protected virtual void SetupLogging()
{
string loggingFolder;
if (string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase))
{
loggingFolder = RunUtilities.GetDatasetParentFolder(DatasetPath);
}
else
{
loggingFolder = Path.Combine(ExecutorParameters.OutputFolderBase, "Logs");
}
try
{
if (!Directory.Exists(loggingFolder))
{
Directory.CreateDirectory(loggingFolder);
}
}
catch (Exception ex)
{
throw new System.IO.IOException("Trying to set up logging folder but there was a critical error. Details:\n\n" + ex.Message, ex);
}
_loggingFileName = Path.Combine(loggingFolder, RunUtilities.GetDatasetName(DatasetPath) + "_log.txt");
}
public void TopDownWorkflowTest1()
{
//see https://jira.pnnl.gov/jira/browse/OMCR-98
string baseFolder =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact";
const string executorParameterFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact\Parameters\topdownExecutorParameters1.xml";
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
executorParameters.ExportChromatogramData = false;
executorParameters.OutputFolderBase =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact";
const string testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact\RawData\Proteus_Peri_intact_ETD.raw";
string testDatasetName = RunUtilities.GetDatasetName(testDatasetPath);
string expectedResultsFilename = executorParameters.OutputFolderBase + "\\IqResults" + "\\" + testDatasetName + "_quant.txt";
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, testDatasetPath);
string proteinSeq =
@"A.VDKTNPYALMEDAAQKTFDKLKTEQPEIRKNPELLREIVQQELLPYVHIKYAGALVLGPYYRNATPAQRDAYFAAFKDYLAQVYGQALAMYEGQEYRIEPAKPFADKSNLTIRVTIIDKNGRPPVRLDFQWRKNSKTGEWQAYDMIAEGVSMITTKQNEWSDILSAKGVDGLTKQLEISAKTPITLDEKK.";
executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.Code == proteinSeq).ToList();
executor.Execute();
Assert.IsNotNull(executor.TargetedWorkflow.Run);
Console.WriteLine("Num targetedResults in Run = " + executor.TargetedWorkflow.Run.ResultCollection.MassTagResultList.Count);
Assert.IsTrue(File.Exists(expectedResultsFilename), "Results file does not exist!");
//TODO: fix _quant.txt output column headers
TopDownTargetedResultFromTextImporter importer = new TopDownTargetedResultFromTextImporter(expectedResultsFilename);
var results = importer.Import();
Assert.IsNotNull(results);
Assert.IsTrue(results.HasResults);
Assert.AreEqual(1, results.Results.Count);
//foreach (var r in results.Results)
//{
// Console.WriteLine(r.TargetID + "\t" + r.ScanLC + "\t" + r.Intensity);
//}
}
public void TopDownWorkflowFullTargetSet()
{
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = false;
executorParameters.DeleteLocalDatasetAfterProcessing = false;
executorParameters.TargetsFilePath = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Targets\fullTargetSet\Proteus_Peri_intact_ETD_MSAlign_ResultTable.Filtered05FDR.txt";
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
executorParameters.ExportChromatogramData = true;
var workflowParameters = new TopDownTargetedWorkflowParameters();
workflowParameters.AreaOfPeakToSumInDynamicSumming = 2;
workflowParameters.ChromatogramCorrelationIsPerformed = false;
workflowParameters.ChromGeneratorMode = Globals1.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
workflowParameters.ChromGenSourceDataPeakBR = 4;
workflowParameters.ChromGenSourceDataSigNoise = 3;
workflowParameters.ChromNETTolerance = 0.025;
workflowParameters.ChromPeakDetectorPeakBR = 0.1;
workflowParameters.ChromPeakDetectorSigNoise = 0.1;
workflowParameters.ChromPeakSelectorMode = Globals1.PeakSelectorMode.Smart;
workflowParameters.ChromSmootherNumPointsInSmooth = 9;
workflowParameters.MaxScansSummedInDynamicSumming = 100;
workflowParameters.MSPeakDetectorPeakBR = 1.3;
workflowParameters.MSPeakDetectorSigNoise = 2;
workflowParameters.ChromGenTolerance = 15;
workflowParameters.MSToleranceInPPM = 25;
workflowParameters.MultipleHighQualityMatchesAreAllowed = true;
workflowParameters.NumChromPeaksAllowedDuringSelection = 10;
workflowParameters.NumMSScansToSum = 5;
workflowParameters.ResultType = Globals1.ResultType.TOPDOWN_TARGETED_RESULT;
workflowParameters.SummingMode = SummingModeEnum.SUMMINGMODE_STATIC;
const string testDatasetPath =
@"\\protoapps\UserData\Fujimoto\TopDownTesting\RawData\Proteus_Peri_intact_ETD.raw";
string resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "Results");
string testDatasetName = RunUtilities.GetDatasetName(testDatasetPath);
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, workflowParameters, testDatasetPath);
executor.Execute();
Assert.IsNotNull(executor.TargetedWorkflow.Run);
Assert.IsTrue(File.Exists(expectedResultsFilename), "Results file does not exist!");
}
protected string TryFindTargetsForCurrentDataset()
{
var datasetName = RunUtilities.GetDatasetName(DatasetPath);
string[] possibleFileSuffixs = { "_iqTargets.txt", "_targets.txt", "_LCMSFeatures.txt", "_MSGFPlus.tsv", "_msgfdb_fht.txt" };
var possibleTargetFiles = new List <FileInfo>();
var targetsBaseFolder = ExecutorParameters.TargetsBaseFolder;
if (string.IsNullOrEmpty(ExecutorParameters.TargetsBaseFolder))
{
targetsBaseFolder = Path.Combine(ExecutorParameters.OutputFolderBase, "Targets");
}
var dirinfo = new DirectoryInfo(targetsBaseFolder);
foreach (var suffix in possibleFileSuffixs)
{
var fileInfos = dirinfo.GetFiles("*" + suffix);
foreach (var fileInfo in fileInfos)
{
if (fileInfo.Name.StartsWith(datasetName, StringComparison.OrdinalIgnoreCase))
{
possibleTargetFiles.Add(fileInfo);
}
}
}
if (possibleTargetFiles.Count == 0)
{
return(string.Empty);
}
else if (possibleTargetFiles.Count == 1)
{
return(possibleTargetFiles.First().FullName);
}
else
{
var sb = new StringBuilder();
sb.Append("Error in getting IQ target file. Multiple files were found for the dataset: " + datasetName + Environment.NewLine);
sb.Append("Candidate IQ target files: " + Environment.NewLine);
foreach (var possibleTargetFile in possibleTargetFiles)
{
sb.Append(possibleTargetFile.FullName + Environment.NewLine);
}
throw new NotSupportedException(sb.ToString());
}
}
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 WorkflowTestUsingParameterFile1()
{
var parameterFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\DeconMSn\ParameterFiles\DeconMSn_LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_scans6000_6050.xml";
var rawdataFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var outputFolder = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\DeconMSn\Output";
var datasetName = RunUtilities.GetDatasetName(rawdataFile);
var expectedResultsFile1 = Path.Combine(outputFolder, datasetName + ".mgf");
var expectedResultsFile2 = Path.Combine(outputFolder, datasetName + "_DeconMSn_log.txt");
var expectedResultsFile3 = Path.Combine(outputFolder, datasetName + "_profile.txt");
if (File.Exists(expectedResultsFile1))
{
File.Delete(expectedResultsFile1);
}
if (File.Exists(expectedResultsFile2))
{
File.Delete(expectedResultsFile2);
}
if (File.Exists(expectedResultsFile3))
{
File.Delete(expectedResultsFile3);
}
var workflow = ScanBasedWorkflow.CreateWorkflow(rawdataFile, parameterFile, outputFolder);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedResultsFile1));
Assert.IsTrue(File.Exists(expectedResultsFile2));
Assert.IsTrue(File.Exists(expectedResultsFile3));
}
public void ExecuteMultipleTargetsTest1()
{
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";
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
executorBaseParameters.ChromGenSourceDataPeakBR = 3;
executorBaseParameters.ChromGenSourceDataSigNoise = 2;
executorBaseParameters.TargetsFilePath = targetsFile;
executorBaseParameters.OutputFolderBase = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled";
var expectedResultsFilename = Path.Combine(executorBaseParameters.OutputFolderBase,
"IqResults",
RunUtilities.GetDatasetName(testFile) + "_iqResults.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
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();
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.ChromNETTolerance = 0.5;
//define workflows for parentTarget and childTargets
var parentWorkflow = new BasicIqWorkflow(run, targetedWorkflowParameters);
var childWorkflow = new BasicIqWorkflow(run, targetedWorkflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);
//Main line for executing IQ:
executor.Execute();
//Test the results...
Assert.IsTrue(File.Exists(expectedResultsFilename), "results file doesn't exist");
var numResultsInResultsFile = 0;
var outputToConsole = true;
using (var reader = new StreamReader(expectedResultsFilename))
{
while (reader.Peek() != -1)
{
var line = reader.ReadLine();
numResultsInResultsFile++;
if (outputToConsole)
{
Console.WriteLine(line);
}
}
}
Assert.IsTrue(numResultsInResultsFile > 1, "No results in output file");
//the Result Tree is flattened out in the results file.
Assert.IsTrue(numResultsInResultsFile == 11);
//the results in the Executor are in the a Result tree. So there should be just 10.
Assert.AreEqual(10, executor.Results.Count);
}
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 TopDownWorkflowTestNoChargeStateList()
{
//see https://jira.pnnl.gov/jira/browse/OMCR-101
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = false;
executorParameters.DeleteLocalDatasetAfterProcessing = false;
executorParameters.TargetsFilePath = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Targets\noChargeStateList\Proteus_Peri_intact_ETD_MSAlign_ResultTable.txt";
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
executorParameters.ExportChromatogramData = true;
var workflowParameters = new TopDownTargetedWorkflowParameters();
workflowParameters.AreaOfPeakToSumInDynamicSumming = 2;
workflowParameters.ChromatogramCorrelationIsPerformed = false;
workflowParameters.ChromGeneratorMode = Globals1.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
workflowParameters.ChromGenSourceDataPeakBR = 4;
workflowParameters.ChromGenSourceDataSigNoise = 3;
workflowParameters.ChromNETTolerance = 0.025;
workflowParameters.ChromPeakDetectorPeakBR = 0.1;
workflowParameters.ChromPeakDetectorSigNoise = 0.1;
workflowParameters.ChromPeakSelectorMode = Globals1.PeakSelectorMode.Smart;
workflowParameters.ChromSmootherNumPointsInSmooth = 9;
workflowParameters.MaxScansSummedInDynamicSumming = 100;
workflowParameters.MSPeakDetectorPeakBR = 1.3;
workflowParameters.MSPeakDetectorSigNoise = 2;
workflowParameters.ChromGenTolerance = 15;
workflowParameters.MSToleranceInPPM = 25;
workflowParameters.MultipleHighQualityMatchesAreAllowed = true;
workflowParameters.NumChromPeaksAllowedDuringSelection = 10;
workflowParameters.NumMSScansToSum = 5;
workflowParameters.ResultType = Globals1.ResultType.TOPDOWN_TARGETED_RESULT;
workflowParameters.SummingMode = SummingModeEnum.SUMMINGMODE_STATIC;
const string testDatasetPath =
@"\\protoapps\UserData\Fujimoto\TopDownTesting\RawData\Proteus_Peri_intact_ETD.raw";
string resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "Results");
string testDatasetName = RunUtilities.GetDatasetName(testDatasetPath);
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, workflowParameters, testDatasetPath);
executor.Execute();
/*
* var currentTarget = executor.TargetedWorkflow.Result.Target;
* Console.WriteLine("Target info:");
* Console.WriteLine(currentTarget.ID + "\t" + currentTarget.MonoIsotopicMass + "\t" + currentTarget.MZ + "\t" + currentTarget.ChargeState + "\t"+ currentTarget.EmpiricalFormula);
* Console.WriteLine("Theor profile");
* TestUtilities.DisplayIsotopicProfileData(executor.TargetedWorkflow.Result.Target.IsotopicProfile);
* TestUtilities.DisplayXYValues(executor.TargetedWorkflow.MassSpectrumXYData);
* TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
* TestUtilities.DisplayPeaks(executor.TargetedWorkflow.ChromPeaksDetected.Select(p=>(Peak)p).ToList());
*/
Assert.IsNotNull(executor.TargetedWorkflow.Run);
Console.WriteLine("Num targetedResults in Run = " + executor.TargetedWorkflow.Run.ResultCollection.MassTagResultList.Count);
Assert.IsTrue(File.Exists(expectedResultsFilename), "Results file does not exist!");
//var resultsfile = new StreamReader(@"\\protoapps\UserData\Fujimoto\TopDownTesting\Results\noChargeStateList\Proteus_Peri_intact_ETD_quant.txt");
//string line = resultsfile.ReadLine();
//line = resultsfile.ReadLine();
//string[] chargestatelist = line.Split('\t');
//Assert.AreEqual("10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22", chargestatelist[2]);
//resultsfile.Close();
}
public void TopDownWorkflowTestMissingChargeState()
{
//see https://jira.pnnl.gov/jira/browse/OMCR-102
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = false;
executorParameters.DeleteLocalDatasetAfterProcessing = false;
executorParameters.TargetsFilePath = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Targets\missingChargeState\Proteus_Peri_intact_ETD_MSAlign_ResultTable.txt";
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
executorParameters.ExportChromatogramData = true;
var workflowParameters = new TopDownTargetedWorkflowParameters();
workflowParameters.AreaOfPeakToSumInDynamicSumming = 2;
workflowParameters.ChromatogramCorrelationIsPerformed = false;
workflowParameters.ChromGeneratorMode = Globals1.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
workflowParameters.ChromGenSourceDataPeakBR = 4;
workflowParameters.ChromGenSourceDataSigNoise = 3;
workflowParameters.ChromNETTolerance = 0.025;
workflowParameters.ChromPeakDetectorPeakBR = 0.1;
workflowParameters.ChromPeakDetectorSigNoise = 0.1;
workflowParameters.ChromPeakSelectorMode = Globals1.PeakSelectorMode.Smart;
workflowParameters.ChromSmootherNumPointsInSmooth = 9;
workflowParameters.MaxScansSummedInDynamicSumming = 100;
workflowParameters.MSPeakDetectorPeakBR = 1.3;
workflowParameters.MSPeakDetectorSigNoise = 2;
workflowParameters.ChromGenTolerance = 15;
workflowParameters.MSToleranceInPPM = 25;
workflowParameters.MultipleHighQualityMatchesAreAllowed = true;
workflowParameters.NumChromPeaksAllowedDuringSelection = 10;
workflowParameters.NumMSScansToSum = 5;
workflowParameters.ResultType = Globals1.ResultType.TOPDOWN_TARGETED_RESULT;
workflowParameters.SummingMode = SummingModeEnum.SUMMINGMODE_STATIC;
const string testDatasetPath =
@"\\protoapps\UserData\Fujimoto\TopDownTesting\RawData\Proteus_Peri_intact_ETD.raw";
string resultsFolderLocation = executorParameters.OutputFolderBase + "\\Results";
string testDatasetName = RunUtilities.GetDatasetName(testDatasetPath);
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, workflowParameters, testDatasetPath);
string proteinSeq1 =
@"A.AENVVHHKLDGMPISEAVEINAGNNLVFLSGKVPTKKSADAPEGELASYGNTEEQTINVLEQIKTNLNNLGLDMKDVVKMQVFLVGGEENNGTMDFKGFMNGYSKFYDASKTNQLPARSAFQVAKLANPAWRVEIEVIAVRPAK.";
executor.Targets.TargetList = executor.Targets.TargetList.Where(p => (p.Code == proteinSeq1)).ToList();
executor.Execute();
Assert.IsNotNull(executor.TargetedWorkflow.Run);
Console.WriteLine("Num targetedResults in Run = " + executor.TargetedWorkflow.Run.ResultCollection.MassTagResultList.Count);
Assert.IsTrue(File.Exists(expectedResultsFilename), "Results file does not exist!");
var resultsfile = new StreamReader(@"\\protoapps\UserData\Fujimoto\TopDownTesting\Results\missingChargeState\Proteus_Peri_intact_ETD_quant.txt");
string line = resultsfile.ReadLine();
line = resultsfile.ReadLine();
string[] chargestatelist = line.Split('\t');
Assert.AreEqual("10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22", chargestatelist[2]);
resultsfile.Close();
}
public new void InitializeWorkflow()
{
//_loggingFileName = GetLogFileName(ExecutorParameters.LoggingFolder);
Check.Require(WorkflowParameters is SipperWorkflowExecutorParameters, "Parameters are not of the right type.");
var db = ((SipperWorkflowExecutorParameters)WorkflowParameters).DbName;
var server = ((SipperWorkflowExecutorParameters)WorkflowParameters).DbServer;
var table = ((SipperWorkflowExecutorParameters)WorkflowParameters).DbTableName;
var massTagIDsForFiltering =
GetMassTagsToFilterOn(((SipperWorkflowExecutorParameters)WorkflowParameters).TargetsToFilterOn).Distinct().ToList();
_loggingFileName = Path.Combine(ExecutorParameters.OutputFolderBase, "Logs", RunUtilities.GetDatasetName(DatasetPath) + "_log.txt");
TargetsAreFromPeakMatchingDataBase = (!String.IsNullOrEmpty(db) && !String.IsNullOrEmpty(server));
var targetsFilePathIsEmpty = (String.IsNullOrEmpty(ExecutorParameters.TargetsFilePath));
if (TargetsAreFromPeakMatchingDataBase)
{
Targets = LoadTargetsFromPeakMatchingResultsForGivenDataset(RunUtilities.GetDatasetName(DatasetPath));
}
else
{
if (targetsFilePathIsEmpty)
{
var currentTargetsFilePath = TryFindTargetsForCurrentDataset(); //check for a _targets file specifically associated with dataset
if (String.IsNullOrEmpty(currentTargetsFilePath))
{
Targets = null;
}
else
{
Targets = GetLcmsFeatureTargets(currentTargetsFilePath);
}
}
else
{
Targets = GetLcmsFeatureTargets(ExecutorParameters.TargetsFilePath);
}
}
Check.Ensure(Targets != null && Targets.TargetList.Count > 0, "Failed to initialize - Target list is empty. Please check parameter file.");
if (massTagIDsForFiltering.Count > 0)
{
Targets.TargetList =
(from n in Targets.TargetList
where massTagIDsForFiltering.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
select n).ToList();
}
MassTagIDsinTargets = Targets.TargetList.Select(p => (long)((LcmsFeatureTarget)p).FeatureToMassTagID).Where(n => n > 0).ToList();
if (TargetsAreFromPeakMatchingDataBase)
{
var mtImporter = new MassTagFromSqlDbImporter(db, server, MassTagIDsinTargets);
MassTagsForReference = mtImporter.Import();
}
else
{
MassTagsForReference = GetMassTagTargets(((SipperWorkflowExecutorParameters)WorkflowParameters).ReferenceDataForTargets, MassTagIDsinTargets.Select(p => (int)p).ToList());
}
MassTagsForReference.TargetList = (from n in MassTagsForReference.TargetList
group n by new
{
n.ID,
n.ChargeState
}
into grp
select grp.First()).ToList();
UpdateTargetMissingInfo();
_resultsFolder = GetResultsFolder(ExecutorParameters.OutputFolderBase);
_workflowParameters = WorkflowParameters.CreateParameters(ExecutorParameters.WorkflowParameterFile);
_workflowParameters.LoadParameters(ExecutorParameters.WorkflowParameterFile);
TargetedWorkflow = TargetedWorkflow.CreateWorkflow(_workflowParameters);
}
public void ExecutorTest1()
{
Console.WriteLine(Environment.CurrentDirectory);
var util = new IqTargetUtilities();
var testFile = @"\\proto-5\External_Waters_TOF_Xfer\MzML_Files\130716_iPRG14_004.mzML";
//string 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\Fujimoto\SangtaeBottomUp\msgfPlus\C~~data~iPRG 2014~130716_iPRG14_004.raw.-1_Filtered.tsv";
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
executorBaseParameters.ChromGenSourceDataPeakBR = 3;
executorBaseParameters.ChromGenSourceDataSigNoise = 2;
executorBaseParameters.TargetsFilePath = targetsFile;
executorBaseParameters.OutputFolderBase =
@"\\protoapps\UserData\Fujimoto\SangtaeBottomUp\Results";
var expectedResultsFilename = Path.Combine(executorBaseParameters.OutputFolderBase,
"IqResults",
RunUtilities.GetDatasetName(testFile) + "_iqResults.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var run = new RunFactory().CreateRun(testFile);
var executor = new IqExecutor(executorBaseParameters, run);
//executor.ChromSourceDataFilePath = peaksTestFile;
executor.LoadAndInitializeTargets(targetsFile);
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.ChromNETTolerance = 0.05;
//define workflows for parentTarget and childTargets
var parentWorkflow = new ChromPeakDeciderIqWorkflow(run, targetedWorkflowParameters);
var childWorkflow = new ChargeStateChildIqWorkflow(run, targetedWorkflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);
//SipperDataDump.DataDumpSetup(@"\\pnl\projects\MSSHARE\Merkley_Eric\For_Grant\IqResults\EXP6B_F1_CSCL_LIGHT_130520020056\EXP6B_F1_CSCL_LIGHT_FULLRESULTS.txt");
//Main line for executing IQ:
executor.Execute();
//Test the results...
var numResultsInResultsFile = 0;
var outputToConsole = true;
using (var reader = new StreamReader(expectedResultsFilename))
{
while (reader.Peek() != -1)
{
var line = reader.ReadLine();
numResultsInResultsFile++;
if (outputToConsole)
{
Console.WriteLine(line);
}
}
}
}