public void TestGetModifiedSequence()
{
var seq = "NIDVLEGNEQFINAAKIITHPNFNGNTLDND";
var modifications = "X;X;X;X;X;X;X;X;X;X;X;X;X;X;X;Dimethyl (K);X;X;X;X;X;X;X;X;X;X;X;X;X;X;X";
var actual = MaxQuantPeptideTextReader.GetModifiedSequence(seq, modifications);
Assert.AreEqual("NIDVLEGNEQFINAAK(Dimethyl)IITHPNFNGNTLDND", actual);
}
public void TestRead()
{
MaxQuantPeptideTextReader reader = new MaxQuantPeptideTextReader();
var spectra = reader.ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/maxquant_sites.txt");
Assert.AreEqual(162, spectra.Count);
Assert.AreEqual("LQR_SCS_Nu_CA_SAX_Online_071226_06", spectra[0].Query.FileScan.Experimental);
Assert.AreEqual(12044, spectra[0].Query.FileScan.FirstScan);
Assert.AreEqual(0.000888, spectra[0].ExpectValue, 0.000001);
Assert.AreEqual(21.4, spectra[0].Score, 0.0001);
Assert.AreEqual("ASEDES*DLEDEEEKSQEDTEQK", spectra[0].Sequence);
Assert.AreEqual("#S*GEDEQQEQTIAEDLVVTK", spectra[15].Sequence);
Assert.AreEqual("*", reader.ModificationMap["(ph)"]);
Assert.AreEqual("#", reader.ModificationMap["(ac)"]);
Assert.AreEqual("@", reader.ModificationMap["(ox)"]);
}
public override IEnumerable <string> Process()
{
var spectra = new MaxQuantPeptideTextReader().ReadFromFile(options.SiteFile);
spectra.RemoveAll(m => m.DeltaScore < options.MinDeltaScore || m.Probability < options.MinProbability);
spectra = (from g in spectra.GroupBy(m => m.Query.FileScan.ShortFileName)
select g.OrderBy(l => l.Score).Last()).ToList();
if (options.IsSILAC)
{
var spmap = spectra.ToDictionary(m => m.Query.FileScan.ShortFileName);
var existModificationChar = (from sp in spectra
from c in sp.Sequence
where !char.IsLetter(c)
select c).Distinct().Count();
Dictionary <char, char> labelChars = new Dictionary <char, char>();
foreach (var c in options.SILACAminoacids)
{
labelChars[c] = ModificationConsts.MODIFICATION_CHAR[++existModificationChar];
}
using (var sr = new StreamReader(options.MSMSFile))
{
var headers = sr.ReadLine().Split('\t');
var rawIndex = Array.IndexOf(headers, "Raw file");
var scanIndex = Array.IndexOf(headers, "Scan number");
string line;
while ((line = sr.ReadLine()) != null)
{
if (string.IsNullOrWhiteSpace(line))
{
break;
}
var parts = line.Split('\t');
var raw = parts[rawIndex];
var scan = int.Parse(parts[scanIndex]);
var sf = new SequestFilename(raw, scan, scan, 0, "");
var name = sf.ShortFileName;
IIdentifiedSpectrum sp;
if (spmap.TryGetValue(name, out sp))
{
foreach (var pep in sp.Peptides)
{
var seq = pep.Sequence;
StringBuilder sb = new StringBuilder();
for (int i = seq.Length - 1; i >= 0; i--)
{
char heavyChar;
if (labelChars.TryGetValue(seq[i], out heavyChar))
{
sb.Append(heavyChar);
}
sb.Append(seq[i]);
}
pep.Sequence = SequenceUtils.GetReversedSequence(sb.ToString());
}
}
}
}
}
string resultFilename = options.SiteFile + ".peptides";
new MascotPeptideTextFormat("\t\"File, Scan(s)\"\tSequence\tCharge\tScore\tDeltaScore\tExpectValue\tPValue\tModification").WriteToFile(resultFilename, spectra);
return(new[] { resultFilename });
}
