public ProteinDbForDataGrid(DbForDigestion uu) { FilePath = uu.FilePath; FileName = uu.FileName; }
public static void SingleDatabase() { Loaders.LoadElements(); string subFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DigestionTest"); Directory.CreateDirectory(subFolder); string databasePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "Databases", "TestDatabase_1.fasta"); DbForDigestion database = new DbForDigestion(databasePath); Parameters param = new Parameters(); param.MinPeptideLengthAllowed = 1; param.MaxPeptideLengthAllowed = 100; param.NumberOfMissedCleavagesAllowed = 0; param.TreatModifiedPeptidesAsDifferent = false; param.ProteasesForDigestion.Add(ProteaseDictionary.Dictionary["trypsin"]); param.OutputFolder = subFolder; DigestionTask digestion = new DigestionTask(); digestion.DigestionParameters = param; var digestionResults = digestion.RunSpecific(subFolder, new List <DbForDigestion>() { database }); Assert.AreEqual(1, digestionResults.PeptideByFile.Count); Assert.AreEqual(1, digestionResults.PeptideByFile.Values.Count); Assert.AreEqual(2, digestionResults.PeptideByFile[database.FileName][param.ProteasesForDigestion.First().Name].Count); foreach (var entry in digestionResults.PeptideByFile[database.FileName][param.ProteasesForDigestion.First().Name]) { if (entry.Key.Accession == "testProtein_1") { Assert.AreEqual(26, entry.Value.Count); Assert.AreEqual("MSFVNGNEIFTAAR", entry.Value[0].BaseSequence); Assert.IsFalse(entry.Value[0].Unique); Assert.IsFalse(entry.Value[0].UniqueAllDbs); Assert.IsTrue(entry.Value[0].SeqOnlyInThisDb); Assert.AreEqual("QGHYAVGAFNTNNLEWTR", entry.Value[1].BaseSequence); Assert.IsTrue(entry.Value[1].Unique); Assert.IsTrue(entry.Value[1].UniqueAllDbs); Assert.IsTrue(entry.Value[1].SeqOnlyInThisDb); Assert.AreEqual("AILK", entry.Value[2].BaseSequence); Assert.IsTrue(entry.Value[2].Unique); Assert.IsTrue(entry.Value[2].UniqueAllDbs); Assert.IsTrue(entry.Value[2].SeqOnlyInThisDb); Assert.AreEqual("AAQEK", entry.Value[3].BaseSequence); Assert.IsFalse(entry.Value[3].Unique); Assert.IsFalse(entry.Value[3].UniqueAllDbs); Assert.IsTrue(entry.Value[3].SeqOnlyInThisDb); Assert.AreEqual("NTPVLIQVSMGAAK", entry.Value[4].BaseSequence); Assert.IsFalse(entry.Value[4].Unique); Assert.IsFalse(entry.Value[4].UniqueAllDbs); Assert.IsTrue(entry.Value[4].SeqOnlyInThisDb); Assert.AreEqual("YMGDYK", entry.Value[5].BaseSequence); Assert.IsFalse(entry.Value[5].Unique); Assert.IsFalse(entry.Value[5].UniqueAllDbs); Assert.IsTrue(entry.Value[5].SeqOnlyInThisDb); Assert.AreEqual("LVK", entry.Value[6].BaseSequence); Assert.IsFalse(entry.Value[6].Unique); Assert.IsFalse(entry.Value[6].UniqueAllDbs); Assert.IsTrue(entry.Value[6].SeqOnlyInThisDb); Assert.AreEqual("TLVEEEMR", entry.Value[7].BaseSequence); Assert.IsTrue(entry.Value[7].Unique); Assert.IsTrue(entry.Value[7].UniqueAllDbs); Assert.IsTrue(entry.Value[7].SeqOnlyInThisDb); } else if (entry.Key.Accession == "testProtein_2") { Assert.AreEqual(27, entry.Value.Count); Assert.AreEqual("MSFVNGNEIFTAAR", entry.Value[0].BaseSequence); Assert.IsFalse(entry.Value[0].Unique); Assert.IsFalse(entry.Value[0].UniqueAllDbs); Assert.IsTrue(entry.Value[0].SeqOnlyInThisDb); Assert.AreEqual("QGHPPGAFNTNNLEWTR", entry.Value[1].BaseSequence); Assert.IsTrue(entry.Value[1].Unique); Assert.IsTrue(entry.Value[1].UniqueAllDbs); Assert.IsTrue(entry.Value[1].SeqOnlyInThisDb); Assert.AreEqual("AIVK", entry.Value[2].BaseSequence); Assert.IsTrue(entry.Value[2].Unique); Assert.IsTrue(entry.Value[2].UniqueAllDbs); Assert.IsTrue(entry.Value[2].SeqOnlyInThisDb); Assert.AreEqual("AAQEK", entry.Value[3].BaseSequence); Assert.IsFalse(entry.Value[3].Unique); Assert.IsFalse(entry.Value[3].UniqueAllDbs); Assert.IsTrue(entry.Value[3].SeqOnlyInThisDb); Assert.AreEqual("NTPVLIQVSMGAAK", entry.Value[4].BaseSequence); Assert.IsFalse(entry.Value[4].Unique); Assert.IsFalse(entry.Value[4].UniqueAllDbs); Assert.IsTrue(entry.Value[4].SeqOnlyInThisDb); Assert.AreEqual("YMGDYK", entry.Value[5].BaseSequence); Assert.IsFalse(entry.Value[5].Unique); Assert.IsFalse(entry.Value[5].UniqueAllDbs); Assert.IsTrue(entry.Value[5].SeqOnlyInThisDb); Assert.AreEqual("LVK", entry.Value[6].BaseSequence); Assert.IsFalse(entry.Value[6].Unique); Assert.IsFalse(entry.Value[6].UniqueAllDbs); Assert.IsTrue(entry.Value[6].SeqOnlyInThisDb); Assert.AreEqual("TLVEPPMR", entry.Value[7].BaseSequence); Assert.IsTrue(entry.Value[7].Unique); Assert.IsTrue(entry.Value[7].UniqueAllDbs); Assert.IsTrue(entry.Value[7].SeqOnlyInThisDb); } } Directory.Delete(subFolder, true); }