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 });
}
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 option = new SilacQuantificationSummaryOption()
{
MinimumPeptideRSquare = this.MinPeptideRegressionCorrelation
};
spectra.ForEach(m =>
{
m.SetEnabled(option.IsPeptideRatioValid(m) && !option.IsPeptideOutlier(m));
var dupSpectra = m.GetDuplicatedSpectra();
dupSpectra.ForEach(n => n.SetEnabled(option.IsPeptideRatioValid(n) && !option.IsPeptideOutlier(n)));
});
var calc = new ExtendSilacProteinRatioCalculator();
Dictionary <string, string> datasetMap = new Dictionary <string, string>();
foreach (var ds in datasets)
{
var lst = ds.Value;
lst.ForEach(m => datasetMap[m] = ds.Key);
}
foreach (IIdentifiedProteinGroup mpg in sr)
{
var realSpectra = new List <IIdentifiedSpectrum>(mpg.GetPeptides());
foreach (var spectrum in realSpectra)
{
var dupSpectra = spectrum.GetDuplicatedSpectra();
mpg.AddIdentifiedSpectra(dupSpectra);
}
ProteinQuantificationResult pr = new ProteinQuantificationResult();
foreach (var ds in datasets)
{
var lst = ds.Value;
pr.Items[ds.Key] = calc.Calculate(mpg, m => lst.Contains(m.Query.FileScan.Experimental));
}
bool valid = pr.Items.Values.FirstOrDefault(m => m.Enabled) != null;
foreach (IIdentifiedProtein protein in mpg)
{
protein.SetEnabled(valid);
protein.Annotations[SilacQuantificationConstants.SILAC_KEY] = pr;
}
}
var finalSpectra = sr.GetSpectra();
finalSpectra.ForEach(m => m.SetDataset(datasetMap[m.Query.FileScan.Experimental]));
resultFormat.InitializeByResult(sr);
resultFormat.WriteToFile(resultFile, sr);
return(new[] { resultFile });
}
