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 TestErnestosData1()
{
string baseFolder = @"\\protoapps\DataPkgs\Public\2012\573_O16O18_Data_analysis_of_ubiquintated_peptides";
string outputFolder = @"D:\Temp\TargetedTesting";
BasicTargetedWorkflowExecutorParameters executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.TargetsBaseFolder = Path.Combine(baseFolder, "Targets");
executorParameters.WorkflowParameterFile = Path.Combine(baseFolder, "Parameters", "O16O18WorkflowParameters_2011_08_23_sum5.xml");
executorParameters.OutputFolderBase = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowTesting\Output";
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
string testDatasetPath = @"\\protoapps\UserData\Slysz\Data\O16O18\Ernesto\PSI_LRW_18O_02A_18Jun12_Falcon_12-03-34.RAW";
testDatasetPath = @"D:\Data\O16O18\Ernesto\PSI_LRW_1to1_03A_6Jul12_Falcon_12-06-04.raw";
string outputtedParameterFile =
@"\\protoapps\DataPkgs\Public\2012\573_O16O18_Data_analysis_of_ubiquintated_peptides\Parameters\ExecutorParameters1.xml";
//executorParameters.SaveParametersToXML(outputtedParameterFile);
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
}
public void DemoParameterTest1()
{
var outputFileName = baseFolder + @"\BasicTargetedWorkflowExecutorParameters_autoGenerated.xml";
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.SaveParametersToXML(outputFileName);
}
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 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 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 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 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 MSAlignTargetDataTest()
{
var testFile = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\SBEP_STM_001_02222012_Aragon.raw";
var targetsFile = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\salmonella_top_target.txt";
var resultsFolder = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\Results";
//Backend.Utilities.SipperDataDump.DataDumpSetup(@"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\Results\detailed_results.txt");
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
executorBaseParameters.ChromGenSourceDataPeakBR = 3;
executorBaseParameters.ChromGenSourceDataSigNoise = 2;
executorBaseParameters.TargetsFilePath = targetsFile;
executorBaseParameters.OutputFolderBase = resultsFolder;
var run = new RunFactory().CreateRun(testFile);
var executor = new TopDownMSAlignExecutor(executorBaseParameters, run);
var s = Stopwatch.StartNew();
executor.LoadAndInitializeTargets(targetsFile);
s.Stop();
var rt = s.Elapsed;
Console.WriteLine("import: " + rt);
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.ChromNETTolerance = 0.05;
targetedWorkflowParameters.ChromatogramCorrelationIsPerformed = true;
targetedWorkflowParameters.ChromSmootherNumPointsInSmooth = 15;
targetedWorkflowParameters.MSToleranceInPPM = 15;
targetedWorkflowParameters.NumMSScansToSum = 5;
//define workflows for parentTarget and childTargets
var parentWorkflow = new ChromPeakDeciderTopDownIqWorkflow(run, targetedWorkflowParameters);
var childWorkflow = new ChargeStateChildTopDownIqWorkflow(run, targetedWorkflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);
var stopwatch = Stopwatch.StartNew();
//Main line for executing IQ:
executor.Execute();
stopwatch.Stop();
var runtime = stopwatch.Elapsed;
Console.WriteLine("Runtime: " + runtime);
}
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 ChromCorrelatorTest1()
{
var rawFilename = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw";
var run = new RunFactory().CreateRun(rawFilename);
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new IqExecutor(executorBaseParameters, run);
executor.LoadChromData(run);
var workflowAssigner = new IqWorkflowAssigner();
TargetedWorkflowParameters workflowParameters = new O16O18WorkflowParameters();
IqWorkflow workflow = new O16O18IqWorkflow(run, workflowParameters);
IqTarget iqTarget = new IqChargeStateTarget();
iqTarget.EmpiricalFormula = "C58H100N18O20";
iqTarget.Code = "GAAQNIIPASTGAAK";
iqTarget.ID = 1093;
iqTarget.ChargeState = 0;
var iqTargetList = new List <IqTarget>();
iqTargetList.Add(iqTarget);
var utilities = new IqTargetUtilities();
utilities.CreateChildTargets(iqTargetList);
workflowAssigner.AssignWorkflowToParent(workflow, iqTargetList);
workflowAssigner.AssignWorkflowToChildren(workflow, iqTargetList);
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
foreach (var target in iqTarget.ChildTargets())
{
utilities.UpdateTargetMissingInfo(target);
target.TheorIsotopicProfile = theorFeatureGenerator.GenerateTheorProfile(target.EmpiricalFormula, target.ChargeState);
}
foreach (var childTarget in iqTarget.ChildTargets())
{
var result = childTarget.CreateResult();
var correlator = new O16O18ChromCorrelator(7, 0.1, 20, Globals.ToleranceUnit.PPM);
var corrData = correlator.CorrelateData(run, result, 5700, 6500);
var corrDataItem1 = corrData.CorrelationDataItems.First();
Console.WriteLine("z= \t" + childTarget.ChargeState + "\tCorrelationData (slope,intercept,rsquared)= \t" + corrDataItem1);
}
}
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 JoinTargetsTest1()
{
var targetsFileName =
@"\\proto-7\VOrbi05\2013_2\mhp_plat_test_1_14April13_Frodo_12-12-04\MSG201305011339_Auto939903\mhp_plat_test_1_14April13_Frodo_12-12-04_msgfdb_fht.txt";
var massTagFilename =
@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set1_P890_targets.txt";
var rawFile = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw";
IqTargetImporter massTagImporter = new BasicIqTargetImporter(massTagFilename);
var massTagRefs = massTagImporter.Import().OrderBy(p => p.Code).ToList();
WorkflowExecutorBaseParameters parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.TargetsFilePath = targetsFileName;
var run = new RunFactory().CreateRun(rawFile);
var massAndNetAligner = new IqMassAndNetAligner(parameters, run);
massAndNetAligner.LoadAndInitializeTargets();
var testNET = massAndNetAligner.Targets.First().ElutionTimeTheor;
var query = (from massTag in massTagRefs
join target in massAndNetAligner.Targets on massTag.Code equals target.Code
select new
{
MassTag = massTag,
MSGFTarget = target
}).ToList();
foreach (var thing in query)
{
thing.MSGFTarget.ID = thing.MassTag.ID;
thing.MSGFTarget.ElutionTimeTheor = thing.MassTag.ElutionTimeTheor;
}
var targets = query.Select(p => p.MSGFTarget).ToList();
var testNETAfter = massAndNetAligner.Targets.First().ElutionTimeTheor;
Console.WriteLine("NET before= " + testNET);
Console.WriteLine("NET before= " + testNETAfter);
}
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 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 targetedWorkflow_alignUsingDataFromFiles_localVersion()
{
//TODO: figure out result is correct
//TODO: get MS and Chrom in Jira
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.TargetsFilePath =
@"C:\Users\d3x720\Documents\Data\QCShew\IQ\QCShew_Formic_MassTags_Bin10_MT24702_Z3.txt";
executorParameters.TargetedAlignmentIsPerformed = true;
var workflowParameters = new BasicTargetedWorkflowParameters();
workflowParameters.ChromSmootherNumPointsInSmooth = 9;
workflowParameters.ChromPeakDetectorPeakBR = 1;
workflowParameters.ChromPeakDetectorSigNoise = 1;
workflowParameters.ChromGenTolerance = 20;
workflowParameters.ChromNETTolerance = 0.025;
workflowParameters.MSToleranceInPPM = 20;
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);
executor.Execute();
var expectedResultsFilename =
@"C:\Users\d3x720\Documents\Data\QCShew\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_results.txt";
var result = executor.TargetedWorkflow.Result;
Console.WriteLine("theor monomass= \t" + result.Target.MonoIsotopicMass);
Console.WriteLine("monomass= \t" + result.IsotopicProfile.MonoIsotopicMass);
Console.WriteLine("ppmError before= \t" + result.MassErrorBeforeAlignment);
Console.WriteLine("ppmError after= \t" + result.MassErrorAfterAlignment);
Console.WriteLine("Database NET= " + result.Target.NormalizedElutionTime);
Console.WriteLine("Result NET= " + result.GetNET());
Console.WriteLine("Result NET Error= " + result.GetNETAlignmentError());
Console.WriteLine("NumChromPeaksWithinTol= " + result.NumChromPeaksWithinTolerance);
//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 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 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 ExecutorCreatingTargetsTest1()
{
var util = new IqTargetUtilities();
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_scans5500-6500_peaks.txt";
var targetsFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var resultsFolder = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Results";
var expectedResultsFilename = Path.Combine(resultsFolder, RunUtilities.GetDatasetName(testFile) + "_iqResults.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
executorBaseParameters.ChromGenSourceDataPeakBR = 3;
executorBaseParameters.ChromGenSourceDataSigNoise = 2;
executorBaseParameters.TargetsFilePath = targetsFile;
//create no more than two charge state targets per peptide
executorBaseParameters.MaxNumberOfChargeStateTargetsToCreate = 2;
var run = new RunFactory().CreateRun(testFile);
var executor = new IqExecutor(executorBaseParameters, run);
executor.ChromSourceDataFilePath = peaksTestFile;
executor.LoadAndInitializeTargets(targetsFile);
executor.Targets = (from n in executor.Targets where n.ElutionTimeTheor > 0.305 && n.ElutionTimeTheor < 0.325 select n).Take(10).ToList();
foreach (var iqTarget in executor.Targets)
{
var numChildTargets = iqTarget.GetChildCount();
Assert.IsTrue(numChildTargets <= 2); //MaxNumberOfChargeStateTargetsToCreate = 2;
Console.WriteLine(iqTarget + "\t" + numChildTargets);
}
}
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 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 ProblemTesting_correlationProb1()
{
//see JIRA https://jira.pnnl.gov/jira/browse/OMCS-628
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
var testDatasetPath =
@"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1B_8Apr13_Cougar_13-03-25.raw";
executorParameters.IsMassAlignmentPerformed = true;
executorParameters.IsNetAlignmentPerformed = true;
executorParameters.ReferenceTargetsFilePath =
@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set3_P892_targets.txt";
var run = new RunFactory().CreateRun(testDatasetPath);
var executor = new IqExecutor(executorParameters, run);
var targetsFile =
@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set3_P892_targets.txt";
executor.LoadAndInitializeTargets(targetsFile);
executor.SetupMassAndNetAlignment();
var testTarget = 6955012;
executor.Targets = (from n in executor.Targets where n.ID == testTarget select n).ToList();
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.LoadParameters(@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Parameters\O16O18WorkflowParameters_2011_08_23_sum5.xml");
//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();
}
public void GlycanProcessingTest1()
{
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.WorkflowParameterFile = @"D:\Data\From_Scott\BasicTargetedWorkflowParameters1.xml";
executorParameters.TargetsFilePath = @"D:\Data\From_Scott\Glycan_targets.txt";
//executorParameters.TargetType = Globals.TargetType.LcmsFeature;
var testDatasetPath = @"D:\Data\From_Scott\Gly08_Velos4_Jaguar_200nL_Sp01_3X_7uL_1000A_31Aug12.raw";
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, testDatasetPath);
//executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.ID == 18).ToList();
executor.Execute();
}
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 ChromPeakAnalyzerWorkflowTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var run = new RunFactory().CreateRun(testFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var testTarget = new ChromPeakIqTarget();
ITheorFeatureGenerator TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
var testPeak = new ChromPeak(5184, 840963, 50, 0);
var executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new TopDownMSAlignExecutor(executorBaseParameters, run);
executor.ChromSourceDataFilePath = peaksTestFile;
var workflow = new ChromPeakAnalyzerIqWorkflow(run, parameters);
testTarget.SetWorkflow(workflow);
testTarget.ID = 1;
testTarget.Code = "NGIIMMENR";
testTarget.EmpiricalFormula = "C43H76N14O14S2";
testTarget.MonoMassTheor = 1076.510631;
testTarget.ChromPeak = testPeak;
testTarget.ChargeState = 1;
testTarget.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(testTarget.EmpiricalFormula, testTarget.ChargeState);
var testTargetList = new List <IqTarget>();
IqTarget testParent = new IqChargeStateTarget();
testParent.AddTarget(testTarget);
testTargetList.Add(testTarget);
executor.Execute(testTargetList);
var result = testTarget.GetResult();
Assert.NotNull(result.LCScanSetSelected);
Assert.AreNotEqual(1, result.FitScore);
Assert.AreEqual(true, result.IsotopicProfileFound);
}
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());
}
