public void TestAlignedSequenceToString()
{
IList <ISequence> seqList = new List <ISequence>();
seqList.Add(new Sequence(Alphabets.DNA, "CAAAAGGGATTGC---TGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC"));
seqList.Add(new Sequence(Alphabets.DNA, "CAAAAGGGATTGC---"));
seqList.Add(new Sequence(Alphabets.DNA, "TAGTAGTTCTGCTATATACATTTG"));
seqList.Add(new Sequence(Alphabets.DNA, "GTTATCATGCGAACAATTCAACAGACACTGTAGA"));
NucmerPairwiseAligner num = new NucmerPairwiseAligner();
num.BreakLength = 8;
num.FixedSeparation = 0;
num.MinimumScore = 0;
num.MaximumSeparation = 0;
num.SeparationFactor = 0;
num.LengthOfMUM = 8;
IList <ISequence> sequenceList = seqList;
IList <ISequenceAlignment> alignmentObj = num.Align(sequenceList);
AlignedSequence alignedSeqs = (AlignedSequence)alignmentObj[0].AlignedSequences[0];
string actualString = alignedSeqs.ToString();
string expectedString = "CAAAAGGGATTGC---\r\nCAAAAGGGATTGC---\r\nCAAAAGGGATTGC---\r\n";
Assert.AreEqual(actualString, expectedString);
}
public void ValidateAlignedSequenceToString()
{
IList <ISequence> seqList = new List <ISequence>();
string actualAlignedSeqString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.AlignedSeqActualNode);
seqList.Add(new Sequence(Alphabets.DNA,
actualAlignedSeqString));
seqList.Add(new Sequence(Alphabets.DNA, "CAAAAGGGATTGC---"));
seqList.Add(new Sequence(Alphabets.DNA, "TAGTAGTTCTGCTATATACATTTG"));
seqList.Add(new Sequence(Alphabets.DNA, "GTTATCATGCGAACAATTCAACAGACACTGTAGA"));
var num = new NucmerPairwiseAligner();
num.BreakLength = 8;
num.FixedSeparation = 0;
num.MinimumScore = 0;
num.MaximumSeparation = 0;
num.SeparationFactor = 0;
num.LengthOfMUM = 8;
IList <ISequence> sequenceList = seqList;
IList <ISequenceAlignment> alignmentObj = num.Align(sequenceList);
var alignedSeqs = (AlignedSequence)alignmentObj[0].AlignedSequences[0];
string actualString = alignedSeqs.ToString();
string expectedString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.AlignedSeqExpectedNode);
Assert.AreEqual(actualString, expectedString.Replace("\\r\\n", System.Environment.NewLine));
}
public void TestNUCmer3MultipleReferences()
{
Sequence referenceSeq = null;
Sequence searchSeq = null;
List <ISequence> referenceSeqs = null;
List <ISequence> searchSeqs = null;
referenceSeqs = new List <ISequence>();
string reference = "ATGCGCATCCCC";
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R1";
referenceSeqs.Add(referenceSeq);
reference = "TAGCT";
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R11";
referenceSeqs.Add(referenceSeq);
searchSeqs = new List <ISequence>();
string search = "CCGCGCCCCCTCAGCT";
searchSeq = new Sequence(Alphabets.DNA, search);
searchSeq.ID = "Q1";
searchSeqs.Add(searchSeq);
NucmerPairwiseAligner nucmer = new NucmerPairwiseAligner();
nucmer.FixedSeparation = 0;
nucmer.MinimumScore = 2;
nucmer.SeparationFactor = -1;
nucmer.LengthOfMUM = 3;
IList <IPairwiseSequenceAlignment> result = nucmer.Align(referenceSeqs, searchSeqs).Select(a => a as IPairwiseSequenceAlignment).ToList();
// Check if output is not null
Assert.AreNotEqual(null, result);
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "GCGCATCCCC");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "GCGC--CCCC");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "GCGCATCCCC");
alignedSeq.Score = -5;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "AGCT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "AGCT");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "AGCT");
alignedSeq.Score = 12;
alignedSeq.FirstOffset = 11;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
public void TestAlignedSequenceToString()
{
var seqList = new List <ISequence>
{
new Sequence(Alphabets.DNA, "CAAAAGGGATTGC---TGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC"),
new Sequence(Alphabets.DNA, "CAAAAGGGATTGC---"),
new Sequence(Alphabets.DNA, "TAGTAGTTCTGCTATATACATTTG"),
new Sequence(Alphabets.DNA, "GTTATCATGCGAACAATTCAACAGACACTGTAGA")
};
NucmerPairwiseAligner num = new NucmerPairwiseAligner
{
BreakLength = 8,
FixedSeparation = 0,
MinimumScore = 0,
MaximumSeparation = 0,
SeparationFactor = 0,
LengthOfMUM = 8
};
IList <ISequence> sequenceList = seqList;
IList <ISequenceAlignment> alignmentObj = num.Align(sequenceList);
Assert.AreNotEqual(0, alignmentObj.Count);
var alignedSeqs = (AlignedSequence)alignmentObj[0].AlignedSequences[0];
string actualString = alignedSeqs.ToString();
string ExpectedString = "CAAAAGGGATTGC---\r\nCAAAAGGGATTGC---\r\nCAAAAGGGATTGC---\r\n".Replace("\r\n", Environment.NewLine);
Assert.AreEqual(ExpectedString, actualString);
}
public static void AssignContigToMTDNA(ISequence contig)
{
var delts = GetDeltaAlignments(contig).SelectMany(x => x).ToList();
StringBuilder sb = new StringBuilder();
int alnCounts = delts.Count;
if (alnCounts > 0)
{
var alns = NucmerPairwiseAligner.ConvertDeltaToAlignment(delts);
contig.Metadata[DELTA_ALIGNMENT_METADATAKEY] = alns;
sb.Append("ALNS=" + alnCounts.ToString());
foreach (var d in alns)
{
//if(d.IsReverseQueryDirection)
//{sb.Append("R;");}
//else{sb.Append("F;");}
var alnLength = d.FirstSequence.Count;
sb.Append(d.FirstOffset.ToString() + "-" + (d.FirstOffset + alnLength).ToString() + ";" + d.SecondOffset.ToString() + "-" + (d.SecondOffset + alnLength).ToString() + ";" + d.Score.ToString());
}
}
else
{
sb.Append("No Alignments");
}
contig.ID = contig.ID + " " + sb.ToString();
}
/// <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 ValidateNUCmerAlignGeneralTestCases(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();
var nucmerObj = new NucmerPairwiseAligner();
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMLengthNode);
// Update other values for NUCmer object
nucmerObj.MaximumSeparation = 0;
nucmerObj.MinimumScore = 2;
nucmerObj.SeparationFactor = 0.12f;
nucmerObj.BreakLength = 2;
nucmerObj.LengthOfMUM = long.Parse(mumLength, null);
nucmerObj.MinimumScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MinimumScoreNode), null);
try
{
nucmerObj.Align(refSeqList, searchSeqList);
Assert.Fail("Expected Exception: ArgumentException");
}
catch (ArgumentException)
{
}
}
public void TestNUCmer3SingleCluster()
{
string reference = "AGAAAAGTTTTCA";
string search = "TTTTGAGATAAAATC";
Sequence referenceSeq = null;
Sequence searchSeq = null;
List <ISequence> referenceSeqs = null;
List <ISequence> searchSeqs = null;
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R1";
searchSeq = new Sequence(Alphabets.DNA, search);
searchSeq.ID = "Q1";
referenceSeqs = new List <ISequence>();
referenceSeqs.Add(referenceSeq);
searchSeqs = new List <ISequence>();
searchSeqs.Add(searchSeq);
NucmerPairwiseAligner nucmer = new NucmerPairwiseAligner();
nucmer.FixedSeparation = 0;
nucmer.MinimumScore = 2;
nucmer.SeparationFactor = -1;
nucmer.LengthOfMUM = 3;
nucmer.ForwardOnly = true;
IList <IPairwiseSequenceAlignment> result = nucmer.Align(referenceSeqs, searchSeqs).Select(a => a as IPairwiseSequenceAlignment).ToList();
// Check if output is not null
Assert.AreNotEqual(null, result);
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "AG--AAAA");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "AGATAAAA");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "AGATAAAA");
alignedSeq.Score = -11;
alignedSeq.FirstOffset = 5;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "TTTT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "TTTT");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "TTTT");
alignedSeq.Score = 12;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 7;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
}
/// <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>
void ValidateNUCmerAlignGeneralTestCases(string nodeName)
{
string mumLength = String.Empty;
bool exThrown = false;
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 = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.ReferenceSequencesNode);
searchSequences = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
for (int i = 0; i < referenceSequences.Length; i++)
{
ISequence referSeq = new Sequence(seqAlphabet, encodingObj.GetBytes(referenceSequences[i]));
refSeqList.Add(referSeq);
}
for (int i = 0; i < searchSequences.Length; i++)
{
ISequence searchSeq = new Sequence(seqAlphabet, encodingObj.GetBytes(searchSequences[i]));
searchSeqList.Add(searchSeq);
}
NucmerPairwiseAligner nucmerObj = new NucmerPairwiseAligner();
mumLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMLengthNode);
// Update other values for NUCmer object
nucmerObj.MaximumSeparation = 0;
nucmerObj.MinimumScore = 2;
nucmerObj.SeparationFactor = 0.12f;
nucmerObj.BreakLength = 2;
nucmerObj.LengthOfMUM = long.Parse(mumLength, null);
nucmerObj.MinimumScore = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MinimumScoreNode), (IFormatProvider)null);
try
{
nucmerObj.Align(refSeqList, searchSeqList);
Assert.Fail();
}
catch (ArgumentException ex)
{
exThrown = true;
Assert.IsTrue(exThrown, String.Format((IFormatProvider)null,
"NUCmer P2: {0}", ex.Message));
}
}
public void NUCmerAlignGreaterMumLength()
{
string mumLength = String.Empty;
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 = utilityObj.xmlUtil.GetTextValues(Constants.GreaterMumLengthSequence,
Constants.ReferenceSequencesNode);
searchSequences = utilityObj.xmlUtil.GetTextValues(Constants.GreaterMumLengthSequence,
Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(Constants.GreaterMumLengthSequence,
Constants.AlphabetNameNode));
for (int i = 0; i < referenceSequences.Length; i++)
{
ISequence referSeq = new Sequence(seqAlphabet, encodingObj.GetBytes(referenceSequences[i]));
refSeqList.Add(referSeq);
}
for (int i = 0; i < searchSequences.Length; i++)
{
ISequence searchSeq = new Sequence(seqAlphabet, encodingObj.GetBytes(searchSequences[i]));
searchSeqList.Add(searchSeq);
}
NucmerPairwiseAligner nucmerObj = new NucmerPairwiseAligner();
mumLength = utilityObj.xmlUtil.GetTextValue(Constants.GreaterMumLengthSequence, Constants.MUMLengthNode);
// Update other values for NUCmer object
nucmerObj.MaximumSeparation = 0;
nucmerObj.MinimumScore = 2;
nucmerObj.SeparationFactor = 0.12f;
nucmerObj.BreakLength = 2;
nucmerObj.LengthOfMUM = long.Parse(mumLength, null);
nucmerObj.MinimumScore = int.Parse(utilityObj.xmlUtil.GetTextValue(Constants.GreaterMumLengthSequence,
Constants.MinimumScoreNode), (IFormatProvider)null);
IList <ISequenceAlignment> seqAlign = nucmerObj.Align(refSeqList, searchSeqList);
if (seqAlign.Count == 0)
{
Console.WriteLine("NUCmer P2 : Successfully validated the invalid mumlength");
ApplicationLog.WriteLine("NUCmer P2 : Successfully validated the invalid mumlength");
}
else
{
Assert.Fail();
}
}
public void NUCmerAlignSmallSizeAlignSequence()
{
// Gets the reference sequence from the FastA file
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.SmallSizeSequenceNodeName,
Constants.FilePathNode);
Assert.IsNotNull(filePath);
FastAParser parser = new FastAParser();
IEnumerable <ISequence> refSeqList = parser.Parse(filePath);
// Gets the query sequence from the FastA file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(Constants.SmallSizeSequenceNodeName,
Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
FastAParser queryParser = new FastAParser();
IEnumerable <ISequence> searchSeqList = queryParser.Parse(queryFilePath);
string mumLength = this.utilityObj.xmlUtil.GetTextValue(Constants.SmallSizeSequenceNodeName, Constants.MUMAlignLengthNode);
NucmerPairwiseAligner nucmerObj = new NucmerPairwiseAligner
{
MaximumSeparation = 0,
MinimumScore = 2,
SeparationFactor = 0.12f,
BreakLength = 2,
LengthOfMUM = long.Parse(mumLength, null)
};
IList <ISequenceAlignment> align = nucmerObj.Align(refSeqList.ElementAt(0), searchSeqList);
string expectedSequences = this.utilityObj.xmlUtil.GetFileTextValue(Constants.SmallSizeSequenceNodeName,
Constants.ExpectedSequencesNode);
string[] expSeqArray = expectedSequences.Split(',');
int j = 0;
// Gets all the aligned sequences in comma separated format
foreach (IPairwiseSequenceAlignment seqAlignment in align)
{
foreach (PairwiseAlignedSequence alignedSeq in seqAlignment)
{
Assert.AreEqual(expSeqArray[j], alignedSeq.FirstSequence.ConvertToString());
++j;
Assert.AreEqual(expSeqArray[j], alignedSeq.SecondSequence.ConvertToString());
j++;
}
}
}
public void NUCmerAlignerProperties()
{
NucmerPairwiseAligner nucmerObj = new NucmerPairwiseAligner();
Assert.AreEqual(Constants.NUCLength, nucmerObj.LengthOfMUM.ToString((IFormatProvider)null));
Assert.AreEqual(200, nucmerObj.BreakLength);
Assert.AreEqual(-8, nucmerObj.GapExtensionCost);
Assert.AreEqual(-13, nucmerObj.GapOpenCost);
Assert.AreEqual(Constants.NUCFixedSeperation, nucmerObj.FixedSeparation.ToString(CultureInfo.InvariantCulture));
Assert.AreEqual(Constants.NUCMaximumSeparation, nucmerObj.MaximumSeparation.ToString(CultureInfo.InvariantCulture));
Assert.AreEqual(Constants.NUCMinimumScore, nucmerObj.MinimumScore.ToString(CultureInfo.InvariantCulture));
Assert.AreEqual(Constants.NUCSeparationFactor, nucmerObj.SeparationFactor.ToString(CultureInfo.InvariantCulture));
}
/// <summary>
/// Validates the NUCmer align method for several test cases for the parameters passed.
/// </summary>
/// <param name="sequenceList">List of Input Sequences</param>
private static void ValidateNUCmerEmptyAlignGeneralTestCases(IEnumerable <ISequence> sequenceList)
{
var nucmerObj = new NucmerPairwiseAligner();
try
{
IList <ISequenceAlignment> result = nucmerObj.Align(sequenceList);
ApplicationLog.WriteLine("NUCmer P2 : Exception not thrown");
Assert.Fail("ArgumentNullException not thrown.");
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine("NUCmer P2: Successfully validated empty SequenceList");
}
}
/// <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.");
}
public void NUCmerAlignerProperties()
{
NucmerPairwiseAligner nucmerObj = new NucmerPairwiseAligner();
Assert.AreEqual(Constants.NUCLength,
nucmerObj.LengthOfMUM.ToString((IFormatProvider)null));
Assert.AreEqual(200, nucmerObj.BreakLength);
Assert.AreEqual(-8, nucmerObj.GapExtensionCost);
Assert.AreEqual(-13, nucmerObj.GapOpenCost);
Assert.AreEqual(Constants.NUCFixedSeperation,
nucmerObj.FixedSeparation.ToString((IFormatProvider)null));
Assert.AreEqual(Constants.NUCMaximumSeparation,
nucmerObj.MaximumSeparation.ToString((IFormatProvider)null));
Assert.AreEqual(Constants.NUCMinimumScore,
nucmerObj.MinimumScore.ToString((IFormatProvider)null));
Assert.AreEqual(Constants.NUCSeparationFactor,
nucmerObj.SeparationFactor.ToString((IFormatProvider)null));
ApplicationLog.WriteLine("Successfully validated all the properties of NUCmer Aligner class.");
}
public void NUCmerAlignGreaterMumLength()
{
// Gets the reference & search sequences from the configuration file
string[] referenceSequences = this.utilityObj.xmlUtil.GetTextValues(Constants.GreaterMumLengthSequence, Constants.ReferenceSequencesNode);
string[] searchSequences = this.utilityObj.xmlUtil.GetTextValues(Constants.GreaterMumLengthSequence, Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(Constants.GreaterMumLengthSequence, 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();
string mumLength = this.utilityObj.xmlUtil.GetTextValue(Constants.GreaterMumLengthSequence, Constants.MUMLengthNode);
var nucmerObj = new NucmerPairwiseAligner
{
MaximumSeparation = 0,
SeparationFactor = 0.12f,
BreakLength = 2,
LengthOfMUM = long.Parse(mumLength, null),
MinimumScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(Constants.GreaterMumLengthSequence, Constants.MinimumScoreNode), null)
};
IList <ISequenceAlignment> seqAlign = nucmerObj.Align(refSeqList, searchSeqList);
Assert.AreEqual(0, seqAlign.Count);
}
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 = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.ReferenceSequencesNode);
searchSequences = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(
utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
for (int i = 0; i < referenceSequences.Length; i++)
{
ISequence referSeq = new Sequence(seqAlphabet,
encodingObj.GetBytes(referenceSequences[i]));
refSeqList.Add(referSeq);
}
for (int i = 0; i < searchSequences.Length; i++)
{
ISequence searchSeq = new Sequence(seqAlphabet,
encodingObj.GetBytes(searchSequences[i]));
searchSeqList.Add(searchSeq);
}
// Gets the mum length from the xml
string mumLength = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MUMAlignLengthNode);
NucmerPairwiseAligner nucmerObj = new NucmerPairwiseAligner();
// Update other values for NUCmer object
nucmerObj.MaximumSeparation = int.Parse
(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), (IFormatProvider)null);
nucmerObj.MinimumScore = int.Parse(
utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), (IFormatProvider)null);
nucmerObj.SeparationFactor = int.Parse(
utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), (IFormatProvider)null);
nucmerObj.BreakLength = int.Parse(
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 = 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++;
}
}
Console.WriteLine(
"NUCmer BVT : Successfully validated all the aligned sequences.");
ApplicationLog.WriteLine(
"NUCmer BVT : Successfully validated all the aligned sequences.");
}
void ValidateNUCmerAlignGeneralTestCases(string nodeName, bool isFilePath)
{
string[] referenceSequences = null;
string[] searchSequences = null;
IEnumerable <ISequence> refSeqList = new List <ISequence>();
IEnumerable <ISequence> searchSeqList = new List <ISequence>();
if (isFilePath)
{
// Gets the reference sequence from the FastA file
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"NUCmer BVT : Successfully validated the File Path '{0}'.", filePath));
FastAParser parser = new FastAParser(filePath);
refSeqList = parser.Parse();
// Gets the query sequence from the FastA file
string queryFilePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"NUCmer BVT : Successfully validated the File Path '{0}'.", queryFilePath));
FastAParser queryParser = new FastAParser(queryFilePath);
searchSeqList = queryParser.Parse();
}
else
{
// Gets the reference & search sequences from the configurtion file
referenceSequences = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.ReferenceSequencesNode);
searchSequences = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
IList <ISequence> tempRefSeqList = new List <ISequence>();
for (int i = 0; i < referenceSequences.Length; i++)
{
ISequence referSeq = new Sequence(seqAlphabet, encodingObj.GetBytes(referenceSequences[i]));
referSeq.ID = "ref " + i;
tempRefSeqList.Add(referSeq);
}
refSeqList = (IEnumerable <ISequence>)tempRefSeqList;
IList <ISequence> tempSearchSeqList = new List <ISequence>();
for (int i = 0; i < searchSequences.Length; i++)
{
ISequence searchSeq = new Sequence(seqAlphabet, encodingObj.GetBytes(searchSequences[i]));
searchSeq.ID = "qry " + i;
tempSearchSeqList.Add(searchSeq);
}
searchSeqList = (IEnumerable <ISequence>)tempSearchSeqList;
}
string mumLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode);
NucmerPairwiseAligner nucmerObj = new NucmerPairwiseAligner();
nucmerObj.MaximumSeparation = 0;
nucmerObj.MinimumScore = 2;
nucmerObj.SeparationFactor = 0.12f;
nucmerObj.BreakLength = 2;
nucmerObj.LengthOfMUM = long.Parse(mumLength, null);
IList <ISequenceAlignment> align = nucmerObj.Align(refSeqList, searchSeqList);
string expectedSequences = string.Empty;
if (isFilePath)
{
expectedSequences = utilityObj.xmlUtil.GetFileTextValue(nodeName,
Constants.ExpectedSequencesNode);
}
else
{
expectedSequences = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequencesNode);
}
string[] expSeqArray = expectedSequences.Split(',');
// Gets all the aligned sequences in comma seperated format
foreach (IPairwiseSequenceAlignment seqAlignment in align)
{
foreach (PairwiseAlignedSequence alignedSeq in seqAlignment)
{
string actualStr = new string(alignedSeq.FirstSequence.Select(a => (char)a).ToArray());
Assert.IsTrue(expSeqArray.Contains(actualStr));
actualStr = new string(alignedSeq.SecondSequence.Select(a => (char)a).ToArray());
Assert.IsTrue(expSeqArray.Contains(actualStr));
}
}
Console.WriteLine("NUCmer BVT : Successfully validated all the aligned sequences.");
ApplicationLog.WriteLine("NUCmer BVT : Successfully validated all the aligned sequences.");
}
public void NUCmerAlignSmallSizeAlignSequence()
{
IEnumerable <ISequence> refSeqList = new List <ISequence>();
IEnumerable <ISequence> searchSeqList = new List <ISequence>();
// Gets the reference sequence from the FastA file
string filePath = utilityObj.xmlUtil.GetTextValue(Constants.SmallSizeSequenceNodeName,
Constants.FilePathNode);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"NUCmer BVT : Successfully validated the File Path '{0}'.", filePath));
FastAParser parser = new FastAParser(filePath);
refSeqList = parser.Parse();
// Gets the query sequence from the FastA file
string queryFilePath = utilityObj.xmlUtil.GetTextValue(Constants.SmallSizeSequenceNodeName,
Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"NUCmer BVT : Successfully validated the File Path '{0}'.", queryFilePath));
FastAParser queryParser = new FastAParser(queryFilePath);
searchSeqList = queryParser.Parse();
string mumLength = utilityObj.xmlUtil.GetTextValue(Constants.SmallSizeSequenceNodeName, Constants.MUMAlignLengthNode);
NucmerPairwiseAligner nucmerObj = new NucmerPairwiseAligner();
nucmerObj.MaximumSeparation = 0;
nucmerObj.MinimumScore = 2;
nucmerObj.SeparationFactor = 0.12f;
nucmerObj.BreakLength = 2;
nucmerObj.LengthOfMUM = long.Parse(mumLength, null);
IList <ISequenceAlignment> align = nucmerObj.Align(refSeqList.ElementAt(0), searchSeqList);
string expectedSequences = string.Empty;
expectedSequences = utilityObj.xmlUtil.GetFileTextValue(Constants.SmallSizeSequenceNodeName,
Constants.ExpectedSequencesNode);
string[] expSeqArray = expectedSequences.Split(',');
int j = 0;
// Gets all the aligned sequences in comma seperated format
foreach (IPairwiseSequenceAlignment seqAlignment in align)
{
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++;
}
}
Console.WriteLine("NUCmer BVT : Successfully validated all the aligned sequences.");
ApplicationLog.WriteLine("NUCmer BVT : 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="isFilePath">Is Sequence saved in File</param>
void ValidateNUCmerAlignGeneralTestCases(string nodeName, bool isFilePath)
{
IList <ISequence> refSeqList, searchSeqList;
if (isFilePath)
{
// Gets the reference sequence from the FastA file
string filePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
Assert.IsNotNull(filePath);
Assert.IsTrue(File.Exists(filePath));
ApplicationLog.WriteLine(string.Format(null, "NUCmer BVT : Successfully validated the File Path '{0}'.", filePath));
FastAParser parser = new FastAParser();
refSeqList = parser.Parse(filePath).ToList();
// Gets the query sequence from the FastA file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
Assert.IsTrue(File.Exists(queryFilePath));
ApplicationLog.WriteLine(string.Format(null, "NUCmer BVT : Successfully validated the File Path '{0}'.", queryFilePath));
searchSeqList = parser.Parse(queryFilePath).ToList();
}
else
{
// Gets the reference & search sequences from the configuration file
IAlphabet seqAlphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
string[] sequences = this.utilityObj.xmlUtil.GetTextValues(nodeName, Constants.ReferenceSequencesNode);
refSeqList = sequences.Select((t, i) => new Sequence(seqAlphabet, this.encodingObj.GetBytes(t))
{
ID = "ref " + i
}).Cast <ISequence>().ToList();
sequences = this.utilityObj.xmlUtil.GetTextValues(nodeName, Constants.SearchSequencesNode);
searchSeqList = sequences.Select((t, i) => new Sequence(seqAlphabet, this.encodingObj.GetBytes(t))
{
ID = "qry " + i
}).Cast <ISequence>().ToList();
}
var aligner = new NucmerPairwiseAligner
{
MaximumSeparation = 0,
MinimumScore = 2,
SeparationFactor = 0.12f,
BreakLength = 2,
LengthOfMUM = long.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode), null)
};
IList <ISequenceAlignment> align = aligner.Align(refSeqList, searchSeqList);
string expectedSequences = isFilePath
? this.utilityObj.xmlUtil.GetFileTextValue(nodeName, Constants.ExpectedSequencesNode)
: this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequencesNode);
string[] expSeqArray = expectedSequences.Split(',');
// Gets all the aligned sequences in comma separated format
foreach (IPairwiseSequenceAlignment seqAlignment in align)
{
foreach (PairwiseAlignedSequence alignedSeq in seqAlignment)
{
string actualStr = alignedSeq.FirstSequence.ConvertToString();
Assert.IsTrue(expSeqArray.Contains(actualStr));
actualStr = alignedSeq.SecondSequence.ConvertToString();
Assert.IsTrue(expSeqArray.Contains(actualStr));
}
}
}
public void TestNUCmer3CustomBreakLength()
{
Sequence referenceSeq = null;
Sequence searchSeq = null;
List <ISequence> referenceSeqs = null;
List <ISequence> searchSeqs = null;
referenceSeqs = new List <ISequence>();
string reference = "CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGT";
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R1";
referenceSeqs.Add(referenceSeq);
reference = "CCCCCCCCC";
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R2";
referenceSeqs.Add(referenceSeq);
reference = "TTTTT";
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R3";
referenceSeqs.Add(referenceSeq);
searchSeqs = new List <ISequence>();
string search = "CATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAA";
searchSeq = new Sequence(Alphabets.DNA, search);
searchSeq.ID = "Q1";
searchSeqs.Add(searchSeq);
search = "CAAAGTCTCTATCAGAATGCAGATGCAGATGTTTTTGTGGGGTCATCAAGATATAGCAAGAAGTTCAAGC";
searchSeq = new Sequence(Alphabets.DNA, search);
searchSeq.ID = "Q2";
searchSeqs.Add(searchSeq);
search = "AAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGC";
searchSeq = new Sequence(Alphabets.DNA, search);
searchSeq.ID = "Q3";
searchSeqs.Add(searchSeq);
NucmerPairwiseAligner nucmer = new NucmerPairwiseAligner();
nucmer.MaximumSeparation = 0;
nucmer.MinimumScore = 2;
nucmer.SeparationFactor = 0.12F;
nucmer.LengthOfMUM = 5;
nucmer.BreakLength = 2;
IList <IPairwiseSequenceAlignment> result = nucmer.Align(referenceSeqs, searchSeqs).Select(a => a as IPairwiseSequenceAlignment).ToList();
// Check if output is not null
Assert.AreNotEqual(null, result);
List <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "AAAGGGA");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "AAAGGGA");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "AAAGGGA");
alignedSeq.Score = 21;
alignedSeq.FirstOffset = 8;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "CATTA");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "CATTA");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "CATTA");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 31;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "ATGTT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "ATGTT");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "ATGTT");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 13;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "GAATGC");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "GAATGC");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "GAATGC");
alignedSeq.Score = 18;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 11;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "TTTTT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "TTTTT");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "TTTTT");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 31;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "CAAAA");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "CAAAA");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "CAAAA");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 3;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "GGATT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "GGATT");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "GGATT");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 45;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "GCAAA");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "GCAAA");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "GCAAA");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 9;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "TTACC");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "TTACC");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "TTACC");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 22;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
public void ValidatePairwiseAlignedSequenceMultipleRefQuery()
{
var referenceSeqs = new List <ISequence>()
{
new Sequence(Alphabets.DNA, "ATGCGCATCCCC")
{
ID = "R1"
},
new Sequence(Alphabets.DNA, "TAGCT")
{
ID = "R2"
}
};
var searchSeqs = new List <ISequence>()
{
new Sequence(Alphabets.DNA, "CCGCGCCCCCTC")
{
ID = "Q1"
},
new Sequence(Alphabets.DNA, "AGCT")
{
ID = "Q2"
}
};
var nucmer = new NucmerPairwiseAligner
{
FixedSeparation = 0,
MinimumScore = 2,
SeparationFactor = -1,
LengthOfMUM = 3,
ForwardOnly = true,
};
IList <IPairwiseSequenceAlignment> result = nucmer.Align(referenceSeqs, searchSeqs).Select(a => a as IPairwiseSequenceAlignment).ToList();
// Check if output is not null
Assert.AreNotEqual(null, result);
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
var alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "GCGCATCCCC"),
SecondSequence = new Sequence(Alphabets.DNA, "GCGC--CCCC"),
Consensus = new Sequence(Alphabets.DNA, "GCGCATCCCC"),
Score = -5,
FirstOffset = 0,
SecondOffset = 0
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "AGCT"),
SecondSequence = new Sequence(Alphabets.DNA, "AGCT"),
Consensus = new Sequence(Alphabets.DNA, "AGCT"),
Score = 12,
FirstOffset = 0,
SecondOffset = 1
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
ApplicationLog.WriteLine("PairwiseAlignedSequence P1: Successfully validated Sequence with Multiple Reference.");
}
public NucmerAlignerProvider(ISequenceProvider provider, NucmerPairwiseAligner aligner)
{
_provider = provider;
_aligner = aligner;
}
public void ValidatePairwiseAlignedSequenceCustomBreakLength()
{
var referenceSeqs = new List <ISequence>()
{
new Sequence(Alphabets.DNA, "CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGT")
{
ID = "R1"
},
new Sequence(Alphabets.DNA, "CCCCCCCCC")
{
ID = "R2"
},
new Sequence(Alphabets.DNA, "TTTTT")
{
ID = "R3"
}
};
var searchSeqs = new List <ISequence>()
{
new Sequence(Alphabets.DNA, "CATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAA")
{
ID = "Q1"
},
new Sequence(Alphabets.DNA, "CAAAGTCTCTATCAGAATGCAGATGCAGATGTTTTTGTGGGGTCATCAAGATATAGCAAGAAGTTCAAGC")
{
ID = "Q2"
},
new Sequence(Alphabets.DNA, "AAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGC")
{
ID = "Q3"
},
};
var nucmer = new NucmerPairwiseAligner
{
MaximumSeparation = 0,
MinimumScore = 2,
SeparationFactor = 0.12F,
LengthOfMUM = 5,
BreakLength = 2,
ForwardOnly = true,
};
var result = nucmer.Align(referenceSeqs, searchSeqs).Select(a => a as IPairwiseSequenceAlignment).ToList();
// Check if output is not null
Assert.AreNotEqual(null, result);
var expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "AAAGGGA"),
SecondSequence = new Sequence(Alphabets.DNA, "AAAGGGA"),
Consensus = new Sequence(Alphabets.DNA, "AAAGGGA"),
Score = 21,
FirstOffset = 8,
SecondOffset = 0
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "CATTA"),
SecondSequence = new Sequence(Alphabets.DNA, "CATTA"),
Consensus = new Sequence(Alphabets.DNA, "CATTA"),
Score = 15,
FirstOffset = 0,
SecondOffset = 31
});
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "ATGTT"),
SecondSequence = new Sequence(Alphabets.DNA, "ATGTT"),
Consensus = new Sequence(Alphabets.DNA, "ATGTT"),
Score = 15,
FirstOffset = 13,
SecondOffset = 0
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "GAATGC"),
SecondSequence = new Sequence(Alphabets.DNA, "GAATGC"),
Consensus = new Sequence(Alphabets.DNA, "GAATGC"),
Score = 18,
FirstOffset = 0,
SecondOffset = 11
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "TTTTT"),
SecondSequence = new Sequence(Alphabets.DNA, "TTTTT"),
Consensus = new Sequence(Alphabets.DNA, "TTTTT"),
Score = 15,
FirstOffset = 31,
SecondOffset = 0
});
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "CAAAA"),
SecondSequence = new Sequence(Alphabets.DNA, "CAAAA"),
Consensus = new Sequence(Alphabets.DNA, "CAAAA"),
Score = 15,
FirstOffset = 3,
SecondOffset = 0
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "GGATT"),
SecondSequence = new Sequence(Alphabets.DNA, "GGATT"),
Consensus = new Sequence(Alphabets.DNA, "GGATT"),
Score = 15,
FirstOffset = 45,
SecondOffset = 0
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "GCAAA"),
SecondSequence = new Sequence(Alphabets.DNA, "GCAAA"),
Consensus = new Sequence(Alphabets.DNA, "GCAAA"),
Score = 15,
FirstOffset = 0,
SecondOffset = 9
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "TTACC"),
SecondSequence = new Sequence(Alphabets.DNA, "TTACC"),
Consensus = new Sequence(Alphabets.DNA, "TTACC"),
Score = 15,
FirstOffset = 22,
SecondOffset = 0
});
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
ApplicationLog.WriteLine("PairwiseAlignedSequence P1: Successfully validated Sequence with Custom Break Length.");
}
