public void CompactFormReading2()
{
Assert.AreEqual(2, PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "sampleModFileDouble2.txt"), out var errors).Count());
}
public static void TestEverythingRunner()
{
foreach (var modFile in Directory.GetFiles(@"Mods"))
{
GlobalVariables.AddMods(PtmListLoader.ReadModsFromFile(modFile, out var fmww), false);
}
CalibrationTask task1 = new CalibrationTask
{
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain)),
CalibrationParameters = new CalibrationParameters
{
WriteIntermediateFiles = true,
NumFragmentsNeededForEveryIdentification = 6,
}
};
GptmdTask task2 = new GptmdTask
{
CommonParameters = new CommonParameters()
};
SearchTask task3 = new SearchTask
{
CommonParameters = new CommonParameters(),
SearchParameters = new SearchParameters
{
DoParsimony = true,
SearchTarget = true,
SearchType = SearchType.Modern
}
};
SearchTask task4 = new SearchTask
{
CommonParameters = new CommonParameters(),
SearchParameters = new SearchParameters
{
SearchType = SearchType.Modern,
}
};
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)> {
("task1", task1),
("task2", task2),
("task3", task3),
("task4", task4),
};
List <Modification> variableModifications = GlobalVariables.AllModsKnown.OfType <Modification>().Where(b => task1.CommonParameters.ListOfModsVariable.Contains((b.ModificationType, b.IdWithMotif))).ToList();
List <Modification> fixedModifications = GlobalVariables.AllModsKnown.OfType <Modification>().Where(b => task1.CommonParameters.ListOfModsFixed.Contains((b.ModificationType, b.IdWithMotif))).ToList();
// Generate data for files
Protein ParentProtein = new Protein("MPEPTIDEKANTHE", "accession1");
var digestedList = ParentProtein.Digest(task1.CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList();
Assert.AreEqual(3, digestedList.Count);
PeptideWithSetModifications pepWithSetMods1 = digestedList[0];
PeptideWithSetModifications pepWithSetMods2 = digestedList[2];
var dictHere = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
dictHere.Add(3, new List <Modification> {
new Modification(_originalId: "21", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 21.981943)
});
Protein ParentProteinToNotInclude = new Protein("MPEPTIDEK", "accession2", "organism", new List <Tuple <string, string> >(), dictHere);
digestedList = ParentProteinToNotInclude.Digest(task1.CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList();
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetMods1, pepWithSetMods2, digestedList[1]
});
Protein proteinWithChain = new Protein("MAACNNNCAA", "accession3", "organism", new List <Tuple <string, string> >(), new Dictionary <int, List <Modification> >(), new List <ProteolysisProduct> {
new ProteolysisProduct(4, 8, "chain")
}, "name2", "fullname2");
string mzmlName = @"ok.mzML";
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlName, false);
string xmlName = "okk.xml";
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), new List <Protein> {
ParentProtein, proteinWithChain
}, xmlName);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestEverythingRunner");
// RUN!
var engine = new EverythingRunnerEngine(taskList, new List <string> {
mzmlName
}, new List <DbForTask> {
new DbForTask(xmlName, false)
}, outputFolder);
engine.Run();
File.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, mzmlName));
File.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, xmlName));
Directory.Delete(outputFolder, true);
}
public static void CompactFormReadingGeneral(string filename)
{
Assert.AreEqual(2, PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", filename), out var errors).Count());
}
public static void SampleModFileLoadingFail1General(string filename)
{
var a = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", filename), out var errors).ToList();
Assert.AreEqual(0, a.Count);
}
public void get_theoretical_proteoforms(string current_directory)
{
if (!ready_to_make_database(current_directory))
{
return;
}
//Clear out data from potential previous runs
foreach (ProteoformCommunity community in Sweet.lollipop.decoy_proteoform_communities.Values)
{
community.theoretical_proteoforms = new TheoreticalProteoform[0];
}
theoretical_proteins.Clear();
//Read the UniProt-XML and ptmlist
var psiModDeserialized = Loaders.LoadPsiMod(Path.Combine(current_directory, "Mods", "PSI-MOD.obo.xml"));
Dictionary <string, int> formalChargesDictionary = Loaders.GetFormalChargesDictionary(psiModDeserialized);
List <Modification> all_known_modifications = Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.PtmList)
.SelectMany(file => PtmListLoader.ReadModsFromFile(file.complete_path, formalChargesDictionary, out List <(Modification, string)> filteredModificationsWithWarnings))
.ToList();
uniprotModifications = make_modification_dictionary(all_known_modifications);
Parallel.ForEach(Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.ProteinDatabase).ToList(), database =>
{
if (database.extension == ".xml")
{
lock (theoretical_proteins)
theoretical_proteins.Add(database, ProteinDbLoader.LoadProteinXML(database.complete_path, true, DecoyType.None, all_known_modifications, database.ContaminantDB, Sweet.lollipop.mod_types_to_exclude, out Dictionary <string, Modification> um).ToArray());
lock (all_known_modifications) all_known_modifications.AddRange(ProteinDbLoader.GetPtmListFromProteinXml(database.complete_path).Where(m => !Sweet.lollipop.mod_types_to_exclude.Contains(m.ModificationType)));
}
else if (database.extension == ".fasta")
{
lock (theoretical_proteins)
theoretical_proteins.Add(database, ProteinDbLoader.LoadProteinFasta(database.complete_path, true, DecoyType.None, database.ContaminantDB, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors).ToArray());
}
});
foreach (string filename in Directory.GetFiles(Path.Combine(current_directory, "Mods")))
{
List <Modification> new_mods = !filename.EndsWith("variable.txt") || Sweet.lollipop.methionine_oxidation ?
PtmListLoader.ReadModsFromFile(filename, formalChargesDictionary, out List <(Modification, string)> filteredModificationsWithWarnings).ToList() :
new List <Modification>(); // Empty variable modifications if not selected
if (filename.EndsWith("variable.txt"))
{
variableModifications = new_mods;
}
all_known_modifications.AddRange(new_mods);
}
all_known_modifications = new HashSet <Modification>(all_known_modifications).ToList();
uniprotModifications = make_modification_dictionary(all_known_modifications);
all_mods_with_mass = uniprotModifications.SelectMany(kv => kv.Value).Concat(variableModifications).ToList();
Sweet.lollipop.modification_ranks = rank_mods(theoretical_proteins, variableModifications, all_mods_with_mass);
unlocalized_lookup = make_unlocalized_lookup(all_mods_with_mass.Concat(new List <Modification> {
new Ptm().modification
}));
load_unlocalized_names(Path.Combine(Environment.CurrentDirectory, "Mods", "stored_mods.modnames"));
//this is for ptmsets --> used in RELATIONS
all_possible_ptmsets = PtmCombos.generate_all_ptmsets(2, all_mods_with_mass, Sweet.lollipop.modification_ranks, Sweet.lollipop.mod_rank_first_quartile / 2).ToList();
for (int i = 2; i <= Math.Max(ptmset_max_number_of_a_kind, Sweet.lollipop.max_ptms); i++) // the method above doesn't make 2 or more of a kind, so we make it here
{
all_possible_ptmsets.AddRange(all_mods_with_mass.Select(m => new PtmSet(Enumerable.Repeat(new Ptm(-1, m), i).ToList(), Sweet.lollipop.modification_ranks, Sweet.lollipop.mod_rank_first_quartile / 2)));
}
//Generate lookup table for ptm sets based on rounded mass of eligible PTMs -- used in forming ET relations
possible_ptmset_dictionary = make_ptmset_dictionary();
make_theoretical_proteoforms();
}
public static void SampleModFileLoadingFail3General(string filename, string errorMessage)
{
Assert.That(() =>
PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", filename), out var errors).ToList(),
Throws.TypeOf <MzLibException>().With.Property("Message").EqualTo(errorMessage));
}
public static void SampleModFileLoadingFail5General_missingPosition()
{
var a = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "sampleModFileFail_missingPosition.txt")).ToList();
Assert.AreEqual(0, a.Count()); // ID is missing
}
public void SampleModFileLoading()
{
PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "sampleModFile.txt"));
}
public static void LoadModWithNl()
{
var hah = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "cfInNL.txt")).First() as ModificationWithMassAndCf;
Assert.AreEqual(2, hah.neutralLosses.Count);
}
public static void SampleModFileLoadingFail1General() //TG is not valide
{
var a = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "sampleModFileFail1.txt")).ToList();
Assert.AreEqual(0, a.Count());
}
public void CompactFormReading()
{
Assert.AreEqual(2, PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "sampleModFileDouble.txt")).Count());
}
public void get_theoretical_proteoforms(string current_directory)
{
if (!ready_to_make_database(current_directory))
{
return;
}
//Clear out data from potential previous runs
foreach (ProteoformCommunity community in SaveState.lollipop.decoy_proteoform_communities.Values)
{
community.theoretical_proteoforms = new TheoreticalProteoform[0];
}
theoretical_proteins.Clear();
//Read the UniProt-XML and ptmlist
List <ModificationWithLocation> all_known_modifications = SaveState.lollipop.get_files(SaveState.lollipop.input_files, Purpose.PtmList).SelectMany(file => PtmListLoader.ReadModsFromFile(file.complete_path)).ToList();
uniprotModifications = make_modification_dictionary(all_known_modifications);
Dictionary <string, Modification> um;
Parallel.ForEach(SaveState.lollipop.get_files(SaveState.lollipop.input_files, Purpose.ProteinDatabase).ToList(), database =>
{
lock (theoretical_proteins) theoretical_proteins.Add(database, ProteinDbLoader.LoadProteinXML(database.complete_path, false, all_known_modifications, database.ContaminantDB, SaveState.lollipop.mod_types_to_exclude, out um).ToArray());
lock (all_known_modifications) all_known_modifications.AddRange(ProteinDbLoader.GetPtmListFromProteinXml(database.complete_path).OfType <ModificationWithLocation>().Where(m => !SaveState.lollipop.mod_types_to_exclude.Contains(m.modificationType)));
});
foreach (string filename in Directory.GetFiles(Path.Combine(current_directory, "Mods")))
{
var new_mods = !filename.EndsWith("variable.txt") || SaveState.lollipop.methionine_oxidation ?
PtmListLoader.ReadModsFromFile(filename) :
new List <ModificationWithLocation>(); // Empty variable modifications if not selected
if (filename.EndsWith("variable.txt"))
{
variableModifications = new_mods.OfType <ModificationWithMass>().ToList();
}
if (filename.EndsWith("intact_mods.txt"))
{
List <double> old_mods = all_known_modifications.OfType <ModificationWithMass>().Select(m => m.monoisotopicMass).ToList();
new_mods = new_mods.OfType <ModificationWithMass>().Where(m => !old_mods.Contains(m.monoisotopicMass)); // get rid of the unlocalized mods if they're already present
}
all_known_modifications.AddRange(new_mods);
}
all_known_modifications = new HashSet <ModificationWithLocation>(all_known_modifications).ToList();
uniprotModifications = make_modification_dictionary(all_known_modifications);
all_mods_with_mass = uniprotModifications.SelectMany(kv => kv.Value).OfType <ModificationWithMass>().Concat(variableModifications).ToList();
SaveState.lollipop.modification_ranks = rank_mods(theoretical_proteins, variableModifications, all_mods_with_mass);
unlocalized_lookup = make_unlocalized_lookup(all_mods_with_mass.Concat(new List <ModificationWithMass> {
new Ptm().modification
}));
load_unlocalized_names(Path.Combine(Environment.CurrentDirectory, "Mods", "stored_mods.modnames"));
//Generate all two-member sets and all three-member (or greater) sets of the same modification (three-member combinitorics gets out of hand for assignment)
all_possible_ptmsets = PtmCombos.generate_all_ptmsets(Math.Min(2, SaveState.lollipop.max_ptms), all_mods_with_mass, SaveState.lollipop.modification_ranks, SaveState.lollipop.mod_rank_first_quartile / 2).ToList();
for (int i = 2; i < SaveState.lollipop.max_ptms + 1; i++)
{
all_possible_ptmsets.AddRange(all_mods_with_mass.Select(m => new PtmSet(Enumerable.Repeat(new Ptm(-1, m), i).ToList(), SaveState.lollipop.modification_ranks, SaveState.lollipop.mod_rank_first_quartile / 2)));
}
//Generate lookup table for ptm sets based on rounded mass of eligible PTMs -- used in forming ET relations
possible_ptmset_dictionary = make_ptmset_dictionary();
expanded_proteins = expand_protein_entries(theoretical_proteins.Values.SelectMany(p => p).ToArray());
aaIsotopeMassList = new AminoAcidMasses(SaveState.lollipop.carbamidomethylation, SaveState.lollipop.natural_lysine_isotope_abundance, SaveState.lollipop.neucode_light_lysine, SaveState.lollipop.neucode_heavy_lysine).AA_Masses;
if (SaveState.lollipop.combine_identical_sequences)
{
expanded_proteins = group_proteins_by_sequence(expanded_proteins);
}
expanded_proteins = expanded_proteins.OrderBy(x => x.OneBasedPossibleLocalizedModifications.Count).ToArray(); // Take on harder problems first to use parallelization more effectively
process_entries(expanded_proteins, variableModifications);
process_decoys(expanded_proteins, variableModifications);
if (SaveState.lollipop.combine_theoretical_proteoforms_byMass)
{
SaveState.lollipop.target_proteoform_community.theoretical_proteoforms = group_proteoforms_by_mass(SaveState.lollipop.target_proteoform_community.theoretical_proteoforms);
foreach (ProteoformCommunity community in SaveState.lollipop.decoy_proteoform_communities.Values)
{
community.theoretical_proteoforms = group_proteoforms_by_mass(community.theoretical_proteoforms);
}
}
}
public static Dictionary <string, List <Modification> > read_mods()
{
Loaders.LoadElements();
List <Modification> all_modifications = Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.PtmList).SelectMany(file => PtmListLoader.ReadModsFromFile(file.complete_path, out List <(Modification, string)> filteredModificationsWithWarnings)).ToList();
return(Sweet.lollipop.theoretical_database.make_modification_dictionary(all_modifications));
}
public static void CNBrProteinDigestion()
{
var proteaseMods = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", "ProteaseMods.txt"), out var errors).ToList();
var prot = new Protein("PEPTIDEMPEPTIDEM", null);
var prot2 = new Protein("MPEPTIDEMPEPTIDE", null);
string path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DoubleProtease.tsv");
Assert.That(File.Exists(path));
var proteaseDict = ProteaseDictionary.LoadProteaseDictionary(path, proteaseMods);
ProteaseDictionary.Dictionary = ProteaseDictionary.LoadProteaseDictionary(Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "ProteolyticDigestion", "proteases.tsv"), proteaseMods);
var protease1 = proteaseDict["CNBr"];
DigestionParams digestionParams1 = new DigestionParams(
protease: protease1.Name,
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <Modification> variableModifications1 = new List <Modification>();
var protease2 = proteaseDict["CNBr_old"];
DigestionParams digestionParams2 = new DigestionParams(
protease: protease2.Name,
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <Modification> variableModifications2 = new List <Modification>();
var protease3 = proteaseDict["CNBr_N"];
DigestionParams digestionParams3 = new DigestionParams(
protease: protease3.Name,
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <Modification> variableModifications3 = new List <Modification>();
var peps1 = prot.Digest(digestionParams1, new List <Modification>(), variableModifications1).ToList();
var peps2 = prot.Digest(digestionParams2, new List <Modification>(), variableModifications2).ToList();
var peps3 = prot2.Digest(digestionParams3, new List <Modification>(), variableModifications1).ToList();
Assert.AreNotEqual(null, protease3.CleavageMod);
Assert.AreEqual("M", protease3.CleavageMod.Target.ToString());
Assert.AreNotEqual(peps3[0].MonoisotopicMass, peps3[1].MonoisotopicMass);
Assert.AreEqual(882.39707781799996, peps3[1].MonoisotopicMass);
Assert.AreEqual(930.400449121, peps3[0].MonoisotopicMass);
Assert.AreEqual(null, protease2.CleavageMod);
Assert.AreNotEqual(null, protease1.CleavageMod);
Assert.AreEqual("M", protease1.CleavageMod.Target.ToString());
Assert.AreEqual(peps1[1].MonoisotopicMass, peps2[1].MonoisotopicMass);
Assert.AreEqual(peps1[1].MonoisotopicMass, peps2[0].MonoisotopicMass);
Assert.AreEqual(peps2[0].MonoisotopicMass, peps2[1].MonoisotopicMass);
Assert.AreNotEqual(peps1[0].MonoisotopicMass, peps1[1].MonoisotopicMass);
Assert.AreNotEqual(peps1[0].MonoisotopicMass, peps2[0].MonoisotopicMass);
Assert.AreNotEqual(peps1[0].MonoisotopicMass, peps2[1].MonoisotopicMass);
Assert.AreEqual(882.39707781799996, peps1[0].MonoisotopicMass);
Assert.AreEqual(930.400449121, peps1[1].MonoisotopicMass);
}
public static void SampleModFileLoadingFail5General_missingMonoisotopicMassAndChemicalFormula()
{
var a = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "sampleModFileFail_missingChemicalFormulaAndMonoisotopicMass.txt")).ToList();
Assert.AreEqual(0, a.Count()); // ID is missing
}
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(2639, 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);
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();
Assert.AreEqual(334, uniprotPtms.Count()); // UniProt PTM list may be updated at some point, causing the unit test to fail
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();
Assert.AreEqual(2973, sampleModList.Count());
string s = "";
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);
}
public static Dictionary <string, List <Modification> > read_mods()
{
Loaders.LoadElements(Path.Combine(TestContext.CurrentContext.TestDirectory, "elements.dat"));
List <ModificationWithLocation> all_modifications = SaveState.lollipop.get_files(SaveState.lollipop.input_files, Purpose.PtmList).SelectMany(file => PtmListLoader.ReadModsFromFile(file.complete_path)).ToList();
return(SaveState.lollipop.theoretical_database.make_modification_dictionary(all_modifications));
}
public void SampleModFileLoadingFail2()
{
var b = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "sampleModFileFail2.txt"));
Assert.AreEqual(0, b.Count());
}
public void SampleModFileLoading()
{
var sampleModList = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "sampleModFile.txt")).ToList();
Console.WriteLine(sampleModList.First().ToString());
}
