public void TestRead()
{
var result = new ProteinProphetXmlReader().ReadFromFile(@"../../../data/proteinprophet.xml");
var filters = result.GetProteinSummaryDataFilterList();
Assert.AreEqual(16, filters.Count);
Assert.AreEqual(1.0, filters.Last().MinProbability);
Assert.AreEqual(0.493, filters.Last().Sensitivity);
Assert.AreEqual(0.000, filters.Last().FalsePositiveErrorRate);
Assert.AreEqual(1982, filters.Last().PredictedNumCorrect);
Assert.AreEqual(0, filters.Last().PredictedNumIncorrect);
var group = result[0];
Assert.AreEqual("sp|A2A791|ZMYM4_MOUSE", group[0].Name);
Assert.AreEqual(6.3, group[0].Coverage);
Assert.AreEqual("Zinc finger MYM-type protein 4 OS=Mus musculus GN=Zmym4 PE=1 SV=1", group[0].Description);
var items = group[0].Peptides;
Assert.AreEqual(8, items.Count);
Assert.AreEqual("GETEQDLEADFPSESFDPLNK", items[0].Sequence);
Assert.AreEqual(0.9990, items[0].Spectrum.Probability);
Assert.AreEqual(2, items[0].Spectrum.Charge);
Assert.AreEqual("GETEQDLEADFPSESFDPLNK*", items[1].Sequence);
Assert.AreEqual(0.9990, items[1].Spectrum.Probability);
Assert.AreEqual(2, items[1].Spectrum.Charge);
}
public void TestRead()
{
var result = new ProteinProphetXmlReader().ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/proteinprophet.xml");
var filters = result.GetProteinSummaryDataFilterList();
Assert.AreEqual(16, filters.Count);
Assert.AreEqual(1.0, filters.Last().MinProbability);
Assert.AreEqual(0.493, filters.Last().Sensitivity);
Assert.AreEqual(0.000, filters.Last().FalsePositiveErrorRate);
Assert.AreEqual(1982, filters.Last().PredictedNumCorrect);
Assert.AreEqual(0, filters.Last().PredictedNumIncorrect);
var group = result[0];
Assert.AreEqual("sp|A2A791|ZMYM4_MOUSE", group[0].Name);
Assert.AreEqual(6.3, group[0].Coverage);
Assert.AreEqual("Zinc finger MYM-type protein 4 OS=Mus musculus GN=Zmym4 PE=1 SV=1", group[0].Description);
var items = group[0].Peptides;
Assert.AreEqual(8, items.Count);
Assert.AreEqual("GETEQDLEADFPSESFDPLNK", items[0].Sequence);
Assert.AreEqual(0.9990, items[0].Spectrum.Probability);
Assert.AreEqual(2, items[0].Spectrum.Charge);
Assert.AreEqual("GETEQDLEADFPSESFDPLNK*", items[1].Sequence);
Assert.AreEqual(0.9990, items[1].Spectrum.Probability);
Assert.AreEqual(2, items[1].Spectrum.Charge);
}
public override IEnumerable <string> Process(string fileName)
{
var result = new ProteinProphetXmlReader().ReadFromFile(fileName);
for (int i = result.Count - 1; i >= 0; i--)
{
if (result[i].Probability < min_probability)
{
result.RemoveAt(i);
}
}
result.Sort();
result.BuildGroupIndex();
var resultFile = FileUtils.ChangeExtension(fileName, "noredundant");
var format = new MascotResultTextFormat(MascotHeader.PROTEINPROPHET_PROTEIN_HEADER, MascotHeader.PROTEINPROPHET_PEPTIDE_HEADER);
format.WriteToFile(resultFile, result);
return(new string[] { resultFile });
}
