public static void TestMetaDrawReadPsmFile()
{
SearchTask searchTask = new SearchTask();
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra.mzml");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DbForPrunedDb.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("AllPSMs.psmtsv"));
List <PsmFromTsv> parsedPsms = PsmTsvReader.ReadTsv(psmFile, out var warnings);
Assert.AreEqual(11, parsedPsms.Count);
Assert.AreEqual(0, warnings.Count);
Directory.Delete(folderPath, true);
}
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 ReadOGlycoPsms()
{
string psmFile = @"TestData\oglyco.psmtsv";
List <PsmFromTsv> parsedPsms = PsmTsvReader.ReadTsv(psmFile, out var warnings);
Assert.AreEqual(9, parsedPsms.Count);
}
private void LoadAndDisplayPsms(string filename)
{
allPsms.Clear();
string fileNameWithExtension = Path.GetFileName(spectraFilePath);
string fileNameWithoutExtension = Path.GetFileNameWithoutExtension(spectraFilePath);
try
{
// TODO: print warnings
foreach (var psm in PsmTsvReader.ReadTsv(filename, out List <string> warnings))
{
if (spectraFilePath == null || psm.Filename == fileNameWithExtension || psm.Filename == fileNameWithoutExtension || psm.Filename.Contains(fileNameWithoutExtension))
{
allPsms.Add(psm);
FilterPsm(psm);
}
}
GroupAmbiguousPsms();
}
catch (Exception e)
{
MessageBox.Show("Could not open PSM file:\n" + e.Message);
}
}
public static void TestMetaDrawErrors()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestMetaDrawErrors");
string proteinDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta");
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML");
Directory.CreateDirectory(outputFolder);
// run search task
var searchtask = new SearchTask();
searchtask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(proteinDatabase, false)
}, new List <string> {
spectraFile
}, "");
var psmFile = Path.Combine(outputFolder, @"AllPSMs.psmtsv");
// load results into metadraw (skipping spectra file, to produce an error msg)
var metadrawLogic = new MetaDrawLogic();
metadrawLogic.PsmResultFilePaths.Add(psmFile);
// this should produce an error because an expected spectra file is not present
var errors = metadrawLogic.LoadFiles(loadSpectra: true, loadPsms: true);
Assert.That(errors.Any());
Assert.That(!metadrawLogic.FilteredListOfPsms.Any());
// this should not produce an error because we said not to load spectra
errors = metadrawLogic.LoadFiles(loadSpectra: false, loadPsms: true);
Assert.That(!errors.Any());
var psmsFromTsv = PsmTsvReader.ReadTsv(psmFile, out var warnings);
var plotView = new OxyPlot.Wpf.PlotView();
var canvas = new Canvas();
var parentChildScanPlotsView = new ParentChildScanPlotsView();
// plotting PSM should produce an error because spectra are not loaded
metadrawLogic.DisplaySpectrumMatch(plotView, canvas, psmsFromTsv.First(), parentChildScanPlotsView, out errors);
Assert.That(errors.Any());
// export to PDF should produce an error because spectra are not loaded
metadrawLogic.ExportToPdf(plotView, canvas, new List <PsmFromTsv> {
psmsFromTsv.First()
}, parentChildScanPlotsView, outputFolder, out errors);
Assert.That(errors.Any());
// clean up resources
metadrawLogic.CleanUpResources();
// delete output
Directory.Delete(outputFolder, true);
}
private void LoadPsms(out List <string> errors, bool haveLoadedSpectra)
{
errors = new List <string>();
HashSet <string> fileNamesWithoutExtension = new HashSet <string>(
SpectraFilePaths.Select(p => System.IO.Path.GetFileName(p.Replace(GlobalVariables.GetFileExtension(p), string.Empty))));
List <PsmFromTsv> psmsThatDontHaveMatchingSpectraFile = new List <PsmFromTsv>();
try
{
foreach (var resultsFile in PsmResultFilePaths)
{
lock (ThreadLocker)
{
foreach (PsmFromTsv psm in PsmTsvReader.ReadTsv(resultsFile, out List <string> warnings))
{
if (fileNamesWithoutExtension.Contains(psm.FileNameWithoutExtension) || !haveLoadedSpectra)
{
AllPsms.Add(psm);
}
else
{
psmsThatDontHaveMatchingSpectraFile.Add(psm);
}
if (PsmsGroupedByFile.TryGetValue(psm.FileNameWithoutExtension, out var psmsForThisFile))
{
psmsForThisFile.Add(psm);
}
else
{
PsmsGroupedByFile.Add(psm.FileNameWithoutExtension, new ObservableCollection <PsmFromTsv> {
psm
});
}
}
}
}
}
catch (Exception e)
{
errors.Add("Error reading PSM file:\n" + e.Message);
}
if (psmsThatDontHaveMatchingSpectraFile.Any())
{
foreach (var file in psmsThatDontHaveMatchingSpectraFile.GroupBy(p => p.FileNameWithoutExtension))
{
errors.Add(file.Count() + " PSMs from " + file.Key + " were not loaded because this spectra file was not found");
}
}
FilterPsms();
}
private void LoadPsms(string filename, bool loadPsmsOfAllSpectraFiles)
{
allPsms.Clear();
string fileNameWithExtension = Path.GetFileName(spectraFilePath);
string fileNameWithoutExtension = Path.GetFileNameWithoutExtension(spectraFilePath);
try
{
// TODO: print warnings
foreach (var psm in PsmTsvReader.ReadTsv(filename, out List <string> warnings))
{
if (loadPsmsOfAllSpectraFiles || Path.GetFileName(psm.Filename) == fileNameWithExtension || psm.Filename == fileNameWithExtension || psm.Filename == fileNameWithoutExtension || psm.Filename.Equals(fileNameWithoutExtension + "-calib")) // in case results are from a calibrated file
{
allPsms.Add(psm);
}
}
}
catch (Exception e)
{
MessageBox.Show("Could not open PSM file:\n" + e.Message);
}
}
public static void TestFindVariantCrossingIons()
{
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\VariantCrossTest.psmtsv");
List <string> warnings = new List <string>();
List <PsmFromTsv> psms;
psms = PsmTsvReader.ReadTsv(myFile, out warnings); // test will fail if the order of psms is changed to something other than top to bottom row
// check that variant psm properties are being parsed correctly
Assert.AreEqual("", psms[0].IdentifiedSequenceVariations);
Assert.AreEqual("A147T", psms[1].IdentifiedSequenceVariations);
Assert.AreEqual("541-541", psms[0].SpliceSites);
Assert.AreEqual("", psms[1].SpliceSites);
// check that the correct ions are being added to VariantCrossingIons
List <List <string> > expected = new List <List <string> >();
expected.Add(new List <string>()
{
}); // no variant (7527)
expected.Add(new List <string>()
{
"b3"
}); // b fragments before and after variant (4211)
expected.Add(new List <string>()
{
"y3"
}); // y fragments before and after variant (7759)
expected.Add(new List <string>()
{
"b4", "b16"
}); // variant at 1st position (9221)
expected.Add(new List <string>()
{
"y1", "y9"
}); // variant at last position (6778)
expected.Add(new List <string>()
{
"b4", "y35"
}); // peptide comes from multiple proteins (8613)
expected.Add(new List <string>()
{
"b1", "b10", "y1", "y6"
}); // variation spans the whole peptide (8765)
expected.Add(new List <string>()
{
}); // variant before peptide (8169)
expected.Add(new List <string>()
{
}); // variant after peptide (6532)
expected.Add(new List <string>()
{
"a3"
}); // a fragments before and after variant (4212)
expected.Add(new List <string>()
{
"c3"
}); // c fragments before and after variant (4213)
expected.Add(new List <string>()
{
"x3"
}); // x fragments before and after variant (7760)
expected.Add(new List <string>()
{
"zDot3"
}); // z fragments before and after variant (7761)
expected.Add(new List <string>()
{
}); // M fragment with length almost the whole peptide and variant in the middle (7762)
expected.Add(new List <string>()
{
}); // D fragment with length almost the whole peptide and variant in the middle (7763)
for (int i = 0; i < psms.Count; i++)
{
IEnumerable <string> actualIons = psms[i].VariantCrossingIons.Select(p => p.NeutralTheoreticalProduct.Annotation);
foreach (string expectedIon in expected[i])
{
Assert.IsTrue(actualIons.Contains(expectedIon),
"VariantCrossingIons should contain ion " + expectedIon + " in file " + psms[i].Filename + ".");
}
foreach (string actualIon in actualIons)
{
Assert.IsTrue(expected[i].Contains(actualIon),
"VariantCrossingIons should not contain ion " + actualIon + " in file " + psms[i].Filename + ".");
}
}
}
public static void InternalFragmentIonTest()
{
SearchTask searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
MinAllowedInternalFragmentLength = 1
},
CommonParameters = new CommonParameters(
digestionParams: new DigestionParams("top-down"),
listOfModsVariable: new List <(string, string)> {
("Common Variable", "Oxidation on M"),
("Common Biological", "Acetylation on K"),
("Common Biological", "Acetylation on X")
})
};
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\InternalTest.mgf");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\InternalTest.fasta");
DbForTask db = new DbForTask(myDatabase, false);
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)> {
("TestInternal", searchTask)
};
var engine = new EverythingRunnerEngine(taskList, new List <string> {
myFile
}, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, Environment.CurrentDirectory);
engine.Run();
string outputPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestInternal\AllPSMs.psmtsv");
//var output = File.ReadAllLines(outputPath);
//read the psmtsv
List <PsmFromTsv> psms = PsmTsvReader.ReadTsv(outputPath, out var warning);
Assert.IsTrue(psms.Count == 1);
//check that it's been disambiguated
Assert.IsFalse(psms[0].FullSequence.Contains("|"));
int numTotalFragments = psms[0].MatchedIons.Count;
//test again but no variable acetyl on K. Make sure that internal fragments are still searched even without ambiguity
searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
MinAllowedInternalFragmentLength = 1
},
CommonParameters = new CommonParameters(
digestionParams: new DigestionParams("top-down"),
listOfModsVariable: new List <(string, string)> {
("Common Variable", "Oxidation on M"),
("Common Biological", "Acetylation on X")
})
};
taskList = new List <(string, MetaMorpheusTask)> {
("TestInternal", searchTask)
};
engine = new EverythingRunnerEngine(taskList, new List <string> {
myFile
}, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, Environment.CurrentDirectory);
engine.Run();
psms = PsmTsvReader.ReadTsv(outputPath, out warning);
Assert.IsTrue(psms.Count == 1);
Assert.IsTrue(psms[0].MatchedIons.Count == numTotalFragments);
Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestInternal"), true);
}
