public static void GenerateDefaultTaskTomls(string folderLocation)
{
try
{
if (!Directory.Exists(folderLocation))
{
Directory.CreateDirectory(folderLocation);
}
CalibrationTask c = new CalibrationTask();
Toml.WriteFile(c, Path.Combine(folderLocation, @"CalibrationTask.toml"), MetaMorpheusTask.tomlConfig);
GptmdTask g = new GptmdTask();
Toml.WriteFile(g, Path.Combine(folderLocation, @"GptmdTask.toml"), MetaMorpheusTask.tomlConfig);
SearchTask s = new SearchTask();
Toml.WriteFile(s, Path.Combine(folderLocation, @"SearchTask.toml"), MetaMorpheusTask.tomlConfig);
XLSearchTask xl = new XLSearchTask();
Toml.WriteFile(xl, Path.Combine(folderLocation, @"XLSearchTask.toml"), MetaMorpheusTask.tomlConfig);
GlycoSearchTask glyco = new GlycoSearchTask();
Toml.WriteFile(glyco, Path.Combine(folderLocation, @"GlycoSearchTask.toml"), MetaMorpheusTask.tomlConfig);
}
catch (Exception e)
{
throw new MetaMorpheusException("Default tomls could not be written: " + e.Message);
}
}
public static void GlyTest_RunTask()
{
GlycoSearchTask task = new GlycoSearchTask();
task._glycoSearchParameters.GlycoSearchType = GlycoSearchType.NGlycanSearch;
Directory.CreateDirectory(Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData"));
DbForTask db = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData/Q9C0Y4.fasta"), false);
string raw = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData/yeast_glycan_25170.mgf");
new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("Task", task)
}, new List <string> {
public GlycoSearchTaskWindow(GlycoSearchTask task)
{
InitializeComponent();
PopulateChoices();
TheTask = task ?? new GlycoSearchTask();
UpdateFieldsFromTask(TheTask);
if (task == null)
{
this.saveButton.Content = "Add GlycoSearch Task";
}
DataContextForSearchTaskWindow = new DataContextForSearchTaskWindow()
{
ExpanderTitle = string.Join(", ", SearchModesForThisTask.Where(b => b.Use).Select(b => b.Name)),
AnalysisExpanderTitle = "Some analysis properties...",
SearchModeExpanderTitle = "Some search properties..."
};
this.DataContext = DataContextForSearchTaskWindow;
SearchModifications.Timer.Tick += new EventHandler(TextChangeTimerHandler);
base.Closing += this.OnClosing;
}
private void UpdateFieldsFromTask(GlycoSearchTask task)
{
RbtOGlycoSearch.IsChecked = task._glycoSearchParameters.GlycoSearchType == EngineLayer.GlycoSearch.GlycoSearchType.OGlycanSearch;
RbtNGlycoSearch.IsChecked = task._glycoSearchParameters.GlycoSearchType == EngineLayer.GlycoSearch.GlycoSearchType.NGlycanSearch;
Rbt_N_O_GlycoSearch.IsChecked = task._glycoSearchParameters.GlycoSearchType == EngineLayer.GlycoSearch.GlycoSearchType.N_O_GlycanSearch;
TbMaxOGlycanNum.Text = task._glycoSearchParameters.MaximumOGlycanAllowed.ToString(CultureInfo.InvariantCulture);
CkbOxoniumIonFilt.IsChecked = task._glycoSearchParameters.OxoniumIonFilt;
txtTopNum.Text = task._glycoSearchParameters.GlycoSearchTopNum.ToString(CultureInfo.InvariantCulture);
CmbOGlycanDatabase.SelectedItem = task._glycoSearchParameters.OGlycanDatabasefile;
CmbNGlycanDatabase.SelectedItem = task._glycoSearchParameters.NGlycanDatabasefile;
cbbPrecusorMsTl.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
PrecusorMsTlTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
TopNPeaksTextBox.Text = task.CommonParameters.NumberOfPeaksToKeepPerWindow == int.MaxValue || !task.CommonParameters.NumberOfPeaksToKeepPerWindow.HasValue ? "" : task.CommonParameters.NumberOfPeaksToKeepPerWindow.Value.ToString(CultureInfo.InvariantCulture);
MinRatioTextBox.Text = task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak == double.MaxValue || !task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.HasValue ? "" : task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.Value.ToString(CultureInfo.InvariantCulture);
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
ChildScanDissociationTypeComboBox.SelectedItem = "Null";
if (task.CommonParameters.MS2ChildScanDissociationType != DissociationType.Unknown)
{
ChildScanDissociationTypeComboBox.SelectedItem = task.CommonParameters.MS2ChildScanDissociationType.ToString();
}
CheckBoxDecoy.IsChecked = task._glycoSearchParameters.DecoyType != DecoyType.None;
RadioButtonReverseDecoy.IsChecked = task._glycoSearchParameters.DecoyType == DecoyType.Reverse;
RadioButtonSlideDecoy.IsChecked = task._glycoSearchParameters.DecoyType == DecoyType.Slide;
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
TxtBoxMaxModPerPep.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
numberOfDatabaseSearchesTextBox.Text = task.CommonParameters.TotalPartitions.ToString(CultureInfo.InvariantCulture);
maxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
public static void MetaDraw_GlycoSearchTaskWithChildScansTest()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"MetaDraw_GlycoSearchTaskTest");
string proteinDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\leukosialin.fasta");
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\sliced_glyco_hcd_ethcd.raw");
// run task
CommonParameters commonParameters = new CommonParameters(dissociationType: DissociationType.HCD, ms2childScanDissociationType: DissociationType.EThcD);
Directory.CreateDirectory(outputFolder);
var glycoSearchTask = new GlycoSearchTask()
{
CommonParameters = commonParameters
};
glycoSearchTask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(proteinDatabase, false)
}, new List <string> {
spectraFile
}, "");
var psmFile = Path.Combine(outputFolder, @"oglyco.psmtsv");
// load results into metadraw
var metadrawLogic = new MetaDrawLogic();
metadrawLogic.SpectraFilePaths.Add(spectraFile);
metadrawLogic.PsmResultFilePaths.Add(psmFile);
var errors = metadrawLogic.LoadFiles(true, true);
Assert.That(!errors.Any());
Assert.That(metadrawLogic.FilteredListOfPsms.Any());
// test results filter
MetaDrawSettings.QValueFilter = 0.01;
MetaDrawSettings.ShowDecoys = false;
metadrawLogic.FilterPsms();
Assert.That(metadrawLogic.FilteredListOfPsms.All(p => p.DecoyContamTarget == "T"));
Assert.That(metadrawLogic.FilteredListOfPsms.All(p => p.QValue <= 0.01));
// test text search filter (filter by full sequence)
string filterString = @"STTAVQ";
metadrawLogic.FilterPsmsByString(filterString);
int c = 0;
foreach (var filteredPsm in metadrawLogic.PeptideSpectralMatchesView)
{
var psmObj = (PsmFromTsv)filteredPsm;
Assert.That(psmObj.FullSequence.Contains(filterString));
c++;
}
Assert.Greater(c, 0);
// test text search filter (filter by MS2 scan number)
filterString = @"2";
metadrawLogic.FilterPsmsByString(filterString);
c = 0;
foreach (var filteredPsm in metadrawLogic.PeptideSpectralMatchesView)
{
var psmObj = (PsmFromTsv)filteredPsm;
Assert.That(psmObj.Ms2ScanNumber.ToString().Contains(filterString));
c++;
}
Assert.Greater(c, 0);
// draw PSM
var plotView = new OxyPlot.Wpf.PlotView();
var canvas = new Canvas();
var parentChildView = new ParentChildScanPlotsView();
var psm = metadrawLogic.FilteredListOfPsms.First();
metadrawLogic.DisplaySpectrumMatch(plotView, canvas, psm, parentChildView, out errors);
Assert.That(errors == null || !errors.Any());
// test that plot was drawn
var peak = (LineSeries)plotView.Model.Series[0]; // the first m/z peak
var peakPoints = peak.Points;
Assert.That(Math.Round(peakPoints[0].X, 2) == 101.07); // m/z
Assert.That(Math.Round(peakPoints[1].X, 2) == 101.07);
Assert.That((int)peakPoints[0].Y == 0); // intensity
Assert.That((int)peakPoints[1].Y == 3847);
var plotAxes = plotView.Model.Axes;
Assert.AreEqual(2, plotAxes.Count);
// test that base sequence annotation was drawn
Assert.Greater(canvas.Children.Count, 0);
// test that the plots were drawn in the parent/child view
Assert.AreEqual(2, parentChildView.Plots.Count);
// test parent scan
var parentPlot = parentChildView.Plots[0];
Assert.AreEqual("Scan: 27 Dissociation Type: HCD MsOrder: 2 Selected Mz: 924.12 Retention Time: 32.65", parentPlot.SpectrumLabel);
int numAnnotatedResidues = psm.BaseSeq.Length;
int numAnnotatedIons = psm.MatchedIons.Count(p => p.NeutralTheoreticalProduct.ProductType != ProductType.M &&
p.NeutralTheoreticalProduct.ProductType != ProductType.D);
int numAnnotatedMods = psm.FullSequence.Count(p => p == '[');
Assert.AreEqual(numAnnotatedResidues + numAnnotatedIons + numAnnotatedMods, parentPlot.TheCanvas.Children.Count);
peak = (LineSeries)parentPlot.Plot.Model.Series[0]; // the first m/z peak
peakPoints = peak.Points;
Assert.AreEqual(101.07, Math.Round(peakPoints[0].X, 2)); // m/z
Assert.AreEqual(101.07, (Math.Round(peakPoints[1].X, 2)));
Assert.AreEqual(0, (int)peakPoints[0].Y); // intensity
Assert.AreEqual(3847, (int)peakPoints[1].Y);
// test child scan
var childPlot = parentChildView.Plots[1];
Assert.AreEqual("Scan: 30 Dissociation Type: EThcD MsOrder: 2 Selected Mz: 924.12 RetentionTime: 32.66",
childPlot.SpectrumLabel);
Assert.Greater(childPlot.TheCanvas.Children.Count, 0);
numAnnotatedResidues = psm.BaseSeq.Length;
numAnnotatedIons = psm.ChildScanMatchedIons[30]
.Count(p => p.NeutralTheoreticalProduct.ProductType != ProductType.M &&
p.NeutralTheoreticalProduct.ProductType != ProductType.D);
numAnnotatedMods = psm.FullSequence.Count(p => p == '[');
Assert.AreEqual(numAnnotatedResidues + numAnnotatedIons + numAnnotatedMods, childPlot.TheCanvas.Children.Count);
peak = (LineSeries)childPlot.Plot.Model.Series[0]; // the first m/z peak
peakPoints = peak.Points;
Assert.AreEqual(126.06, Math.Round(peakPoints[0].X, 2)); // m/z
Assert.AreEqual(126.06, Math.Round(peakPoints[1].X, 2));
Assert.AreEqual(0, (int)peakPoints[0].Y); // intensity
Assert.AreEqual(8496, (int)peakPoints[1].Y);
// write pdf
var psmsToExport = metadrawLogic.FilteredListOfPsms.Where(p => p.FullSequence == "STTAVQTPTSGEPLVST[O-Glycosylation:H1N1 on X]SEPLSSK").ToList();
metadrawLogic.ExportToPdf(plotView, canvas, psmsToExport, parentChildView, outputFolder, out errors);
// test that pdf exists
Assert.That(File.Exists(Path.Combine(outputFolder, @"27_STTAVQTPTSGEPLVST[O-Glycosylat.pdf"))); // parent scan
Assert.That(File.Exists(Path.Combine(outputFolder, @"30_STTAVQTPTSGEPLVST[O-Glycosylat.pdf"))); // child scan
// clean up resources
metadrawLogic.CleanUpResources();
Assert.That(!metadrawLogic.FilteredListOfPsms.Any());
Assert.That(!metadrawLogic.PsmResultFilePaths.Any());
Assert.That(!metadrawLogic.SpectraFilePaths.Any());
// delete output
Directory.Delete(outputFolder, true);
}
