private static void LoadModifications()
{
_AllModsKnown = new List <Modification>();
_AllModTypesKnown = new HashSet <string>();
ErrorsReadingMods = new List <string>();
AllModsKnownDictionary = new Dictionary <string, Modification>();
UnimodDeserialized = Loaders.LoadUnimod(Path.Combine(DataDir, @"Data", @"unimod.xml")).ToList();
PsiModDeserialized = Loaders.LoadPsiMod(Path.Combine(DataDir, @"Data", @"PSI-MOD.obo.xml"));
var formalChargesDictionary = Loaders.GetFormalChargesDictionary(PsiModDeserialized);
UniprotDeseralized = Loaders.LoadUniprot(Path.Combine(DataDir, @"Data", @"ptmlist.txt"), formalChargesDictionary).ToList();
foreach (var modFile in Directory.GetFiles(Path.Combine(DataDir, @"Mods")))
{
AddMods(PtmListLoader.ReadModsFromFile(modFile, out var errorMods), false);
}
AddMods(UniprotDeseralized.OfType <Modification>(), false);
AddMods(UnimodDeserialized.OfType <Modification>(), false);
foreach (Modification mod in AllModsKnown)
{
if (!AllModsKnownDictionary.ContainsKey(mod.IdWithMotif))
{
AllModsKnownDictionary.Add(mod.IdWithMotif, mod);
}
// no error thrown if multiple mods with this ID are present - just pick one
}
ProteaseMods = UsefulProteomicsDatabases.PtmListLoader.ReadModsFromFile(Path.Combine(DataDir, @"Mods", @"ProteaseMods.txt"), out var errors).ToList();
ProteaseDictionary.Dictionary = ProteaseDictionary.LoadProteaseDictionary(Path.Combine(DataDir, @"ProteolyticDigestion", @"proteases.tsv"), ProteaseMods);
}
public void FilesLoading()
{
Loaders.LoadElements(Path.Combine(TestContext.CurrentContext.TestDirectory, "elements.dat"));
Loaders.LoadUnimod(Path.Combine(TestContext.CurrentContext.TestDirectory, "unimod_tables.xml"));
Loaders.LoadPsiMod(Path.Combine(TestContext.CurrentContext.TestDirectory, "PSI-MOD.obo.xml"));
Loaders.LoadUniprot(Path.Combine(TestContext.CurrentContext.TestDirectory, "ptmlist.txt"));
}
public void FilesLoading()
{
Loaders.LoadElements(Path.Combine(TestContext.CurrentContext.TestDirectory, "elements2.dat"));
var unimodMods = Loaders.LoadUnimod(Path.Combine(TestContext.CurrentContext.TestDirectory, "unimod_tables2.xml")).ToList();
Assert.AreEqual(2, (unimodMods.First(b => b.id.Equals("HexNAc(2) on N at Any")) as ModificationWithMass).neutralLosses.Count);
var psiModDeserialized = Loaders.LoadPsiMod(Path.Combine(TestContext.CurrentContext.TestDirectory, "PSI-MOD.obo2.xml"));
// N6,N6,N6-trimethyllysine
var trimethylLysine = psiModDeserialized.Items.OfType <UsefulProteomicsDatabases.Generated.oboTerm>().First(b => b.id.Equals("MOD:00083"));
Assert.AreEqual("1+", trimethylLysine.xref_analog.First(b => b.dbname.Equals("FormalCharge")).name);
// Phosphoserine
Assert.IsFalse(psiModDeserialized.Items.OfType <UsefulProteomicsDatabases.Generated.oboTerm>().First(b => b.id.Equals("MOD:00046")).xref_analog.Any(b => b.dbname.Equals("FormalCharge")));
Dictionary <string, int> formalChargesDictionary = Loaders.GetFormalChargesDictionary(psiModDeserialized);
var uniprotPtms = Loaders.LoadUniprot(Path.Combine(TestContext.CurrentContext.TestDirectory, "ptmlist2.txt"), formalChargesDictionary).ToList();
using (StreamWriter w = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "test.txt")))
{
foreach (var nice in uniprotPtms)
{
w.WriteLine(nice.ToString());
w.WriteLine("//");
}
foreach (var nice in unimodMods)
{
w.WriteLine(nice.ToString());
w.WriteLine("//");
}
}
var sampleModList = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "test.txt")).ToList();
string stringRepresentation = "ID (3R)-3-hydroxyarginine\r\nMT UniProt\r\nPP Anywhere.\r\nDR RESID; AA0601\r\nDR PSI-MOD; MOD:01956\r\nDR UniProt; PTM-0476\r\nTG R\r\nMM 15.994915\r\nCF O";
Assert.AreEqual(stringRepresentation, sampleModList.First().ToString());
// N,N,N-trimethylalanine
var thisMod = sampleModList.First(b => b.id.Equals(@"N,N,N-trimethylalanine")) as ModificationWithMass;
Assert.IsTrue(thisMod.monoisotopicMass > 42);
Assert.IsTrue(thisMod.monoisotopicMass < 43);
}
public void FilesLoading() //delete mzLib\Test\bin\x64\Debug to update your local unimod list
{
Loaders.LoadElements();
string uniModPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "unimod_tables2.xml");
string psiModPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "PSI-MOD.obo2.xml");
string uniProtPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "ptmlist2.txt");
// UniModPTMs
var unimodMods = Loaders.LoadUnimod(uniModPath).ToList();
Assert.AreEqual(2677, unimodMods.Count); // UniMod PTM list may be updated at some point, causing the unit test to fail
List <Modification> myList = unimodMods.Where(m => m.OriginalId.Equals("HexNAc(2)")).ToList();
Modification testMod = myList.First();
int neutralLossCount = 0;
if (testMod.NeutralLosses.Count != 0)
{
foreach (KeyValuePair <MassSpectrometry.DissociationType, List <double> > item in testMod.NeutralLosses)
{
foreach (double loss in item.Value)
{
neutralLossCount++;
}
}
}
Assert.AreEqual(2, neutralLossCount);
// PsiMod PTMs
var psiModDeserialized = Loaders.LoadPsiMod(psiModPath);
// N6,N6,N6-trimethyllysine
var trimethylLysine = psiModDeserialized.Items.OfType <UsefulProteomicsDatabases.Generated.oboTerm>().First(b => b.id.Equals("MOD:00083"));
Assert.AreEqual("1+", trimethylLysine.xref_analog.First(b => b.dbname.Equals("FormalCharge")).name);
// Phosphoserine
Assert.IsFalse(psiModDeserialized.Items.OfType <UsefulProteomicsDatabases.Generated.oboTerm>().First(b => b.id.Equals("MOD:00046")).xref_analog.Any(b => b.dbname.Equals("FormalCharge")));
Dictionary <string, int> formalChargesDictionary = Loaders.GetFormalChargesDictionary(psiModDeserialized);
// UniProt PTMs
var uniprotPtms = Loaders.LoadUniprot(uniProtPath, formalChargesDictionary).ToList();
Assert.AreEqual(345, uniprotPtms.Count()); // UniProt PTM list may be updated at some point, causing the unit test to fail
// write UniProt and UniMod PTMs to a file
using (StreamWriter w = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "test.txt")))
{
foreach (var nice in uniprotPtms)
{
w.WriteLine(nice.ToString());
w.WriteLine("//");
}
foreach (var nice in unimodMods)
{
w.WriteLine(nice.ToString());
w.WriteLine("//");
}
}
// read in the file and make sure that it has the same number of PTMs
var sampleModList = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "test.txt"), out var errors).ToList();
Assert.AreEqual(uniprotPtms.Count + unimodMods.Count, sampleModList.Count());
List <Modification> myOtherList = new List <Modification>();
foreach (Modification mod in sampleModList)
{
if (mod.IdWithMotif != null && mod.IdWithMotif.Contains("Acetyl"))
{
myOtherList.Add(mod);
}
}
var thisMod = myOtherList.First();
Assert.IsTrue(thisMod.MonoisotopicMass > 42);
Assert.IsTrue(thisMod.MonoisotopicMass < 43);
File.Delete(uniModPath);
File.Delete(psiModPath);
File.Delete(uniProtPath);
}
