Exemplo n.º 1
0
        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);
        }
Exemplo n.º 2
0
        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;
        }
Exemplo n.º 3
0
        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);            
        }