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 Test() { PseudoSequenceBuilder builder = new PseudoSequenceBuilder("KR", false); Sequence seq = new Sequence("TEST", "EISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSK"); builder.Build(seq); Assert.AreEqual("EISQVFEIALRKNLPVNFEVAERSGPPHMNKFVTVKSVGEFVGEGEGSKK", seq.SeqString); }
private void ProcessFile(ref int index, StreamWriter sw, string fastaFile, bool isContaminant) { FastaFormat ff = new FastaFormat(); using (StreamReader sr = new StreamReader(fastaFile)) { Progress.SetRange(0, sr.BaseStream.Length); Sequence seq; while ((seq = ff.ReadSequence(sr)) != null) { Progress.SetPosition(StreamUtils.GetCharpos(sr)); if (isContaminant) { if (!seq.Reference.StartsWith("CON_")) { seq.Reference = "CON_" + seq.Reference; } } if (combined) { ff.WriteSequence(sw, seq); } if (pseudoAminoacid) { builder.Build(seq); } index++; Sequence reversedSeq = SequenceUtils.GetReversedSequence(seq.SeqString, index); ff.WriteSequence(sw, reversedSeq); } } }