public void FastaTrimRegex2() { Sequence seqObj = new Sequence(Alphabets.DNA, "TTTAAAGATTACATTTAAA"); Sequence expected = new Sequence(Alphabets.DNA, "TTTAAAGATTACA"); TrimByRegex target = new TrimByRegex(new FastAParser(), new FastAFormatter(), new FastAFormatter(), @"TTTAAA$"); ISequence actual = target.Trim(seqObj); Assert.AreEqual(BioHelper.GetStringSequence(expected), BioHelper.GetStringSequence(actual)); }
public void FastqTrimRegex1() { QualitativeSequence seqObj = new QualitativeSequence(Alphabets.DNA, FastQFormatType.Sanger, "GGGCCCGATTACATTTAAA", "ABCABCIIIIIIIABCABC"); QualitativeSequence expected = new QualitativeSequence(Alphabets.DNA, FastQFormatType.Sanger, "GGGCCCTTTAAA", "ABCABCABCABC"); TrimByRegex target = new TrimByRegex(new FastQParser(), new FastQFormatter(), new FastQFormatter(), "GATTACA"); ISequence actual = target.Trim(seqObj); Assert.AreEqual(BioHelper.GetStringSequence(expected), BioHelper.GetStringSequence(actual)); Assert.AreEqual(BioHelper.GetEncodedQualityScoreStringSequence(expected), BioHelper.GetEncodedQualityScoreStringSequence(actual as QualitativeSequence)); }