public void ImportIqTargetsFromMsgfTest1()
{
var targetsFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\Yellow_C13_070_23Mar10_Griffin_10-01-28_msgfplus.tsv";
var importer = new BasicIqTargetImporter(targetsFile);
var targets = importer.Import();
Assert.IsNotNull(targets);
Assert.IsTrue(targets.Any());
var utilities = new IqTargetUtilities();
foreach (var iqTarget in targets)
{
utilities.UpdateTargetMissingInfo(iqTarget, false);
}
Assert.IsTrue(targets.Count > 10);
foreach (var iqTarget in targets.Take(10))
{
Console.WriteLine(iqTarget.ToString() + "\t" + iqTarget.ScanLC + "\t" + iqTarget.QualityScore);
}
}
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 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);
}