private void SetupUniProt()
{
var parser = new UniProtPtmListParser();
UniprotModification[] modifications = parser.Parse(File.ReadAllText(UniProtTests.GetPtmListPath())).ToArray();
_uniProtMod312 = modifications.Single(x => x.Id == "PTM-0312");
//_uniProtModLookup = UniProtModificationLookup.CreateFromModifications(new[] { _uniProtMod312 },
// _elementProvider);
_uniProtModLookup = UniProtModificationLookup.CreateFromModifications(modifications,
_elementProvider);
}
public void BasicModificationFileParse()
{
var parser = new UniProtPtmListParser();
var entries = parser.Parse(File.ReadAllText(GetPtmListPath())).ToList();
Assert.AreEqual(676, entries.Count);
// Make sure we parse first and last
var mod0 = entries[0];
var mod675 = entries[675];
Assert.AreEqual("(2-aminosuccinimidyl)acetic acid (Asn-Gly)", mod0.Name);
Assert.AreEqual("S-linked (HexNAc...) cysteine", mod675.Name);
// Confirm missing Resid, Unimod, and PSI-MOD mappings
Assert.IsNull(mod675.Resid);
Assert.IsNull(mod675.Unimod);
Assert.IsNull(mod675.PsiMod);
UniprotModification mod3 = entries[3];
Assert.AreEqual("(3R)-3-hydroxyasparagine", mod3.Identifier);
Assert.AreEqual("PTM-0369", mod3.Accession);
Assert.AreEqual(UniprotFeatureType.ModifiedResidue, mod3.FeatureKey);
Assert.AreEqual("Asparagine", mod3.Target);
Assert.AreEqual("Amino acid side chain", mod3.AminoAcidPosition);
Assert.AreEqual("Anywhere", mod3.PolypeptidePosition);
Assert.AreEqual("O1", mod3.CorrectionFormula);
Assert.AreEqual(15.994915, mod3.MonoisotopicMassDifference);
Assert.AreEqual(16.00, mod3.AverageMassDifference);
Assert.AreEqual("Intracellular localisation or Extracellular and lumenal localisation", mod3.CellularLocation);
Assert.AreEqual(1, mod3.TaxonomicRanges.Count);
Assert.AreEqual("Eukaryota; taxId:40674 (Mammalia)", mod3.TaxonomicRanges.Single());
Assert.AreEqual(1, mod3.Keywords.Count);
Assert.AreEqual("Hydroxylation", mod3.Keywords.Single());
Assert.AreEqual("AA0026", mod3.Resid);
Assert.AreEqual("MOD:00035", mod3.PsiMod);
Assert.AreEqual("35", mod3.Unimod);
}
public void Setup()
{
var unimodOboParser = new UnimodOboParser();
UnimodModification[] modifications = unimodOboParser.Parse(UnimodTest.GetUnimodFilePath()).ToArray();
NistElementParser nistParser = new NistElementParser();
IElement[] elements = nistParser.ParseFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "elements.dat")).ToArray();
_elementProvider = new InMemoryElementProvider(elements);
_residueProvider = new IupacAminoAcidProvider(_elementProvider);
var atomProvider = new UnimodHardCodedAtomProvider(_elementProvider);
_lookup = new CompositeModificationLookup(new IProteoformModificationLookup[]
{
UnimodModificationLookup.CreateFromModifications(modifications, atomProvider),
new FormulaLookup(_elementProvider),
new MassLookup(),
new BrnoModificationLookup(_elementProvider),
new IgnoreKeyModificationLookup(ProFormaKey.Info),
});
ProFormaParser proFormaParser = new ProFormaParser();
ProteoformGroupFactory proteoformGroupFactory = new ProteoformGroupFactory(_elementProvider, _residueProvider);
var mapper = new RelayAccessionMapper(d =>
{
if (d == "B:ac")
{
return(Tuple.Create(ProFormaEvidenceType.PsiMod, "MOD:00394")); // acetylated residue
}
return(Tuple.Create(ProFormaEvidenceType.None, d));
});
var parser = new UniProtPtmListParser();
var entries = parser.Parse(File.ReadAllText(UniProtTests.GetPtmListPath())).ToList();
_chemicalProteoformHashGenerator = new ChemicalProteoformHashGenerator(proFormaParser, proteoformGroupFactory, _lookup, mapper);
}
