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();
}