public void TestCalculateQValue()
{
var peptides = new MascotPeptideTextFormat().ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/QTOF_Ecoli.LowRes.t.xml.peptides");
peptides.RemoveAll(m => m.ExpectValue > 0.05 || m.Peptide.PureSequence.Length < 6);
peptides.ForEach(m => m.FromDecoy = m.Proteins.Any(l => l.Contains("REVERSE_")));
IdentifiedSpectrumUtils.CalculateQValue(peptides, new ExpectValueFunction(), new TargetFalseDiscoveryRateCalculator());
Assert.AreEqual(0.0267, peptides[0].QValue, 0.0001);
}
public override IEnumerable <string> Process()
{
var evidences = new MascotPeptideTextFormat().ReadFromFile(options.InputFile);
//Remove the PSM without mapped to proteins, usually it is from decoy database.
evidences.RemoveAll(m => string.IsNullOrWhiteSpace(m.Annotations["Proteins"] as string));
if (options.RemoveContanimant)
{
evidences.RemoveAll(m => (m.Annotations["Proteins"] as string).Contains("CON_"));
}
foreach (var spectrum in evidences)
{
ParseMaxQuantEvidencePeptide(spectrum);
}
new MascotPeptideTextFormat("\tFileScan\tSequence\tObs\tMH+\tDiff(MH+)\tDiffPPM\tCharge\tRank\tScore\tExpectValue\tReference\tMissCleavage\tModification\tMatchCount\tNumProteaseTermini").WriteToFile(options.OutputFile, evidences);
return(new string[] { options.OutputFile });
}
public override IEnumerable <string> Process(string fileName)
{
var peps = new MascotPeptideTextFormat().ReadFromFile(fileName);
peps.RemoveAll(m => !(m.Annotations["Number of Phospho (STY)"] as string).Equals("1"));
var silac = new MascotResultTextFormat().ReadFromFile(silacFile);
var silacPeps = silac.GetSpectra();
silacPeps.RemoveAll(m => m.GetQuantificationItem() == null || !m.GetQuantificationItem().HasRatio);
Regex reg = new Regex(@"Cx_(.+)");
var silacMap = silacPeps.ToGroupDictionary(m => m.Peptide.PureSequence + GetModificationCount(m.Peptide, "STY"));
int found = 0;
int missed = 0;
var matchFile = fileName + ".match";
using (StreamWriter sw = new StreamWriter(matchFile))
{
sw.Write("Sequence");
var mq = peps[0].GetMaxQuantItemList();
foreach (var mqi in mq)
{
sw.Write("\tm_" + mqi.Name);
sw.Write("\ts_" + mqi.Name);
}
sw.WriteLine();
foreach (var p in peps)
{
var pureSeqKey = p.Peptide.PureSequence + p.Annotations["Number of Phospho (STY)"].ToString();
if (silacMap.ContainsKey(pureSeqKey))
{
found++;
Console.WriteLine("Find - " + pureSeqKey);
var findPep = silacMap[pureSeqKey];
var findPepMap = findPep.ToGroupDictionary(m => reg.Match(m.Query.FileScan.Experimental).Groups[1].Value);
mq = p.GetMaxQuantItemList();
sw.Write(p.Peptide.PureSequence);
foreach (var mqi in mq)
{
if (string.IsNullOrEmpty(mqi.Ratio))
{
sw.Write("\t");
}
else
{
sw.Write("\t{0:0.00}", Math.Log(MyConvert.ToDouble(mqi.Ratio)));
}
if (!findPepMap.ContainsKey(mqi.Name))
{
sw.Write("\t");
}
else
{
var spectra = findPepMap[mqi.Name];
spectra.Sort((m1, m2) => m2.GetQuantificationItem().Correlation.CompareTo(m1.GetQuantificationItem().Correlation));
sw.Write("\t{0:0.00}", -Math.Log(spectra[0].GetQuantificationItem().Ratio));
}
}
sw.WriteLine();
}
else
{
missed++;
Console.WriteLine("Missed - " + pureSeqKey);
}
}
}
Console.WriteLine("Found = {0}; Missed = {1}", found, missed);
// Regex reg =new Regex(@"Cx_(.+)");
return(new string[] { });
}
public void TestCalculateQValue()
{
var peptides = new MascotPeptideTextFormat().ReadFromFile("../../../data/QTOF_Ecoli.LowRes.t.xml.peptides");
peptides.RemoveAll(m => m.ExpectValue > 0.05 || m.Peptide.PureSequence.Length < 6);
peptides.ForEach(m => m.FromDecoy = m.Proteins.Any(l => l.Contains("REVERSE_")));
IdentifiedSpectrumUtils.CalculateQValue(peptides, new ExpectValueFunction(), new TargetFalseDiscoveryRateCalculator());
Assert.AreEqual(0.0267, peptides[0].QValue, 0.0001);
}
