public override IEnumerable <string> Process(string filename)
{
string resultFile = filename + ".SILACsummary";
FileInfo resultFI = new FileInfo(resultFile);
DirectoryInfo detailDir = new DirectoryInfo(resultFI.DirectoryName + "\\" + resultFI.Name + ".details");
if (!detailDir.Exists)
{
detailDir.Create();
}
builder.Progress = this.Progress;
var spectra = resultFormat.ReadFromFile(filename);
builder.Quantify(spectra, detailDir.FullName);
SilacQuantificationSummaryOption summaryOption = new SilacQuantificationSummaryOption()
{
MinimumPeptideRSquare = this.MinPeptideRegressionCorrelation
};
spectra.ForEach(m =>
{
summaryOption.SetPeptideRatioValid(m, summaryOption.HasPeptideRatio(m) && !summaryOption.IsPeptideOutlier(m));
});
resultFormat.Initialize(spectra);
resultFormat.WriteToFile(resultFile, spectra);
return(new[] { resultFile });
}
public override IEnumerable <string> Process(string filename)
{
string resultFile = filename + ".SILACsummary";
FileInfo resultFI = new FileInfo(resultFile);
DirectoryInfo detailDir = new DirectoryInfo(resultFI.DirectoryName + "\\" + resultFI.Name + ".details");
if (!detailDir.Exists)
{
detailDir.Create();
}
builder.Progress = this.Progress;
IIdentifiedResult sr = resultFormat.ReadFromFile(filename);
var spectra = sr.GetSpectra();
builder.Quantify(spectra, detailDir.FullName);
SilacQuantificationSummaryOption summaryOption = new SilacQuantificationSummaryOption()
{
MinimumPeptideRSquare = this.MinPeptideRegressionCorrelation
};
spectra.ForEach(m =>
{
summaryOption.SetPeptideRatioValid(m, summaryOption.HasPeptideRatio(m) && !summaryOption.IsPeptideOutlier(m));
});
foreach (IIdentifiedProteinGroup mpg in sr)
{
calc.Calculate(mpg, m => true);
}
if (option.KeepPeptideWithMostScan)
{
foreach (var pgroup in sr)
{
var gspec = pgroup.GetPeptides().GroupBy(l => l.Query.FileScan.Experimental + "_" + l.Sequence + "_" + l.Query.Charge).ToList();
HashSet <IIdentifiedSpectrum> kept = new HashSet <IIdentifiedSpectrum>();
foreach (var spec in gspec)
{
if (spec.Count() == 1)
{
kept.Add(spec.First());
}
else
{
var maxScan = spec.Max(l => (l.Annotations["S_RATIO"] as QuantificationItem).ScanCount);
var maxSpecs = spec.Where(l => (l.Annotations["S_RATIO"] as QuantificationItem).ScanCount == maxScan).ToList();
foreach (var maxSpec in maxSpecs)
{
kept.Add(maxSpec);
}
}
}
foreach (var p in pgroup)
{
p.Peptides.RemoveAll(l => !kept.Contains(l.Spectrum));
}
}
}
resultFormat.InitializeByResult(sr);
resultFormat.WriteToFile(resultFile, sr);
return(new[] { resultFile });
}