public void test1() { string path = @"C:\Users\Rui Zhang\Downloads\ZC_20171218_C16_R1.raw"; ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader(); reader.Init(path); ISpectrum ms2 = reader.GetSpectrum(7638); //IProcess processer = new LocalNeighborPicking(); IProcess processer = new WeightedAveraging(new LocalNeighborPicking()); //RidgeLineFinder coeffMatrix = new RidgeLineFinder(1.0, 2, 1, 2); //IProcess processer = new PeakPickingCWT(coeffMatrix); ms2 = processer.Process(ms2); using (StreamWriter outputFile = new StreamWriter(@"C:\Users\Rui Zhang\Downloads\peak.csv")) { outputFile.WriteLine("mz,intensity"); foreach (IPeak pk in ms2.GetPeaks()) { outputFile.WriteLine(pk.GetMZ().ToString() + "," + pk.GetIntensity().ToString()); } } }
public void ParallelRun(string path, string outputDir, AveragineType type, ChargerType chargerType) { string file = Path.GetFileNameWithoutExtension(path) + ".mgf"; string output = Path.Combine(outputDir, file); ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader(); LocalMaximaPicking picking = new LocalMaximaPicking(ms1PrcisionPPM); reader.Init(path); Dictionary <int, List <int> > scanGroup = new Dictionary <int, List <int> >(); int current = -1; int start = reader.GetFirstScan(); int end = reader.GetLastScan(); for (int i = start; i < end; i++) { if (reader.GetMSnOrder(i) == 1) { current = i; scanGroup[i] = new List <int>(); } else if (reader.GetMSnOrder(i) == 2) { scanGroup[current].Add(i); } } List <MS2Info> ms2Infos = new List <MS2Info>(); Parallel.ForEach(scanGroup, (scanPair) => { if (scanPair.Value.Count > 0) { ISpectrum ms1 = reader.GetSpectrum(scanPair.Key); foreach (int i in scanPair.Value) { double mz = reader.GetPrecursorMass(i, reader.GetMSnOrder(i)); List <IPeak> ms1Peaks = FilterPeaks(ms1.GetPeaks(), mz, searchRange); if (ms1Peaks.Count() == 0) { continue; } // insert pseudo peaks for large gap List <IPeak> peaks = new List <IPeak>(); double precision = 0.02; double last = ms1Peaks.First().GetMZ(); foreach (IPeak peak in ms1Peaks) { if (peak.GetMZ() - last > precision) { peaks.Add(new GeneralPeak(last + precision / 2, 0)); peaks.Add(new GeneralPeak(peak.GetMZ() - precision / 2, 0)); } peaks.Add(peak); last = peak.GetMZ(); } List <IPeak> majorPeaks = picking.Process(peaks); ICharger charger = new Patterson(); if (chargerType == ChargerType.Fourier) { charger = new Fourier(); } else if (chargerType == ChargerType.Combined) { charger = new PattersonFourierCombine(); } int charge = charger.Charge(peaks, 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(type); BrainCSharp braincs = new BrainCSharp(); MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs); MonoisotopicScore result = searcher.Search(mz, charge, cluster); double precursorMZ = result.GetMZ(); // write mgf ISpectrum ms2 = reader.GetSpectrum(i); IProcess processer = new WeightedAveraging(new LocalNeighborPicking()); ms2 = processer.Process(ms2); MS2Info ms2Info = new MS2Info { PrecursorMZ = result.GetMZ(), PrecursorCharge = charge, Scan = ms2.GetScanNum(), Retention = ms2.GetRetention(), Peaks = ms2.GetPeaks() }; lock (resultLock) { ms2Infos.Add(ms2Info); } } } readingProgress.Add(scanGroup.Count); }); ms2Infos = ms2Infos.OrderBy(m => m.Scan).ToList(); using (FileStream ostrm = new FileStream(output, FileMode.OpenOrCreate, FileAccess.Write)) { using (StreamWriter writer = new StreamWriter(ostrm)) { foreach (MS2Info ms2 in ms2Infos) { WriteMGF(writer, path + ",SCANS=" + ms2.Scan.ToString() + ",PRECURSOR=" + ms2.PrecursorMZ, ms2.PrecursorMZ, ms2.PrecursorCharge, ms2.Scan, ms2.Retention * 60, reader.GetActivation(ms2.Scan), ms2.Peaks); writer.Flush(); } } } // update progress progress.Add(); }
public Run Read(string path, AveragineType type, ChargerType charger, string defaultDataProcessingRef, ProgressUpdate updater) { Run data = new Run(); // init reader ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader(); LocalMaximaPicking picking = new LocalMaximaPicking(ms1PrcisionPPM); IProcess process = new WeightedAveraging(new LocalNeighborPicking()); reader.Init(path); data.spectrumList = new SpectrumList(); Dictionary <int, Spectrum> spectrumMap = new Dictionary <int, Spectrum>(); int start = reader.GetFirstScan(); int end = reader.GetLastScan(); Dictionary <int, List <int> > scanGroup = new Dictionary <int, List <int> >(); int current = -1; for (int i = start; i < end; i++) { if (reader.GetMSnOrder(i) == 1) { current = i; scanGroup[i] = new List <int>(); } else if (reader.GetMSnOrder(i) == 2) { scanGroup[current].Add(i); } } Parallel.ForEach(scanGroup, (scanPair) => { if (scanPair.Value.Count > 0) { int parentScan = scanPair.Key; ISpectrum ms1 = null; List <IPeak> majorPeaks = new List <IPeak>(); Spectrum ms1Spectrum = ThermoRawRunFactoryHelper.GetMS1Spectrum(ref reader, parentScan, ref ms1); if (ms1Spectrum != null) { lock (resultLock) { spectrumMap[parentScan] = ms1Spectrum; } } foreach (int scan in scanPair.Value) { Spectrum ms2Spectrum = ThermoRawRunFactoryHelper.GetMS2Spectrum(ref reader, scan, type, charger, picking, process, ms1); if (ms2Spectrum != null) { lock (resultLock) { spectrumMap[scan] = ms2Spectrum; } } } } updater(scanGroup.Count); }); List <Spectrum> spectrumList = spectrumMap.OrderBy(s => s.Key).Select(s => s.Value).ToList(); data.spectrumList.spectrum = new Spectrum[spectrumList.Count]; spectrumList = spectrumList.OrderBy(x => int.Parse(x.id.Substring(5))).ToList(); for (int i = 0; i < spectrumList.Count; i++) { int scan = int.Parse(spectrumList[i].id.Substring(5)); data.spectrumList.spectrum[i] = spectrumList[i]; data.spectrumList.spectrum[i].index = (scan - 1).ToString(); data.spectrumList.spectrum[i].defaultArrayLength = spectrumList[i].defaultArrayLength; } data.spectrumList.count = spectrumList.Count.ToString(); data.spectrumList.defaultDataProcessingRef = defaultDataProcessingRef; return(data); }
void GenerateTasks() { if (Path.GetExtension(msPath) == ".mgf") { MGFSpectrumReader reader = new MGFSpectrumReader(); reader.Init(msPath); Dictionary <int, MS2Spectrum> spectraData = reader.GetSpectrum(); foreach (int scan in spectraData.Keys) { MS2Spectrum spectrum = spectraData[scan]; SearchTask searchTask = new SearchTask(spectrum, spectrum.PrecursorMZ(), spectrum.PrecursorCharge()); tasks.Enqueue(searchTask); readingCounter.Add(spectraData.Count); } } else { ISpectrumReader reader = new ThermoRawSpectrumReader(); LocalMaximaPicking picking = new LocalMaximaPicking(); IProcess process = new WeightedAveraging(new LocalNeighborPicking()); reader.Init(msPath); int start = reader.GetFirstScan(); int end = reader.GetLastScan(); Dictionary <int, List <int> > scanGroup = new Dictionary <int, List <int> >(); int current = -1; for (int i = start; i < end; i++) { if (reader.GetMSnOrder(i) == 1) { current = i; scanGroup[i] = new List <int>(); } else if (reader.GetMSnOrder(i) == 2) { scanGroup[current].Add(i); } } Parallel.ForEach(scanGroup, new ParallelOptions { MaxDegreeOfParallelism = SearchingParameters.Access.ThreadNums }, (scanPair) => { if (scanPair.Value.Count > 0) { ISpectrum ms1 = reader.GetSpectrum(scanPair.Key); foreach (int i in scanPair.Value) { double mz = reader.GetPrecursorMass(i, reader.GetMSnOrder(i)); List <IPeak> ms1Peaks = FilterPeaks(ms1.GetPeaks(), mz, searchRange); if (ms1Peaks.Count() == 0) { continue; } ICharger charger = new Patterson(); int charge = charger.Charge(ms1Peaks, mz - searchRange, mz + searchRange); // insert pseudo peaks for large gap List <IPeak> peaks = new List <IPeak>(); double precision = 0.02; double last = ms1Peaks.First().GetMZ(); foreach (IPeak peak in ms1Peaks) { if (peak.GetMZ() - last > precision) { peaks.Add(new GeneralPeak(last + precision / 2, 0)); peaks.Add(new GeneralPeak(peak.GetMZ() - precision / 2, 0)); } peaks.Add(peak); last = peak.GetMZ(); } List <IPeak> majorPeaks = picking.Process(peaks); // 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); SearchTask searchTask = new SearchTask(ms2, precursorMZ, charge); tasks.Enqueue(searchTask); } } readingCounter.Add(scanGroup.Count); }); } }