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 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);
}