public void TestGetDatabaseComposition() { Dictionary <char, double> actual = SequenceUtils.GetDatabaseComposition(TestContext.CurrentContext.TestDirectory + "/../../../data//test.fasta"); Assert.AreEqual(0.5, actual['A']); Assert.AreEqual(0.5, actual['B']); }
public void TestGetReversedSequence4() { Sequence seq = SequenceUtils.GetReversedSequence("ABCDE", "REV_", 2, 5); Assert.AreEqual("REV_05", seq.Name); Assert.AreEqual("EDCBA", seq.SeqString); }
public void TestReadFromFasta() { FastaFormat ff = new FastaFormat(); List <Sequence> seqs = SequenceUtils.Read(ff, @TestContext.CurrentContext.TestDirectory + "/../../../data//Standard_Protein_FIT_060222.noredundant.fasta"); Assert.AreEqual(43, seqs.Count); }
public void TestRead() { List <Sequence> seqs = SequenceUtils.Read(new FastaFormat(), TestContext.CurrentContext.TestDirectory + "/../../../data//test.fasta"); Assert.AreEqual(2, seqs.Count); Assert.AreEqual("test1 description of test1", seqs[0].Reference); Assert.AreEqual("AAAAA", seqs[0].SeqString); Assert.AreEqual("test2 description of test2", seqs[1].Reference); Assert.AreEqual("BBBBB", seqs[1].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); } } }
public void TestGetReversedSequence1() { Assert.AreEqual("EDCBA", SequenceUtils.GetReversedSequence("ABCDE")); }