public static void GlyTest_GetKindString()
{
byte[] kind = new byte[] { 3, 4, 0, 0, 1, 0, 0, 0, 0, 0 };
string kindString = Glycan.GetKindString(kind);
Assert.AreEqual("H3N4F1", kindString);
}
public static List <Product> GetGlycanYIons(double precursorMass, Glycan glycan)
{
List <Product> YIons = new List <Product>();
YIons.Add(new Product(ProductType.M, FragmentationTerminus.Both, precursorMass - (double)glycan.Mass / 1E5, 0, 0, (double)glycan.Mass / 1E5)); //Y0 ion. Glycan totally loss.
foreach (var ion in glycan.Ions)
{
Product product = new Product(ProductType.M, FragmentationTerminus.Both, precursorMass - (double)ion.LossIonMass / 1E5, 0, 0, (double)ion.LossIonMass / 1E5);
YIons.Add(product);
}
return(YIons);
}
public static void GlyTest_GlyGetTheoreticalFragments()
{
Protein pep = new Protein("TKPREEQYNSTYR", "accession");
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 7);
var aPeptideWithSetModifications = pep.Digest(digestionParams, new List <Modification>(), new List <Modification>());
string[] motifs = new string[] { "Nxs", "Nxt" };
var sites = GlycoSpectralMatch.GetPossibleModSites(aPeptideWithSetModifications.Last(), motifs);
Glycan glycan = Glycan.Struct2Glycan("(N(F)(N(H(H(N))(H(N)))))", 0);
//using (StreamWriter output = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "GlycanFragmentions.txt")))
//{
// foreach (var product in fragmentIons)
// {
// foreach (var ion in product.Item2)
// {
// output.WriteLine(ion.Annotation + "\t" + ion.NeutralLoss.ToString() + "\t" + ion.NeutralMass.ToString());
// }
// }
//}
CommonParameters commonParameters = new CommonParameters(deconvolutionMassTolerance: new PpmTolerance(20), trimMsMsPeaks: false);
string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData/Glyco_3383.mgf"); //"25170.mgf"
MyFileManager myFileManager = new MyFileManager(true);
var msDataFile = myFileManager.LoadFile(filePath, commonParameters);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(msDataFile, filePath, commonParameters).ToArray();
var glycanMod = Glycan.NGlycanToModification(glycan);
var glycopep = GlycoPeptides.GenerateGlycopeptide(sites[0], aPeptideWithSetModifications.Last(), glycan);
List <Product> fragmentIons = new List <Product>();
glycopep.Fragment(DissociationType.HCD, FragmentationTerminus.Both, fragmentIons);
var glycanYIons = GlycoPeptides.GetGlycanYIons(listOfSortedms2Scans[0].PrecursorMass, glycan);
var matchedGlycanYIons = MetaMorpheusEngine.MatchFragmentIons(listOfSortedms2Scans[0], glycanYIons, commonParameters);
Assert.AreEqual(matchedGlycanYIons.Count, 14);
//TO DO: The neutroloss is not annotated well.
var matchedFragmentIons = MetaMorpheusEngine.MatchFragmentIons(listOfSortedms2Scans[0], fragmentIons, commonParameters);
var coreIons = GlycoPeptides.ScanGetTrimannosylCore(matchedFragmentIons, glycan);
Assert.AreEqual(coreIons.Count, 6);
var filter = GlycoPeptides.ScanTrimannosylCoreFilter(matchedFragmentIons, glycan);
Assert.AreEqual(filter, true);
var NGlycans = GlycanDatabase.LoadGlycan(GlobalVariables.NGlycanLocations[0], true, false);
var bestGlycans = GlycoPeptides.MatchBestGlycan(listOfSortedms2Scans[0], NGlycans.ToArray(), commonParameters).Where(p => p != null && p.Item2 >= 2).OrderByDescending(p => p.Item2).Take(100).OrderBy(p => p.Item3).ToArray();;
}
public static void OGlycoTest_GetKPerWithDuplicate()
{
List <int> input = new List <int> {
3, 5, 2, 7
};
int[] ids = new int[3] {
2, 2, 3
};
var perWithDuplicate = GlycoPeptides.GetPermutations(input, ids);
var allPermutation = Glycan.GetPermutations(input, ids.Length);
Assert.That(perWithDuplicate.Count() == allPermutation.Count() / 2);
}
//The function here is to calculate permutation localization which could be used to compare with Graph-Localization.
public static List <int[]> GetPermutations(List <int> allModPos, int[] glycanBoxId)
{
var length = glycanBoxId.Length;
var indexes = Enumerable.Range(0, length).ToArray();
int[] orderGlycan = new int[length];
List <int[]> permutateModPositions = new List <int[]>();
var combinations = Glycan.GetKCombs(allModPos, length);
foreach (var com in combinations)
{
var permutation = Glycan.GetPermutations(com, length);
HashSet <string> keys = new HashSet <string>();
foreach (var per in permutation)
{
Array.Sort(indexes);
var orderedPer = per.ToArray();
Array.Sort(orderedPer, indexes);
for (int i = 0; i < length; i++)
{
orderGlycan[i] = glycanBoxId[indexes[i]];
}
var key = string.Join(",", orderGlycan.Select(p => p.ToString()));
if (!keys.Contains(key))
{
keys.Add(key);
permutateModPositions.Add(per.ToArray());
}
}
}
return(permutateModPositions);
}
public static PeptideWithSetModifications GenerateGlycopeptide(int position, PeptideWithSetModifications peptide, Glycan glycan)
{
Modification modification = Glycan.NGlycanToModification(glycan);
Dictionary <int, Modification> testMods = new Dictionary <int, Modification> {
{ position, modification }
};
if (!peptide.AllModsOneIsNterminus.Keys.Contains(position))
{
foreach (var mod in peptide.AllModsOneIsNterminus)
{
testMods.Add(mod.Key, mod.Value);
}
}
var testPeptide = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams, peptide.OneBasedStartResidueInProtein,
peptide.OneBasedEndResidueInProtein, peptide.CleavageSpecificityForFdrCategory, peptide.PeptideDescription, peptide.MissedCleavages, testMods, peptide.NumFixedMods);
return(testPeptide);
}
public static void OGlycoTest_GetK()
{
List <int> input = new List <int> {
1, 2, 3, 4, 5
};
//Combination test
var kcombs = Glycan.GetKCombs(input, 3);
Assert.AreEqual(kcombs.Count(), 10);
var allcombs = Glycan.GetKCombs(input, 5);
Assert.AreEqual(allcombs.Count(), 1);
//Combination test with repetition
var kcombs_rep = Glycan.GetKCombsWithRept(input, 3);
Assert.AreEqual(kcombs_rep.Count(), 35);
var allcombs_rep = Glycan.GetKCombsWithRept(input, 5);
Assert.AreEqual(allcombs_rep.Count(), 126);
//Permutation test
var kperm = Glycan.GetPermutations(input, 3);
Assert.AreEqual(kperm.Count(), 60);
var allperm = Glycan.GetPermutations(input, 5).ToList();
Assert.AreEqual(allperm.Count(), 120);
//Permutation test with repetition
var kperm_rep = Glycan.GetPermutationsWithRept(input, 3);
Assert.AreEqual(kperm_rep.Count(), 125);
}
public override string ToString()
{
var sb = new StringBuilder();
sb.Append(FullFilePath + "\t");
sb.Append(ScanNumber + "\t");
sb.Append(ScanRetentionTime + "\t");
sb.Append(PrecursorScanNumber + "\t");
sb.Append(ScanPrecursorMonoisotopicPeakMz + "\t");
sb.Append(ScanPrecursorCharge + "\t");
sb.Append(ScanPrecursorMass + "\t");
var proteinAccessionString = ProteinAccession ?? PsmTsvWriter.Resolve(BestMatchingPeptides.Select(p => p.Peptide.Protein.Accession), FullSequence).ResolvedString;
sb.Append(proteinAccessionString + "\t");
sb.Append(Organism + "\t");
sb.Append(PsmTsvWriter.Resolve(BestMatchingPeptides.Select(b => b.Peptide.Protein.FullName), FullSequence).ResolvedString + "\t");
int _FirstOneBasedStartResidueInProtein = OneBasedStartResidueInProtein.HasValue ? OneBasedStartResidueInProtein.Value : BestMatchingPeptides.First().Peptide.OneBasedStartResidueInProtein;
int _FirstOneBasedEndResidueInProtein = OneBasedEndResidueInProtein.HasValue ? OneBasedEndResidueInProtein.Value : BestMatchingPeptides.First().Peptide.OneBasedEndResidueInProtein;;
if (OneBasedStartResidueInProtein.HasValue)
{
sb.Append("[" + OneBasedStartResidueInProtein.Value.ToString() + " to " + OneBasedEndResidueInProtein.Value.ToString() + "]" + '\t');
}
else
{
sb.Append("\t");
}
sb.Append(BaseSequence + "\t");
sb.Append(BestMatchingPeptides.First().Peptide.PreviousAminoAcid + "," + BestMatchingPeptides.First().Peptide.NextAminoAcid + "\t");
sb.Append(FullSequence + "\t");
sb.Append(BestMatchingPeptides.First().Peptide.AllModsOneIsNterminus.Count + "\t");
sb.Append((PeptideMonisotopicMass.HasValue ? PeptideMonisotopicMass.Value.ToString() : "---")); sb.Append("\t");
sb.Append(Score + "\t");
sb.Append(Rank + "\t");
if (ChildMatchedFragmentIons == null)
{
foreach (var mid in MatchedIonDataDictionary(this.MatchedFragmentIons))
{
sb.Append(mid.Value);
sb.Append("\t");
}
}
else
{
StringBuilder[] scanFragmentStringbuilder = new StringBuilder[6];
int i = 0;
foreach (var mid in MatchedIonDataDictionary(this.MatchedFragmentIons))
{
scanFragmentStringbuilder[i] = new StringBuilder();
scanFragmentStringbuilder[i].Append("{" + ScanNumber + "@" + mid.Value + "}");
i++;
}
foreach (var childScan in ChildMatchedFragmentIons)
{
int j = 0;
int oneBasedScan = childScan.Key;
foreach (var mid in MatchedIonDataDictionary(childScan.Value))
{
scanFragmentStringbuilder[j].Append("{" + oneBasedScan + "@" + mid.Value + "}");
j++;
}
}
foreach (var s in scanFragmentStringbuilder)
{
sb.Append(s.ToString() + "\t");
}
}
sb.Append((IsDecoy) ? "D" : (IsContaminant) ? "C" : "T"); sb.Append("\t");
sb.Append(FdrInfo != null? FdrInfo.QValue.ToString() : "-1"); sb.Append("\t");
sb.Append("0" + "\t");
sb.Append("0" + "\t");
if (NGlycan != null)
{
sb.Append(PeptideScore + "\t");
sb.Append(GlycanScore + "\t");
sb.Append(DiagnosticIonScore + "\t");
sb.Append((double)NGlycan.First().Mass / 1E5); sb.Append("\t");
sb.Append(Glycan.GetKindString(NGlycan.First().Kind)); sb.Append("\t");
sb.Append(R138vs144.ToString()); sb.Append("\t");
if (NGlycan.First().Struc != null)
{
sb.Append(NGlycan.First().Struc); sb.Append("\t");
}
}
if (Routes != null)
{
sb.Append(LocalizationGraphs.First().TotalScore + "\t");
sb.Append(GlycanScore + "\t");
sb.Append(DiagnosticIonScore + "\t");
var glycanBox = GlycanBox.OGlycanBoxes[Routes.First().ModBoxId];
sb.Append(glycanBox.NumberOfMods + "\t");
sb.Append(LocalizationGraphs.First().ModPos.Length + "\t");
sb.Append(glycanBox.Mass + "\t");
sb.Append(Glycan.GetKindString(glycanBox.Kind)); sb.Append("\t");
var NSiteExist = MotifExist(BaseSequence, new string[] { "Nxt", "Nxs" });
sb.Append(NSiteExist); sb.Append("\t");
sb.Append(R138vs144.ToString()); sb.Append("\t");
//Get glycans
var glycans = new Glycan[glycanBox.NumberOfMods];
for (int i = 0; i < glycanBox.NumberOfMods; i++)
{
glycans[i] = GlycanBox.GlobalOGlycans[glycanBox.ModIds[i]];
}
if (glycans.First().Struc != null)
{
sb.Append(string.Join(",", glycans.Select(p => p.Struc.ToString()).ToArray()));
}
sb.Append("\t");
sb.Append(CorrectLocalizationLevel(SiteSpeciLocalProb, LocalizationGraphs.First(), Routes.First(), LocalizedGlycan, LocalizationLevel)); sb.Append("\t");
//string localizedGlycan = LocalizedGlycan.Where(p=>p.Item3).Count() > 0 ? "[" + string.Join(",", LocalizedGlycan.Where(p => p.Item3).Select(p => p.Item1.ToString() + "-" + p.Item2.ToString())) + "]" : "";
//sb.Append(localizedGlycan); sb.Append("\t");
string local_peptide = "";
string local_protein = "";
LocalizedSiteSpeciLocalInfo(SiteSpeciLocalProb, LocalizedGlycan, OneBasedStartResidueInProtein, ref local_peptide, ref local_protein);
sb.Append(local_peptide); sb.Append("\t");
sb.Append(local_protein); sb.Append("\t");
sb.Append(AllLocalizationInfo(Routes)); sb.Append("\t");
sb.Append(SiteSpeciLocalInfo(SiteSpeciLocalProb));
}
return(sb.ToString());
}
public static List <Product> GetGlycanYIons(PeptideWithSetModifications peptide, Glycan glycan)
{
double possiblePeptideMass = peptide.MonoisotopicMass;
List <Product> YIons = new List <Product>();
YIons.Add(new Product(ProductType.M, FragmentationTerminus.Both, possiblePeptideMass + (double)glycan.Mass / 1E5, 0, 0, (double)glycan.Mass / 1E5));
foreach (var ion in glycan.Ions)
{
Product product = new Product(ProductType.M, FragmentationTerminus.Both, possiblePeptideMass + (double)glycan.Mass / 1E5, 0, 0, (double)ion.LossIonMass / 1E5);
YIons.Add(product);
}
return(YIons);
}
public static bool ScanTrimannosylCoreFilter(List <MatchedFragmentIon> matchedFragmentIons, Glycan glycan)
{
Dictionary <int, double> cores = ScanGetTrimannosylCore(matchedFragmentIons, glycan);
if (cores.Count > 2)
{
return(true);
}
else if (cores.Keys.Contains(83) && cores.Keys.Contains(203))
{
return(true);
}
return(false);
}
public static Dictionary <int, double> ScanGetTrimannosylCore(List <MatchedFragmentIon> matchedFragmentIons, Glycan glycan)
{
Dictionary <int, double> cores = new Dictionary <int, double>();
foreach (var fragment in matchedFragmentIons.Where(p => p.NeutralTheoreticalProduct.ProductType == ProductType.M))
{
if (Glycan.TrimannosylCores.ContainsKey((int)((double)glycan.Mass / 1E5 - fragment.NeutralTheoreticalProduct.NeutralLoss)))
{
var pair = Glycan.TrimannosylCores.Where(p => p.Key == (int)((double)glycan.Mass / 1E5 - fragment.NeutralTheoreticalProduct.NeutralLoss)).FirstOrDefault();
if (!cores.ContainsKey(pair.Key))
{
cores.Add(pair.Key, pair.Value);
}
}
}
return(cores);
}