public static void TestMetaDrawReadCrossPsmFile()
{
XLSearchTask searchTask = new XLSearchTask();
searchTask.XlSearchParameters.Crosslinker = GlobalVariables.Crosslinkers.ToList()[1];
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\BSA_DSS_23747.mzML");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\BSA.fasta");
string folderPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestMetaDrawReadPsmFile");
DbForTask db = new DbForTask(myDatabase, false);
Directory.CreateDirectory(folderPath);
searchTask.RunTask(folderPath, new List <DbForTask> {
db
}, new List <string> {
myFile
}, "metadraw");
string psmFile = Directory.GetFiles(folderPath).First(f => f.Contains("XL_Intralinks.tsv"));
List <PsmFromTsv> parsedPsms = PsmTsvReader.ReadTsv(psmFile, out var warnings);
Directory.Delete(folderPath, true);
}
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 XLSearchTaskWindow()
{
InitializeComponent();
PopulateChoices();
TheTask = new XLSearchTask();
UpdateFieldsFromTask(TheTask);
this.saveButton.Content = "Add the XLSearch Task";
dataContextForSearchTaskWindow = new DataContextForSearchTaskWindow()
{
ExpanderTitle = string.Join(", ", SearchModesForThisTask.Where(b => b.Use).Select(b => b.Name)),
//ModExpanderTitle =
//"fixed: "
//+ string.Join(",", ModFileListInWindow.Where(b => b.Fixed).Select(b => b.FileName))
//+ " variable: "
//+ string.Join(",", ModFileListInWindow.Where(b => b.Variable).Select(b => b.FileName))
//+ " localize: "
//+ string.Join(",", ModFileListInWindow.Where(b => b.Localize).Select(b => b.FileName)),
AnalysisExpanderTitle = "Some analysis properties...",
SearchModeExpanderTitle = "Some search properties..."
};
this.DataContext = dataContextForSearchTaskWindow;
}
public XLSearchTaskWindow(XLSearchTask task)
{
InitializeComponent();
PopulateChoices();
TheTask = task;
UpdateFieldsFromTask(TheTask);
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;
}
public static void WriteTsvTest()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlOutputTestFile");
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\2017-11-21_XL_DSSO_Ribosome_RT60min_28800-28898.mzML");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\RibosomeGO.fasta");
Directory.CreateDirectory(outputFolder);
XLSearchTask xLSearch = new XLSearchTask();
xLSearch.XlSearchParameters.CrosslinkAtCleavageSite = true;
xLSearch.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, new List <string> {
myFile
}, "test");
var resultsPath = File.ReadAllLines(Path.Combine(outputFolder, @"XL_Intralinks.tsv"));
var sections = resultsPath[1].Split('\t');
Assert.That(resultsPath.Length > 1);
Assert.That(sections.Length == 47);
var resultsPath_Inter = File.ReadAllLines(Path.Combine(outputFolder, @"XL_Interlinks.tsv"));
Assert.That(resultsPath_Inter.Length > 1);
var resultsPath_Deadend = File.ReadAllLines(Path.Combine(outputFolder, @"Deadends.tsv"));
Assert.That(resultsPath_Deadend.Length > 1);
var resultsPath_loop = File.ReadAllLines(Path.Combine(outputFolder, @"Looplinks.tsv"));
Assert.That(resultsPath_loop.Length > 1);
var resultsPath_single = File.ReadAllLines(Path.Combine(outputFolder, @"SinglePeptides.tsv"));
Assert.That(resultsPath_single.Length > 1);
Directory.Delete(outputFolder, true);
}
public XLSearchTaskWindow(XLSearchTask task)
{
InitializeComponent();
PopulateChoices();
TheTask = task ?? new XLSearchTask();
UpdateFieldsFromTask(TheTask);
if (task == null)
{
this.saveButton.Content = "Add the XLSearch 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;
}
public static void WriteTsvTest()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlOutputTest1");
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\BSA_DSS_23747.mzML");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\BSA.fasta");
Directory.CreateDirectory(outputFolder);
XLSearchTask xLSearch = new XLSearchTask();
xLSearch.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, new List <string> {
myFile
}, "test");
var resultsPath = File.ReadAllLines(Path.Combine(outputFolder, @"XL_Interlinks.tsv"));
var sections = resultsPath[1].Split('\t');
Assert.That(resultsPath.Length == 2);
Assert.That(sections.Length == 45);
Directory.Delete(outputFolder, true);
}
public static void XlTest_BSA_DSSO()
{
//Generate parameters
var commonParameters = new CommonParameters(doPrecursorDeconvolution: false, cIons: true, zDotIons: true, scoreCutoff: 2, digestionParams: new DigestionParams(minPeptideLength: 5));
var xlSearchParameters = new XlSearchParameters {
XlCharge_2_3_PrimeFragment = true
};
//Create databases contain two protein.
var proteinList = new List <Protein> {
new Protein("EKVLTSSAR", "Fake01"), new Protein("LSQKFPK", "Fake02")
};
ModificationMotif.TryGetMotif("M", out ModificationMotif motif1);
ModificationWithMass mod1 = new ModificationWithMass("Oxidation of M", "Common Variable", motif1, TerminusLocalization.Any, 15.99491461957);
ModificationMotif.TryGetMotif("C", out ModificationMotif motif2);
ModificationWithMass mod2 = new ModificationWithMass("Carbamidomethyl of C", "Common Fixed", motif2, TerminusLocalization.Any, 57.02146372068994);
var variableModifications = new List <ModificationWithMass>()
{
mod1
};
var fixedModifications = new List <ModificationWithMass>()
{
mod2
};
var localizeableModifications = new List <ModificationWithMass>();
var lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y, ProductType.C, ProductType.Zdot
};
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int i = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
//Generate digested peptide lists.
List <PeptideWithSetModifications> digestedList = new List <PeptideWithSetModifications>();
foreach (var item in proteinList)
{
var digested = item.Digest(commonParameters.DigestionParams, fixedModifications, variableModifications).ToList();
digestedList.AddRange(digested);
}
foreach (var fdfd in digestedList)
{
fdfd.CompactPeptide(TerminusType.None);
}
//Run index engine
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, lp, 1, DecoyType.Reverse, new List <DigestionParams>
{
commonParameters.DigestionParams
}, commonParameters, 30000, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
var fragmentIndexCount = indexResults.FragmentIndex.Count(p => p != null);
var fragmentIndexAll = indexResults.FragmentIndex.Select((s, j) => new { j, s }).Where(p => p.s != null).Select(t => t.j).ToList();
Assert.IsTrue(fragmentIndexAll.Count() > 0);
//Get MS2 scans.
var myMsDataFile = new XLTestDataFile();
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, commonParameters.DoPrecursorDeconvolution, commonParameters.UseProvidedPrecursorInfo, commonParameters.DeconvolutionIntensityRatio, commonParameters.DeconvolutionMaxAssumedChargeState, commonParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
//Generate crosslinker, which is DSSO here.
CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass();
crosslinker.SelectCrosslinker(xlSearchParameters.CrosslinkerType);
//TwoPassCrosslinkSearchEngine.Run().
List <PsmCross> newPsms = new List <PsmCross>();
new TwoPassCrosslinkSearchEngine(newPsms, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, lp, 0, commonParameters, false, xlSearchParameters.XlPrecusorMsTl, crosslinker, xlSearchParameters.CrosslinkSearchTop, xlSearchParameters.CrosslinkSearchTopNum, xlSearchParameters.XlQuench_H2O, xlSearchParameters.XlQuench_NH2, xlSearchParameters.XlQuench_Tris, xlSearchParameters.XlCharge_2_3, xlSearchParameters.XlCharge_2_3_PrimeFragment, new List <string> {
}).Run();
var compactPeptideToProteinPeptideMatch = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >();
new CrosslinkAnalysisEngine(newPsms, compactPeptideToProteinPeptideMatch, proteinList, variableModifications, fixedModifications, lp, null, crosslinker, TerminusType.None, commonParameters, new List <string> {
}).Run();
foreach (var item in newPsms)
{
item.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
}
//Test newPsms
Assert.AreEqual(newPsms.Count(), 3);
//Test Output
var task = new XLSearchTask();
task.WriteAllToTsv(newPsms, TestContext.CurrentContext.TestDirectory, "allPsms", new List <string> {
});
task.WritePepXML_xl(newPsms, proteinList, null, variableModifications, fixedModifications, null, TestContext.CurrentContext.TestDirectory, "pep.XML", new List <string> {
});
task.WriteSingleToTsv(newPsms.Where(p => p.CrossType == PsmCrossType.Singe).ToList(), TestContext.CurrentContext.TestDirectory, "singlePsms", new List <string> {
});
//Test PsmCross.XlCalculateTotalProductMasses.
var psmCrossAlpha = new PsmCross(digestedList[1].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0], commonParameters.DigestionParams);
var psmCrossBeta = new PsmCross(digestedList[2].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0], commonParameters.DigestionParams);
var linkPos = PsmCross.XlPosCal(psmCrossAlpha.compactPeptide, crosslinker.CrosslinkerModSites);
var productMassesAlphaList = PsmCross.XlCalculateTotalProductMasses(psmCrossAlpha, psmCrossBeta.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass, crosslinker, lp, true, false, linkPos);
Assert.AreEqual(productMassesAlphaList[0].ProductMz.Length, 99);
}
private void UpdateFieldsFromTask(XLSearchTask task)
{
//Crosslink search para
//RbSearchCrosslink.IsChecked = !task.XlSearchParameters.SearchGlyco;
//RbSearchGlyco.IsChecked = task.XlSearchParameters.SearchGlyco;
cbCrosslinkers.SelectedItem = task.XlSearchParameters.Crosslinker;
ckbXLTopNum.IsChecked = task.XlSearchParameters.RestrictToTopNHits;
txtXLTopNum.Text = task.XlSearchParameters.CrosslinkSearchTopNum.ToString(CultureInfo.InvariantCulture);
ckbCrosslinkAtCleavageSite.IsChecked = task.XlSearchParameters.CrosslinkAtCleavageSite;
ckbQuenchH2O.IsChecked = task.XlSearchParameters.XlQuench_H2O;
ckbQuenchNH2.IsChecked = task.XlSearchParameters.XlQuench_NH2;
ckbQuenchTris.IsChecked = task.XlSearchParameters.XlQuench_Tris;
cbbXLprecusorMsTl.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
XLPrecusorMsTlTextBox.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();
if (task.CommonParameters.ChildScanDissociationType != DissociationType.Unknown)
{
ChildScanDissociationTypeComboBox.SelectedItem = task.CommonParameters.ChildScanDissociationType.ToString();
}
checkBoxDecoy.IsChecked = task.XlSearchParameters.DecoyType != DecoyType.None;
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);
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;
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
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);
ckbPercolator.IsChecked = task.XlSearchParameters.WriteOutputForPercolator;
ckbPepXML.IsChecked = task.XlSearchParameters.WritePepXml;
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();
}
}
private void UpdateFieldsFromTask(XLSearchTask task)
{
//Crosslink search para
cbCrosslinker.SelectedIndex = (int)task.XlSearchParameters.CrosslinkerType;
//cbFragmentation.SelectedIndex = (int)task.XlSearchParameters.FragmentationType;
ckbXLTopNum.IsChecked = task.XlSearchParameters.CrosslinkSearchTop;
txtXLTopNum.Text = task.XlSearchParameters.CrosslinkSearchTopNum.ToString(CultureInfo.InvariantCulture);
ckbQuenchH2O.IsChecked = task.XlSearchParameters.XlQuench_H2O;
ckbQuenchNH2.IsChecked = task.XlSearchParameters.XlQuench_NH2;
ckbQuenchTris.IsChecked = task.XlSearchParameters.XlQuench_Tris;
//ckbSearchWithXLAllBeta.IsChecked = task.XlSearchParameters.CrosslinkSearchWithAllBeta;
txtUdXLKerName.Text = task.XlSearchParameters.UdXLkerName;
ckbUdXLkerCleavable.IsChecked = task.XlSearchParameters.UdXLkerCleavable;
txtUdXLkerTotalMs.Text = task.XlSearchParameters.UdXLkerTotalMass.HasValue ? task.XlSearchParameters.UdXLkerTotalMass.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerShortMass.Text = task.XlSearchParameters.UdXLkerShortMass.HasValue ? task.XlSearchParameters.UdXLkerShortMass.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerLongMass.Text = task.XlSearchParameters.UdXLkerLongMass.HasValue ? task.XlSearchParameters.UdXLkerLongMass.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerLoopMass.Text = task.XlSearchParameters.UdXLkerLoopMass.HasValue ? task.XlSearchParameters.UdXLkerLoopMass.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerAminoAcid.Text = task.XlSearchParameters.UdXLkerResidue.ToString();
txtUdXLkerDeadendH2O.Text = task.XlSearchParameters.UdXLkerDeadendMassH2O.HasValue ? task.XlSearchParameters.UdXLkerDeadendMassH2O.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerDeadendNH2.Text = task.XlSearchParameters.UdXLkerDeadendMassNH2.HasValue ? task.XlSearchParameters.UdXLkerDeadendMassNH2.Value.ToString(CultureInfo.InvariantCulture) : "";
txtUdXLkerDeadendTris.Text = task.XlSearchParameters.UdXLkerDeadendMassTris.HasValue ? task.XlSearchParameters.UdXLkerDeadendMassTris.Value.ToString(CultureInfo.InvariantCulture) : "";
cbbXLprecusorMsTl.SelectedIndex = task.XlSearchParameters.XlPrecusorMsTl is AbsoluteTolerance ? 0 : 1;
txtXLPrecusorMsTl.Text = task.XlSearchParameters.XlPrecusorMsTl.Value.ToString(CultureInfo.InvariantCulture);
//cbbXLBetaprecusorMsTl.SelectedIndex = task.XlSearchParameters.XlPrecusorMsTl is AbsoluteTolerance ? 0 : 1;
//txtXLBetaPrecusorMsTl.Text = task.XlSearchParameters.XlPrecusorMsTl.Value.ToString(CultureInfo.InvariantCulture);
trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
TopNPeaksCheckBox.Text = task.CommonParameters.TopNpeaks.HasValue ? task.CommonParameters.TopNpeaks.Value.ToString(CultureInfo.InvariantCulture) : "";
MinRatioCheckBox.Text = task.CommonParameters.MinRatio.HasValue ? task.CommonParameters.MinRatio.Value.ToString(CultureInfo.InvariantCulture) : "";
ckbCharge_2_3.IsChecked = task.XlSearchParameters.XlCharge_2_3;
ckbCharge_2_3_PrimeFragments.IsChecked = task.XlSearchParameters.XlCharge_2_3_PrimeFragment;
checkBoxDecoy.IsChecked = task.XlSearchParameters.DecoyType != DecoyType.None;
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
txtMinPeptideLength.Text = task.CommonParameters.DigestionParams.MinPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MinPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
txtMaxPeptideLength.Text = task.CommonParameters.DigestionParams.MaxPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MaxPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.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;
bCheckBox.IsChecked = task.CommonParameters.BIons;
yCheckBox.IsChecked = task.CommonParameters.YIons;
cCheckBox.IsChecked = task.CommonParameters.CIons;
zdotCheckBox.IsChecked = task.CommonParameters.ZdotIons;
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
ckbAllResults.IsChecked = task.XlSearchParameters.XlOutAll;
ckbPercolator.IsChecked = task.XlSearchParameters.XlOutPercolator;
ckbCrosslink.IsChecked = task.XlSearchParameters.XlOutCrosslink;
ckbPepXML.IsChecked = task.XlSearchParameters.XlOutPepXML;
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.DisplayName.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.DisplayName.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));
}
}
localizeAllCheckBox.IsChecked = task.CommonParameters.LocalizeAll;
if (task.CommonParameters.LocalizeAll)
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
}
else
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
if (task.CommonParameters.ListOfModTypesLocalize.Contains(heh.DisplayName))
{
heh.Use = true;
}
else
{
heh.Use = false;
}
}
}
foreach (var ye in variableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in fixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
public static void XlTest_BSA_DSSO()
{
//Generate parameters
var commonParameters = new CommonParameters(doPrecursorDeconvolution: false, dissociationType: DissociationType.EThcD,
scoreCutoff: 1, digestionParams: new DigestionParams(minPeptideLength: 5), precursorMassTolerance: new PpmTolerance(10));
var xlSearchParameters = new XlSearchParameters();
//Create databases contain two protein.
var proteinList = new List <Protein> {
new Protein("EKVLTSSAR", "Fake01"), new Protein("LSQKFPK", "Fake02")
};
ModificationMotif.TryGetMotif("M", out ModificationMotif motif1);
Modification mod1 = new Modification(_originalId: "Oxidation of M", _modificationType: "Common Variable", _target: motif1, _locationRestriction: "Anywhere.", _monoisotopicMass: 15.99491461957);
ModificationMotif.TryGetMotif("C", out ModificationMotif motif2);
Modification mod2 = new Modification(_originalId: "Carbamidomethyl of C", _modificationType: "Common Fixed", _target: motif2, _locationRestriction: "Anywhere.", _monoisotopicMass: 57.02146372068994);
var variableModifications = new List <Modification>()
{
mod1
};
var fixedModifications = new List <Modification>()
{
mod2
};
var localizeableModifications = new List <Modification>();
//Run index engine
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, 1, DecoyType.Reverse, commonParameters, 30000, false, new List <FileInfo>(), new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
var indexedFragments = indexResults.FragmentIndex.Where(p => p != null).SelectMany(v => v).ToList();
Assert.AreEqual(82, indexedFragments.Count);
Assert.AreEqual(3, indexResults.PeptideIndex.Count);
//Get MS2 scans.
var myMsDataFile = new XLTestDataFile();
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//Generate crosslinker, which is DSSO here.
Crosslinker crosslinker = GlobalVariables.Crosslinkers.Where(p => p.CrosslinkerName == "DSSO").First();
CrosslinkSpectralMatch[] possiblePsms = new CrosslinkSpectralMatch[listOfSortedms2Scans.Length];
new CrosslinkSearchEngine(possiblePsms, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, commonParameters, crosslinker, xlSearchParameters.RestrictToTopNHits, xlSearchParameters.CrosslinkSearchTopNum, xlSearchParameters.XlQuench_H2O, xlSearchParameters.XlQuench_NH2, xlSearchParameters.XlQuench_Tris, new List <string> {
}).Run();
var newPsms = possiblePsms.Where(p => p != null).ToList();
foreach (var item in newPsms)
{
item.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
}
//Test newPsms
Assert.AreEqual(3, newPsms.Count);
//Test Output
var task = new XLSearchTask();
task.WritePepXML_xl(newPsms, proteinList, null, variableModifications, fixedModifications, null, TestContext.CurrentContext.TestDirectory, "pep.XML", new List <string> {
});
//Test PsmCross.XlCalculateTotalProductMasses
//var psmCrossAlpha = new CrosslinkSpectralMatch(digestedList[1], 0, 0, 0, listOfSortedms2Scans[0], commonParameters.DigestionParams, new List<MatchedFragmentIon>());
//var psmCrossBeta = new CrosslinkSpectralMatch(digestedList[2], 0, 0, 0, listOfSortedms2Scans[0], commonParameters.DigestionParams, new List<MatchedFragmentIon>());
//var linkPos = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), digestedList[1]);
//var productMassesAlphaList = CrosslinkedPeptide.XlGetTheoreticalFragments(DissociationType.EThcD, false, crosslinker, linkPos, digestedList[2].MonoisotopicMass, digestedList[1]);
//Assert.AreEqual(productMassesAlphaList.First().Value.Count, 50); //TO DO: The number here should be manually verified.
File.Delete(@"singlePsms.tsv");
File.Delete(@"pep.XML.pep.xml");
File.Delete(@"allPsms.tsv");
}
public static void MetaDraw_XlSearchTaskWithChildScansTest()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"MetaDraw_XlSearchTaskTest");
string proteinDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\BSA.fasta");
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\ms2mixed_bsa_xlink.mzML");
// run task
CommonParameters commonParameters = new CommonParameters(dissociationType: DissociationType.CID, ms2childScanDissociationType: DissociationType.ETD,
trimMsMsPeaks: false);
Directory.CreateDirectory(outputFolder);
var xlSearchTask = new XLSearchTask()
{
CommonParameters = commonParameters
};
xlSearchTask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(proteinDatabase, false)
}, new List <string> {
spectraFile
}, "");
//TODO: test other files (XL_Interlinks.tsv, Deadends.tsv, Looplinks.tsv, SinglePeptides.tsv)
var csmFile = Path.Combine(outputFolder, @"XL_Intralinks.tsv");
// load results into metadraw
var metadrawLogic = new MetaDrawLogic();
metadrawLogic.SpectraFilePaths.Add(spectraFile);
metadrawLogic.PsmResultFilePaths.Add(csmFile);
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 = @"SLGKVGTR";
metadrawLogic.FilterPsmsByString(filterString);
int c = 0;
foreach (var filteredPsm in metadrawLogic.PeptideSpectralMatchesView)
{
var psmObj = (PsmFromTsv)filteredPsm;
Assert.That(psmObj.FullSequence.Contains(filterString));
c++;
}
Assert.That(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.That(c > 0);
// draw PSM
var plotView = new OxyPlot.Wpf.PlotView();
var canvas = new Canvas();
var parentChildView = new ParentChildScanPlotsView();
var csm = metadrawLogic.FilteredListOfPsms.First();
metadrawLogic.DisplaySpectrumMatch(plotView, canvas, csm, 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) == 142.12); // m/z
Assert.That(Math.Round(peakPoints[1].X, 2) == 142.12);
Assert.That((int)peakPoints[0].Y == 0); // intensity
Assert.That((int)peakPoints[1].Y == 1114);
var plotAxes = plotView.Model.Axes;
Assert.That(plotAxes.Count == 2);
// test that base sequence annotation was drawn
Assert.That(canvas.Children.Count > 0);
// test that the plots were drawn in the parent/child view
Assert.That(parentChildView.Plots.Count == 2);
// test parent scan
var parentPlot = parentChildView.Plots[0];
Assert.That(parentPlot.SpectrumLabel == "Scan: 2 Dissociation Type: CID MsOrder: 2 Selected Mz: 492.02 Retention Time: 23.9");
int numAnnotatedResidues = csm.BaseSeq.Length;
int numAnnotatedIons = csm.MatchedIons.Count(p => p.NeutralTheoreticalProduct.ProductType != ProductType.M);
int numAnnotatedMods = csm.FullSequence.Count(p => p == '[');
Assert.That(parentPlot.TheCanvas.Children.Count == numAnnotatedResidues + numAnnotatedIons + numAnnotatedMods);
peak = (LineSeries)parentPlot.Plot.Model.Series[0]; // the first m/z peak
peakPoints = peak.Points;
Assert.That(Math.Round(peakPoints[0].X, 2) == 142.12); // m/z
Assert.That(Math.Round(peakPoints[1].X, 2) == 142.12);
Assert.That((int)peakPoints[0].Y == 0); // intensity
Assert.That((int)peakPoints[1].Y == 1114);
// test child scan
var childPlot = parentChildView.Plots[1];
Assert.That(childPlot.SpectrumLabel == "Scan: 3 Dissociation Type: ETD MsOrder: 2 Selected Mz: 492.02 RetentionTime: 23.9");
Assert.That(childPlot.TheCanvas.Children.Count > 0);
numAnnotatedResidues = csm.BaseSeq.Length;
numAnnotatedIons = csm.ChildScanMatchedIons[3].Concat(csm.BetaPeptideChildScanMatchedIons[3])
.Count(p => p.NeutralTheoreticalProduct.ProductType != ProductType.M);
numAnnotatedMods = csm.FullSequence.Count(p => p == '[');
Assert.That(childPlot.TheCanvas.Children.Count == numAnnotatedResidues + numAnnotatedIons + numAnnotatedMods);
peak = (LineSeries)childPlot.Plot.Model.Series[0]; // the first m/z peak
peakPoints = peak.Points;
Assert.That(Math.Round(peakPoints[0].X, 2) == 122.92); // m/z
Assert.That(Math.Round(peakPoints[1].X, 2) == 122.92);
Assert.That((int)peakPoints[0].Y == 0); // intensity
Assert.That((int)peakPoints[1].Y == 857);
// write pdf
var psmsToExport = metadrawLogic.FilteredListOfPsms.Where(p => p.FullSequence == "SLGKVGTR(4)").ToList();
metadrawLogic.ExportToPdf(plotView, canvas, psmsToExport, parentChildView, outputFolder, out errors);
// test that pdf exists
Assert.That(File.Exists(Path.Combine(outputFolder, @"2_SLGKVGTR(4).pdf"))); // parent scan
Assert.That(File.Exists(Path.Combine(outputFolder, @"3_SLGKVGTR(4).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);
}
