public void ValidateSangerFormatTypeDnaReverseComplement()
{
// Gets the actual sequence and the alphabet from the Xml
IAlphabet alphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.AlphabetNameNode));
FastQFormatType expectedFormatType = Utility.GetFastQFormatType(
utilityObj.xmlUtil.GetTextValue(Constants.SimpleDnaSangerNode, Constants.FastQFormatType));
string inputSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.inputSequenceNode);
string compSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.ComplementQualSeqNode);
string expectedRevCompSeq = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.RevComplement);
string expectedRevSeq = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.ReverseQualSeq);
string inputQuality = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.InputByteArrayNode);
byte[] byteArray = Encoding.UTF8.GetBytes(inputQuality);
QualitativeSequence createdQualitativeSequence =
new QualitativeSequence(alphabet, expectedFormatType,
inputSequence, inputQuality);
ISequence revSeq = createdQualitativeSequence.GetReversedSequence();
ISequence revCompSeq = createdQualitativeSequence.GetReverseComplementedSequence();
ISequence compSeq = createdQualitativeSequence.GetComplementedSequence();
Assert.AreEqual(expectedRevSeq, new string(revSeq.Select(a => (char)a).ToArray()));
Assert.AreEqual(expectedRevCompSeq, new string(revCompSeq.Select(a => (char)a).ToArray()));
Assert.AreEqual(compSequence, new string(compSeq.Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine("Qualitative BVT: Successfully validated Reverse, Complement and ReverseComplement sequence");
}
public void ValidateSangerFormatTypeDnaReverseComplement()
{
// Gets the actual sequence and the alphabet from the Xml
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.AlphabetNameNode));
FastQFormatType expectedFormatType = Utility.GetFastQFormatType(
this.utilityObj.xmlUtil.GetTextValue(Constants.SimpleDnaSangerNode, Constants.FastQFormatType));
string inputSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.inputSequenceNode);
string compSequence = this.utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.ComplementQualSeqNode);
string expectedRevCompSeq = this.utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.RevComplement);
string expectedRevSeq = this.utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.ReverseQualSeq);
string inputQuality = this.utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaSangerNode, Constants.InputByteArrayNode);
byte[] byteArray = Encoding.UTF8.GetBytes(inputQuality);
QualitativeSequence createdQualitativeSequence =
new QualitativeSequence(alphabet, expectedFormatType,
inputSequence, inputQuality);
ISequence revSeq = createdQualitativeSequence.GetReversedSequence();
ISequence revCompSeq = createdQualitativeSequence.GetReverseComplementedSequence();
ISequence compSeq = createdQualitativeSequence.GetComplementedSequence();
Assert.AreEqual(expectedRevSeq, new string(revSeq.Select(a => (char)a).ToArray()));
Assert.AreEqual(expectedRevCompSeq, new string(revCompSeq.Select(a => (char)a).ToArray()));
Assert.AreEqual(compSequence, new string(compSeq.Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine("Qualitative BVT: Successfully validated Reverse, Complement and ReverseComplement sequence");
}
