public void TestPsm()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
const char pre = 'R';
const string sequence = "LENWPPASLADDL";
const char post = 'A';
const string annotation = "R.LENWPPASLADDL._";
const int charge = 2;
const int ms2ScanNum = 25534;
var aaSet = new AminoAcidSet();
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 0, 0);
var ms2Scorer = new ProductScorerBasedOnDeconvolutedSpectra(run, 1, 2, 10, 0, 1.1);
ms2Scorer.DeconvoluteAllProductSpectra();
var scorer = ms2Scorer.GetMs2Scorer(ms2ScanNum);
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
graph.SetSink(0);
var score = graph.GetFragmentScore(scorer);
Console.WriteLine("Fast search score: " + score);
var composition = graph.GetSinkSequenceCompositionWithH2O();
var informedScorer = new InformedBottomUpScorer(run, aaSet, 1, 15, new Tolerance(10));
var refinedScore = informedScorer.GetScores(pre, sequence, post, composition, charge, ms2ScanNum);
Console.WriteLine("RefinedScores: {0}", refinedScore);
}
public bool RunSearch(double corrThreshold)
{
var sw = new Stopwatch();
ErrorMessage = string.Empty;
Console.Write(@"Reading raw file...");
sw.Start();
_run = InMemoryLcMsRun.GetLcMsRun(SpecFilePath, 1.4826, 1.4826);
_bottomUpScorer = new InformedBottomUpScorer(_run, AminoAcidSet, MinProductIonCharge, MaxProductIonCharge, ProductIonTolerance);
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Determining precursor masses...");
sw.Start();
var ms1Filter = new Ms1IsotopeAndChargeCorrFilter(_run, PrecursorIonTolerance, MinPrecursorIonCharge, MaxPrecursorIonCharge,
400, 5000, corrThreshold, 0, 0);
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Deconvoluting MS2 spectra...");
sw.Start();
_ms2ScorerFactory = new ProductScorerBasedOnDeconvolutedSpectra(
_run,
MinProductIonCharge, MaxProductIonCharge,
new Tolerance(10),
0
);
_ms2ScorerFactory.DeconvoluteAllProductSpectra();
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
// Target database
var targetDb = new FastaDatabase(DatabaseFilePath);
// string dirName = OutputDir ?? Path.GetDirectoryName(SpecFilePath);
var baseName = Path.GetFileNameWithoutExtension(SpecFilePath);
var targetOutputFilePath = Path.Combine(OutputDir, baseName + TargetFileExtension);
var decoyOutputFilePath = Path.Combine(OutputDir, baseName + DecoyFileExtension);
var tdaOutputFilePath = Path.Combine(OutputDir, baseName + TdaFileExtension);
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Target))
{
sw.Reset();
Console.Write(@"Reading the target database...");
sw.Start();
targetDb.Read();
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.WriteLine(@"Searching the target database");
sw.Start();
var targetMatches = RunSearch(GetAnnotationsAndOffsets(targetDb), ms1Filter, false);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Target database search elapsed time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Rescoring and writing target results...");
sw.Start();
WriteResultsToFile(targetMatches, targetOutputFilePath, targetDb);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed time: {0:f4} sec", sec);
}
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Decoy))
{
// Decoy database
sw.Reset();
Console.Write(@"Reading the decoy database...");
sw.Start();
var decoyDb = targetDb.Decoy(Enzyme);
decoyDb.Read();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.WriteLine(@"Searching the decoy database");
sw.Start();
var decoyMatches = RunSearch(GetAnnotationsAndOffsets(decoyDb), ms1Filter, true);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Decoy database search elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Rescoring and writing decoy results...");
sw.Start();
WriteResultsToFile(decoyMatches, decoyOutputFilePath, decoyDb);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed time: {0:f4} sec", sec);
}
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Both))
{
var fdrCalculator = new FdrCalculator(targetOutputFilePath, decoyOutputFilePath);
if (fdrCalculator.HasError())
{
ErrorMessage = fdrCalculator.ErrorMessage;
Console.WriteLine(@"Error computing FDR: " + fdrCalculator.ErrorMessage);
return false;
}
fdrCalculator.WriteTo(tdaOutputFilePath);
}
Console.WriteLine(@"Done");
return true;
}
public void TestLogLikelihoodScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
//const string seqStr = "IAHESDDEKGHAAK";
//var composition = Composition.Parse("C(62) H(98) N(20) O(24) S(0)");
//const int charge = 4;
//const int ms2ScanNum = 12901;
var aaSet = new AminoAcidSet();
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 0);
var scorer = new InformedBottomUpScorer(run, aaSet, 1, 2, new Tolerance(10));
//var refinedScore = scorer.GetScores(AminoAcid.PeptideNTerm, seqStr, AminoAcid.PeptideCTerm, composition,
// charge, ms2ScanNum);
// Console.WriteLine("RefinedScores: {0}", refinedScore.Score);
}
