private void btnLoad_Click(object sender, EventArgs e) { if (rawFile.Exists) { if (reader != null) { reader.Close(); } reader = RawFileFactory.GetRawFileReader(rawFile.FullName); lastScan = reader.GetLastSpectrumNumber(); } if (ms3MatchedFile.Exists) { items = (from line in File.ReadAllLines(ms3MatchedFile.FullName).Skip(1) let parts = line.Split('\t') let pm = int.Parse(parts[6]) where pm > 0 select new MS3MatchItem() { Category = parts[0], Sequence1 = parts[1], Scan1 = int.Parse(parts[2]), Sequence2 = parts[3], Scan2 = int.Parse(parts[4]), MinMz = parts[5].StringAfter(">=").Trim(), PrecursorMatched = pm, MS3Matched = int.Parse(parts[7]) }).ToList(); gvPeptides.DataSource = items; } }
public FileData3 ReadFromFile(string fileName) { FileData3 result = new FileData3(); result.FileName = new FileInfo(fileName).Name; rawFile.Open(fileName); try { for (int scan = rawFile.GetFirstSpectrumNumber(); scan <= rawFile.GetLastSpectrumNumber(); scan++) { PeakList <Peak> pkl = rawFile.GetPeakList(scan, minPeakMz - 1, maxPeakMz + 1); result.AddPeaks(minPeakMz, maxPeakMz, scan, pkl); } } finally { rawFile.Close(); } return(result); }
private void btnLoad_Click(object sender, EventArgs e) { if (rawFile.Exists) { if (reader != null) { reader.Close(); } reader = RawFileFactory.GetRawFileReader(rawFile.FullName); lastScan = reader.GetLastSpectrumNumber(); } if (ms3xcorrFile.Exists) { items = (from line in File.ReadAllLines(ms3xcorrFile.FullName).Skip(1) let parts = line.Split('\t') select new MS3XcorrItem() { Category = parts[0], Sequence1 = parts[1], MS2Scan1 = int.Parse(parts[2]), MS2Precursor1 = double.Parse(parts[3]), MS3Scan1 = int.Parse(parts[4]), MS3Precursor1 = double.Parse(parts[5]), Sequence2 = parts[6], MS2Scan2 = int.Parse(parts[7]), MS2Precursor2 = double.Parse(parts[8]), MS3Scan2 = int.Parse(parts[9]), MS3Precursor2 = double.Parse(parts[10]), Xcorr = double.Parse(parts[11]) }).ToList(); items.RemoveAll(m => m.MS3Precursor1 < 250); items = items.OrderBy(m => m.Category).ThenBy(m => m.Sequence1).ThenBy(m => m.MS3Precursor1).ToList(); gvPeptides.DataSource = items; } }
public override IEnumerable <string> Process(string fileName) { string resultFile = new FileInfo(targetDir + "\\" + FileUtils.ChangeExtension(new FileInfo(fileName).Name, ".txt")).FullName; reader.Open(fileName); try { using (StreamWriter sw = new StreamWriter(resultFile)) { sw.NewLine = "\n"; sw.WriteLine(); sw.WriteLine("FUNCTION 1"); int firstScan = reader.GetFirstSpectrumNumber(); int lastScan = reader.GetLastSpectrumNumber(); for (int i = firstScan; i <= lastScan; i++) { var pkl = reader.GetPeakList(i); sw.WriteLine(""); sw.WriteLine("Scan\t\t{0}", i); sw.WriteLine("Retention Time\t{0:0.000}", reader.ScanToRetentionTime(i)); sw.WriteLine(""); foreach (var peak in pkl) { sw.WriteLine("{0:0.0000}\t{1:0}", peak.Mz, peak.Intensity); } } } } finally { reader.Close(); } return(new string[] { resultFile }); }
private List <SrmScan> GetMRMScans(string directory) { var fileName = GetPeakFileName(directory); if (File.Exists(fileName)) { SetProgressMessage("Reading scan from " + fileName + " ..."); return(new SrmScanFileFormat().ReadFromFile(fileName)); } else { List <PeakList <Peak> > pkls = new List <PeakList <Peak> >(); SetProgressMessage("Reading scan from " + directory + " ..."); IRawFile reader = RawFileFactory.GetRawFileReader(directory); try { var firstCount = reader.GetFirstSpectrumNumber(); var lastCount = reader.GetLastSpectrumNumber(); Progress.SetRange(firstCount, lastCount); Progress.SetPosition(firstCount); for (int i = firstCount; i <= lastCount; i++) { if (reader.GetMsLevel(i) != 2) { continue; } if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } Progress.Increment(1); var pkl = reader.GetPeakList(i); var precursor = reader.GetPrecursorPeak(i); if (precursor != null) { pkl.PrecursorMZ = precursor.Mz; pkl.PrecursorCharge = precursor.Charge; } pkl.ScanTimes.Add(new ScanTime(i, reader.ScanToRetentionTime(i))); pkls.Add(pkl); } List <SrmScan> result = new List <SrmScan>(); pkls.ForEach(m => m.ForEach(n => result.Add(new SrmScan(m.PrecursorMZ, n.Mz, m.ScanTimes[0].RetentionTime, n.Intensity, true)))); new SrmScanFileFormat().WriteToFile(fileName, result); SetProgressMessage("finished."); return(result); } finally { reader.Close(); } } }
public void Quantify(string rawFileName, List <IIdentifiedSpectrum> spectra, string detailDir) { if (!Directory.Exists(detailDir)) { Directory.CreateDirectory(detailDir); } var experimental = RawFileFactory.GetExperimental(rawFileName); Dictionary <string, DifferentRetentionTimeEnvelopes> spectrumKeyMap = new Dictionary <string, DifferentRetentionTimeEnvelopes>(); Dictionary <SilacEnvelopes, List <IIdentifiedSpectrum> > envelopeSpectrumGroup = new Dictionary <SilacEnvelopes, List <IIdentifiedSpectrum> >(); double precursorPPM = GetPrecursorPPM(spectra); try { _rawReader.Open(rawFileName); int firstScanNumber = _rawReader.GetFirstSpectrumNumber(); int lastScanNumber = _rawReader.GetLastSpectrumNumber(); Progress.SetRange(1, spectra.Count); int pepCount = 0; for (int s = 0; s < spectra.Count; s++) { Console.WriteLine(s); IIdentifiedSpectrum spectrum = spectra[s]; SilacQuantificationSummaryItem.ClearAnnotation(spectrum); if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } int startScan = spectrum.Query.FileScan.FirstScan; if (startScan > lastScanNumber) { spectrum.GetOrCreateQuantificationItem().RatioStr = "OUT_OF_RANGE"; continue; } Progress.SetPosition(pepCount++); IIdentifiedPeptide sp = spectrum.Peptide; string seq = GetMatchSequence(spectrum); IPeptideInfo peptideInfo = new IdentifiedPeptideInfo(seq, spectrum.TheoreticalMH, spectrum.Query.Charge); SilacCompoundInfo sci = GetSilacCompoundInfo(peptideInfo); //如果轻重离子理论质荷比一样,忽略 if (!sci.IsSilacData()) { spectrum.GetOrCreateQuantificationItem().RatioStr = "NOT_SILAC"; continue; } //如果轻重离子理论质荷比与观测值不一致,忽略 if (!sci.IsMzEquals(spectrum.ObservedMz, MAX_DELTA_MZ)) { ValidateModifications(seq); spectrum.GetOrCreateQuantificationItem().RatioStr = "WRONG_IDENTIFICATION"; continue; } //如果没有找到相应的FullScan,忽略 int identifiedFullScan = _rawReader.FindPreviousFullScan(startScan, firstScanNumber); if (-1 == identifiedFullScan) { spectrum.GetOrCreateQuantificationItem().RatioStr = "NO_PROFILE"; continue; } DifferentRetentionTimeEnvelopes pkls = FindEnvelopes(spectrumKeyMap, spectrum, sci); SilacEnvelopes envelope = pkls.FindSilacEnvelope(identifiedFullScan); //如果该scan被包含在已经被定量的结果中,忽略 if (envelope != null) { envelope.SetScanIdentified(identifiedFullScan, spectrum.IsExtendedIdentification()); envelopeSpectrumGroup[envelope].Add(spectrum); continue; } //从原始文件中找出该spectrum的定量信息 int maxIndex = Math.Min(option.ProfileLength - 1, pkls.LightProfile.FindMaxIndex()); double mzTolerance = PrecursorUtils.ppm2mz(sci.Light.Mz, option.PPMTolerance); //如果FullScan没有相应的离子,忽略。(鉴定错误或者扩展定量时候,会出现找不到pair的现象) SilacPeakListPair splp = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, identifiedFullScan); if (null == splp) { spectrum.GetOrCreateQuantificationItem().RatioStr = "NO_PROFILE"; continue; } splp.IsIdentified = true; splp.IsExtendedIdentification = spectrum.IsExtendedIdentification(); SilacEnvelopes envelopes = new SilacEnvelopes(); envelopes.Add(splp); //向前查找定量信息 int fullScan = identifiedFullScan; int scanNumber = 0; while ((fullScan = _rawReader.FindPreviousFullScan(fullScan - 1, firstScanNumber)) != -1) { if (_rawReader.IsBadDataScan(fullScan)) { continue; } scanNumber++; var item = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, fullScan, scanNumber <= MinScanNumber); if (null == item) { break; } envelopes.Add(item); } envelopes.Reverse(); //向后查找定量信息 fullScan = identifiedFullScan; scanNumber = 0; while ((fullScan = _rawReader.FindNextFullScan(fullScan + 1, lastScanNumber)) != -1) { if (_rawReader.IsBadDataScan(fullScan)) { continue; } scanNumber++; var item = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, fullScan, scanNumber <= MinScanNumber); if (null == item) { break; } envelopes.Add(item); } //对每个scan计算轻重的离子丰度 envelopes.ForEach(m => m.CalculateIntensity(pkls.LightProfile, pkls.HeavyProfile)); pkls.Add(envelopes); envelopeSpectrumGroup.Add(envelopes, new List <IIdentifiedSpectrum>()); envelopeSpectrumGroup[envelopes].Add(spectrum); } } finally { _rawReader.Close(); } foreach (string key in spectrumKeyMap.Keys) { DifferentRetentionTimeEnvelopes pkls = spectrumKeyMap[key]; foreach (SilacEnvelopes envelopes in pkls) { if (0 == envelopes.Count) { continue; } List <IIdentifiedSpectrum> mps = envelopeSpectrumGroup[envelopes]; double mzTolerance = PrecursorUtils.ppm2mz(mps[0].Query.ObservedMz, option.PPMTolerance); string scanStr = GetScanRange(envelopes); string resultFilename = detailDir + "\\" + mps[0].Query.FileScan.Experimental + "." + PeptideUtils.GetPureSequence(mps[0].Sequence) + "." + mps[0].Query.Charge + scanStr + ".silac"; IPeptideInfo peptideInfo = new IdentifiedPeptideInfo(mps[0].GetMatchSequence(), mps[0].TheoreticalMH, mps[0].Query.Charge); SilacCompoundInfo sci = GetSilacCompoundInfo(peptideInfo); SilacQuantificationSummaryItem item = new SilacQuantificationSummaryItem(sci.Light.IsSample); item.RawFilename = rawFileName; item.SoftwareVersion = this.SoftwareVersion; item.PeptideSequence = mps[0].Sequence; item.Charge = mps[0].Charge; item.LightAtomComposition = sci.Light.Composition.ToString(); item.HeavyAtomComposition = sci.Heavy.Composition.ToString(); item.LightProfile = pkls.LightProfile; item.HeavyProfile = pkls.HeavyProfile; item.ObservedEnvelopes = envelopes; item.ValidateScans(sci, precursorPPM); item.Smoothing(); item.CalculateRatio(); new SilacQuantificationSummaryItemXmlFormat().WriteToFile(resultFilename, item); int maxScoreItemIndex = FindMaxScoreItemIndex(mps); for (int i = 0; i < mps.Count; i++) { if (maxScoreItemIndex == i) { item.AssignToAnnotation(mps[i], resultFilename); } else { item.AssignDuplicationToAnnotation(mps[i], resultFilename); } } } } foreach (IIdentifiedSpectrum mph in spectra) { mph.InitializeRatioEnabled(); } }
public override IEnumerable <string> Process(string targetDir) { foreach (var raw in rawFiles) { List <SimplePeakChro> waitingPeaks = new List <SimplePeakChro>(); foreach (var peak in targetPeaks) { string file = GetTargetFile(targetDir, raw, peak); if (force || !File.Exists(file)) { waitingPeaks.Add(peak); } else { var p = new SimplePeakChroXmlFormat().ReadFromFile(file); peak.MaxRetentionTime = p.MaxRetentionTime; peak.Peaks = p.Peaks; } } if (waitingPeaks.Count == 0) { continue; } rawReader.Open(raw); try { int firstScan = rawReader.GetFirstSpectrumNumber(); int lastScan = rawReader.GetLastSpectrumNumber(); var lastRt = rawReader.ScanToRetentionTime(lastScan); waitingPeaks.ForEach(m => { m.Peaks.Clear(); m.MaxRetentionTime = lastRt; }); Progress.SetMessage("Processing chromotograph extracting..."); Progress.SetRange(firstScan, lastScan); for (int scan = firstScan; scan <= lastScan; scan++) { if (rawReader.GetMsLevel(scan) != 1) { continue; } Progress.SetPosition(scan); if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } PeakList <Peak> pkl = rawReader.GetPeakList(scan); double rt = rawReader.ScanToRetentionTime(scan); foreach (var peak in waitingPeaks) { var env = pkl.FindPeak(peak.Mz, peak.MzTolerance); Peak findPeak = new Peak(peak.Mz, 0.0, 0); if (env.Count > 0) { if (env.Count == 1) { findPeak = env[0]; } else { var charge = env.FindCharge(peak.Charge); if (charge.Count > 0) { if (charge.Count == 1) { findPeak = charge[0]; } else { findPeak = charge.FindMaxIntensityPeak(); } } else { findPeak = env.FindMaxIntensityPeak(); } } } peak.Peaks.Add(new ScanPeak() { Mz = findPeak.Mz, Intensity = findPeak.Intensity, Scan = scan, RetentionTime = rt, Charge = findPeak.Charge, PPMDistance = PrecursorUtils.mz2ppm(peak.Mz, findPeak.Mz - peak.Mz) }); } } waitingPeaks.ForEach(m => m.TrimPeaks(minRetentionTime)); } finally { rawReader.Close(); } Progress.SetMessage("Saving ... "); foreach (var peak in waitingPeaks) { string file = GetTargetFile(targetDir, raw, peak); new SimplePeakChroXmlFormat().WriteToFile(file, peak); } Progress.SetMessage("Finished."); Progress.End(); } return(new string[] { targetDir }); }
public override IEnumerable <string> Process(string rawFilename) { string ms1Filename = GetResultFilename(rawFilename); string ms1IndexFilename = ms1Filename + ".index"; rawFile.Open(rawFilename); try { int firstScan = rawFile.GetFirstSpectrumNumber(); int lastScan = rawFile.GetLastSpectrumNumber(); int firstFullScan = 0; for (firstFullScan = firstScan; firstFullScan < lastScan; firstFullScan++) { if (rawFile.GetMsLevel(firstFullScan) == 1) { break; } } if (firstFullScan >= lastScan) { return(new List <string>()); } Progress.SetRange(firstScan, lastScan); using (var sw = new StreamWriter(ms1Filename)) { //write header sw.Write("H\tCreationDate\t{0:m/dd/yyyy HH:mm:ss}\n", DateTime.Now); sw.Write("H\tExtractor\t{0}\n", GetProgramName()); sw.Write("H\tExtractorVersion\t{0}\n", GetProgramVersion()); sw.Write("H\tComments\t{0} written by Quanhu Sheng, 2008-2009\n", GetProgramName()); sw.Write("H\tExtractorOptions\tMS1\n"); sw.Write("H\tAcquisitionMethod\tData-Dependent\n"); sw.Write("H\tDataType\tCentriod\n"); sw.Write("H\tScanType\tMS1\n"); sw.Write("H\tFirstScan\t{0}\n", firstScan); sw.Write("H\tLastScan\t{0}\n", lastScan); using (var swIndex = new StreamWriter(ms1IndexFilename)) { for (int scan = firstScan; scan <= lastScan; scan++) { if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } Progress.SetPosition(scan); if (rawFile.GetMsLevel(scan) == 1) { sw.Flush(); swIndex.Write("{0}\t{1}\n", scan, sw.BaseStream.Position); sw.Write("S\t{0}\t{0}\n", scan); sw.Write("I\tRetTime\t{0:0.####}\n", rawFile.ScanToRetentionTime(scan)); PeakList <Peak> pkl = rawFile.GetPeakList(scan); foreach (Peak p in pkl) { sw.Write("{0:0.0000} {1:0.0} {2}\n", p.Mz, p.Intensity, p.Charge); } } } } } } finally { rawFile.Close(); } Progress.End(); return(new[] { ms1Filename }); }
public void CloseFile() { reader.Close(); }
public override IEnumerable <string> Process(string targetDir) { foreach (var raw in rawFiles) { List <RetentionTimePeak> waitingPeaks = new List <RetentionTimePeak>(); foreach (var peak in targetPeaks) { string file = GetTargetFile(targetDir, raw, peak); if (force || !File.Exists(file)) { waitingPeaks.Add(peak); } } if (waitingPeaks.Count == 0) { continue; } rawReader.Open(raw); try { int firstScan = rawReader.GetFirstSpectrumNumber(); int lastScan = rawReader.GetLastSpectrumNumber(); waitingPeaks.ForEach(m => m.Chromotographs.Clear()); for (int scan = firstScan; scan <= lastScan; scan++) { if (rawReader.GetMsLevel(scan) != 1) { continue; } if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } PeakList <Peak> pkl = rawReader.GetPeakList(scan); double rt = rawReader.ScanToRetentionTime(scan); var st = new ScanTime(scan, rt); foreach (var peak in waitingPeaks) { var env = pkl.FindEnvelopeDirectly(peak.PeakEnvelope, peak.MzTolerance, () => new Peak()); env.ScanTimes.Add(st); peak.Chromotographs.Add(env); } } waitingPeaks.ForEach(m => m.TrimPeaks()); } finally { rawReader.Close(); } foreach (var peak in waitingPeaks) { string file = GetTargetFile(targetDir, raw, peak); new RetentionTimePeakXmlFormat().WriteToFile(file, peak); } } return(new string[] { targetDir }); }
public override void Update(object sender, UpdateQuantificationItemEventArgs e) { var summary = e.Item as O18QuantificationSummaryItem; if (summary == null) { throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null"); } panel.InitGraphPane(this.title, "m/z", "Intensity", true, 0.0); ZedGraphicExtension.ClearData(zgcGraph, false); try { var envelope = summary.ObservedEnvelopes.Find(m => m.IsSelected); if (envelope == null) { return; } panel.InitGraphPane(this.title + ", Scan=" + envelope.Scan.ToString(), "m/z", "Intensity", true, 0.0); double minMz = envelope[0].Mz - 1.0; double maxMz = envelope[envelope.Count - 1].Mz + 1.0; zgcGraph.GraphPane.XAxis.Scale.Min = minMz; zgcGraph.GraphPane.XAxis.Scale.Max = maxMz; var ppl = new PointPairList(); envelope.ForEach(p => { if (p.Intensity > 0) { ppl.Add(p.Mz, p.Intensity); } }); panel.AddIndividualLine("Isotopic Envelope", ppl, Color.Red); panel.AddTextUp(ppl, 5, (m => m.X.ToString("0.0000"))); var halfMax = (from env in envelope select env.Intensity).Max() / 2; ppl.Clear(); envelope.ForEach(p => { if (p.Intensity == 0) { ppl.Add(p.Mz, halfMax); } }); panel.AddIndividualLine("", ppl, defaultColor: Color.Red, dStyle: DashStyle.Dash); panel.AddTextUp(ppl, 5, (m => m.X.ToString("0.0000"))); if (File.Exists(summary.RawFilename)) { if (rawFile == null) { rawFile = RawFileFactory.GetRawFileReader(summary.RawFilename); } else if (!rawFile.FileName.Equals(summary.RawFilename)) { rawFile.Close(); rawFile = RawFileFactory.GetRawFileReader(summary.RawFilename); } PeakList <Peak> pkl = rawFile.GetPeakList(envelope.ScanTimes[0].Scan); var pplRaw = new PointPairList(); for (int i = 0; i < pkl.Count; i++) { if (pkl[i].Mz < minMz) { continue; } else if (pkl[i].Mz > maxMz) { break; } pplRaw.Add(pkl[i].Mz, -pkl[i].Intensity); } panel.AddIndividualLine("PeakList From RawFile", pplRaw, Color.Blue); panel.AddTextDown(pplRaw, 5, (m => m.X.ToString("0.0000"))); /* * foreach (var p in ppl) * { * if (p.Y == 0) * { * double ppm = double.MaxValue; * double ppmAbs = Math.Abs(ppm); * foreach (var pp in pplRaw) * { * double ppmCur = PrecursorUtils.mz2ppm(pp.X, pp.X - p.X); * double ppmCurAbs = Math.Abs(ppmCur); * if (Math.Abs(ppmCur) < ppmAbs) * { * ppm = ppmCur; * ppmAbs = ppmCurAbs; * } * * if (pp.X > p.X) * { * break; * } * } * * p.Z = ppm; * } * } */ } } finally { ZedGraphicExtension.UpdateGraph(zgcGraph); } }