public void TestConvertingFromSolexaToSanger()
{
string sequencestr = "GCCCCCCCCCCCCCCCCCGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGAAAAA";
string solexaQualScores = ";<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~";
string sangerQaulScores = "!\"##$$%%&&'()*++,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_";
QualitativeSequence solexaSeq = new QualitativeSequence(Alphabets.DNA,
FastQFormatType.Solexa,
sequencestr,
ASCIIEncoding.ASCII.GetBytes(solexaQualScores));
QualitativeSequence sangerSeq = solexaSeq.ConvertTo(FastQFormatType.Sanger);
string testSanger = ASCIIEncoding.ASCII.GetString(sangerSeq.Scores);
Assert.AreEqual(testSanger, sangerQaulScores);
}
public void TestConvertingFromSolexaToIllumina()
{
string sequencestr = "GCCCCCCCCCCCCCCCCCGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGAAAAA";
string solexaQualScores = ";<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~";
string illuminaQualScores = "@ABBCCDDEEFGHIJJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~";
QualitativeSequence solexaSeq = new QualitativeSequence(Alphabets.DNA,
FastQFormatType.Solexa,
sequencestr,
ASCIIEncoding.ASCII.GetBytes(solexaQualScores));
QualitativeSequence illuminaSeq = solexaSeq.ConvertTo(FastQFormatType.Illumina);
string testillumina = ASCIIEncoding.ASCII.GetString(illuminaSeq.Scores);
Assert.AreEqual(testillumina, illuminaQualScores);
}
public void TestConvertingFromSangerToIllumina()
{
string sequencestr = "ACGTAAAAAAAGGGGGGGGGGGGGGGGCCCCCCCCCCCCCCCCCGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGAAAAA";
string sangerQaulScores = "!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~";
string illuminaQualScores = "@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~";
QualitativeSequence sangerSeq = new QualitativeSequence(Alphabets.DNA,
FastQFormatType.Sanger,
sequencestr,
ASCIIEncoding.ASCII.GetBytes(sangerQaulScores));
QualitativeSequence illuminaSeq = sangerSeq.ConvertTo(FastQFormatType.Illumina);
string testIllumina = ASCIIEncoding.ASCII.GetString(illuminaSeq.Scores);
Assert.AreEqual(testIllumina, illuminaQualScores);
}
public void ConvertSolexaToSangerAndIllumina()
{
// Gets the actual sequence and the Qual score from the Xml
string solexaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SolexaSequence);
string expectedSangerSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SangerSequence);
string expectedIlluminaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.IlluminaSequence);
string solexaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SolexaQualScore);
string expectedSangerQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SangerQualScore);
string expectedIlluminaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.IlluminaQualScore);
byte[] byteValue = Encoding.UTF8.GetBytes(solexaQualScore);
string sangerQualScore = null;
string illuminaQualScore = null;
byte[] qualScores = new byte[solexaSequence.Count()];
for (int i = 0; i < solexaSequence.Count(); i++)
{
qualScores[i] = (byte)'{';
}
Byte[] solexaSequenceinBytes = Encoding.UTF8.GetBytes(solexaSequence);
// Create a Solexa qualitative sequence.
QualitativeSequence solexaQualSequence = new QualitativeSequence(Alphabets.DNA,
FastQFormatType.Solexa_Illumina_v1_0, solexaSequenceinBytes, byteValue);
// Convert Solexa to Sanger.
QualitativeSequence sangerQualSequence = solexaQualSequence.ConvertTo(
FastQFormatType.Sanger);
var scores = sangerQualSequence.GetEncodedQualityScores();
sangerQualScore = Encoding.UTF8.GetString(scores, 0, scores.Length);
Assert.AreEqual(expectedSangerQualScore, sangerQualScore);
Assert.AreEqual(new string(sangerQualSequence.Select(a => (char)a).ToArray()), expectedSangerSequence);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Sanger score type {0} is as expected.",
sangerQualScore));
// Convert Solexa to Illumina.
QualitativeSequence illuminaQualSequence =
solexaQualSequence.ConvertTo(FastQFormatType.Illumina_v1_3);
scores = illuminaQualSequence.GetEncodedQualityScores();
illuminaQualScore = Encoding.UTF8.GetString(scores, 0, scores.Length);
Assert.AreEqual(expectedIlluminaQualScore, illuminaQualScore);
string illuminaQualseq = new string(illuminaQualSequence.Select(a => (char)a).ToArray());
// Validate converted illumina score.
Assert.AreEqual(illuminaQualScore, expectedIlluminaQualScore);
Assert.AreEqual(illuminaQualseq, expectedIlluminaSequence);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Illumina score type {0} is as expected.",
illuminaQualScore));
}
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 = Encoding.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_Illumina_v1_0);
byte[] sangerToSolexa = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Sanger, FastQFormatType.Solexa_Illumina_v1_0, scoreValue);
var scores = solexaQualSequence.GetEncodedQualityScores();
solexaQualScore = Encoding.UTF8.GetString(scores, 0, scores.Length);
// Validate converted solexa score.
string qualSequence = new string(Encoding.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(null,
"Qualitative Sequence BVT:Qualitative Solexa score type {0} is as expected.",
solexaQualScore));
// Convert Sanger to Illumina.
QualitativeSequence illuminaQualSequence = sangerQualSequence.ConvertTo(
FastQFormatType.Illumina_v1_3);
scores = illuminaQualSequence.GetEncodedQualityScores();
illuminaQualScore = Encoding.UTF8.GetString(scores, 0, scores.Length);
byte[] sangerToIllumina = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Sanger, FastQFormatType.Illumina_v1_3, 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(Encoding.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));
}
public void ConvertSolexaToSangerAndIllumina()
{
// Gets the actual sequence and the Qual score from the Xml
string solexaSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SolexaSequence);
string expectedSangerSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SangerSequence);
string expectedIlluminaSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.IlluminaSequence);
string solexaQualScore = this.utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SolexaQualScore);
string expectedSangerQualScore = this.utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SangerQualScore);
string expectedIlluminaQualScore = this.utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.IlluminaQualScore);
byte[] byteValue = Encoding.UTF8.GetBytes(solexaQualScore);
string sangerQualScore = null;
string illuminaQualScore = null;
byte[] qualScores = new byte[solexaSequence.Count()];
for (int i = 0; i < solexaSequence.Count(); i++)
{
qualScores[i] = (byte)'{';
}
Byte[] solexaSequenceinBytes = Encoding.UTF8.GetBytes(solexaSequence);
// Create a Solexa qualitative sequence.
QualitativeSequence solexaQualSequence = new QualitativeSequence(Alphabets.DNA,
FastQFormatType.Solexa_Illumina_v1_0, solexaSequenceinBytes, byteValue);
// Convert Solexa to Sanger.
QualitativeSequence sangerQualSequence = solexaQualSequence.ConvertTo(
FastQFormatType.Sanger);
var scores = sangerQualSequence.GetEncodedQualityScores();
sangerQualScore = Encoding.UTF8.GetString(scores, 0, scores.Length);
Assert.AreEqual(expectedSangerQualScore, sangerQualScore);
Assert.AreEqual(new string(sangerQualSequence.Select(a => (char)a).ToArray()), expectedSangerSequence);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Sanger score type {0} is as expected.",
sangerQualScore));
// Convert Solexa to Illumina.
QualitativeSequence illuminaQualSequence =
solexaQualSequence.ConvertTo(FastQFormatType.Illumina_v1_3);
scores = illuminaQualSequence.GetEncodedQualityScores();
illuminaQualScore = Encoding.UTF8.GetString(scores, 0, scores.Length);
Assert.AreEqual(expectedIlluminaQualScore, illuminaQualScore);
string illuminaQualseq=new string(illuminaQualSequence.Select(a => (char)a).ToArray());
// Validate converted illumina score.
Assert.AreEqual(illuminaQualScore, expectedIlluminaQualScore);
Assert.AreEqual(illuminaQualseq, expectedIlluminaSequence);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Illumina score type {0} is as expected.",
illuminaQualScore));
}
public void ConvertSangerToSolexaAndIllumina()
{
// Gets the actual sequence and the Qual score from the Xml
string sangerSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SangerSequence);
string expectedSolexaSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SolexaSequence);
string expectedIlluminaSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.IlluminaSequence);
string sangerQualScore = this.utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SangerQualScore);
string expectedSolexaQualScore = this.utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SolexaQualScore);
string expectedIlluminaQualScore = this.utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.IlluminaQualScore);
string solexaQualScore = null;
string illuminaQualScore = null;
byte[] scoreValue = Encoding.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_Illumina_v1_0);
byte[] sangerToSolexa = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Sanger, FastQFormatType.Solexa_Illumina_v1_0, scoreValue);
var scores = solexaQualSequence.GetEncodedQualityScores();
solexaQualScore = Encoding.UTF8.GetString(scores, 0, scores.Length);
// Validate converted solexa score.
string qualSequence = new string(Encoding.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(null,
"Qualitative Sequence BVT:Qualitative Solexa score type {0} is as expected.",
solexaQualScore));
// Convert Sanger to Illumina.
QualitativeSequence illuminaQualSequence = sangerQualSequence.ConvertTo(
FastQFormatType.Illumina_v1_3);
scores = illuminaQualSequence.GetEncodedQualityScores();
illuminaQualScore = Encoding.UTF8.GetString(scores, 0, scores.Length);
byte[] sangerToIllumina = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Sanger, FastQFormatType.Illumina_v1_3, 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(Encoding.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));
}
