public void TestConvertFromSangerToSolexa()
{
byte[] bs;
byte[] bs1 = new byte[2];
bs1[0] = (byte)34;
bs1[1] = (byte)34;
bs = QualitativeSequence.ConvertFromSangerToSolexa(bs1);
Assert.IsNotNull((object)bs);
Assert.AreEqual <int>(2, bs.Length);
Assert.AreEqual <byte>((byte)59, bs[0]);
Assert.AreEqual <byte>((byte)59, bs[1]);
}
public void TestConvertFromSangerToSolexa()
{
byte[] solexaScores;
byte[] sangerScores = new byte[2];
sangerScores[0] = (byte)34;
sangerScores[1] = (byte)34;
solexaScores = QualitativeSequence.ConvertFromSangerToSolexa(sangerScores);
Assert.IsNotNull((object)solexaScores);
Assert.AreEqual <int>(2, solexaScores.Length);
Assert.AreEqual <byte>((byte)59, solexaScores[0]);
Assert.AreEqual <byte>((byte)59, solexaScores[1]);
}
public void ConvertSangerToSolexaAndIllumina()
{
// Gets the actual sequence and the Qual score from the Xml
string sangerSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SangerSequence);
string expectedSolexaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SolexaSequence);
string expectedIlluminaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.IlluminaSequence);
string sangerQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SangerQualScore);
string expectedSolexaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SolexaQualScore);
string expectedIlluminaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.IlluminaQualScore);
//string solexaQualScore = null;
//string illuminaQualScore = null;
byte[] scoreValue = ASCIIEncoding.ASCII.GetBytes(sangerQualScore);
// Create a Sanger qualitative sequence.
//QualitativeSequence sangerQualSequence = new QualitativeSequence(
// Alphabets.DNA, FastQFormatType.Sanger, sangerSequence, scoreValue);
//QualitativeSequence sangerQualSequence = new QualitativeSequence(*********************
// Alphabets.DNA, FastQFormatType.Sanger, sangerSequence, sangerQualScore);
// Convert Sanger to Solexa.
//QualitativeSequence solexaQualSequence = sangerQualSequence.ConvertTo(
// FastQFormatType.Solexa);
byte[] sangerToSolexa = QualitativeSequence.ConvertFromSangerToSolexa(scoreValue);
//solexaQualScore = ASCIIEncoding.ASCII.GetString(solexaQualSequence.Scores);
// Validate converted solexa score.
string qualSequence = new string(encodingObj.GetChars(sangerToSolexa));
Assert.AreEqual(expectedSolexaQualScore, qualSequence);
//Assert.AreEqual(solexaQualScore, expectedSolexaQualScore);
//Assert.AreEqual(solexaQualSequence.ToString(), expectedSolexaSequence);
//ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
// "Qualitative Sequence BVT:Qualitative Solexa score type {0} is as expected.",
// solexaQualScore));
//Console.WriteLine(string.Format((IFormatProvider)null,
// "Qualitative Sequence BVT:Qualitative Solexa score type {0} is as expected.",
//solexaQualSequence.ToString()));
// Convert Sanger to Illumina.
//QualitativeSequence illuminaQualSequence = sangerQualSequence.ConvertTo(
// FastQFormatType.Illumina);
//illuminaQualScore = ASCIIEncoding.ASCII.GetString(illuminaQualSequence.Scores);
byte[] sangerToIllumina = QualitativeSequence.ConvertFromSangerToIllumina(scoreValue);
//// Validate converted illumina score.
//Assert.AreEqual(illuminaQualScore, expectedIlluminaQualScore);
//Assert.AreEqual(illuminaQualSequence.ToString(), expectedIlluminaSequence);
string sangerToIlluminaString = new string(encodingObj.GetChars(sangerToIllumina));
Assert.AreEqual(expectedIlluminaQualScore, sangerToIlluminaString);
//ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
// "Qualitative Sequence BVT:Qualitative Illumina score type {0} is as expected.",
// illuminaQualScore));
//Console.WriteLine(string.Format((IFormatProvider)null,
// "Qualitative Sequence BVT:Qualitative Illumina score type {0} is as expected.",
// illuminaQualSequence.ToString()));
}
public void ConvertSangerToSolexaAndIllumina()
{
// Gets the actual sequence and the Qual score from the Xml
string sangerSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SangerSequence);
string expectedSolexaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SolexaSequence);
string expectedIlluminaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.IlluminaSequence);
string sangerQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SangerQualScore);
string expectedSolexaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SolexaQualScore);
string expectedIlluminaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.IlluminaQualScore);
string solexaQualScore = null;
string illuminaQualScore = null;
byte[] scoreValue = UTF8Encoding.UTF8.GetBytes(sangerQualScore);
// Create a Sanger qualitative sequence.
QualitativeSequence sangerQualSequence = new QualitativeSequence(Alphabets.DNA,
FastQFormatType.Sanger, sangerSequence, sangerQualScore);
// Convert Sanger to Solexa.
QualitativeSequence solexaQualSequence = sangerQualSequence.ConvertTo(
FastQFormatType.Solexa);
byte[] sangerToSolexa = QualitativeSequence.ConvertFromSangerToSolexa(scoreValue);
var scores = solexaQualSequence.QualityScores.ToArray();
solexaQualScore = UTF8Encoding.UTF8.GetString(scores, 0, scores.Length);
// Validate converted solexa score.
string qualSequence = new string(UTF8Encoding.UTF8.GetChars(sangerToSolexa));
Assert.AreEqual(expectedSolexaQualScore, qualSequence);
Assert.AreEqual(solexaQualScore, expectedSolexaQualScore);
string solexaQualString = new string(solexaQualSequence.Select(a => (char)a).ToArray());
Assert.AreEqual(solexaQualString, expectedSolexaSequence);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Solexa score type {0} is as expected.",
solexaQualScore));
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Solexa score type {0} is as expected.",
solexaQualString));
// Convert Sanger to Illumina.
QualitativeSequence illuminaQualSequence = sangerQualSequence.ConvertTo(
FastQFormatType.Illumina);
scores = illuminaQualSequence.QualityScores.ToArray();
illuminaQualScore = UTF8Encoding.UTF8.GetString(scores, 0, scores.Length);
byte[] sangerToIllumina = QualitativeSequence.ConvertFromSangerToIllumina(scoreValue);
string illuminaQualSeq = new string(illuminaQualSequence.Select(a => (char)a).ToArray());
//// Validate converted illumina score.
Assert.AreEqual(illuminaQualScore, expectedIlluminaQualScore);
Assert.AreEqual(illuminaQualSeq, expectedIlluminaSequence);
string sangerToIlluminaString = new string(UTF8Encoding.UTF8.GetChars(sangerToIllumina));
Assert.AreEqual(expectedIlluminaQualScore, sangerToIlluminaString);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Illumina score type {0} is as expected.",
illuminaQualScore));
Console.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Illumina score type {0} is as expected.",
illuminaQualSeq));
}