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 }); }