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 virtual void LoadAndInitializeTargets(string targetsFilePath)
{
if (TargetImporter == null)
{
TargetImporter = new BasicIqTargetImporter(targetsFilePath);
}
IqLogger.Log.Info("Target Loading Started...");
Targets = TargetImporter.Import();
foreach (var iqTarget in Targets)
{
iqTarget.ChargeState = 0; //parent has a 0 charge state
if (Parameters.TargetType == Globals.TargetType.LcmsFeature)
{
iqTarget.ElutionTimeTheor = Run.NetAlignmentInfo.GetNETValueForScan(iqTarget.ScanLC);
}
}
_targetUtilities.CreateChildTargets(Targets, Parameters.MinMzForDefiningChargeStateTargets,
Parameters.MaxMzForDefiningChargeStateTargets, Parameters.MaxNumberOfChargeStateTargetsToCreate, IqTargetsAreCysteineModified);
IqLogger.Log.Info("Targets Loaded Successfully. Total targets loaded= " + Targets.Count);
}
public void JoinTargetsTest1()
{
var targetsFileName =
@"\\proto-7\VOrbi05\2013_2\mhp_plat_test_1_14April13_Frodo_12-12-04\MSG201305011339_Auto939903\mhp_plat_test_1_14April13_Frodo_12-12-04_msgfdb_fht.txt";
var massTagFilename =
@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set1_P890_targets.txt";
var rawFile = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw";
IqTargetImporter massTagImporter = new BasicIqTargetImporter(massTagFilename);
var massTagRefs = massTagImporter.Import().OrderBy(p => p.Code).ToList();
WorkflowExecutorBaseParameters parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.TargetsFilePath = targetsFileName;
var run = new RunFactory().CreateRun(rawFile);
var massAndNetAligner = new IqMassAndNetAligner(parameters, run);
massAndNetAligner.LoadAndInitializeTargets();
var testNET = massAndNetAligner.Targets.First().ElutionTimeTheor;
var query = (from massTag in massTagRefs
join target in massAndNetAligner.Targets on massTag.Code equals target.Code
select new
{
MassTag = massTag,
MSGFTarget = target
}).ToList();
foreach (var thing in query)
{
thing.MSGFTarget.ID = thing.MassTag.ID;
thing.MSGFTarget.ElutionTimeTheor = thing.MassTag.ElutionTimeTheor;
}
var targets = query.Select(p => p.MSGFTarget).ToList();
var testNETAfter = massAndNetAligner.Targets.First().ElutionTimeTheor;
Console.WriteLine("NET before= " + testNET);
Console.WriteLine("NET before= " + testNETAfter);
}
protected TargetCollection GetMassTagTargets(string massTagFileName, List <int> targetIDsToFilterOn)
{
if (String.IsNullOrEmpty(massTagFileName) || !File.Exists(massTagFileName))
{
return(new TargetCollection());
}
if (massTagFileName.ToLower().Contains("_msgfplus.tsv"))
{
var iqTargetImporter = new BasicIqTargetImporter(massTagFileName);
var iqTargets = iqTargetImporter.Import();
var targetUtilities = new IqTargetUtilities();
var targetCollection = new TargetCollection
{
TargetList = new List <TargetBase>()
};
foreach (var iqTarget in iqTargets)
{
if (iqTarget.QualityScore > MsgfFdrScoreCutoff)
{
continue;
}
targetUtilities.UpdateTargetMissingInfo(iqTarget);
TargetBase oldStyleTarget = new PeptideTarget();
oldStyleTarget.ChargeState = (short)iqTarget.ChargeState;
oldStyleTarget.Code = iqTarget.Code;
oldStyleTarget.EmpiricalFormula = iqTarget.EmpiricalFormula;
oldStyleTarget.ID = iqTarget.ID;
oldStyleTarget.MZ = iqTarget.MZTheor;
oldStyleTarget.MonoIsotopicMass = iqTarget.MonoMassTheor;
oldStyleTarget.ScanLCTarget = iqTarget.ScanLC;
oldStyleTarget.NormalizedElutionTime = (float)iqTarget.ElutionTimeTheor;
oldStyleTarget.ElutionTimeUnit = DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum;
targetCollection.TargetList.Add(oldStyleTarget);
}
return(targetCollection);
}
var importer = new MassTagFromTextFileImporter(massTagFileName);
return(importer.Import(targetIDsToFilterOn));
}
private void SetMassTagReferencesForNetAlignment()
{
if (!string.IsNullOrEmpty(Parameters.ReferenceTargetsFilePath))
{
IqTargetImporter massTagImporter = new BasicIqTargetImporter(Parameters.ReferenceTargetsFilePath);
var massTagRefs = massTagImporter.Import();
IqMassAndNetAligner.SetMassTagReferences(massTagRefs);
IqLogger.Log.Info("IQ Net aligner - " + massTagRefs.Count + " reference targets were loaded successfully.");
}
else
{
IqLogger.Log.Info("IQ Net aligner INACTIVE - no reference tags were loaded. You need to define 'TargetsUsedForLookupFilePath'");
}
}
public void ImportUnlabeledIqTargetsTest1()
{
var targetsFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var importer = new BasicIqTargetImporter(targetsFile);
var targets = importer.Import();
Assert.IsNotNull(targets);
Assert.IsTrue(targets.Any());
Assert.IsTrue(targets.Count > 10);
foreach (var iqTarget in targets.Take(10))
{
Console.WriteLine(iqTarget.ToString());
}
}
public void ImportUnlabeledIqTargetsFromResultsFileTest1()
{
var targetsFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Results\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ForImportOnly_iqResults.txt";
var importer = new BasicIqTargetImporter(targetsFile);
var targets = importer.Import();
Assert.IsNotNull(targets);
Assert.IsTrue(targets.Any());
Assert.IsTrue(targets.Count > 0);
foreach (var iqTarget in targets.Take(10))
{
Console.WriteLine(iqTarget.ToString());
}
}
protected virtual TargetCollection GetLcmsFeatureTargets(string targetsFilePath)
{
if (targetsFilePath.ToLower().Contains("_msgf"))
{
var iqTargetImporter = new BasicIqTargetImporter(targetsFilePath);
var iqTargets = iqTargetImporter.Import();
var targetUtilities = new IqTargetUtilities();
var targetCollection = new TargetCollection();
targetCollection.TargetList = new List <TargetBase>();
foreach (var iqTarget in iqTargets)
{
if (iqTarget.QualityScore > MsgfFdrScoreCutoff)
{
continue;
}
targetUtilities.UpdateTargetMissingInfo(iqTarget);
TargetBase oldStyleTarget = new LcmsFeatureTarget();
oldStyleTarget.ChargeState = (short)iqTarget.ChargeState;
oldStyleTarget.Code = iqTarget.Code;
oldStyleTarget.EmpiricalFormula = iqTarget.EmpiricalFormula;
oldStyleTarget.ID = iqTarget.ID;
oldStyleTarget.MZ = iqTarget.MZTheor;
oldStyleTarget.MonoIsotopicMass = iqTarget.MonoMassTheor;
oldStyleTarget.ScanLCTarget = iqTarget.ScanLC;
oldStyleTarget.NormalizedElutionTime = (float)iqTarget.ElutionTimeTheor;
oldStyleTarget.ElutionTimeUnit = DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum;
targetCollection.TargetList.Add(oldStyleTarget);
}
return(targetCollection);
}
var importer =
new LcmsTargetFromFeaturesFileImporter(targetsFilePath);
var lcmsTargetCollection = importer.Import();
return(lcmsTargetCollection);
}
public void Test1()
{
var targetsFileName =
@"\\proto-7\VOrbi05\2013_2\mhp_plat_test_1_14April13_Frodo_12-12-04\MSG201305011339_Auto939903\mhp_plat_test_1_14April13_Frodo_12-12-04_msgfdb_fht.txt";
var massTagFilename =
@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set1_P890_targets.txt";
var rawFile = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw";
WorkflowExecutorBaseParameters parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.TargetsFilePath = targetsFileName;
var run = new RunFactory().CreateRun(rawFile);
var massAndNetAligner = new IqMassAndNetAligner(parameters, run);
massAndNetAligner.LoadAndInitializeTargets();
IqTargetImporter massTagImporter = new BasicIqTargetImporter(massTagFilename);
var massTagRefs = massTagImporter.Import();
massAndNetAligner.SetMassTagReferences(massTagRefs);
//massAligner.Targets = massAligner.Targets.Take(1).ToList();
massAndNetAligner.ExecuteAlignment();
var sb = new StringBuilder();
var usefulResults = new List <IqResult>();
foreach (var iqResult in massAndNetAligner.Results)
{
var childresults = iqResult.ChildResults();
foreach (var childresult in childresults)
{
if (childresult.ObservedIsotopicProfile == null)
{
continue;
}
sb.Append(childresult.Target.ID);
sb.Append("\t");
if (childresult.ObservedIsotopicProfile == null)
{
sb.Append("[null]");
sb.Append(Environment.NewLine);
}
else
{
usefulResults.Add(childresult);
sb.Append(childresult.ChromPeakSelected.XValue);
sb.Append("\t");
sb.Append(childresult.ElutionTimeObs);
sb.Append("\t");
sb.Append(childresult.ParentResult.Target.ElutionTimeTheor);
sb.Append("\t");
sb.Append(childresult.MZObs.ToString("0.00000"));
sb.Append("\t");
sb.Append(childresult.MonoMassObs.ToString("0.00000"));
sb.Append("\t");
sb.Append(childresult.MassErrorBefore.ToString("0.00000"));
sb.Append("\t");
sb.Append(childresult.FitScore.ToString("0.000"));
sb.Append(Environment.NewLine);
}
}
}
var averageMassError = usefulResults.Average(p => p.MassErrorBefore);
var stdev = MathUtils.GetStDev(usefulResults.Select(p => p.MassErrorBefore).ToList());
//Console.WriteLine(sb.ToString());
Console.WriteLine("avg mass error= " + averageMassError);
Console.WriteLine("stdev= " + stdev);
Console.WriteLine("----------- mass alignment ------------");
TestUtilities.DisplayXYValues(massAndNetAligner.MassAlignmentInfo.ScanAndPpmShiftVals);
Console.WriteLine("------------NET alignment --------------");
DisplayNetAlignmentInfo(massAndNetAligner.NetAlignmentInfo);
}
public void AlignUsingMsgfOutputFullProcessingTest1()
{
var targetsFileName =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_msgfdb_fht.txt";
var massTagFilename =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_ProdTest_Formic_P823_PMT3.txt";
var rawFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
WorkflowExecutorBaseParameters parameters = new BasicTargetedWorkflowExecutorParameters();
parameters.TargetsFilePath = targetsFileName;
parameters.ReferenceTargetsFilePath = massTagFilename;
var run = new RunFactory().CreateRun(rawFile);
var massAndNetAligner = new IqMassAndNetAligner(parameters, run);
massAndNetAligner.LoadAndInitializeTargets();
massAndNetAligner.Targets = massAndNetAligner.Targets.Take(2000).ToList();
var exportedAlignmentResultsFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_iqAlignmentResults.txt";
if (!File.Exists(exportedAlignmentResultsFile))
{
File.Delete(exportedAlignmentResultsFile);
}
IqTargetImporter massTagImporter = new BasicIqTargetImporter(massTagFilename);
var massTagRefs = massTagImporter.Import();
massAndNetAligner.SetMassTagReferences(massTagRefs);
//massAligner.Targets = massAligner.Targets.Take(1).ToList();
massAndNetAligner.ExecuteAlignment();
var sb = new StringBuilder();
var usefulResults = new List <IqResult>();
massAndNetAligner.ExportResults(exportedAlignmentResultsFile);
foreach (var iqResult in massAndNetAligner.Results)
{
var childresults = iqResult.ChildResults();
foreach (var childresult in childresults)
{
if (childresult.ObservedIsotopicProfile == null)
{
continue;
}
sb.Append(childresult.Target.ID);
sb.Append("\t");
if (childresult.ObservedIsotopicProfile == null)
{
sb.Append("[null]");
sb.Append(Environment.NewLine);
}
else
{
usefulResults.Add(childresult);
sb.Append(childresult.ChromPeakSelected.XValue);
sb.Append("\t");
sb.Append(childresult.ElutionTimeObs);
sb.Append("\t");
sb.Append(childresult.ParentResult.Target.ElutionTimeTheor);
sb.Append("\t");
sb.Append(childresult.MZObs.ToString("0.00000"));
sb.Append("\t");
sb.Append(childresult.MonoMassObs.ToString("0.00000"));
sb.Append("\t");
sb.Append(childresult.MassErrorBefore.ToString("0.00000"));
sb.Append("\t");
sb.Append(childresult.FitScore.ToString("0.000"));
sb.Append(Environment.NewLine);
}
}
}
var averageMassError = usefulResults.Average(p => p.MassErrorBefore);
var stdev = MathUtils.GetStDev(usefulResults.Select(p => p.MassErrorBefore).ToList());
Console.WriteLine(sb.ToString());
Console.WriteLine("avg mass error= " + averageMassError);
Console.WriteLine("stdev= " + stdev);
Console.WriteLine("----------- mass alignment ------------");
TestUtilities.DisplayXYValues(massAndNetAligner.MassAlignmentInfo.ScanAndPpmShiftVals);
Console.WriteLine("------------NET alignment --------------");
DisplayNetAlignmentInfo(massAndNetAligner.NetAlignmentInfo);
}
