public void TestKeepMaxScorePeptideOnly()
{
List <IIdentifiedSpectrum> spectra = new List <IIdentifiedSpectrum>();
spectra.Add(new IdentifiedSpectrum()
{
Score = 3.0
});
spectra.Add(new IdentifiedSpectrum()
{
Score = 2.0
});
spectra.ForEach(m =>
{
m.AddPeptide(new IdentifiedPeptide(m)
{
Sequence = "A1"
});
m.Charge = 2;
});
IdentifiedSpectrum other = new IdentifiedSpectrum()
{
Score = 2.0, Charge = 2
};
other.AddPeptide(new IdentifiedPeptide(other)
{
Sequence = "B1"
});
spectra.Add(other);
List <IIdentifiedSpectrum> filtered = UniquePeptideDistiller.KeepMaxScorePeptideOnly(spectra);
Assert.AreEqual(2, filtered.Count);
Assert.AreEqual(3.0, filtered[0].Score);
Assert.AreEqual("A1", filtered[0].Sequence);
Assert.AreEqual(2.0, filtered[1].Score);
Assert.AreEqual("B1", filtered[1].Sequence);
}
public override IEnumerable <string> Process(string fileName)
{
var format = new SequestResultTextFormat();
format.Progress = this.Progress;
Progress.SetMessage("Reading identified result from " + fileName + " ...");
IIdentifiedResult ir = format.ReadFromFile(fileName);
Progress.SetMessage("Removing duplicated peptide ...");
Progress.SetRange(0, ir.Count);
for (int i = 0; i < ir.Count; i++)
{
Progress.SetPosition(i);
IIdentifiedProteinGroup group = ir[i];
List <IIdentifiedSpectrum> peps = UniquePeptideDistiller.KeepMaxScorePeptideOnly(group.GetPeptides());
foreach (var protein in group)
{
protein.Peptides.RemoveAll(m => !peps.Contains(m.Spectrum));
}
}
string resultFileName = fileName + ".unique";
Progress.SetMessage("Saving proteins to " + resultFileName + " ...");
format.WriteToFile(resultFileName, ir);
List <IIdentifiedSpectrum> spectra = ir.GetSpectra();
var peptideFormat = new SequestPeptideTextFormat(format.PeptideFormat.GetHeader());
string peptideFileName = fileName + ".unique.peptides";
Progress.SetMessage("Saving peptides to " + peptideFileName + " ...");
peptideFormat.WriteToFile(peptideFileName, spectra);
Progress.SetMessage("Finished.");
return(new[] { resultFileName, peptideFileName });
}
