public void ChromatogramExportTest() { var testFilesDir = new TestFilesDir(TestContext, TEST_ZIP_PATH); string chromExportDoc = testFilesDir.GetTestPath("ChromToExport.sky"); string fileExpected1 = testFilesDir.GetTestPathLocale(EXPORT_1); string fileActual1 = GetActualName(fileExpected1); string fileExpected2 = testFilesDir.GetTestPathLocale(EXPORT_2); string fileActual2 = GetActualName(fileExpected2); string fileExpectedAll = testFilesDir.GetTestPathLocale(EXPORT_ALL); string fileActualAll = GetActualName(fileExpectedAll); SrmDocument doc = ResultsUtil.DeserializeDocument(chromExportDoc); // Load an empty doc, so that we can make a change and // cause the .skyd to be loaded var docContainer = new ResultsTestDocumentContainer(null, chromExportDoc); docContainer.SetDocument(doc, null, true); docContainer.AssertComplete(); SrmDocument docResults = docContainer.Document; if (IsSaveAll) { // For regenerating all of the required expected files, if things change SaveChrom(docResults, testFilesDir.GetTestPath(EXPORT_1), FILE_NAMES_1.ToList(), CultureInfo.GetCultureInfo("en-US"), EXTRACTOR_1, SOURCES_1); SaveChrom(docResults, testFilesDir.GetTestPath(EXPORT_2), FILE_NAMES_2.ToList(), CultureInfo.GetCultureInfo("en-US"), EXTRACTOR_2, SOURCES_2); SaveChrom(docResults, testFilesDir.GetTestPath(EXPORT_ALL), FILE_NAMES_ALL.ToList(), CultureInfo.GetCultureInfo("en-US"), EXTRACTOR_ALL, SOURCES_ALL); SaveChrom(docResults, testFilesDir.GetTestPathIntl(EXPORT_1), FILE_NAMES_1.ToList(), CultureInfo.GetCultureInfo("fr-FR"), EXTRACTOR_1, SOURCES_1); SaveChrom(docResults, testFilesDir.GetTestPathIntl(EXPORT_2), FILE_NAMES_2.ToList(), CultureInfo.GetCultureInfo("fr-FR"), EXTRACTOR_2, SOURCES_2); SaveChrom(docResults, testFilesDir.GetTestPathIntl(EXPORT_ALL), FILE_NAMES_ALL.ToList(), CultureInfo.GetCultureInfo("fr-FR"), EXTRACTOR_ALL, SOURCES_ALL); } SaveChrom(docResults, fileActual1, FILE_NAMES_1.ToList(), LocalizationHelper.CurrentCulture, EXTRACTOR_1, SOURCES_1); SaveChrom(docResults, fileActual2, FILE_NAMES_2.ToList(), LocalizationHelper.CurrentCulture, EXTRACTOR_2, SOURCES_2); SaveChrom(docResults, fileActualAll, FILE_NAMES_ALL.ToList(), LocalizationHelper.CurrentCulture, EXTRACTOR_ALL, SOURCES_ALL); AssertEx.FileEquals(fileExpected1, fileActual1); AssertEx.FileEquals(fileExpected2, fileActual2); AssertEx.FileEquals(fileExpectedAll, fileActualAll); // Close the .skyd file docContainer.Release(); }
public void TestMProphetResultsHandler() { var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE); var documentFile = testFilesDir.GetTestPath("MProphetGold-trained.sky"); SrmDocument doc = ResultsUtil.DeserializeDocument(documentFile); // Load libraries doc = doc.ChangeSettings(doc.Settings.ChangePeptideLibraries(libraries => { var lib = libraries.Libraries[0]; return libraries.ChangeLibrarySpecs(new LibrarySpec[] { new BiblioSpecLiteSpec(lib.Name, testFilesDir.GetTestPath(lib.FileNameHint)) }); })); // Load an empty doc, so that we can make a change and // cause the .skyd to be loaded var docContainer = new ResultsTestDocumentContainer(null, documentFile); docContainer.SetDocument(doc, null, true); docContainer.AssertComplete(); SrmDocument docOriginal = docContainer.Document; var peakScoringModel = docOriginal.Settings.PeptideSettings.Integration.PeakScoringModel; var resultsHandler = new MProphetResultsHandler(docOriginal, peakScoringModel) { QValueCutoff = Q_CUTOFF }; // 1. Reintegrate and export report produces expected file resultsHandler.ScoreFeatures(); var docNew = resultsHandler.ChangePeaks(); var reportSpec = MakeReportSpec(); if (IsSaveAll) { // For regenerating expected files if things change ReportToCsv(reportSpec, docNew, testFilesDir.GetTestPath(REPORT_EXPECTED), CultureInfo.GetCultureInfo("en-US")); ReportToCsv(reportSpec, docNew, testFilesDir.GetTestPathIntl(REPORT_EXPECTED), CultureInfo.GetCultureInfo("fr-FR")); } string docNewActual = testFilesDir.GetTestPath(REPORT_ACTUAL); string docNewExpected = testFilesDir.GetTestPathLocale(REPORT_EXPECTED); ReportToCsv(reportSpec, docNew, docNewActual, CultureInfo.CurrentCulture); AssertEx.FileEquals(docNewExpected, docNewActual); // 2. Reintegrating again gives no change in document var resultsHandlerRepeat = new MProphetResultsHandler(docNew, peakScoringModel) { QValueCutoff = Q_CUTOFF }; resultsHandlerRepeat.ScoreFeatures(); var docRepeat = resultsHandlerRepeat.ChangePeaks(); Assert.AreSame(docRepeat, docNew); Assert.AreNotSame(docOriginal, docNew); // 3. Export mProphet results gives expected file var calcs = peakScoringModel.PeakFeatureCalculators; var mProphetActual = testFilesDir.GetTestPath(MPROPHET_ACTUAL); var mProphetExpected = testFilesDir.GetTestPathLocale(MPROPHET_EXPECTED); if (IsSaveAll) { // For regenerating files SaveMProphetFeatures(resultsHandler, testFilesDir.GetTestPath(MPROPHET_EXPECTED), CultureInfo.GetCultureInfo("en-US"), calcs); SaveMProphetFeatures(resultsHandler, testFilesDir.GetTestPathIntl(MPROPHET_EXPECTED), CultureInfo.GetCultureInfo("fr-FR"), calcs); } SaveMProphetFeatures(resultsHandler, mProphetActual, CultureInfo.CurrentCulture, calcs); AssertEx.FileEquals(mProphetExpected, mProphetActual); // 4. Export mProphet -> Import Peak Boundaries leads to same result as reintegrate var resultsHandlerQAll = new MProphetResultsHandler(docOriginal, peakScoringModel) {QValueCutoff = 1.0}; resultsHandlerQAll.ScoreFeatures(); var docNewQAll = resultsHandlerQAll.ChangePeaks(); var peakBoundaryImporter = new PeakBoundaryImporter(docNewQAll); long lineCount = Helpers.CountLinesInFile(mProphetActual); peakBoundaryImporter.Import(mProphetActual, null, lineCount); var docImport = peakBoundaryImporter.Document; // Serialized documents are easier to debug when something is different string strDocNew = SerializeDoc(docNewQAll); string strDocImport = SerializeDoc(docImport); AssertEx.NoDiff(strDocNew, strDocImport); Assert.AreSame(docNewQAll, docImport); // 5. Reintegration with q value cutoff of <0 causes all peaks set to null var handlerAllNull = new MProphetResultsHandler(docOriginal, peakScoringModel) {QValueCutoff = -0.001}; handlerAllNull.ScoreFeatures(); var docNull = handlerAllNull.ChangePeaks(); foreach (var transitionNode in docNull.PeptideTransitions) foreach(var chromInfo in transitionNode.ChromInfos) Assert.IsTrue(chromInfo.IsEmpty || transitionNode.IsDecoy); // 6. Reintegration adjusts example peak to null at q=0.005 cutoff, but adjusts it to a non-null peak at q=0.20 const int groupNum = 11; var midQNode = resultsHandler.Document.PeptideTransitionGroups.ToList()[groupNum]; foreach (var chromInfo in midQNode.Transitions.SelectMany(transition => transition.ChromInfos)) Assert.IsTrue(chromInfo.IsEmpty); resultsHandler.QValueCutoff = Q_CUTOFF_HIGH; resultsHandler.ChangePeaks(); var midQNodeNew = resultsHandler.Document.PeptideTransitionGroups.ToList()[groupNum]; foreach (var chromInfo in midQNodeNew.Transitions.SelectMany(transition => transition.ChromInfos)) Assert.IsFalse(chromInfo.IsEmpty); // 7. Labeled peptide pairs still have matching peaks foreach (var peptideNode in resultsHandler.Document.Peptides) { Assert.AreEqual(2, peptideNode.TransitionGroupCount); var groupList = peptideNode.TransitionGroups.ToList(); var lightGroup = groupList[0]; var heavyGroup = groupList[0]; var lightChromInfo = lightGroup.ChromInfos.ToList()[0]; var heavyChromInfo = heavyGroup.ChromInfos.ToList()[0]; Assert.AreEqual(lightChromInfo.StartRetentionTime, heavyChromInfo.StartRetentionTime); Assert.AreEqual(lightChromInfo.EndRetentionTime, heavyChromInfo.EndRetentionTime); Assert.AreEqual(lightChromInfo.RetentionTime, heavyChromInfo.RetentionTime); } // 8. Verify that chosen peaks and q values are the same as those in mProphet paper: // http://www.nature.com/nmeth/journal/v8/n5/full/nmeth.1584.html#/supplementary-information // TODO: Grab this data from the mProphet paper // Release open streams docContainer.Release(); }