private static void SaveMProphetFeatures(MProphetResultsHandler resultsHandler,
string saveFile,
CultureInfo cultureInfo,
IList <IPeakFeatureCalculator> calcs)
{
using (var saver = new FileSaver(saveFile))
using (var writer = new StreamWriter(saver.SafeName))
{
resultsHandler.WriteScores(writer, cultureInfo, calcs);
writer.Flush();
writer.Close();
saver.Commit();
}
}
public static void WriteFeatures(string filePath,
MProphetResultsHandler resultsHandler,
IList <IPeakFeatureCalculator> calcs,
CultureInfo cultureInfo,
bool bestOnly,
bool includeDecoys,
IProgressMonitor progressMonitor)
{
using (var fs = new FileSaver(filePath))
using (var writer = new StreamWriter(fs.SafeName))
{
resultsHandler.ScoreFeatures(progressMonitor);
resultsHandler.WriteScores(writer, cultureInfo, calcs, bestOnly, includeDecoys, progressMonitor);
writer.Close();
fs.Commit();
}
}
public void ScorePeptides(SrmDocument doc, IProgressMonitor progressMonitor)
{
var model = doc.Settings.PeptideSettings.Integration.PeakScoringModel;
if (model == null || !model.IsTrained)
{
model = LegacyScoringModel.DEFAULT_MODEL;
}
var mProphetResultsHandler = new MProphetResultsHandler(doc, model);
mProphetResultsHandler.ScoreFeatures(progressMonitor, true);
if (progressMonitor.IsCanceled)
{
return;
}
var scoredPeptidesDict = new Dictionary <Target, ScoredPeptide>();
foreach (var nodePep in doc.Molecules.Where(pep => pep.PercentileMeasuredRetentionTime.HasValue && !pep.IsDecoy))
{
var allStats = doc.MeasuredResults.MSDataFileInfos
.Select(info => mProphetResultsHandler.GetPeakFeatureStatistics(nodePep.Id.GlobalIndex, info.FileId.GlobalIndex))
.Where(stats => stats != null).ToArray();
var value = float.MaxValue;
if (allStats.Length > 0)
{
value = model is MProphetPeakScoringModel
? allStats.Select(stats => stats.QValue.Value).Max()
: -allStats.Select(stats => stats.BestScore).Min();
}
if (!scoredPeptidesDict.TryGetValue(nodePep.ModifiedTarget, out var existing) || value < existing.Score)
{
scoredPeptidesDict[nodePep.ModifiedTarget] = new ScoredPeptide(
new MeasuredPeptide(doc.Settings.GetModifiedSequence(nodePep), nodePep.PercentileMeasuredRetentionTime.Value), nodePep, value);
}
}
_scoredPeptides = scoredPeptidesDict.Values.OrderBy(pep => pep.Peptide.RetentionTime).ToArray();
_cirtPeptides = _scoredPeptides.Where(pep => _cirtAll.ContainsKey(pep.Peptide.Target)).ToArray();
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
double qCutoff = double.MaxValue;
if (reintegrateQCutoff.Checked)
{
if (!helper.ValidateDecimalTextBox(textBoxCutoff, 0.0, 1.0, out qCutoff))
{
return;
}
}
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.ReintegrateDlg_OkDialog_Reintegrating,
})
{
try
{
var scoringModel = _driverPeakScoringModel.SelectedItem;
if (Equals(scoringModel, LegacyScoringModel.DEFAULT_UNTRAINED_MODEL))
{
scoringModel = LegacyScoringModel.DEFAULT_MODEL;
}
if (scoringModel == null || !scoringModel.IsTrained)
{
throw new InvalidDataException(Resources.ReintegrateDlg_OkDialog_You_must_train_and_select_a_model_in_order_to_reintegrate_peaks_);
}
var resultsHandler = new MProphetResultsHandler(Document, scoringModel)
{
QValueCutoff = qCutoff,
OverrideManual = checkBoxOverwrite.Checked,
AddAnnotation = checkBoxAnnotation.Checked,
AddMAnnotation = checkBoxAnnotation.Checked
};
longWaitDlg.PerformWork(this, 1000, pm =>
{
resultsHandler.ScoreFeatures(pm);
if (resultsHandler.IsMissingScores())
{
throw new InvalidDataException(Resources.ReintegrateDlg_OkDialog_The_current_peak_scoring_model_is_incompatible_with_one_or_more_peptides_in_the_document___Please_train_a_new_model_);
}
// TODO: Add a checkbox for including decoys. Probably most of the time real users won't want to bother with reintegrating decoys
Document = resultsHandler.ChangePeaks(pm);
});
if (longWaitDlg.IsCanceled)
{
return;
}
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.ReintegrateDlg_OkDialog_Failed_attempting_to_reintegrate_peaks_),
x.Message);
MessageDlg.ShowWithException(this, message, x);
return;
}
}
var newPeakScoringModel = _driverPeakScoringModel.SelectedItem;
if (!Equals(newPeakScoringModel, Document.Settings.PeptideSettings.Integration.PeakScoringModel))
{
Document = Document.ChangeSettings(Document.Settings.ChangePeptideIntegration(
i => i.ChangePeakScoringModel(newPeakScoringModel)));
}
DialogResult = DialogResult.OK;
}
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();
}
public void OkDialog()
{
using (var dlg = new SaveFileDialog
{
Title = Resources.MProphetFeaturesDlg_OkDialog_Export_mProphet_Features,
OverwritePrompt = true,
DefaultExt = EXT,
Filter = TextUtil.FileDialogFilterAll(Resources.MProphetFeaturesDlg_OkDialog_mProphet_Feature_Files, EXT),
})
{
if (!string.IsNullOrEmpty(DocumentFilePath))
{
dlg.InitialDirectory = Path.GetDirectoryName(DocumentFilePath);
dlg.FileName = Path.GetFileNameWithoutExtension(DocumentFilePath) + EXT;
}
if (dlg.ShowDialog(this) == DialogResult.Cancel)
{
return;
}
var displayCalcs = new List <IPeakFeatureCalculator>();
displayCalcs.AddRange(from object calcName in checkedListVars.CheckedItems select GetCalcFromName(calcName.ToString()));
IPeakScoringModel currentPeakScoringModel = Document.Settings.PeptideSettings.Integration.PeakScoringModel;
var mProphetScoringModel = currentPeakScoringModel as MProphetPeakScoringModel;
// if (mProphetScoringModel == null)
// {
// MessageDlg.Show(this, Resources.MProphetFeaturesDlg_OkDialog_To_export_MProphet_features_first_train_an_MProphet_model_);
// return;
// }
var resultsHandler = new MProphetResultsHandler(Document, mProphetScoringModel);
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.SkylineWindow_OpenSharedFile_Extracting_Files,
})
{
try
{
longWaitDlg.PerformWork(this, 1000, b =>
WriteFeatures(dlg.FileName,
resultsHandler,
displayCalcs,
LocalizationHelper.CurrentCulture,
checkBoxBestOnly.Checked,
!checkBoxTargetsOnly.Checked,
b));
if (longWaitDlg.IsCanceled)
{
return;
}
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.MProphetFeaturesDlg_OkDialog_Failed_attempting_to_save_mProphet_features_to__0__, dlg.FileName),
x.Message);
MessageDlg.ShowWithException(this, message, x);
}
}
}
DialogResult = DialogResult.OK;
}
/// <summary>
/// Changing this starts a peak reintegration when it is set on the document.
/// </summary>
public PeptideIntegration ChangeResultsHandler(MProphetResultsHandler prop)
{
return ChangeProp(ImClone(this), im =>
{
if (prop != null)
im.PeakScoringModel = prop.ScoringModel;
im.ResultsHandler = prop;
});
}
