreEqual(1500, (int)executorParameters.MaxMzForDefiningChargeStateTargets);
Assert.AreEqual(100, executorParameters.MaxNumberOfChargeStateTargetsToCreate);
}
public void issue0725_targetedAlignmentProblems()
{
var executorParameterFile = @"D:\Data\Orbitrap\Issue0725_badAlignment\Issue0725_executorWorkflow.xml";
var datasetPath = @"D:\Data\Orbitrap\Issue0725_badAlignment\QC_Shew_10_03-2_100min_06May10_Tiger_10-04-08.RAW";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath);
executor.Execute();
}
public void issue0705_completelyFailedAlignment_multialignErrors()
{
var executorParameterFile = @"\\protoapps\UserData\Slysz\Data\Redmine_Issues\Issue0705_failedAlignment\workflowExecutorParameters.xml";
var datasetPath = @"\\proto-3\LTQ_Orb_3\2010_1\QC_Shew_10_01-pt5-4_12Feb10_Doc_09-12-26\QC_Shew_10_01-pt5-4_12Feb10_Doc_09-12-26.raw";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath);
executor.Execute();
}
public void ExecutorTest2()
{
var executorParamFile = baseFolder + @"\Parameters" + "\\" + @"QCShew_OrbiStandard_workflowExecutorParameters.xml";
var testDatasetPath = baseFolder + "\\" + "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParamFile);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
}
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 Bruker9T_N14N15_executorTest1()
{
var testfile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\RawData\RSPH_PtoA_L_28_rep1_28Feb08_Raptor_08-01-01";
var parameterFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Parameters\ExecutorParameters1 - forTesting.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(parameterFile);
executorParameters.CopyRawFileLocal = false;
var executor = new BasicTargetedWorkflowExecutor(executorParameters, testfile);
executor.Execute();
}
public void TestUIMFTargetedMSMSWorkflowLotsOfTargets()
{
var datasetPath = uimfMsMsFile;
var executorParameterFilename =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\UIMF_Targeted_MSMS_Testing\Parameters\UIMFTargetedMSMSWorkflowExecutorParametersLotsOfMassTags.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFilename);
var executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath);
executor.Execute();
}
public void Test1()
{
string executorParameterFileName = @"D:\Data\IQ_testing\From_SangTae\ExecutorParameters1.xml";
BasicTargetedWorkflowExecutorParameters executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFileName);
string testDataFile = @"D:\Data\IQ_testing\From_SangTae\QC_Shew_12_02_2_1Aug12_Cougar_12-06-11.raw";
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDataFile);
executor.Targets.TargetList = executor.Targets.TargetList.Take(10).ToList();
executor.Execute();
}
public void InvestigateIQFailures()
{
var executorParamFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Parameters\ExecutorParameters1 - Copy.xml";
var executorParameters =
new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParamFile);
var testFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Testing\LNA_A_Expo_Sample_SC_9_LNA_ExpA_Expo_Stat_SeattleBioMed_15Feb13_Cougar_12-12-35.raw";
var run = new RunFactory().CreateRun(testFile);
var iqparameterFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Testing\IQWorkflowParameters1.xml";
var workflowParameters = new BasicTargetedWorkflowParameters();
workflowParameters.LoadParameters(iqparameterFile);
workflowParameters.MSToleranceInPPM = 10;
workflowParameters.ChromPeakDetectorPeakBR = 0.25;
workflowParameters.ChromPeakDetectorSigNoise = 2;
var targetedWorkflow = new BasicTargetedWorkflow(run, workflowParameters);
var executor = new BasicTargetedWorkflowExecutor(executorParameters, targetedWorkflow, testFile);
//int[] testTargets = {349959971, 349951038,349954483 };
//int[] testTargets = { 349951038 };
//int[] testTargets = { 349954483 };
//int[] testTargets = { 2911730 };
int[] testTargets = { 349946881 };
var chargeState = 3;
executor.Targets.TargetList = (from n in executor.Targets.TargetList where testTargets.Contains(n.ID) select n).ToList();
executor.Targets.TargetList = (from n in executor.Targets.TargetList where n.ChargeState == chargeState select n).ToList();
executor.Execute();
//Results of investiga tion! - 349959971 was being missed because the MSTolerance was too narrow. When changed from 5 to 6, it was found. I think we can safely set this at 10.
//Results of investigation! - 349951038 was being missed because it was being flagged (peak to the left) problem.
TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
}
public void importParametersTest1()
{
var importedParametersFile = Path.Combine(FileRefs.ImportedData, "importedBasicTargetedWorkflowExecutorParameters_defaults.xml");
var parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.LoadParameters(importedParametersFile);
Assert.AreEqual(true, parameters.CopyRawFileLocal);
Assert.AreEqual(true, parameters.DeleteLocalDatasetAfterProcessing);
Assert.AreEqual(@"d:\temp\rawdata", parameters.FolderPathForCopiedRawDataset);
Assert.AreEqual(@"d:\temp\MassTags\massTagsToBeTargeted.txt", parameters.TargetsFilePath);
Assert.AreEqual(@"d:\temp\Parameters\targetedAlignmentParameters.xml", parameters.TargetedAlignmentWorkflowParameterFile);
Assert.AreEqual(@"d:\temp\Parameters\WorkflowParameters.xml", parameters.WorkflowParameterFile);
Assert.AreEqual(@"d:\temp", parameters.TargetsBaseFolder);
}
public void TestUIMFTargetedMSMSWorkflowSingleTarget()
{
var datasetPath = uimfMsMsFile;
var executorParameterFilename =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\UIMF_Targeted_MSMS_Testing\Parameters\UIMFTargetedMSMSWorkflowExecutorParameters.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFilename);
var executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath);
executor.Execute();
//TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
}
public void copyToLocalTest1()
{
var executorParameterFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\basicTargetedWorkflowExecutorParameters_CopyToLocalTestCase2.xml";
var datasetPath = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var testDatasetName = "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
var expectedResultsFilename = Path.Combine(executorParameters.OutputFolderBase, "Results", testDatasetName + "_results.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, datasetPath);
executor.Execute();
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new UnlabelledTargetedResultFromTextImporter(expectedResultsFilename);
var repository = importer.Import();
Assert.AreEqual(10, repository.Results.Count);
var result1 = repository.Results[2];
Assert.AreEqual(24702, result1.TargetID);
Assert.AreEqual(3, result1.ChargeState);
Assert.AreEqual(8112, result1.ScanLC);
//Dataset MassTagID ChargeState Scan ScanStart ScanEnd NET NumChromPeaksWithinTol NumQualityChromPeaksWithinTol MonoisotopicMass MonoMZ IntensityRep FitScore IScore FailureType
//QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18 24702 3 8119 8112 8124 0.4172 2 1 2920.53082 974.51755 1379489 0.1136 0.0000
}
public void ExecutorTest3Temp()
{
var executorParamFile =
@"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\Parameters\ExecutorParameters1 - Copy.xml";
var testDatasetPath =
@"\\protoapps\DataPkgs\Public\2012\601_Sipper_paper_data_processing_and_analysis\RawData\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParamFile);
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
}
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 orbitrap_N14N15_executorTest2()
{
var testfile =
@"\\protoapps\UserData\Slysz\Data\N14N15\2012_07_09_VelosOrbi Ponly datasets\RawData\RSPH_Ponly_28_A_8May12_Earth_12-03-11.raw";
var parameterFile =
@"\\protoapps\UserData\Slysz\Data\N14N15\2012_07_09_VelosOrbi Ponly datasets\Parameters\ExecutorParameters1 - forTesting.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(parameterFile);
executorParameters.CopyRawFileLocal = false;
var executor = new BasicTargetedWorkflowExecutor(executorParameters, testfile);
executor.Execute();
//TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
foreach (var chromPeak in executor.TargetedWorkflow.ChromPeaksDetected)
{
Console.WriteLine(chromPeak.XValue + "\t" + chromPeak.Height + "\t" + chromPeak.Width);
}
}
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 targetedWorkflow_noAlignment()
{
//TODO: fix test - it is using previous data for alignment
//TODO: make JIRA issue so we can see chromatogram, etc.
var executorParameterFile = baseFolder + @"\Parameters\QCShew_OrbiStandard_workflowExecutorParameters.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
var resultsFolderLocation = executorParameters.OutputFolderBase + "\\Results";
var testDatasetPath = baseFolder + @"\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var testDatasetName = "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18";
var expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_results.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var rawFileInfo = new FileInfo(testDatasetPath);
//delete alignment files
var mzalignmentFile = Path.Combine(rawFileInfo.DirectoryName, testDatasetName + "_mzAlignment.txt");
var netAlignmentFile = Path.Combine(rawFileInfo.DirectoryName, testDatasetName + "_netAlignment.txt");
if (File.Exists(mzalignmentFile))
{
File.Delete(mzalignmentFile);
}
if (File.Exists(netAlignmentFile))
{
File.Delete(netAlignmentFile);
}
executorParameters.TargetedAlignmentIsPerformed = false; //no targeted alignment
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new UnlabelledTargetedResultFromTextImporter(expectedResultsFilename);
var repository = importer.Import();
Assert.AreEqual(10, repository.Results.Count);
var result1 = repository.Results[0];
Assert.AreEqual(24702, result1.TargetID);
Assert.AreEqual(3, result1.ChargeState);
Assert.AreEqual(8637, result1.ScanLC);
//TODO: confirm/fix this NET value
//Assert.AreEqual(0.41724m, (decimal)Math.Round(result1.NET, 5));
// Assert.AreEqual(0.002534m, (decimal)Math.Round(result1.NETError, 6));
//Assert.AreEqual(974.52068m, (decimal)Math.Round(result1.MonoMZ, 5));
//Assert.AreEqual(2920.53082m, (decimal)Math.Round(result1.MonoMass, 5));
//Assert.AreEqual(2920.53733m, (decimal)Math.Round(result1.MonoMassCalibrated, 5));
//Assert.AreEqual(-1.83m, (decimal)Math.Round(result1.MassErrorInPPM, 2));
}
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);
//}
}
public void targetedWorkflow_withTargetedAlignment_test()
{
var executorParameterFile = baseFolder + @"\Parameters\QCShew_OrbiStandard_workflowExecutorParameters.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
var resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "Results");
var testDatasetPath = baseFolder + @"\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var testDatasetName = "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18";
var expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_results.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var rawFileInfo = new FileInfo(testDatasetPath);
var mzalignmentFile = Path.Combine(rawFileInfo.DirectoryName, testDatasetName + "_mzAlignment.txt");
var netAlignmentFile = Path.Combine(rawFileInfo.DirectoryName, testDatasetName + "_netAlignment.txt");
if (File.Exists(mzalignmentFile))
{
File.Delete(mzalignmentFile);
}
if (File.Exists(netAlignmentFile))
{
File.Delete(netAlignmentFile);
}
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new UnlabelledTargetedResultFromTextImporter(expectedResultsFilename);
var repository = importer.Import();
Assert.AreEqual(10, repository.Results.Count);
var result1 = repository.Results[0];
Assert.AreEqual(24702, result1.TargetID);
Assert.AreEqual(3, result1.ChargeState);
Assert.AreEqual(8627, result1.ScanLC);
//Assert.AreEqual(0.41724m, (decimal)Math.Round(result1.NET, 5));
//Assert.AreEqual(0.002534m, (decimal)Math.Round(result1.NETError, 6));
//Assert.AreEqual(2920.53082m, (decimal)Math.Round(result1.MonoMass, 5));
//Assert.AreEqual(2920.53879m, (decimal)Math.Round(result1.MonoMassCalibrated, 5));
//Assert.AreEqual(-2.33m, (decimal)Math.Round(result1.MassErrorInPPM, 2));
//Dataset MassTagID ChargeState Scan ScanStart ScanEnd NET NumChromPeaksWithinTol NumQualityChromPeaksWithinTol MonoisotopicMass MonoMZ IntensityRep FitScore IScore FailureType
//QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18 24702 3 8119 8112 8124 0.4172 2 1 2920.53082 974.51755 1379489 0.1136 0.0000
}
