public void GetStringSequenceTest()
{
ISequence seqObj = new QualitativeSequence(Alphabets.DNA, FastQFormatType.Sanger,
"GGCGCACTTACACCCTACATCCATTG", "IIIIG1?II;IIIII1IIII1%.I7I");
string expected = "GGCGCACTTACACCCTACATCCATTG";
string actual;
actual = BioHelper.GetStringSequence(seqObj);
Assert.AreEqual(expected, actual);
}
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));
}
public void FastqTrimFromLeftTest2()
{
ISequence seqObj = new QualitativeSequence(Alphabets.DNA, FastQFormatType.Sanger,
"GGCGCACTTACACCCTACATCCATTG", "IIIIG1?II;IIIII1IIII1%.I7I");
ISequence expected = new QualitativeSequence(Alphabets.DNA, FastQFormatType.Sanger,
"G", "I");
double trimLength = 1;
bool trimFromStart = true;
TrimByLength target = new TrimByLength(new FastQParser(), new FastQFormatter(), null, trimLength, trimFromStart);
ISequence actual;
actual = target.Trim(seqObj);
Assert.AreEqual(BioHelper.GetStringSequence(expected), BioHelper.GetStringSequence(actual));
Assert.AreEqual((expected as QualitativeSequence).QualityScores.ToString(), (actual as QualitativeSequence).QualityScores.ToString());
}