public void loadresultsForDatasetTest1() { var dbserver = "pogo"; var dbname = "MT_Yellowstone_Communities_P627"; var tableName = @"[MT_Yellowstone_Communities_P627].[PNL\D3X720].[T_Tmp_Slysz_All_PeakMatchingResults]"; var testDataset = "Yellow_C13_070_23Mar10_Griffin_10-01-28"; var util = new PeakMatchedResultUtilities(dbserver, dbname, tableName); var importedResults = util.LoadResultsForDataset(testDataset); Assert.IsTrue(importedResults.Count > 0); Assert.AreEqual(4184, importedResults.Count); var mtImporter = new MassTagFromSqlDbImporter(dbname, dbserver, importedResults.Select(p => (long)p.MatchedMassTagID).Distinct().ToList()); var targetCollection = mtImporter.Import(); var sb = new StringBuilder(); foreach (var target in targetCollection.TargetList) { sb.Append(target.ID + "\t" + target.Code + "\t" + target.EmpiricalFormula + "\n"); } Console.WriteLine(sb.ToString()); }
public void checkModImport_Test1() { var importer = new MassTagFromSqlDbImporter("MT_Shewanella_ProdTest_P352", "porky", _targetIDList); var targetCollection = importer.Import(); var testPeptide1 = (PeptideTarget)targetCollection.TargetList[70]; Assert.AreEqual(72, targetCollection.TargetList.Count); Assert.AreEqual(189684639, testPeptide1.ID); Assert.AreEqual("QALYEAENVLRDEQIALQK", testPeptide1.Code); Assert.AreEqual(2213.1326995m, (decimal)testPeptide1.MonoIsotopicMass); Assert.AreEqual(1, testPeptide1.ModCount); Assert.AreEqual("NH3_Loss:1", testPeptide1.ModDescription); Assert.AreEqual(true, testPeptide1.ContainsMods); Assert.AreEqual(696, testPeptide1.ObsCount); var peptideUtils = new PeptideUtils(); Assert.AreEqual("C97H159N27O33", peptideUtils.GetEmpiricalFormulaForPeptideSequence(testPeptide1.Code)); Assert.AreNotEqual("C97H159N27O33", testPeptide1.EmpiricalFormula); Assert.AreEqual("C97H156N26O33", testPeptide1.EmpiricalFormula); }
public void Get40MassTagsTest() { var importer = new MassTagFromSqlDbImporter("MT_Shewanella_ProdTest_P352", "porky", _targetIDList); var targetCollection = importer.Import(); var testPeptide1 = (PeptideTarget)targetCollection.TargetList[2]; Assert.AreEqual(72, targetCollection.TargetList.Count); Assert.AreEqual(24917, testPeptide1.ID); Assert.AreEqual("TQLKEFIDAQI", testPeptide1.Code); Assert.AreEqual(1304.6975526m, (decimal)testPeptide1.MonoIsotopicMass); Assert.AreEqual(2, testPeptide1.ChargeState); Assert.AreEqual(3192, testPeptide1.ObsCount); Assert.AreEqual(653.35605279, (decimal)testPeptide1.MZ); Assert.AreEqual(0.3989965, (decimal)testPeptide1.NormalizedElutionTime); Assert.AreEqual(359, testPeptide1.RefID); Assert.AreEqual("thioredoxin 1 (TrxA)", testPeptide1.ProteinDescription); }
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); }