private void RunTest(IFileFormat<List<FeatureItemGroup>> format) { var inputFile = @"../../../data/CMS-001.count.mapped.xml"; var features = format.ReadFromFile(inputFile); var tempFile = inputFile + ".tmp"; format.WriteToFile(tempFile, features); FileAssert.AreEqual(inputFile, tempFile); File.Delete(tempFile); }
public override IEnumerable <string> Process(string optionFile) { this.options = O18QuantificationFileProcessorOptions.Load(optionFile); var calc = options.GetProteinRatioCalculator(); var detailDirectory = options.GetDetailDirectory(); if (!Directory.Exists(detailDirectory)) { Directory.CreateDirectory(detailDirectory); } var format = new MascotResultTextFormat(); IIdentifiedResult mr = format.ReadFromFile(options.ProteinFile); CheckRawFilename(mr, optionFile); Dictionary <string, List <IIdentifiedSpectrum> > filePepMap = GetFilePeptideMap(mr); Dictionary <IIdentifiedPeptide, O18QuantificationSummaryItem> pepResultMap = new Dictionary <IIdentifiedPeptide, O18QuantificationSummaryItem>(); foreach (string filename in filePepMap.Keys) { Progress.SetMessage("Processing " + filename); string rawFilename = filename; if (new FileInfo(filename).Name.Equals("Cmpd.raw")) { rawFilename = FindRawFileName(options.ProteinFile); } string experimental = FileUtils.ChangeExtension(new FileInfo(rawFilename).Name, ""); using (CacheRawFile rawFile = new CacheRawFile(rawFilename)) { int firstScanNumber = rawFile.GetFirstSpectrumNumber(); int lastScanNumber = rawFile.GetLastSpectrumNumber(); List <IIdentifiedSpectrum> peps = filePepMap[filename]; Dictionary <string, DifferentRetentionTimeEnvelopes> peptideChargeMap = new Dictionary <string, DifferentRetentionTimeEnvelopes>(); Dictionary <O18QuanEnvelopes, List <IIdentifiedSpectrum> > pklMpMap = new Dictionary <O18QuanEnvelopes, List <IIdentifiedSpectrum> >(); Progress.SetRange(0, peps.Count); foreach (IIdentifiedSpectrum mphit in peps) { if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } Progress.Increment(1); IIdentifiedPeptide mp = mphit.Peptide; if (mp.Sequence.EndsWith("-")) { //it cannot be O18 labelled, just skip it continue; } int startScan = mphit.Query.FileScan.FirstScan; double theoreticalMz = GetTheoretialO16Mz(gapO18O16, mphit); int theoreticalMass = (int)(theoreticalMz * mphit.Query.Charge + 0.5); string sequenceCharge = PeptideUtils.GetPureSequence(mphit.Sequence) + "." + mphit.Query.Charge + "." + theoreticalMass; if (!peptideChargeMap.ContainsKey(sequenceCharge)) { peptideChargeMap.Add(sequenceCharge, new DifferentRetentionTimeEnvelopes()); } bool bFound = false; DifferentRetentionTimeEnvelopes pkls = peptideChargeMap[sequenceCharge]; foreach (var pklList in pkls) { if (pklList.Count == 0) { continue; } if (pklList[0].Scan > startScan) { continue; } if (pklList[pklList.Count - 1].Scan < startScan) { continue; } pklMpMap[pklList].Add(mphit); bFound = true; bool findIdentified = false; for (int i = 1; i < pklList.Count; i++) { if (pklList[i].ScanTimes[0].Scan > startScan) { pklList[i - 1].IsIdentified = true; findIdentified = true; break; } } if (!findIdentified) { pklList[pklList.Count - 1].IsIdentified = true; } } if (bFound) { continue; } double mzTolerance = PrecursorUtils.ppm2mz(theoreticalMz, options.PPMTolerance); O18QuanEnvelopes envelopes = new O18QuanEnvelopes(); bool bFirst = true; int count = 0; //backward for (int scan = startScan; scan >= firstScanNumber; scan--) { if (1 == rawFile.GetMsLevel(scan)) { O18QuanEnvelope envelope = GetCorrespondingEnvelope(rawFile, theoreticalMz, mphit.Query.Charge, mzTolerance, scan); //At most one invalid scan inside both pre or post identification scan range. if (!IsValidEnvelope(envelope, mphit.Charge)) { if (count > 0) { envelopes.RemoveAt(0); break; } else { count++; } } else { count = 0; } if (bFirst) { envelope.IsIdentified = true; bFirst = false; } envelopes.Insert(0, envelope); } } if (envelopes.Count == 0) { //If the identified scan has no quantification information ,ignore it. continue; } count = 0; //forward for (int scan = startScan + 1; scan <= lastScanNumber; scan++) { if (1 == rawFile.GetMsLevel(scan)) { var envelope = GetCorrespondingEnvelope(rawFile, theoreticalMz, mphit.Query.Charge, mzTolerance, scan); //At most one invalid scan inside both pre or post identification scan range. if (!IsValidEnvelope(envelope, mphit.Charge)) { if (count > 0) { envelopes.RemoveAt(envelopes.Count - 1); break; } else { count = 1; } } else { count = 0; } envelopes.Add(envelope); } } if (envelopes.Count == 0) { continue; } string scanCurr = envelopes.GetScanRange(); //check scan list again bFound = false; foreach (var pklList in pkls) { if (pklList.Count == 0) { continue; } string scanOld = pklList.GetScanRange(); if (scanOld.Equals(scanCurr)) { pklMpMap[pklList].Add(mphit); bFound = true; break; } } if (bFound) { continue; } pkls.Add(envelopes); pklMpMap.Add(envelopes, new List <IIdentifiedSpectrum>()); pklMpMap[envelopes].Add(mphit); } var detailFilePrefix = options.GetDetailDirectory() + "\\" + new FileInfo(options.ProteinFile).Name; foreach (string sequenceCharge in peptideChargeMap.Keys) { DifferentRetentionTimeEnvelopes pkls = peptideChargeMap[sequenceCharge]; foreach (var envelopes in pkls) { if (0 == envelopes.Count) { continue; } List <IIdentifiedSpectrum> mps = pklMpMap[envelopes]; double mzTolerance = PrecursorUtils.ppm2mz(mps[0].Query.ObservedMz, options.PPMTolerance); O18QuantificationPeptideProcessor processor = new O18QuantificationPeptideProcessor(fileFormat, options.IsPostDigestionLabelling, rawFilename, PeptideUtils.GetPureSequence(mps[0].Sequence), options.PurityOfO18Water, envelopes, mzTolerance, "", options.GetScanPercentageStart() / 100, options.GetScanPercentageEnd() / 100); processor.TheoreticalMz = GetTheoretialO16Mz(gapO18O16, mps[0]); processor.Charge = mps[0].Charge; processor.SoftwareVersion = options.SoftwareVersion; var resultFilename = MyConvert.Format("{0}.{1}.{2}.{3}.{4}.O18", detailFilePrefix, experimental, PeptideUtils.GetPureSequence(mps[0].Sequence), mps[0].Charge, envelopes.GetScanRange()); processor.Process(resultFilename); O18QuantificationSummaryItem item = fileFormat.ReadFromFile(resultFilename); int maxScoreItemIndex = FindMaxScoreItemIndex(mps); var relativeFile = Path.Combine(Path.GetFileName(options.GetDetailDirectory()), Path.GetFileName(resultFilename)); for (int i = 0; i < mps.Count; i++) { if (maxScoreItemIndex == i) { item.AssignToAnnotation(mps[i], relativeFile); } else { item.AssignDuplicationToAnnotation(mps[i], relativeFile); } } } } } } List <IIdentifiedSpectrum> peptides = mr.GetSpectra(); foreach (IIdentifiedSpectrum mphit in peptides) { if (!mphit.Annotations.ContainsKey(O18QuantificationConstants.O18_RATIO_SCANCOUNT)) { mphit.Annotations[O18QuantificationConstants.O18_RATIO_SCANCOUNT] = "-"; } mphit.SetEnabled(calc.HasPeptideRatio(mphit)); } calc.Calculate(mr, m => true); string resultFile = FileUtils.ChangeExtension(optionFile, ".O18summary"); format.InitializeByResult(mr); format.ProteinFormat = format.ProteinFormat.GetLineFormat(O18QuantificationConstants.O18_EXPORT_PROTEIN_HEADER); format.WriteToFile(resultFile, mr); Progress.SetMessage("Finished, result was saved to " + resultFile); return(new[] { resultFile }); }