public override IEnumerable <string> Process(string rawFileName)
{
IsobaricResult result = GetTraqResult(rawFileName);
string resultFileName = GetITraqFileName(rawFileName);
ITraqResultFileFormatFactory.GetXmlFormat().WriteToFile(resultFileName, result);
return(new[] { resultFileName });
}
protected List <IIdentifiedSpectrum> GetSpectra(string fileName)
{
Progress.SetMessage("Reading peptides ...");
List <IIdentifiedSpectrum> spectra = format.ReadFromFile(fileName);
Progress.SetMessage("Reading itraq ...");
IsobaricResult itraq = ITraqResultFileFormatFactory.GetXmlFormat().ReadFromFile(rawFileName);
Progress.SetMessage("Matching peptide and itraq ...");
ITraqItemUtils.MatchPeptideWithItraq(itraq, spectra);
return(spectra);
}
/// <summary>
/// 从itraqFile中读取spectra对应的iTRAQ信息。
/// </summary>
/// <param name="spectra"></param>
/// <param name="itraqFile"></param>
/// <param name="progress"></param>
public static void LoadITraq(List <IIdentifiedSpectrum> spectra, string itraqFile, bool readPeaks = false, IProgressCallback progress = null)
{
if (progress == null)
{
progress = new EmptyProgressCallback();
}
var fileNames = new HashSet <string>(from s in spectra
let fs = s.Query.FileScan
select fs.Experimental + "," + fs.FirstScan.ToString());
var reader = ITraqResultFileFormatFactory.GetXmlReader();
reader.ReadPeaks = readPeaks;
reader.Progress = progress;
reader.Open(itraqFile);
progress.SetMessage("Reading iTRAQ from {0} ...", itraqFile);
progress.SetRange(1, spectra.Count);
foreach (var spectrum in spectra)
{
if (progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
progress.Increment(1);
var fs = spectrum.Query.FileScan;
if (reader.Has(fs.Experimental, fs.FirstScan))
{
spectrum.SetIsobaricItem(reader.Read(fs.Experimental, fs.FirstScan));
}
else
{
spectrum.SetIsobaricItem(null);
}
}
}
public IsobaricResult GetTraqResult(string rawFileName)
{
Progress.SetMessage("Processing " + rawFileName + " ...");
string experimental = FileUtils.ChangeExtension(new FileInfo(rawFileName).Name, "");
string originalFileName = GetOriginalITraqFileName(rawFileName);
string paramFileName = originalFileName + ".param";
IsobaricResult result = null;
ITraqFileBuilder builder = new ITraqFileBuilder(itraqReader.PlexType.GetDefinition());
if (!CheckOriginalFile(originalFileName) || !File.Exists(paramFileName))
{
itraqReader.Progress = this.Progress;
Progress.SetMessage("Reading isobaric tag channels from " + new FileInfo(rawFileName).Name + "...");
List <IsobaricItem> pkls = itraqReader.ReadFromFile(rawFileName);
Progress.SetMessage("Reading isobaric tag channels finished.");
if (pkls.Count == 0)
{
throw new Exception(MyConvert.Format("No isobaric tag information readed from file {0}, contact with author.", rawFileName));
}
var accs = builder.GetDistances(from pkl in pkls select pkl.RawPeaks);
if (accs.Count == 0)
{
throw new Exception(MyConvert.Format("No isobaric tag information readed from file {0}, contact with author.", rawFileName));
}
result = builder.GetITraqResult(pkls, accs, SigmaFoldTolerance, 1);
result.Mode = itraqReader.ToString();
result.ForEach(m => m.Experimental = experimental);
ITraqResultFileFormatFactory.GetXmlFormat().WriteToFile(originalFileName, result);
using (StreamWriter sw = new StreamWriter(paramFileName))
{
sw.WriteLine("Ion\tDetectedIon\tDeltaMass\tDeltaPPM\tDetectedSigma");
var ions = builder.Definition.Items;
for (int i = 0; i < ions.Length; i++)
{
sw.WriteLine("{0:0.00000}\t{1:0.00000}\t{2:0.00000}\t{3:0.00}\t{4:0.00000}", ions[i].Mass, ions[i].Mass + accs[i].Mean, accs[i].Mean, PrecursorUtils.mz2ppm(ions[i].Mass, accs[i].Mean), accs[i].StdDev);
}
}
}
else
{
Progress.SetMessage("Read xml information from " + originalFileName + " ...");
var format = ITraqResultFileFormatFactory.GetXmlFormat();
format.Progress = this.Progress;
result = format.ReadFromFile(originalFileName);
}
result.RemoveAll(m => m.PeakCount() < minPeakCount);
result.ForEach(m => calc.Correct(m));
result.RemoveAll(m => m.PeakCount() < minPeakCount);
result.ForEach(m => m.PrecursorPercentage = m.PeakInIsolationWindow.GetPrecursorPercentage(this.precursorPPM));
if (NormalizationBuilder != null)
{
NormalizationBuilder.Normalize(result);
}
return(result);
}