public void SetupMassAndNetAlignment(string alignmentFolder = "")
{
WorkflowExecutorBaseParameters massNetAlignerParameters = new BasicTargetedWorkflowExecutorParameters();
IqMassAndNetAligner = new IqMassAndNetAligner(massNetAlignerParameters, Run);
IqMassAndNetAligner.LoessBandwidthNetAlignment = 0.1;
//check if alignment info exists already
SetupAlignmentFolder(alignmentFolder);
var expectedAlignmentFilename = Path.Combine(_alignmentFolder, Run.DatasetName + "_iqAlignmentResults.txt");
var alignmentResultsExist = (File.Exists(expectedAlignmentFilename));
if (alignmentResultsExist)
{
IqLogger.Log.Info("Using the IQ alignment results from here: " + expectedAlignmentFilename);
IqMassAndNetAligner.LoadPreviousIqResults(expectedAlignmentFilename);
SetMassTagReferencesForNetAlignment();
return;
}
//Get a suitable targets file for alignment. These are grabbed from the ..\AlignmentInfo folder.
var targetFileForAlignment = GetTargetFilePathForIqAlignment();
if (string.IsNullOrEmpty(targetFileForAlignment))
{
IqLogger.Log.Info("Alignment not performed - No suitable target file found for use in alignment.");
return;
}
if (!File.Exists(targetFileForAlignment))
{
IqLogger.Log.Info("Alignment not performed - Target file for alignment has been specified but a FILE NOT FOUND error has occured.");
return;
}
var isFirstHitsFile = targetFileForAlignment.EndsWith("_fht.txt");
if (!isFirstHitsFile)
{
IqLogger.Log.Info("Alignment not performed - target file for alignment must be a first hits file (_fht.txt)");
return;
}
IqMassAndNetAligner.LoadAndInitializeTargets(targetFileForAlignment);
SetMassTagReferencesForNetAlignment();
}
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);
}
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 AlignUsingPreviouslyProcessedOutputTest1()
{
var rawFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var previouslyProcessedResultsFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_iqAlignmentResults.txt";
WorkflowExecutorBaseParameters parameters = new BasicTargetedWorkflowExecutorParameters();
var run = new RunFactory().CreateRun(rawFile);
var massAndNetAligner = new IqMassAndNetAligner(parameters, run);
massAndNetAligner.LoadPreviousIqResults(previouslyProcessedResultsFile);
massAndNetAligner.ExecuteAlignment();
var baseFilenameForImageExport =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18";
massAndNetAligner.ExportGraphs(baseFilenameForImageExport);
}
public void DoAlignment()
{
if (Parameters.IsMassAlignmentPerformed)
{
Run.MassAlignmentInfo = IqMassAndNetAligner.DoMassAlignment();
}
if (Parameters.IsNetAlignmentPerformed)
{
Run.NetAlignmentInfo = IqMassAndNetAligner.DoNetAlignment();
}
if (Parameters.IsMassAlignmentPerformed || Parameters.IsMassAlignmentPerformed)
{
var exportedAlignmentIqResultsFilename = Path.Combine(_alignmentFolder, Run.DatasetName + "_iqAlignmentResults.txt");
IqMassAndNetAligner.ExportResults(exportedAlignmentIqResultsFilename);
var exportedGraphBaseFilename = Path.Combine(_alignmentFolder, Run.DatasetName);
IqMassAndNetAligner.ExportGraphs(exportedGraphBaseFilename);
}
}
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);
}