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 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 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 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);
}