public List <Modification> get_mods(string current_directory)
{
var psiModDeserialized = Loaders.LoadPsiMod(Path.Combine(current_directory, "Mods", "PSI-MOD.obo.xml"));
Dictionary <string, int> formalChargesDictionary = Loaders.GetFormalChargesDictionary(psiModDeserialized);
Loaders.LoadElements();
List <Modification> all_known_modifications = new List <Modification>();
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;
}
if (filename.EndsWith("UniprotGlycanDatabase.txt"))
{
glycan_mods = new_mods;
continue;
}
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();
return(all_known_modifications);
}
public void SampleModFileLoadingFail1()
{
Assert.That(() => PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "sampleModFileFail1.txt")).ToList(),
Throws.TypeOf <PtmListLoaderException>()
.With.Property("Message")
.EqualTo("Could not get motif from NxS"));
}
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 static void Test_ReadAllModsFromFile(string filename, int modCount)
{
string testModificationsFileLocation = Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", filename);
var a = PtmListLoader.ReadModsFromFile(testModificationsFileLocation, out var errors);
Assert.AreEqual(modCount, a.Count());
}
public static void PTMListLoader_ModWithComments_Equals_ModWithoutComments()
{
var a = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "SampleMod_Comments.txt"), out var errors).ToList();
var b = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "SampleMod_NoComments.txt"), out var errors2).ToList();
Assert.IsTrue(a.First().Equals(b.First()));
}
public void TestModificationGeneral_Equals()
{
var a = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", "CommonBiological.txt")).ToList();
var b = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", "CommonBiological.txt")).ToList();
Assert.IsTrue(a.First().Equals(b.First()));
}
public void SampleModFileLoadingFail2()
{
Assert.That(() => PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "sampleModFileFail2.txt")).ToList(),
Throws.TypeOf <MzLibException>()
.With.Property("Message")
.EqualTo("Could not get modification site from Anyplace."));
}
public void load_save_unlocalized()
{
Loaders.LoadElements();
TheoreticalProteoformDatabase tpd = new TheoreticalProteoformDatabase();
List <Modification> mods = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "ptmlist.txt"), out List <(Modification, string)> filteredModificationsWithWarnings).ToList();
foreach (Modification m in mods)
{
if (!Sweet.lollipop.modification_ranks.TryGetValue(Math.Round((double)m.MonoisotopicMass, 5), out int x))
{
Sweet.lollipop.modification_ranks.Add(Math.Round((double)m.MonoisotopicMass, 5), -1);
}
}
tpd.unlocalized_lookup = tpd.make_unlocalized_lookup(mods);
tpd.load_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "stored_mods.modnames"));
tpd.save_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "fake_stored_mods.modnames"));
Modification firstAcetyl = mods.FirstOrDefault(x => x.OriginalId.StartsWith("N-acetyl"));
Assert.AreNotEqual(firstAcetyl.OriginalId, tpd.unlocalized_lookup[firstAcetyl].id);
//Test amending
mods.AddRange(PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "intact_mods.txt"), out filteredModificationsWithWarnings).OfType <Modification>());
Sweet.lollipop.modification_ranks = mods.DistinctBy(m => m.MonoisotopicMass).ToDictionary(m => Math.Round((double)m.MonoisotopicMass, 5), m => - 1);
tpd.unlocalized_lookup = tpd.make_unlocalized_lookup(mods.OfType <Modification>());
tpd.amend_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "fake_stored_mods.modnames"));
}
public void SampleModFileLoadingFail3()
{
Assert.That(() => PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "sampleModFileFail3.txt")).ToList(),
Throws.TypeOf <MzLibException>()
.With.Property("Message")
.EqualTo("Input string for chemical formula was in an incorrect format: $%#$%"));
}
public void SampleModFileLoadingFail4()
{
Assert.That(() => PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "m.txt")).ToList(),
Throws.TypeOf <MzLibException>()
.With.Property("Message")
.EqualTo("0 or 238.229666 is not a valid monoisotopic mass"));
}
public void SampleModFileLoadingFail6()
{
Assert.That(() => PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "sampleModFileFail6.txt")).ToList(),
Throws.TypeOf <MzLibException>()
.With.Property("Message")
.EqualTo("modificationType of lalaMod is null"));
}
public void DoNotWriteSameModTwiceButWriteInHeaderSinceDifferent()
{
Loaders.LoadElements(Path.Combine(TestContext.CurrentContext.TestDirectory, "elements2.dat"));
var sampleModList = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "z.txt")).ToList();
Protein protein = new Protein("MCSSSSSSSSSS", "accession", "organism", new List <Tuple <string, string> >(), new Dictionary <int, List <Modification> > {
{ 2, sampleModList.OfType <Modification>().ToList() }
}, null, "name", "full_name", false, false, new List <DatabaseReference>(), new List <SequenceVariation>(), new List <DisulfideBond>());
Assert.AreEqual(1, protein.OneBasedPossibleLocalizedModifications[2].OfType <ModificationWithMass>().Count());
Dictionary <string, HashSet <Tuple <int, Modification> > > dictWithThisMod = new Dictionary <string, HashSet <Tuple <int, Modification> > >();
HashSet <Tuple <int, Modification> > value = new HashSet <Tuple <int, Modification> >();
ModificationMotif.TryGetMotif("C", out ModificationMotif motif);
ModificationWithMass newMod = new ModificationWithMass("Palmitoylation of C", "mt", motif, TerminusLocalization.Any, double.NaN, null, null);
Assert.AreNotEqual(newMod, sampleModList.First());
value.Add(new Tuple <int, Modification>(2, newMod));
dictWithThisMod.Add("accession", value);
var newModResEntries = ProteinDbWriter.WriteXmlDatabase(dictWithThisMod, new List <Protein> {
protein
}, Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins2.xml"));
Assert.AreEqual(0, newModResEntries.Count);
List <Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins2.xml"), true, DecoyType.None, new List <Modification>(), false, new List <string>(), out Dictionary <string, Modification> um);
Assert.AreEqual(1, new_proteins.Count);
Assert.AreEqual(1, new_proteins[0].OneBasedPossibleLocalizedModifications.Count);
Assert.AreEqual(2, new_proteins[0].OneBasedPossibleLocalizedModifications.SelectMany(kv => kv.Value).Count());
}
public void Modification_read_write_into_proteinDb()
{
Loaders.LoadElements(Path.Combine(TestContext.CurrentContext.TestDirectory, "elements2.dat"));
var sampleModList = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "z.txt")).ToList();
Assert.AreEqual(1, sampleModList.OfType <ModificationWithMass>().Count());
Protein protein = new Protein("MCSSSSSSSSSS", "accession", "organism", new List <Tuple <string, string> >(), new Dictionary <int, List <Modification> > {
{ 2, sampleModList.OfType <Modification>().ToList() }
}, null, "name", "full_name", false, false, new List <DatabaseReference>(), new List <SequenceVariation>(), new List <DisulfideBond>());
Assert.AreEqual(1, protein.OneBasedPossibleLocalizedModifications[2].OfType <ModificationWithMass>().Count());
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), new List <Protein> {
protein
}, Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins.xml"));
List <Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins.xml"), true, DecoyType.None, new List <Modification>(), false, new List <string>(), out Dictionary <string, Modification> um);
Assert.AreEqual(1, new_proteins.Count);
Assert.AreEqual(1, new_proteins[0].OneBasedPossibleLocalizedModifications.Count);
Assert.AreEqual(1, new_proteins[0].OneBasedPossibleLocalizedModifications.SelectMany(kv => kv.Value).Count());
Assert.AreEqual("Type", new_proteins[0].OneBasedPossibleLocalizedModifications.SelectMany(kv => kv.Value).OfType <ModificationWithMass>().First().modificationType);
Assert.AreEqual("Palmitoylation of C", new_proteins[0].OneBasedPossibleLocalizedModifications[2][0].id);
Assert.AreEqual(1, new_proteins[0].OneBasedPossibleLocalizedModifications[2].OfType <ModificationWithMass>().Count());
// Check that Modifications were saved after last load
Assert.AreEqual(1, ProteinDbLoader.GetPtmListFromProteinXml(Path.Combine(TestContext.CurrentContext.TestDirectory, @"test_modifications_with_proteins.xml")).Count);
Assert.True(ProteinDbLoader.GetPtmListFromProteinXml(Path.Combine(TestContext.CurrentContext.TestDirectory, @"test_modifications_with_proteins.xml"))[0] == new_proteins[0].OneBasedPossibleLocalizedModifications.SelectMany(kv => kv.Value).First());
//But that we can still read modifications from other protein XMLs that exist
Assert.AreEqual(0, ProteinDbLoader.GetPtmListFromProteinXml(Path.Combine(TestContext.CurrentContext.TestDirectory, "xml.xml")).Count);
}
public void TestModificationGeneralToString()
{
var a = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", "CommonBiological.txt")).ToList();
char[] myChar = { '"' };
string output = a.First().ToString();
Assert.AreEqual(output.TrimStart(myChar).TrimEnd(myChar), "ID 4-carboxyglutamate on E\r\nMT Biological\r\nTG E\r\nPP Anywhere.\r\nCF CO2\r\nMM 43.989829\r\n");
}
public static void Test_ReadAllModsFromFileGeneral()
{
string testModificationsFileLocation = Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", @"CommonArtifacts.txt");
var a = PtmListLoader.ReadModsFromFile(testModificationsFileLocation);
Assert.AreEqual(33, a.Select(m => m.IdWithMotif).ToList().Count);
testModificationsFileLocation = Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", @"CommonBiological.txt");
var b = PtmListLoader.ReadModsFromFile(testModificationsFileLocation);
Assert.AreEqual(35, b.Select(m => m.IdWithMotif).ToList().Count);
}
public static void Test_ModsFromFileAreSorted(string filename)
{
string testModificationsFileLocation = Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", filename);
var a = PtmListLoader.ReadModsFromFile(testModificationsFileLocation, out var errors);
string id1 = a.First().IdWithMotif;
foreach (string modId in a.Select(m => m.IdWithMotif))
{
Assert.GreaterOrEqual(modId, id1);
}
}
public static void ProteaseLoader()
{
string path1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "ProteaseFilesForLoadingTests", "TestProteases_badMod.tsv");
string path2 = Path.Combine(TestContext.CurrentContext.TestDirectory, "ProteaseFilesForLoadingTests", "TestProteases_badMod_dupName.tsv");
string path3 = Path.Combine(TestContext.CurrentContext.TestDirectory, "ProteaseFilesForLoadingTests", "TestProteases_dupName.tsv");
string path4 = Path.Combine(TestContext.CurrentContext.TestDirectory, "ProteaseFilesForLoadingTests", "TestProteases_Mod_dupName.tsv");
var proteaseMods = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", "ProteaseMods.txt"), out var errors).ToList();
Assert.Throws <MzLibUtil.MzLibException>(() => ProteaseDictionary.LoadProteaseDictionary(path1, proteaseMods));
Assert.Throws <MzLibUtil.MzLibException>(() => ProteaseDictionary.LoadProteaseDictionary(path2, proteaseMods));
Assert.Throws <MzLibUtil.MzLibException>(() => ProteaseDictionary.LoadProteaseDictionary(path3, proteaseMods));
Assert.Throws <MzLibUtil.MzLibException>(() => ProteaseDictionary.LoadProteaseDictionary(path4, proteaseMods));
}
public static void LoadModWithNl()
{
var hah = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "cfInNL.txt"), out var errors).First() as Modification;
int count = 0;
foreach (KeyValuePair <MassSpectrometry.DissociationType, List <double> > item in hah.NeutralLosses)
{
foreach (double loos in item.Value)
{
count++;
}
}
Assert.AreEqual(2, count);
}
public static void TestMultipleFilesRunner()
{
foreach (var modFile in Directory.GetFiles(@"Mods"))
{
GlobalVariables.AddMods(PtmListLoader.ReadModsFromFile(modFile));
}
CalibrationTask task1 = new CalibrationTask
{
CommonParameters = new CommonParameters
(
digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain),
listOfModsVariable: new List <(string, string)> {
("Common Variable", "Oxidation of M")
},
public static void TestInvalidModTypeError()
{
string mod = "ID Deamidation\r\nTG N or Q\r\nPP Anywhere.\r\nMT Mod:\r\nCF H-1 N-1 O1\r\n//";
string filepath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestInvalidModTypeError\ptmlist.txt");
Directory.CreateDirectory(Directory.GetParent(filepath).FullName);
File.WriteAllLines(filepath, new string[] { mod });
var ptms = PtmListLoader.ReadModsFromFile(filepath, out var warnings).ToList();
Assert.That(ptms.Count == 0);
Assert.That(warnings.Count == 2);
Assert.That(warnings.First().Item2.Contains("Modification type cannot contain ':'!"));
}
public static void TestReadingIdWithMotif()
{
string modText = "ID Detached EVK or XleDK\r\nPP Peptide N-terminal.\r\nTG evkX or vekX or ldkX or dlkX or idkX or dikX\r\nMT Detached\r\nNL C16H28N4O5\r\nCF C16H28N4O5\r\n" + @"//";
string path = Path.Combine(TestContext.CurrentContext.TestDirectory, "detacher.txt");
File.WriteAllLines(path, new string[] { modText });
var mods = PtmListLoader.ReadModsFromFile(path, out var errors).ToList();
var motifs = mods.Select(p => p.Target.ToString()).Distinct().ToList();
var ids = mods.Select(p => p.IdWithMotif).Distinct().ToList();
Assert.That(mods.Count == 6);
Assert.That(motifs.Count == 6);
Assert.That(ids.Count == 6);
}
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 static void Test_ModsWithComments()
{
string testModificationsFileLocation = Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", @"ModsWithComments.txt");
var a = PtmListLoader.ReadModsFromFile(testModificationsFileLocation, out var errors).ToList();
Assert.AreEqual(4, a.Select(m => m.IdWithMotif).ToList().Count);
Assert.AreEqual("Deamidation on N", a[0].IdWithMotif.ToString());
Assert.AreEqual("Sodium on D", a[2].IdWithMotif.ToString());//this has trailing whitespace that shouldn't be in the name
//Make sure comments are okay on DR key and that key value pairs are still split correctly
Modification someMod = a[2];
Modification test = someMod;
var residValueTest = test.DatabaseReference.First().Value.First();
var residKeyTest = test.DatabaseReference.First().Key;
Assert.AreEqual("RESID", residKeyTest);
Assert.AreEqual("AA0441", residValueTest);
}
public void load_save_unlocalized()
{
TheoreticalProteoformDatabase tpd = new TheoreticalProteoformDatabase();
tpd.ready_to_make_database(TestContext.CurrentContext.TestDirectory);
List <ModificationWithMass> mods = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "variable.txt")).OfType <ModificationWithMass>().ToList();
SaveState.lollipop.modification_ranks = mods.ToDictionary(m => m.monoisotopicMass, m => - 1);
tpd.unlocalized_lookup = tpd.make_unlocalized_lookup(mods);
tpd.load_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "stored_mods.modnames"));
tpd.save_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "fake_stored_mods.modnames"));
Assert.AreNotEqual(mods.First().id, tpd.unlocalized_lookup.Values.First().id);
//Test amending
mods.AddRange(PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "intact_mods.txt")).OfType <ModificationWithMass>());
SaveState.lollipop.modification_ranks = mods.DistinctBy(m => m.monoisotopicMass).ToDictionary(m => m.monoisotopicMass, m => - 1);
tpd.unlocalized_lookup = tpd.make_unlocalized_lookup(mods.OfType <ModificationWithMass>());
tpd.amend_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "fake_stored_mods.modnames"));
}
private static void BenchmarkDatabaseLoadWrite()
{
Console.WriteLine("Starting benchmark BenchmarkDatabaseLoadWrite");
Stopwatch stopWatch = new Stopwatch();
Loaders.LoadElements("elements2.dat");
IEnumerable <Modification> ya = PtmListLoader.ReadModsFromFile(@"ptmlist.txt").ToList();
stopWatch.Restart();
var a = ProteinDbLoader.LoadProteinXML(@"yeast_160126.xml.gz", true, ya, false, null, out Dictionary <string, Modification> um);
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <System.Tuple <int, ModificationWithMass> > >(), a.Where(p => !p.IsDecoy).ToList(), "rewrite_yeast.xml");
var b = ProteinDbLoader.LoadProteinXML(@"rewrite_yeast.xml", true, ya, false, null, out um);
stopWatch.Stop();
Console.WriteLine("Time for getting formulas: " + stopWatch.Elapsed);
Console.WriteLine("Benchmark BenchmarkDatabaseLoadWrite finished");
}
public void DoNotWriteSameModTwiceAndDoNotWriteInHeaderSinceDifferent()
{
Loaders.LoadElements();
var sampleModList = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "z.txt"), out var errors).ToList();
Protein protein = new Protein("MCSSSSSSSSSS", "accession", "organism", new List <Tuple <string, string> >(), new Dictionary <int, List <Modification> > {
{ 2, sampleModList.OfType <Modification>().ToList() }
}, null, "name", "full_name", false, false, new List <DatabaseReference>(), new List <SequenceVariation>(), disulfideBonds: new List <DisulfideBond>());
Assert.AreEqual(1, protein.OneBasedPossibleLocalizedModifications[2].OfType <Modification>().Count());
Dictionary <string, HashSet <Tuple <int, Modification> > > dictWithThisMod = new Dictionary <string, HashSet <Tuple <int, Modification> > >();
HashSet <Tuple <int, Modification> > value = new HashSet <Tuple <int, Modification> >();
var modReadFromFile = sampleModList.First() as Modification;
ModificationMotif.TryGetMotif("C", out ModificationMotif motif);
Modification newMod = new Modification(_originalId: "Palmitoylation of C", _modificationType: "Type", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: modReadFromFile.ChemicalFormula, _monoisotopicMass: modReadFromFile.MonoisotopicMass, _featureType: "MOD_RES", _fileOrigin: "E:\\GitClones\\mzLib\\Test\\bin\\x64\\Debug\\DatabaseTests\\z.txt");
Assert.IsTrue(newMod.Equals(sampleModList.First()));
Assert.AreEqual(newMod, sampleModList.First());
Assert.AreEqual(sampleModList.First(), newMod);
value.Add(new Tuple <int, Modification>(2, newMod));
dictWithThisMod.Add("accession", value);
var newModResEntries = ProteinDbWriter.WriteXmlDatabase(dictWithThisMod, new List <Protein> {
protein
}, Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins3.xml"));
Assert.AreEqual(0, newModResEntries.Count);
List <Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins3.xml"),
true, DecoyType.None, new List <Modification>(), false, new List <string>(), out Dictionary <string, Modification> um);
Assert.AreEqual(1, new_proteins.Count);
Assert.AreEqual(1, new_proteins[0].OneBasedPossibleLocalizedModifications.Count);
Assert.AreEqual(1, new_proteins[0].OneBasedPossibleLocalizedModifications.SelectMany(kv => kv.Value).Count());
}
public static void TestMultipleFilesRunner()
{
#region Setup tasks
foreach (var modFile in Directory.GetFiles(@"Mods"))
{
GlobalVariables.AddMods(PtmListLoader.ReadModsFromFile(modFile));
}
CalibrationTask task1 = new CalibrationTask
{
CommonParameters = new CommonParameters
{
DigestionParams = new DigestionParams
{
MaxMissedCleavages = 0,
MinPeptideLength = null,
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain
},
ListOfModsVariable = new List <(string, string)> {
("Common Variable", "Oxidation of M")
},
public static void Test_ModsFromFileAreSorted()
{
string testModificationsFileLocation = Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", @"CommonArtifacts.txt");
var a = PtmListLoader.ReadModsFromFile(testModificationsFileLocation);
string id1 = a.First().IdWithMotif.ToString();
foreach (string modId in a.Select(m => m.IdWithMotif))
{
Assert.GreaterOrEqual(modId, id1);
}
testModificationsFileLocation = Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", @"CommonBiological.txt");
var b = PtmListLoader.ReadModsFromFile(testModificationsFileLocation);
string id2 = b.First().IdWithMotif.ToString();
foreach (string modId in b.Select(m => m.IdWithMotif))
{
Assert.GreaterOrEqual(modId, id2);
}
}
public static void AnalyzeMultipleFolders(List <string> folders, string outsuffix)
{
// setup
Loaders.LoadElements(Path.Combine(Environment.CurrentDirectory, "elements.dat"));
var commonMods = PtmListLoader.ReadModsFromFile(Path.Combine(Environment.CurrentDirectory, "aListOfMods.txt"), out var filtered);
// analysis & output
Directory.CreateDirectory(OutputFolder);
string outfile = Path.Combine(OutputFolder, $"out{outsuffix}.txt");
if (File.Exists(outfile))
{
File.Delete(outfile);
}
using (StreamWriter writer = new StreamWriter(File.Create(outfile)))
{
List <AnalysisResults> results = folders.SelectMany(f => AnalyzeResultsFolder(f, commonMods)).ToList();
var table = AnalysisResults.SetUpDataTable();
results.ForEach(r => r.AddToTable(table));
writer.Write(AnalysisResults.ResultsString(table));
}
Console.WriteLine("Hit any key to exit.");
Console.ReadKey();
}
public static void LoadModWithNl()
{
var hah = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "cfInNL.txt")).First() as ModificationWithMassAndCf;
Assert.AreEqual(2, hah.neutralLosses.Count);
}