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);
}
