public void TestConstruction()
{
var table = new SapPtmTable(@TestContext.CurrentContext.TestDirectory + "/../../../data//SAP_PTM.txt");
Assert.AreEqual(13, table.SapPtmMap.Count);
Assert.AreEqual("Formyl", table.GetModification('T', 'E'));
Assert.AreEqual("Formyl", table.GetModification('S', 'D'));
Assert.AreEqual("Acetyl", table.GetModification('S', 'E'));
Assert.AreEqual("Deamidated", table.GetModification('Q', 'E'));
Assert.AreEqual("Deamidated", table.GetModification('N', 'D'));
Assert.AreEqual("Methyl", table.GetModification('D', 'E'));
Assert.AreEqual("Methyl+Deamidated", table.GetModification('N', 'E'));
Assert.AreEqual("ethylamino", table.GetModification('T', 'K'));
Assert.AreEqual("Methyl", table.GetModification('N', 'Q'));
Assert.AreEqual("Dioxidation", table.GetModification('P', 'E'));
Assert.AreEqual("Methyl", table.GetModification('S', 'T'));
Assert.AreEqual("Oxidation", table.GetModification('F', 'Y'));
Assert.AreEqual("Deoxy", table.GetModification('S', 'A'));
}
private string OutputPairedResult(Aminoacids aas, MascotPeptideTextFormat format, Dictionary <string, Sequence> proMap, IClassification <IIdentifiedPeptide> classification, string mutHeader, MascotPeptideTextFormat mutPepFormat, List <List <IGrouping <string, IIdentifiedPeptide> > > pairedMut, string pairedFile)
{
bool dbAnnotation = File.Exists(_uniprotXmlFile);
List <TempResult> tr = new List <TempResult>();
int resIndex = 1;
foreach (var res in pairedMut)
{
var mutCharges = (from r in res[0]
orderby r.Spectrum.Charge
select r.Spectrum.Charge).Distinct().ToList();
var pepCounts = GetPepCount(classification, res[0]);
int peplabel = 0;
bool bFound = false;
for (int pepIndex = 1; pepIndex < res.Count; pepIndex++)
{
var charges = (from r in res[pepIndex]
orderby r.Spectrum.Charge
select r.Spectrum.Charge).Distinct().ToList();
var commonCharges = mutCharges.Intersect(charges).ToList();
if (commonCharges.Count == 0)
{
continue;
}
if (!bFound)
{
bFound = true;
resIndex++;
}
peplabel++;
var curMutSpectrum = (from r in res[0]
where commonCharges.Contains(r.Spectrum.Charge)
orderby r.Spectrum.Score descending
select r).First();
var mutText = mutPepFormat.PeptideFormat.GetString(curMutSpectrum.Spectrum);
var curOriginalSpectrum = (from r in res[pepIndex]
where r.Spectrum.Charge == curMutSpectrum.Spectrum.Charge
orderby r.Spectrum.Score descending
select r).First();
var oriPureSeq = curOriginalSpectrum.PureSequence;
var mutFixSeq = MutationUtils.ReplaceLToI(curMutSpectrum.Sequence, oriPureSeq);
var mutFixPureSeq = PeptideUtils.GetPureSequence(mutFixSeq);
int mutationSite = -1;
string equalsToModification = string.Empty;
string rnaediting = string.Empty;
string databaseannotation = string.Empty;
bool isType1 = mutFixPureSeq.Length == oriPureSeq.Length;
if (isType1)
{
MutationUtils.IsMutationOneIL(mutFixPureSeq, oriPureSeq, ref mutationSite);
equalsToModification = spTable.GetModification(oriPureSeq[mutationSite], mutFixPureSeq[mutationSite]);
SnpCode.IsRnaEditing(aas[oriPureSeq[mutationSite]], aas[mutFixPureSeq[mutationSite]], out rnaediting);
}
else
{
mutationSite = Math.Min(mutFixPureSeq.Length, oriPureSeq.Length) - 1;
}
var pepMutation = MyConvert.Format("{0}{1}{2}", oriPureSeq[mutationSite], mutationSite + 1, mutFixPureSeq[mutationSite]);
List <Sequence> seqs = new List <Sequence>();
foreach (var p in curOriginalSpectrum.Proteins)
{
var ac = acParser.GetValue(p);
if (!proMap.ContainsKey(ac))
{
throw new Exception("Cannot find protein " + p + " in sequence database!");
}
seqs.Add(proMap[ac]);
}
var proMutations = (from p in curOriginalSpectrum.Proteins
let ac = acParser.GetValue(p)
let seq = proMap[ac]
let pos = seq.SeqString.IndexOf(oriPureSeq)
let pmu = MyConvert.Format("{0}{1}{2}", oriPureSeq[mutationSite], pos + mutationSite + 1, mutFixPureSeq[mutationSite])
select new { ProteinName = p, Mutation = pmu }).ToList();
var proMutation = (from pro in proMutations select pro.Mutation).Merge("/");
if (isType1 && dbAnnotation)
{
//sequence variants
foreach (var pro in proMutations)
{
var entry = GetUniprotEntry(pro.ProteinName);
if (entry == null)
{
continue;
}
foreach (var sv in entry.SequenceVariants)
{
var mut = string.Format("{0}{1}{2}", sv.Original, sv.Position, sv.Variation);
if (pro.Mutation.Equals(mut))
{
databaseannotation = string.Format("{0}=SequenceVariant {1}", pro.ProteinName, sv.Description);
break;
}
}
if (databaseannotation != string.Empty)
{
break;
}
}
//sequence conflicts
if (databaseannotation == string.Empty)
{
foreach (var pro in proMutations)
{
var entry = GetUniprotEntry(pro.ProteinName);
if (entry == null)
{
continue;
}
foreach (var sv in entry.SequenceConflicts)
{
if ((sv.BeginPosition != sv.EndPosition) || sv.Original.Length != 1)
{
continue;
}
var mut = string.Format("{0}{1}{2}", sv.Original, sv.BeginPosition, sv.Variation);
if (pro.Mutation.Equals(mut))
{
databaseannotation = string.Format("{0}=SequenceConflict {1}", pro.ProteinName, sv.Description);
break;
}
}
if (databaseannotation != string.Empty)
{
break;
}
}
}
}
List <string> proRefs = seqs.ConvertAll(m => m.Description).ToList();
int mutationCount;
var dnaMutation = aas[oriPureSeq[mutationSite]].TransferTo(aas[mutFixPureSeq[mutationSite]], out mutationCount);
var oriPepCounts = GetPepCount(classification, res[pepIndex]);
var line = string.Format("${0}-{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}\t{13}\t{14}\t{15}\t{16}\t{17}",
resIndex,
peplabel,
mutText,
mutFixSeq,
mutFixPureSeq,
(from p in pepCounts
select p.ToString()).Merge("\t"),
pepMutation,
mutationCount,
dnaMutation,
curOriginalSpectrum.Spectrum.Query.FileScan.ShortFileName,
oriPureSeq,
curOriginalSpectrum.Proteins.Merge("/"),
proRefs.Merge("/"),
(from p in oriPepCounts
select p.ToString()).Merge("\t"),
proMutation,
equalsToModification,
rnaediting,
databaseannotation
);
tr.Add(new TempResult()
{
Line = line,
PepCount = pepCounts.Sum(),
OriginalSequence = oriPureSeq
});
}
var groups = tr.GroupBy(m => m.OriginalSequence).ToList();
groups.Sort((m1, m2) => - m1.Max(n => n.PepCount).CompareTo(m2.Max(n => n.PepCount)));
List <TempResult> lines = new List <TempResult>();
groups.ForEach(g => lines.AddRange(from l in g
orderby l.PepCount descending
select l));
using (StreamWriter sw = new StreamWriter(pairedFile))
{
string pepCountHeader = "";
string originalPepCountHeader = "";
foreach (var key in ClassificationSet.Keys)
{
pepCountHeader = pepCountHeader + "\t" + key + "_PepCount";
originalPepCountHeader = originalPepCountHeader + "\t" + key + "_OriginalCount";
}
sw.WriteLine("Index\t" + mutHeader + "\tSequence\tPureSequence" + pepCountHeader + "\tPepMutation\tDNAMutationCount\tDNAMutation\tOriginalFileScan\tOriginalSequence\tOriginalProteins\tOriginalReferences"
+ originalPepCountHeader + "\tProMutation\tEqualsToModification\tRNA-Editing\tDatabaseAnnotation");
lines.ForEach(m => sw.WriteLine(m.Line));
}
}
var pairedPeptideFile = pairedFile + ".peptides";
SavePeptidesFile(pairedMut, format, pairedPeptideFile);
return(pairedPeptideFile);
}