/// <summary>
/// Validates the NUCmer align method for several test cases for the parameters passed.
/// </summary>
/// <param name="nodeName">Node name to be read from xml</param>
private void ValidateNUCmerAlignSimpleGeneralTestCases(string nodeName)
{
// Gets the reference & search sequences from the configuration file
string[] referenceSequences = this.utilityObj.xmlUtil.GetTextValues(nodeName, Constants.ReferenceSequencesNode);
string[] searchSequences = this.utilityObj.xmlUtil.GetTextValues(nodeName, Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
var refSeqList = referenceSequences.Select(t => new Sequence(seqAlphabet, Encoding.ASCII.GetBytes(t))).Cast<ISequence>().ToList();
var searchSeqList = searchSequences.Select(t => new Sequence(seqAlphabet, Encoding.ASCII.GetBytes(t))).Cast<ISequence>().ToList();
// Gets the mum length from the xml
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode);
var nucmerObj = new NucmerPairwiseAligner
{
MaximumSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), null),
MinimumScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), null),
SeparationFactor = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), null),
BreakLength = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), null),
LengthOfMUM = long.Parse(mumLength, null)
};
IList<ISequence> seqList = refSeqList.ToList();
foreach (ISequence seq in searchSeqList)
{
seqList.Add(seq);
}
IList<ISequenceAlignment> alignSimple = nucmerObj.AlignSimple(seqList);
string expectedSequences = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequencesNode);
string[] expSeqArray = expectedSequences.Split(',');
int j = 0;
// Gets all the aligned sequences in comma separated format
foreach (PairwiseAlignedSequence alignedSeq in alignSimple.Cast<IPairwiseSequenceAlignment>().SelectMany(seqAlignment => seqAlignment))
{
Assert.AreEqual(expSeqArray[j], alignedSeq.FirstSequence.ConvertToString());
++j;
Assert.AreEqual(expSeqArray[j], alignedSeq.SecondSequence.ConvertToString());
j++;
}
ApplicationLog.WriteLine("NUCmer P2 : Successfully validated all the aligned sequences.");
}
private void ValidateNUCmerAlignSimpleGeneralTestCases(string nodeName, bool isFilePath, bool isAlignList)
{
IList<ISequence> refSeqList = new List<ISequence>();
IList<ISequence> searchSeqList = new List<ISequence>();
if (isFilePath)
{
// Gets the reference sequence from the FastA file
string filePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format(null, "NUCmer P1 : Successfully validated the File Path '{0}'.", filePath));
var fastaparserobj = new FastAParser();
IEnumerable<ISequence> referenceSeqList = fastaparserobj.Parse(filePath);
foreach (ISequence seq in referenceSeqList)
{
refSeqList.Add(seq);
}
// Gets the query sequence from the FastA file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format(null,"NUCmer P1 : Successfully validated the File Path '{0}'.", queryFilePath));
var fastaParserobj = new FastAParser();
IEnumerable<ISequence> querySeqList = fastaParserobj.Parse(queryFilePath);
foreach (ISequence seq in querySeqList)
{
searchSeqList.Add(seq);
}
}
else
{
// Gets the reference & search sequences from the configuration file
string[] referenceSequences = this.utilityObj.xmlUtil.GetTextValues(nodeName, Constants.ReferenceSequencesNode);
string[] searchSequences = this.utilityObj.xmlUtil.GetTextValues(nodeName, Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
foreach (Sequence referSeq in referenceSequences.Select(t => new Sequence(seqAlphabet, Encoding.ASCII.GetBytes(t))))
{
refSeqList.Add(referSeq);
}
foreach (Sequence searchSeq in searchSequences.Select(t => new Sequence(seqAlphabet, Encoding.ASCII.GetBytes(t))))
{
searchSeqList.Add(searchSeq);
}
}
// Gets the mum length from the xml
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode);
var nucmerObj = new NucmerPairwiseAligner
{
MaximumSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), null),
MinimumScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), null),
SeparationFactor = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), null),
BreakLength = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), null),
LengthOfMUM = long.Parse(mumLength, null)
};
IList<ISequenceAlignment> alignSimple = null;
if (isAlignList)
{
var listOfSeq = new List<ISequence> {refSeqList[0], searchSeqList[0]};
alignSimple = nucmerObj.AlignSimple(listOfSeq);
}
string expectedSequences = isFilePath
? this.utilityObj.xmlUtil.GetFileTextValue(nodeName, Constants.ExpectedSequencesNode)
: this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequencesNode);
string[] expSeqArray = expectedSequences.Split(',');
int j = 0;
// Gets all the aligned sequences in comma separated format
foreach (PairwiseAlignedSequence alignedSeq in alignSimple.Cast<IPairwiseSequenceAlignment>().SelectMany(seqAlignment => seqAlignment))
{
Assert.AreEqual(expSeqArray[j], alignedSeq.FirstSequence.ConvertToString());
++j;
Assert.AreEqual(expSeqArray[j], alignedSeq.SecondSequence.ConvertToString());
j++;
}
ApplicationLog.WriteLine("NUCmer P1 : Successfully validated all the aligned sequences.");
}
/// <summary>
/// Validates the NUCmer align method for several test cases for the parameters passed.
/// </summary>
/// <param name="nodeName">Node name to be read from xml</param>
/// <param name="isAlignList">Is align method to take list?</param>
void ValidateNUCmerAlignSimpleGeneralTestCases(string nodeName,
bool isAlignList)
{
string[] referenceSequences = null;
string[] searchSequences = null;
List<ISequence> refSeqList = new List<ISequence>();
List<ISequence> searchSeqList = new List<ISequence>();
// Gets the reference & search sequences from the configurtion file
referenceSequences = this.utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.ReferenceSequencesNode);
searchSequences = this.utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(
this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
for (int i = 0; i < referenceSequences.Length; i++)
{
ISequence referSeq = new Sequence(seqAlphabet,
this.encodingObj.GetBytes(referenceSequences[i]));
refSeqList.Add(referSeq);
}
for (int i = 0; i < searchSequences.Length; i++)
{
ISequence searchSeq = new Sequence(seqAlphabet,
this.encodingObj.GetBytes(searchSequences[i]));
searchSeqList.Add(searchSeq);
}
// Gets the mum length from the xml
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MUMAlignLengthNode);
NucmerPairwiseAligner nucmerObj = new NucmerPairwiseAligner();
// Update other values for NUCmer object
nucmerObj.MaximumSeparation = int.Parse
(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), (IFormatProvider)null);
nucmerObj.MinimumScore = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), (IFormatProvider)null);
nucmerObj.SeparationFactor = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), (IFormatProvider)null);
nucmerObj.BreakLength = int.Parse(
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), (IFormatProvider)null);
nucmerObj.LengthOfMUM = long.Parse(mumLength, null);
IList<ISequenceAlignment> alignSimple = null;
if (isAlignList)
{
List<ISequence> listOfSeq = new List<ISequence>();
listOfSeq.Add(refSeqList[0]);
listOfSeq.Add(searchSeqList[0]);
alignSimple = nucmerObj.AlignSimple(listOfSeq);
}
string expectedSequences = string.Empty;
expectedSequences = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequencesNode);
string[] expSeqArray = expectedSequences.Split(',');
int j = 0;
// Gets all the aligned sequences in comma seperated format
foreach (IPairwiseSequenceAlignment seqAlignment in alignSimple)
{
foreach (PairwiseAlignedSequence alignedSeq in seqAlignment)
{
Assert.AreEqual(expSeqArray[j], new string(alignedSeq.FirstSequence.Select(a => (char)a).ToArray()));
++j;
Assert.AreEqual(expSeqArray[j], new string(alignedSeq.SecondSequence.Select(a => (char)a).ToArray()));
j++;
}
}
ApplicationLog.WriteLine("NUCmer BVT : Successfully validated all the aligned sequences.");
}
