public override void LoadAndInitializeTargets(string targetsFilePath)
{
if (string.IsNullOrEmpty(targetsFilePath))
{
IqLogger.Log.Info("IqMassAndNetAligner - no alignment targets were loaded. The inputted targets file path is NULL.");
return;
}
if (!File.Exists(targetsFilePath))
{
IqLogger.Log.Info("IqMassAndNetAligner - no alignment targets were loaded. The inputted targets file path is does not exist.");
return;
}
var importer = new IqTargetsFromFirstHitsFileImporter(targetsFilePath);
Targets = importer.Import().Where(p => p.QualityScore < 0.01).OrderBy(p => p.ID).ToList();
//Targets = Targets.Where(p => p.Code.Contains("FEQDGENYTGTIDGNMGAYAR")).ToList();
var filteredList = new List <IqTarget>();
//calculate empirical formula for targets using Code and then monoisotopic mass
foreach (var iqTarget in Targets)
{
iqTarget.Code = _peptideUtils.CleanUpPeptideSequence(iqTarget.Code);
if (_peptideUtils.ValidateSequence(iqTarget.Code))
{
iqTarget.EmpiricalFormula = _peptideUtils.GetEmpiricalFormulaForPeptideSequence(iqTarget.Code, true, true);
var calcMonoMass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(iqTarget.EmpiricalFormula);
var monoMassFromFirstHitsFile = iqTarget.MonoMassTheor;
var massCalculationsAgree = Math.Abs(monoMassFromFirstHitsFile - calcMonoMass) < 0.02;
if (massCalculationsAgree)
{
iqTarget.MonoMassTheor = calcMonoMass;
iqTarget.ElutionTimeTheor = iqTarget.ScanLC / (double)Run.MaxLCScan;
filteredList.Add(iqTarget);
_targetUtilities.UpdateTargetMissingInfo(iqTarget, true);
var chargeStateTarget = new IqTargetMsgfFirstHit();
_targetUtilities.CopyTargetProperties(iqTarget, chargeStateTarget);
iqTarget.AddTarget(chargeStateTarget);
}
}
}
filteredList = (from n in filteredList
group n by new
{
n.Code,
n.ChargeState
}
into grp
select grp.OrderBy(p => p.QualityScore).First()
).ToList();
Targets = filteredList;
TargetedWorkflowParameters workflowParameters = new BasicTargetedWorkflowParameters();
workflowParameters.ChromNETTolerance = 0.005;
workflowParameters.ChromGenTolerance = 50;
//define workflows for parentTarget and childTargets
var parentWorkflow = new ChromPeakDeciderIqWorkflow(Run, workflowParameters);
var childWorkflow = new ChargeStateChildIqWorkflow(Run, workflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, Targets);
if (Targets.Count > 0)
{
IqLogger.Log.Info("IqMassAndNetAligner - Loaded " + Targets.Count + " targets for use in mass and net alignment");
}
else
{
IqLogger.Log.Info("IqMassAndNetAligner - NOTE - no targets have been loaded.");
}
//IqWorkflowAssigner workflowAssigner = new IqWorkflowAssigner();
//workflowAssigner.AssignWorkflowToParent(workflow, Targets);
}
public void Executor_loadAlignment_Test1()
{
var util = new IqTargetUtilities();
var testFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
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.IsMassAlignmentPerformed = true;
executorBaseParameters.IsNetAlignmentPerformed = true;
executorBaseParameters.OutputFolderBase = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled";
var run = new RunFactory().CreateRun(testFile);
var expectedResultsFilename = executorBaseParameters.OutputFolderBase + "\\IqResults\\" + RunUtilities.GetDatasetName(testFile) + "_iqResults.txt";
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
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();
executor.Targets = (from n in executor.Targets where n.ID == 27168 select n).ToList();
executor.SetupMassAndNetAlignment();
executor.DoAlignment();
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.ChromNETTolerance = 0.1;
//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);
//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 results in the Executor are in the a Result tree. So there should be just 10.
Assert.AreEqual(10, executor.Results.Count);
}
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);
}
}
}
}
