public void Run(string path, Counter counter) { ISpectrumReader reader = new ThermoRawSpectrumReader(); reader.Init(path); IGUIFinder finder = new BinarySearchFinder(PPM); IProcess picking = new LocalNeighborPicking(); Dictionary <int, List <GUI> > pointMaps = new Dictionary <int, List <GUI> >(); int start = reader.GetFirstScan(); int end = reader.GetLastScan(); Parallel.For(start, end, (i) => { if (reader.GetMSnOrder(i) < 2) { ISpectrum spectrum = picking.Process(reader.GetSpectrum(i)); lock (resultLock) { pointMaps[i] = finder.FindGlucoseUnits(spectrum); } } counter.Add(end - start); }); List <List <GUI> > points = pointMaps.OrderBy(p => p.Key).Select(p => p.Value).ToList(); IGUISequencer sequencer = new DynamicProgrammingSequencer(); List <GUI> guiPoints = sequencer.Choose(points); Dictionary <int, GUI> guiSelected = new Dictionary <int, GUI>(); foreach (GUI gui in guiPoints) { if (guiSelected.ContainsKey(gui.Unit)) { if (guiSelected[gui.Unit].Peak.GetIntensity() < gui.Peak.GetIntensity()) { guiSelected[gui.Unit] = gui; } } else { guiSelected[gui.Unit] = gui; } } Retention.Clear(); Guis.Clear(); List <GUI> looped = guiSelected.Values.OrderBy(g => g.Scan).ToList(); string output = Path.Combine(Path.GetDirectoryName(path), Path.GetFileNameWithoutExtension(path) + ".csv"); using (FileStream ostrm = new FileStream(output, FileMode.OpenOrCreate, FileAccess.Write)) { using (StreamWriter writer = new StreamWriter(ostrm)) { writer.WriteLine("scan,time,gui,peak,intensity"); foreach (GUI gui in looped) { int scan = gui.Scan; double time = reader.GetRetentionTime(scan); Retention.Add(time); Guis.Add(gui.Unit); writer.WriteLine(scan.ToString() + "," + time.ToString() + "," + gui.Unit.ToString() + "," + gui.Peak.GetMZ().ToString() + "," + gui.Peak.GetIntensity().ToString()); } writer.Flush(); } } Fitter.Fit(Retention, Guis); }
static List <GUI> Init(ref ICurveFitting Fitter, ISpectrumReader reader) { double ppm = 5; object resultLock = new object(); List <double> Retention = new List <double>(); List <double> Guis = new List <double>(); IGUIFinder finder = new BinarySearchFinder(ppm); IProcess picking = new LocalNeighborPicking(); Dictionary <int, List <GUI> > pointMaps = new Dictionary <int, List <GUI> >(); int start = reader.GetFirstScan(); int end = reader.GetLastScan(); Parallel.For(start, end, (i) => { if (reader.GetMSnOrder(i) < 2) { ISpectrum spectrum = picking.Process(reader.GetSpectrum(i)); lock (resultLock) { pointMaps[i] = finder.FindGlucoseUnits(spectrum); } } }); List <List <GUI> > points = pointMaps.OrderBy(p => p.Key).Select(p => p.Value).ToList(); IGUISequencer sequencer = new DynamicProgrammingSequencer(); List <GUI> GuiPoints = sequencer.Choose(points); Fitter = new PolynomialFitting(); Dictionary <int, GUI> guiSelected = new Dictionary <int, GUI>(); foreach (GUI gui in GuiPoints) { if (guiSelected.ContainsKey(gui.Unit)) { if (guiSelected[gui.Unit].Peak.GetIntensity() < gui.Peak.GetIntensity()) { guiSelected[gui.Unit] = gui; } } else { guiSelected[gui.Unit] = gui; } } Retention.Clear(); Guis.Clear(); List <GUI> guiChoice = guiSelected.Values.OrderBy(g => g.Scan).ToList(); foreach (GUI gui in guiChoice) { int scan = gui.Scan; double time = reader.GetRetentionTime(scan); Retention.Add(time); Guis.Add(gui.Unit); } Fitter.Fit(Retention, Guis); return(GuiPoints); }
public void Test1() { string path = @"C:\Users\Rui Zhang\Downloads\ZC_20171218_C16_R1.raw"; string fasta = @"C:\Users\Rui Zhang\Downloads\haptoglobin.fasta"; // peptides IProteinReader proteinReader = new FastaReader(); List <IProtein> proteins = proteinReader.Read(fasta); List <IProtein> decoyProteins = new List <IProtein>(); foreach (IProtein protein in proteins) { IProtein p = new BaseProtein(); p.SetSequence(Reverse(protein.Sequence())); decoyProteins.Add(p); } List <Proteases> proteases = new List <Proteases>() { Proteases.Trypsin, Proteases.GluC }; HashSet <string> peptides = new HashSet <string>(); ProteinDigest proteinDigest = new ProteinDigest(2, 5, proteases[0]); foreach (IProtein protein in decoyProteins) { peptides.UnionWith(proteinDigest.Sequences(protein.Sequence(), ProteinPTM.ContainsNGlycanSite)); } for (int i = 1; i < proteases.Count; i++) { proteinDigest.SetProtease(proteases[i]); List <string> peptidesList = peptides.ToList(); foreach (string seq in peptidesList) { peptides.UnionWith(proteinDigest.Sequences(seq, ProteinPTM.ContainsNGlycanSite)); } } Assert.True(peptides.Contains("KDNLTYVGDGETR")); // build glycan GlycanBuilder glycanBuilder = new GlycanBuilder(); glycanBuilder.Build(); // search List <SearchResult> searchResults = new List <SearchResult>(); ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader(); LocalMaximaPicking picking = new LocalMaximaPicking(); IProcess process = new LocalNeighborPicking(); reader.Init(path); double searchRange = 2; ISpectrum ms1 = null; List <IPeak> majorPeaks = new List <IPeak>(); ISearch <string> oneSearcher = new BucketSearch <string>(ToleranceBy.PPM, 10); PrecursorMatch precursorMatcher = new PrecursorMatch(oneSearcher); precursorMatcher.Init(peptides.ToList(), glycanBuilder.GlycanMaps()); ISearch <string> moreSearcher = new BucketSearch <string>(ToleranceBy.Dalton, 0.01); SequenceSearch sequenceSearcher = new SequenceSearch(moreSearcher); ISearch <int> extraSearcher = new BucketSearch <int>(ToleranceBy.Dalton, 0.01); GlycanSearch glycanSearcher = new GlycanSearch(extraSearcher, glycanBuilder.GlycanMaps()); SearchAnalyzer searchAnalyzer = new SearchAnalyzer(); for (int i = reader.GetFirstScan(); i < reader.GetLastScan(); i++) { if (reader.GetMSnOrder(i) < 2) { ms1 = reader.GetSpectrum(i); majorPeaks = picking.Process(ms1.GetPeaks()); } else { double mz = reader.GetPrecursorMass(i, reader.GetMSnOrder(i)); if (ms1.GetPeaks() .Where(p => p.GetMZ() > mz - searchRange && p.GetMZ() < mz + searchRange) .Count() == 0) { continue; } Patterson charger = new Patterson(); int charge = charger.Charge(ms1.GetPeaks(), mz - searchRange, mz + searchRange); // find evelope cluster EnvelopeProcess envelope = new EnvelopeProcess(); var cluster = envelope.Cluster(majorPeaks, mz, charge); if (cluster.Count == 0) { continue; } // find monopeak Averagine averagine = new Averagine(AveragineType.GlycoPeptide); BrainCSharp braincs = new BrainCSharp(); MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs); MonoisotopicScore result = searcher.Search(mz, charge, cluster); double precursorMZ = result.GetMZ(); // search ISpectrum ms2 = reader.GetSpectrum(i); ms2 = process.Process(ms2); //precursor match var pre_results = precursorMatcher.Match(precursorMZ, charge); if (pre_results.Count == 0) { continue; } // spectrum search var peptide_results = sequenceSearcher.Search(ms2.GetPeaks(), charge, pre_results); if (peptide_results.Count == 0) { continue; } var glycan_results = glycanSearcher.Search(ms2.GetPeaks(), charge, pre_results); if (glycan_results.Count == 0) { continue; } var temp_results = searchAnalyzer.Analyze(i, ms2.GetPeaks(), peptide_results, glycan_results); break; } } }