public void Test() { PseudoSequenceBuilder builder = new PseudoSequenceBuilder("KR", false); Sequence seq = new Sequence("TEST", "EISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSK"); builder.Build(seq); Assert.AreEqual("EISQVFEIALRKNLPVNFEVAERSGPPHMNKFVTVKSVGEFVGEGEGSKK", seq.SeqString); }
public void TestAddDigestFeatures() { Sequence seq = new Sequence("Test", "AAANESAARBBBNPSBBKFFFNITFFRGGGNDTGGR"); Digest digest = new Digest(); digest.DigestProtease = ProteaseManager.CreateProtease("Trypsin_TestAddDigestFeatures", true, "RK", "P"); digest.ProteinSequence = seq; digest.MaxMissedCleavages = 0; digest.AddDigestFeatures(); List<DigestPeptideInfo> peptides = (List<DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE]; Assert.AreEqual(4, peptides.Count); digest.MaxMissedCleavages = 1; digest.AddDigestFeatures(); List<DigestPeptideInfo> missedPeptides = (List<DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE]; Assert.AreEqual(7, missedPeptides.Count); IRangeLocationFilter nglycanFilter = new NGlycanFilter(); digest.MaxMissedCleavages = 0; digest.Filter = nglycanFilter; digest.AddDigestFeatures(); List<DigestPeptideInfo> nglycanPeptides = (List<DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE]; Assert.AreEqual(2, nglycanPeptides.Count); Assert.AreEqual("AAANESAAR", nglycanPeptides[0].PeptideSeq); Assert.AreEqual("FFFNITFFR", nglycanPeptides[1].PeptideSeq); }
public void TestConstruction() { Sequence seq = new Sequence("test description of test", "ABCDE"); Assert.AreEqual("test", seq.Name); Assert.AreEqual("test description of test", seq.Reference); Assert.AreEqual("description of test", seq.Description); Assert.AreEqual("ABCDE", seq.SeqString); }
public void TestGetReversedSequence() { var options = new ReversedDatabaseBuilderOptions() { DecoyKey = "REVERSED", }; var builder = new ReversedDatabaseBuilder(options); var seq = new Sequence("sp|Q12345 sp protein", "ABCDE"); options.DecoyType = DecoyType.Start; Assert.AreEqual("REVERSED_sp|Q12345", builder.GetReversedSequence(1, seq).Name); options.DecoyType = DecoyType.Middle; Assert.AreEqual("sp|REVERSED_Q12345", builder.GetReversedSequence(1, seq).Name); }
public void WriteSequence(StreamWriter writer, Sequence seq) { }
public void FillSequence(Sequence seq) { //matched exon fill sequence exons.ForEach(m => m.FillSequence(seq, this.Strand)); //fill direct sequence this.DirectExpectSequence = seq.SeqString.Substring((int)this.ExpectStart, (int)(this.ExpectEnd - this.ExpectStart + 1)).ToUpper(); if (this.Strand == '-') { this.DirectExpectSequence = SequenceUtils.GetReverseComplementedSequence(this.DirectExpectSequence); } }
public void Build(Sequence seq) { seq.SeqString = findReg.Replace(seq.SeqString, "$2$1"); }
public void WriteSequence(StreamWriter writer, Sequence seq) { WriteSequence(writer, seq.Reference, seq.SeqString); }