public override IEnumerable <string> Process(string fileName)
{
var summary = new O18QuantificationSummaryItem
{
RawFilename = _rawFilename,
SoftwareVersion = SoftwareVersion,
PeptideSequence = _peptide,
AdditionalFormula = _additionalFormula,
PeptideAtomComposition = _atomComposition.GetFormula(),
PurityOfO18Water = _purityOfO18Water,
PeptideProfile = _profile,
ObservedEnvelopes = _envelopes,
IsPostDigestionLabelling = _isPostDigestionLabelling,
TheoreticalO16Mz = TheoreticalMz,
Charge = Charge,
ScanStartPercentage = _scanPercentageStart,
ScanEndPercentage = _scanPercentageEnd
};
summary.InitializeScanRange();
summary.CalculateSpeciesAbundanceByLinearRegression();
_fileFormat.WriteToFile(fileName, summary);
return(new[] { fileName });
}
public void SetSummaryFilename(string o18SummaryFilename, IAnnotation parentObj)
{
if (this.o18SummaryFilename.Equals(o18SummaryFilename))
{
return;
}
this.parentObj = parentObj;
if (this.summary != null)
{
ClearAllData();
}
this.fileFormat = new O18QuantificationSummaryItemXmlFormat();
this.summary = this.fileFormat.ReadFromFile(o18SummaryFilename);
this.o18SummaryFilename = o18SummaryFilename;
Text = o18SummaryFilename;
this.calc = this.summary.GetCalculator();
this.options = new O18QuantificationSummaryViewerOptions(o18SummaryFilename);
ShowSummary(false);
this.btnSave.Enabled = false;
}
public void WriteToStream(System.IO.StreamWriter sw, IIdentifiedSpectrum peptide)
{
string detailFile = this.detailDirectory + "\\" + peptide.Annotations[O18QuantificationConstants.O18_RATIO_FILE];
if (File.Exists(detailFile))
{
O18QuantificationSummaryItem item = format.ReadFromFile(detailFile);
var calc = item.GetCalculator();
foreach (var scan in item.ObservedEnvelopes)
{
if (scan.Enabled)
{
scan.CalculateFromProfile(item.PeptideProfile, calc);
sw.Write("\t");
foreach (var func in valueFuncs)
{
sw.Write("\t{0}", func(scan));
}
sw.WriteLine();
}
}
}
}
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 });
}
public void TestWriteToFile()
{
var item = new O18QuantificationSummaryItem();
item.RawFilename = @"D:\sqh\Science\Project/4NLFOR.raw";
item.PeptideSequence = "AFATDITDAEEDK";
item.PeptideAtomComposition = "C60H92N14O26";
item.PurityOfO18Water = 0.95;
item.PeptideProfile = IsotopicBuilderFactory.GetBuilder().GetProfile(new AtomComposition(item.PeptideAtomComposition), 1, 10);
item.ObservedEnvelopes = new List <O18QuanEnvelope> ();
var pkl1 = new O18QuanEnvelope();
pkl1.ScanTimes.Add(new ScanTime(6741, 12.34));
pkl1.Enabled = true;
pkl1.IsIdentified = true;
pkl1.Add(new Peak(713.3209, 424345.9));
pkl1.Add(new Peak(713.8254, 198378.3));
pkl1.Add(new Peak(714.3221, 246866.8));
pkl1.Add(new Peak(714.8242, 221648.0));
pkl1.Add(new Peak(715.3243, 107701.3));
pkl1.Add(new Peak(715.8316, 0.0));
item.ObservedEnvelopes.Add(pkl1);
var pkl2 = new O18QuanEnvelope();
pkl2.ScanTimes.Add(new ScanTime(6746, 13.34));
pkl2.Enabled = false;
pkl2.Add(new Peak(713.3209, 796597.7));
pkl2.Add(new Peak(713.8254, 530778.4));
pkl2.Add(new Peak(714.3221, 456099.6));
pkl2.Add(new Peak(714.8242, 339509.8));
pkl2.Add(new Peak(715.3243, 182812.3));
pkl2.Add(new Peak(715.8316, 0.0));
item.ObservedEnvelopes.Add(pkl2);
item.SpeciesAbundance = new SpeciesAbundanceInfo();
item.SpeciesAbundance.O16 = 79184307.0;
item.SpeciesAbundance.O181 = 39464386.0;
item.SpeciesAbundance.O182 = 440969.4;
item.SampleAbundance = new SampleAbundanceInfo();
item.SampleAbundance.LabellingEfficiency = 0.0219;
item.SampleAbundance.Ratio = 50;
item.SampleAbundance.O16 = 0;
item.SampleAbundance.O18 = 922867772.7;
item.SpeciesAbundance.RegressionCorrelation = 0.9999;
item.SpeciesAbundance.RegressionItems.Clear();
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(713.3209, 36513020.6, 36512100.5));
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(713.8254, 26438219.2, 26447909.0));
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(714.3221, 29639265.4, 29595148.6));
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(714.8242, 16687280.4, 16812006.0));
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(715.3243, 7087781.0, 6823450.3));
item.SpeciesAbundance.RegressionItems.Add(new SpeciesRegressionItem(715.8316, 1799203.9, 2164120.0));
new O18QuantificationSummaryItemXmlFormat().WriteToFile(@TestContext.CurrentContext.TestDirectory + "/../../../data//O18QuantificationInformation.xml.tmp", item);
AssertUtils.AssertFileEqual(@TestContext.CurrentContext.TestDirectory + "/../../../data//O18QuantificationInformation.xml.tmp",
@TestContext.CurrentContext.TestDirectory + "/../../../data//O18QuantificationInformation.xml");
new FileInfo(@TestContext.CurrentContext.TestDirectory + "/../../../data//O18QuantificationInformation.xml.tmp").Delete();
}
