public void TestSimpleSequenceAssembler()
{
Trace.Set(Trace.AssemblyDetails); // turn on log dump
// test parameters
int matchScore = 1;
int mismatchScore = -8;
int gapCost = -8;
double mergeThreshold = 4;
double consensusThreshold = 66;
Sequence seq1 = new Sequence(Alphabets.DNA, "GCCAAAATTTAGGC");
Sequence seq2 = new Sequence(Alphabets.DNA, "TTATGGCGCCCACGGA");
Sequence seq3 = new Sequence(Alphabets.DNA, "TATAAAGCGCCAA");
// here is how the above sequences should align:
// TATAAAGCGCCAA
// GCCAAAATTTAGGC
// AGGCACCCGCGGTATT <= reversed
//
// TATAAAGCGCCAAAATTTAGGCACCCGCGGTATT
OverlapDeNovoAssembler assembler = new OverlapDeNovoAssembler();
assembler.MergeThreshold = mergeThreshold;
assembler.OverlapAlgorithm = new PairwiseOverlapAligner();
((IPairwiseSequenceAligner)assembler.OverlapAlgorithm).SimilarityMatrix = new DiagonalSimilarityMatrix(matchScore, mismatchScore);
((IPairwiseSequenceAligner)assembler.OverlapAlgorithm).GapOpenCost = gapCost;
assembler.ConsensusResolver = new SimpleConsensusResolver(consensusThreshold);
assembler.AssumeStandardOrientation = false;
List<ISequence> inputs = new List<ISequence>();
inputs.Add(seq1);
inputs.Add(seq2);
inputs.Add(seq3);
IOverlapDeNovoAssembly seqAssembly = (IOverlapDeNovoAssembly)assembler.Assemble(inputs);
Assert.AreEqual(0, seqAssembly.UnmergedSequences.Count);
Assert.AreEqual(1, seqAssembly.Contigs.Count);
Contig contig0 = seqAssembly.Contigs[0];
Assert.AreEqual("TATAAAGCGCCAAAATTTAGGCACCCGCGGTATT", contig0.Consensus.ConvertToString());
Assert.AreEqual(3, contig0.Sequences.Count);
}
/// <summary>
/// Validate Sequence Assembler Test cases based on additional parameter values
/// </summary>
/// <param name="additionalParameter">Additional parameters</param>
private IOverlapDeNovoAssembly GetSequenceAssembly(string additionalParameter)
{
// Get the parameters from Xml
int matchScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.MatchScoreNode), null);
int mismatchScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.MisMatchScoreNode), null);
int gapCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.GapCostNode), null);
double mergeThreshold = double.Parse(this.utilityObj.xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.MergeThresholdNode), null);
double consensusThreshold = double.Parse(this.utilityObj.xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.ConsensusThresholdNode), null);
string sequence1 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode1);
string sequence2 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode2);
string sequence3 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode3);
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.AlphabetNameNode));
// Log based on the test cases
switch (additionalParameter)
{
case "consensus":
// Logs the sequences
ApplicationLog.WriteLine(string.Format(null,
"SimpleConsensusMethod BVT : Sequence 1 used is '{0}'.",
sequence1));
ApplicationLog.WriteLine(string.Format(null,
"SimpleConsensusMethod BVT : Sequence 2 used is '{0}'.",
sequence2));
ApplicationLog.WriteLine(string.Format(null,
"SimpleConsensusMethod BVT : Sequence 3 used is '{0}'.",
sequence3));
break;
default:
// Logs the sequences
ApplicationLog.WriteLine(string.Format(null,
"SequenceAssembly BVT : Sequence 1 used is '{0}'.", sequence1));
ApplicationLog.WriteLine(string.Format(null,
"SequenceAssembly BVT : Sequence 2 used is '{0}'.", sequence2));
ApplicationLog.WriteLine(string.Format(null,
"SequenceAssembly BVT : Sequence 3 used is '{0}'.", sequence3));
break;
}
var seq1 = new Sequence(alphabet, sequence1);
var seq2 = new Sequence(alphabet, sequence2);
var seq3 = new Sequence(alphabet, sequence3);
// here is how the above sequences should align:
// TATAAAGCGCCAA
// GCCAAAATTTAGGC
// AGGCACCCGCGGTATT <= reversed
//
// TATAAAGCGCCAAAATTTAGGCACCCGCGGTATT
var assembler = new OverlapDeNovoAssembler();
assembler.MergeThreshold = mergeThreshold;
assembler.OverlapAlgorithm = new PairwiseOverlapAligner();
(assembler.OverlapAlgorithm).SimilarityMatrix =
new DiagonalSimilarityMatrix(matchScore, mismatchScore);
(assembler.OverlapAlgorithm).GapOpenCost = gapCost;
assembler.ConsensusResolver = new SimpleConsensusResolver(consensusThreshold);
assembler.AssumeStandardOrientation = false;
var inputs = new List<ISequence>();
inputs.Add(seq1);
inputs.Add(seq2);
inputs.Add(seq3);
// Assembles all the sequences.
return (IOverlapDeNovoAssembly) assembler.Assemble(inputs);
}
public void SimpleConsensusWithMakeConsensusMethod()
{
IOverlapDeNovoAssembly assembly = this.GetSequenceAssembly("consensus");
string contigConsensus = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.ContigConsensusNode);
double consensusThreshold = double.Parse(this.utilityObj.xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.ConsensusThresholdNode), null);
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.AlphabetNameNode));
// Read the contig from Contig method.
Contig contigReadForConsensus = assembly.Contigs[0];
contigReadForConsensus.Consensus = null;
var simpleSeqAssembler = new OverlapDeNovoAssembler();
simpleSeqAssembler.ConsensusResolver = new SimpleConsensusResolver(consensusThreshold);
simpleSeqAssembler.MakeConsensus(alphabet, contigReadForConsensus);
Assert.AreEqual(contigConsensus,
new String(contigReadForConsensus.Consensus.Select(a => (char) a).ToArray()));
// Log the required info.
ApplicationLog.WriteLine(string.Format(null,
"SimpleConsensusMethod BVT : Consensus read is '{0}'.",
contigReadForConsensus.Consensus));
}
/// <summary>
/// Validates the Sequence Assembler for all the general test cases.
/// </summary>
/// <param name="nodeName">Xml Node Name</param>
/// <param name="additionalParameter">
/// Additional Parameter based
/// on which the validations are done.
/// </param>
/// <param name="isSeqAssemblyctr">True if Default contructor is validated or else false.</param>
private void ValidateSequenceAssemblerGeneral(string nodeName,
AssemblyParameters additionalParameter, bool isSeqAssemblyctr)
{
// Get the parameters from Xml
int matchScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MatchScoreNode), null);
int mismatchScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MisMatchScoreNode), null);
int gapCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapCostNode), null);
double mergeThreshold = double.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MergeThresholdNode), null);
double consensusThreshold = double.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ConsensusThresholdNode),
null);
string[] sequences = this.utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SequencesNode);
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
string documentation = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.DocumentaionNode);
var info = new SerializationInfo(typeof (OverlapDeNovoAssembly),
new FormatterConverter());
var context = new StreamingContext(StreamingContextStates.All);
var inputs = new List<ISequence>();
switch (additionalParameter)
{
case AssemblyParameters.Consensus:
for (int i = 0; i < sequences.Length; i++)
{
// Logs the sequences
ApplicationLog.WriteLine(string.Format(null, "SimpleConsensusMethod P1 : Sequence '{0}' used is '{1}'.", i, sequences[i]));
var seq = new Sequence(alphabet, sequences[i]);
inputs.Add(seq);
}
break;
default:
for (int i = 0; i < sequences.Length; i++)
{
// Logs the sequences
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly P1 : Sequence '{0}' used is '{1}'.", i, sequences[i]));
var seq = new Sequence(alphabet, sequences[i]);
inputs.Add(seq);
}
break;
}
// here is how the above sequences should align:
// TATAAAGCGCCAA
// GCCAAAATTTAGGC
// AGGCACCCGCGGTATT <= reversed
//
// TATAAAGCGCCAAAATTTAGGCACCCGCGGTATT
var assembler = new OverlapDeNovoAssembler
{
MergeThreshold = mergeThreshold,
OverlapAlgorithm = new PairwiseOverlapAligner()
};
switch (additionalParameter)
{
case AssemblyParameters.DiagonalSM:
(assembler.OverlapAlgorithm).SimilarityMatrix =
new DiagonalSimilarityMatrix(matchScore, mismatchScore);
break;
case AssemblyParameters.SimilarityMatrix:
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
(assembler.OverlapAlgorithm).SimilarityMatrix = new SimilarityMatrix(new StreamReader(blosumFilePath));
break;
default:
(assembler.OverlapAlgorithm).SimilarityMatrix = new DiagonalSimilarityMatrix(matchScore, mismatchScore);
break;
}
(assembler.OverlapAlgorithm).GapOpenCost = gapCost;
assembler.ConsensusResolver = new SimpleConsensusResolver(consensusThreshold);
assembler.AssumeStandardOrientation = false;
// Assembles all the sequences.
IOverlapDeNovoAssembly assembly = (IOverlapDeNovoAssembly) assembler.Assemble(inputs);
// Set Documentation property.
assembly.Documentation = documentation;
// Get the parameters from Xml in general
int contigSequencesCount = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ContigSequencesCountNode), null);
string contigConsensus = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ContigConsensusNode);
switch (additionalParameter)
{
case AssemblyParameters.Consensus:
// Read the contig from Contig method.
Contig contigReadForConsensus = assembly.Contigs[0];
contigReadForConsensus.Consensus = null;
var simpleSeqAssembler = new OverlapDeNovoAssembler
{
ConsensusResolver = new SimpleConsensusResolver(consensusThreshold)
};
simpleSeqAssembler.MakeConsensus(alphabet, contigReadForConsensus);
// Log the required info.
ApplicationLog.WriteLine(string.Format(null, "SimpleConsensusMethod BVT : Consensus read is '{0}'.", contigReadForConsensus.Consensus));
Assert.AreEqual(contigConsensus, new String(contigReadForConsensus.Consensus.Select(a => (char) a).ToArray()));
break;
default:
// Get the parameters from Xml for Assemble() method test cases.
int unMergedCount = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.UnMergedSequencesCountNode),
null);
int contigsCount = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ContigsCountNode), null);
Assert.AreEqual(unMergedCount, assembly.UnmergedSequences.Count);
Assert.AreEqual(contigsCount, assembly.Contigs.Count);
Assert.AreEqual(documentation, assembly.Documentation);
Contig contigRead = assembly.Contigs[0];
// Logs the consensus
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Un Merged Sequences Count is '{0}'.", assembly.UnmergedSequences.Count));
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Contigs Count is '{0}'.", assembly.Contigs.Count));
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Contig Sequences Count is '{0}'.", contigRead.Sequences.Count));
ApplicationLog.WriteLine(string.Format(null, "SequenceAssembly BVT : Consensus read is '{0}'.", contigRead.Consensus));
Assert.AreEqual(contigConsensus, new String(contigRead.Consensus.Select(a => (char) a).ToArray()));
Assert.AreEqual(contigSequencesCount, contigRead.Sequences.Count);
break;
}
}
/// <summary>
/// This method runs assembly on the list of sequences passed.
/// Additionally the user is allowed to select the
/// alignment algorithm.
/// </summary>
/// <param name="input">Input for the assembly process.</param>
/// <param name="worker">The Assembly parser thread</param>
/// <returns>IDeNovoAssembly instance.</returns>
private static IDeNovoAssembly RunAssembly(AssemblyInputEventArgs input, BackgroundWorker worker)
{
double mergeThreshold = input.MergeThreshold;
List<ISequence> sequence = input.Sequences.ToList();
var assemble = new OverlapDeNovoAssembler();
assemble.OverlapAlgorithm = input.Aligner;
// Special casing for SW alignment.
if (assemble.OverlapAlgorithm is SmithWatermanAligner)
{
// If we set the Threshold value lesser than the Max score, then the result will be “JUNK”.
// So setting the threshold value to 25 approximately supports sequence length of 15,0000.
mergeThreshold = 25;
}
assemble.MergeThreshold = mergeThreshold;
assemble.OverlapAlgorithm.SimilarityMatrix = input.AlignerInput.SimilarityMatrix;
assemble.OverlapAlgorithm.GapOpenCost = input.AlignerInput.GapCost;
assemble.OverlapAlgorithm.GapExtensionCost = input.AlignerInput.GapExtensionCost;
assemble.ConsensusResolver = new SimpleConsensusResolver(input.ConsensusThreshold);
assemble.AssumeStandardOrientation = false;
AssignAlignerParameter(assemble.OverlapAlgorithm, input.AlignerInput);
IDeNovoAssembly assemblyOutput = assemble.Assemble(sequence);
if (worker != null && worker.CancellationPending)
{
return null;
}
return assemblyOutput;
}
public void ValidateOverlapDenovoAssemblyToString()
{
const int matchScore = 5;
const int mismatchScore = -4;
const int gapCost = -10;
const double mergeThreshold = 4;
const double consensusThreshold = 66;
ISequence seq1 = new Sequence(Alphabets.DNA,
this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.Seq1StrNode));
ISequence seq2 = new Sequence(Alphabets.DNA,
this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.Seq2StrNode));
var assembler = new OverlapDeNovoAssembler
{
MergeThreshold = mergeThreshold,
OverlapAlgorithm = new NeedlemanWunschAligner
{
SimilarityMatrix =
new DiagonalSimilarityMatrix(matchScore,
mismatchScore),
GapOpenCost = gapCost
},
ConsensusResolver = new SimpleConsensusResolver(consensusThreshold),
AssumeStandardOrientation = false
};
var inputs = new List<ISequence> {seq1, seq2};
var seqAssembly = (IOverlapDeNovoAssembly) assembler.Assemble(inputs);
Assert.AreEqual(0, seqAssembly.UnmergedSequences.Count);
Assert.AreEqual(1, seqAssembly.Contigs.Count);
assembler.OverlapAlgorithm = new SmithWatermanAligner
{
SimilarityMatrix =
new DiagonalSimilarityMatrix(matchScore, mismatchScore),
GapOpenCost = gapCost
};
seqAssembly = (OverlapDeNovoAssembly) assembler.Assemble(inputs);
string actualString = seqAssembly.ToString();
const string expectedString = "ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATG... +[1678]";
Assert.AreEqual(expectedString, actualString.Replace(System.Environment.NewLine, ""));
// Get the parameters from Xml
int matchScore1 =
int.Parse(
this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName, Constants.MatchScoreNode), null);
int mismatchScore1 =
int.Parse(
this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName, Constants.MisMatchScoreNode),
null);
int gapCost1 =
int.Parse(this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName, Constants.GapCostNode),
null);
double mergeThreshold1 =
double.Parse(
this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName, Constants.MergeThresholdNode),
null);
double consensusThreshold1 =
double.Parse(
this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.ConsensusThresholdNode), null);
string sequence1 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode1);
string sequence2 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode2);
string sequence3 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode3);
IAlphabet alphabet =
Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.AlphabetNameNode));
var seq4 = new Sequence(alphabet, sequence1);
var seq5 = new Sequence(alphabet, sequence2);
var seq6 = new Sequence(alphabet, sequence3);
var assembler1 = new OverlapDeNovoAssembler
{
MergeThreshold = mergeThreshold1,
OverlapAlgorithm = new PairwiseOverlapAligner
{
SimilarityMatrix =
new DiagonalSimilarityMatrix(matchScore1,
mismatchScore1),
GapOpenCost = gapCost1,
},
ConsensusResolver = new SimpleConsensusResolver(consensusThreshold1),
AssumeStandardOrientation = false,
};
var inputs1 = new List<ISequence> {seq4, seq5, seq6};
// Assembles all the sequences.
seqAssembly = (OverlapDeNovoAssembly) assembler1.Assemble(inputs1);
Assert.AreEqual(0, seqAssembly.UnmergedSequences.Count);
Assert.AreEqual(1, seqAssembly.Contigs.Count);
assembler1.OverlapAlgorithm = new SmithWatermanAligner();
seqAssembly = (OverlapDeNovoAssembly) assembler1.Assemble(inputs1);
string expectedString1 = "TYMKWRRGCGCCAAAATTTAGGC" + System.Environment.NewLine;
actualString = seqAssembly.ToString();
Assert.AreEqual(expectedString1, actualString);
}
public void ValidateContigToString()
{
const int matchScore = 5;
const int mismatchScore = -4;
const int gapCost = -10;
const double mergeThreshold = 4;
const double consensusThreshold = 66;
string seq2Str = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName, Constants.Seq2StrNode);
string seq1Str = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName, Constants.Seq1StrNode);
ISequence seq1 = new Sequence(Alphabets.DNA, seq1Str);
ISequence seq2 = new Sequence(Alphabets.DNA, seq2Str);
var assembler = new OverlapDeNovoAssembler
{
MergeThreshold = mergeThreshold,
OverlapAlgorithm = new NeedlemanWunschAligner
{
SimilarityMatrix =
new DiagonalSimilarityMatrix(matchScore,
mismatchScore),
GapOpenCost = gapCost
},
ConsensusResolver = new SimpleConsensusResolver(consensusThreshold),
AssumeStandardOrientation = false
};
var seqAssembly = (IOverlapDeNovoAssembly) assembler.Assemble(new List<ISequence> {seq1, seq2});
Contig contig0 = seqAssembly.Contigs[0];
string actualString = contig0.ToString();
string expectedString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.OverlapDenovoExpectedNode);
Assert.AreEqual(expectedString.Replace("\\r\\n", ""), actualString.Replace("\r\n", ""));
// Get the parameters from Xml
int matchScore1 =
int.Parse(
this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName, Constants.MatchScoreNode), null);
int mismatchScore1 =
int.Parse(
this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName, Constants.MisMatchScoreNode),
null);
int gapCost1 =
int.Parse(this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName, Constants.GapCostNode),
null);
double mergeThreshold1 =
double.Parse(
this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName, Constants.MergeThresholdNode),
null);
double consensusThreshold1 =
double.Parse(
this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.ConsensusThresholdNode), null);
string sequence1 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode1);
string sequence2 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode2);
string sequence3 = this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode3);
IAlphabet alphabet =
Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.AlphabetNameNode));
ISequence seq4 = new Sequence(alphabet, sequence1);
ISequence seq5 = new Sequence(alphabet, sequence2);
ISequence seq6 = new Sequence(alphabet, sequence3);
var assembler1 = new OverlapDeNovoAssembler
{
MergeThreshold = mergeThreshold1,
OverlapAlgorithm = new PairwiseOverlapAligner
{
SimilarityMatrix =
new DiagonalSimilarityMatrix(matchScore1,
mismatchScore1),
GapOpenCost = gapCost1
},
ConsensusResolver = new SimpleConsensusResolver(consensusThreshold1),
AssumeStandardOrientation = false
};
// Assembles all the sequences.
var seqAssembly1 = (IOverlapDeNovoAssembly) assembler1.Assemble(new List<ISequence> {seq4, seq5, seq6});
Contig contig1 = seqAssembly1.Contigs[0];
string actualString1 = contig1.ToString();
const string expectedString1 = "TATAAAGCGCCAAAATTTAGGCACCCGCGGTATT";
Assert.AreEqual(expectedString1, actualString1);
}
public void TestSimpleSequenceAssemblerWithSwineflu()
{
Trace.Set(Trace.AssemblyDetails); // turn on log dump
// test parameters
const int matchScore = 5;
const int mismatchScore = -4;
const int gapCost = -10;
const double mergeThreshold = 4;
const double consensusThreshold = 66;
ISequence seq2 = new Sequence(Alphabets.DNA, "ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGAGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATATAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATATACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCGAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAA");
ISequence seq1 = new Sequence(Alphabets.DNA, "ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAATTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA");
OverlapDeNovoAssembler assembler = new OverlapDeNovoAssembler
{
MergeThreshold = mergeThreshold,
OverlapAlgorithm = new NeedlemanWunschAligner
{
SimilarityMatrix = new DiagonalSimilarityMatrix(matchScore, mismatchScore),
GapOpenCost = gapCost
},
ConsensusResolver = new SimpleConsensusResolver(consensusThreshold),
AssumeStandardOrientation = false
};
var inputs = new List<ISequence> {seq1, seq2};
var seqAssembly = (IOverlapDeNovoAssembly)assembler.Assemble(inputs);
Assert.AreEqual(0, seqAssembly.UnmergedSequences.Count);
Assert.AreEqual(1, seqAssembly.Contigs.Count);
Contig contig0 = seqAssembly.Contigs[0];
string expected = "AYRAARGCAAYAMWARTRRWKSYRMTAYWWRYAKTTSYRMYMKMWAMWKYWGMMACMKYAWRTRYAGRYWMWYWWKSKAWMRRTTMWMMWGMSAMYRWWKMMACAGWMMYWGWARASAMWGTAMYAGWAAMRMAYKYWRYWRWMMYWCWMKMWGWYAASCWTMWMGRRRAMMWRYRYAAMSKRARASKRKKMRMMCYAWKRSRWKTRGSYMMATKKMAYWTKGSTRRMTGKAWCMTKGSWRRYYSRRWSYKKGRAWMWCYMKMSWSWGMAWSMYYMTSSWCMKMMAKYKYRKRRWCMTMYAKTKYRGAMAMWKSWASKTSWKACMMWGGARMKTKYWWCSMWKRWGAKKWSMTMRRWKAKSARKWGMKMWSAGWGYMATYRWKYKMARKGTYWKMRWTWKWMMSSWWKRMRAKWTYMYSSMMSAMWMRTKMMTSGMMCAAWSRTGWMWCGRMMRMAKGTSYWMMKGCWGSAKSWMMWMRYKYYKRMRMAAAWWKMWTMTRSMWARWTWWAAWAKGRMWWKYWWAMMMARRRMWYWSMWAMYCMWASMTYARYRAWWMMKRSAWWRAWGWYMWMGKGMWAKRRGKCMTYSWSCWWYSRKSYAYTMRYSMTSMMYMWMMWAGTSYYKAYCARMAWRSWSWYKMWYAKRWTKYWGWKGSRWMWKYWWKWKWSRGSWMRWMRWKMWAKMSSRARAWRKYMAWRMSRSMMAWAGYRAKRRRWCMMRAAGKGAGRRWKMAMKAWKRSWGRAYRMWMKWWKASYSGRSASWMRWARWRMCRKKMGAMRMAAYWRSAWWYSWAGYRRYWSSRARWYWWGYRKTMSCRAKRKAWRSAWWYGCWRKRKMWRGWAWTRYYRKWTCWGRTAYWMYMRTYYMMGATWSMMMWRYMMMYKRTYRSAMWMCMAMKKGTSMKAYAMMCAMSRGYSYYMYAWWYMMSARYMTMCMWYYKMWSAMWATWSRWMMRWKYMCAAWWKRWRWAWRWMSMAMAWAWKTRARAMKSRCMAMAKKRWKRMKGRMYRYMSSRTYKAKKMAWKYYMSRKSYMTWYWWKSKRSMRKYSYMKKTKKSRYYRWWGSSGGKTKSAYWGRRRKGGKRKRKRSAKGGWWSGKWKATSRMYRKYAMRRTKAKCASSRKYMARRWKAKSMRGSSKMMSKRWAKRSMRCMSASMWKRMSAKYRMMSAGAWTRCYAWYRAMGWRAWTWCTRWYAWWGWAAAKWYKRWTAYWSARWWSAYRRMWRTASRKWWMRMRKYMRWMSRYMWRGARWWMARMMWMSWGRAWWWAARWAWARARAWTKWWRATRRWWWMSTKGAYRWTKGKWYYYWSRAYRYYKRRMYKTWSRWTSYMKWRSWRWWKGWWMKAWYKKWRRAYKAMMRMRMTTYRRAYKWSMASRAYTYRWATGWRAAGRWMWKAWRYSARWWRRWAARMARYSMSMWRRAAAWYRRWRMCRRSKRMWTTGRAWWYKRCYRCWWWKRMKWTWACMMSWRMWKSGAWARYRYSWRMAWKGRRASTKWYRAMWAYSSRAMWTAYKMMKASSMARMAWAMTYARASRRAGMARAAWTARAYRGRGWARARMTRGAWKSRRYAARGMTKKAMYMRAYWWKGRYKWWCYAKWYWWYKGYSRYCWRTTCAWYKGTMSYSRKWKYMTYSSTRSKGGYARTCWSYYTSKGGRYRWKCWSTWWYKGGWYKYKMYMKWRTRGRWYWYKWMWKTRWAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAA";
Assert.AreEqual(expected, contig0.Consensus.ConvertToString(), "NeedlemanWunschAligner");
Assert.AreEqual(2, contig0.Sequences.Count);
assembler.OverlapAlgorithm = new SmithWatermanAligner();
seqAssembly = (IOverlapDeNovoAssembly)assembler.Assemble(inputs);
Assert.AreEqual(0, seqAssembly.UnmergedSequences.Count);
Assert.AreEqual(1, seqAssembly.Contigs.Count);
contig0 = seqAssembly.Contigs[0];
expected = "ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGRGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGWCATCAAGATAYAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATAYACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAARTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCRAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGYTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAA";
Assert.AreEqual(expected, contig0.Consensus.ConvertToString(), "SmithwatermanAligner");
Assert.AreEqual(2, contig0.Sequences.Count);
assembler.OverlapAlgorithm = new PairwiseOverlapAligner();
seqAssembly = (IOverlapDeNovoAssembly)assembler.Assemble(inputs);
Assert.AreEqual(0, seqAssembly.UnmergedSequences.Count);
Assert.AreEqual(1, seqAssembly.Contigs.Count);
contig0 = seqAssembly.Contigs[0];
expected = "ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGRGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGWCATCAAGATAYAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATAYACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAARTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCRAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGYTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAA";
Assert.AreEqual(expected, contig0.Consensus.ConvertToString(), "PairwiseOverlapAligner");
Assert.AreEqual(2, contig0.Sequences.Count);
assembler.OverlapAlgorithm = new MUMmerAligner();
seqAssembly = (IOverlapDeNovoAssembly)assembler.Assemble(inputs);
Assert.AreEqual(0, seqAssembly.UnmergedSequences.Count);
Assert.AreEqual(1, seqAssembly.Contigs.Count);
contig0 = seqAssembly.Contigs[0];
Assert.AreEqual(expected, contig0.Consensus.ConvertToString(), "MUMmerAligner");
Assert.AreEqual(2, contig0.Sequences.Count);
}
public void TestAssemblerProperties()
{
IDeNovoAssembler assembler = new OverlapDeNovoAssembler();
Assert.AreEqual(assembler.Name, Properties.Resource.SIMPLE_NAME);
Assert.AreEqual(assembler.Description, Properties.Resource.SIMPLE_DESCRIPTION);
}
public void TestSimpleSequenceAssemblerWithRandomSequence()
{
// Test parameters.
//
// In theory, as long as all positions in the master sequence are
// covered by at least one read, we should be able to pass this test.
// But some parameter settings will make the test fail, for
// various reasons, including:
// 1. Short reads, caused by the strategy used to ensure full coverage
// at the ends, might not score well enough to merge.
// 2. Uncovered positions are always possible due to the random
// generation of reads. (Increasing the number of reads helps with this)
// 3. The assembler might construct the reverse or complement (or both)
// of the master sequence.
// 4. Too low a merge threshold could cause incorrect merges, which
// the algorithm will not repair.
int matchScore = 1;
int mismatchScore = -8;
int gapCost = -8;
double mergeThreshold = 3;
double consensusThreshold = 99;
const int MasterLength = 100;
const int MinReadLength = 10;
const int MaxReadLength = 30;
const int NumReads = 200;
const bool AssumeOrientedReads = true;
// if this is uncommented, assembly details appear in log.
// this is extremely verbose.
// Trace.Set(Trace.AssemblyDetails);
// make random master sequence
// (use seed for repeatability, or omit seed for
// different test each time)
// Random randGen = new Random();
Random randGen = new Random(654321);
StringBuilder randSeq = new StringBuilder();
for (int i = 0; i < MasterLength; ++i)
{
int randm = randGen.Next(8);
if (randm < 2)
{
randSeq.Append('A');
}
else if (randm < 4)
{
randSeq.Append('C');
}
else if (randm < 6)
{
randSeq.Append('G');
}
else
{
randSeq.Append('T');
}
}
Sequence master = new Sequence(Alphabets.AmbiguousDNA, randSeq.ToString());
// create the reads
List<ISequence> inputs = new List<ISequence>();
for (int i = 0; i < NumReads; ++i)
{
// try for uniform coverage clear to the ends (this can lead to short reads, though)
int rndPos = Math.Max(0, randGen.Next(-MinReadLength, MasterLength - 1));
int rndLen = Math.Min(MasterLength - rndPos, randGen.Next(MinReadLength, MaxReadLength + 1));
string data = master.ConvertToString().Substring(Math.Max(0, rndPos), rndLen);
bool revcomp = randGen.Next(2) > 0;
bool reverse = randGen.Next(2) > 0 && !AssumeOrientedReads;
ISequence read;
if (reverse && revcomp)
{
Sequence tmp = new Sequence(Alphabets.DNA, data);
read = new Sequence(Alphabets.DNA, tmp.GetReversedSequence().ConvertToString());
}
else if (revcomp)
{
Sequence tmp = new Sequence(Alphabets.DNA, data);
read = new Sequence(Alphabets.DNA, tmp.GetReverseComplementedSequence().ConvertToString());
}
else
{
read = new Sequence(Alphabets.DNA, data);
}
ApplicationLog.WriteLine("read {0}: {1}", i, read);
inputs.Add(read);
}
OverlapDeNovoAssembler assembler = new OverlapDeNovoAssembler();
assembler.MergeThreshold = mergeThreshold;
assembler.OverlapAlgorithm = new PairwiseOverlapAligner();
((IPairwiseSequenceAligner)assembler.OverlapAlgorithm).SimilarityMatrix = new DiagonalSimilarityMatrix(matchScore, mismatchScore);
((IPairwiseSequenceAligner)assembler.OverlapAlgorithm).GapOpenCost = gapCost;
assembler.ConsensusResolver = new SimpleConsensusResolver(consensusThreshold);
assembler.AssumeStandardOrientation = AssumeOrientedReads;
IOverlapDeNovoAssembly seqAssembly = (IOverlapDeNovoAssembly)assembler.Assemble(inputs);
ApplicationLog.WriteLine(
"Assembly finished. Contigs: {0}. Unmerged sequences: {1}.",
seqAssembly.Contigs.Count,
seqAssembly.UnmergedSequences.Count);
Contig contig0 = seqAssembly.Contigs[0];
ApplicationLog.WriteLine("master sequence and contig 0 consensus:");
ApplicationLog.WriteLine(master.ConvertToString());
ApplicationLog.WriteLine(contig0.Consensus.ConvertToString());
Assert.AreEqual(2, seqAssembly.UnmergedSequences.Count);
Assert.AreEqual(1, seqAssembly.Contigs.Count);
// note that this is tricky, esp. without oriented reads - consensus
// could be reversed and/or complemented relative to original
Assert.AreEqual(master.ConvertToString(), contig0.Consensus.ConvertToString());
}
public void TestSimpleSequenceAssemblerWithSemiRandomSequence()
{
// test parameters
int matchScore = 1;
int mismatchScore = -8;
int gapCost = -8;
double mergeThreshold = 4;
double consensusThreshold = 66;
const int MasterLength = 30;
const int ReadLength = 10;
const int NumReads = 5;
const bool AssumeOrientedReads = false;
// if this is uncommented, assembly details appear in log.
// this is extremely verbose.
Trace.Set(Trace.AssemblyDetails);
// make random master sequence
// (use seed for repeatability, or omit seed for
// different test each time)
// Random randGen = new Random();
Random randGen = new Random(654321);
StringBuilder randSeq = new StringBuilder();
for (int i = 0; i < MasterLength; ++i)
{
int randm = randGen.Next(8);
if (randm < 2)
{
randSeq.Append('A');
}
else if (randm < 4)
{
randSeq.Append('C');
}
else if (randm < 6)
{
randSeq.Append('G');
}
else
{
randSeq.Append('T');
}
}
Sequence master = new Sequence(Alphabets.DNA, randSeq.ToString());
// create the reads
List<ISequence> inputs = new List<ISequence>();
for (int i = 0; i < NumReads; ++i)
{
int pos = 5 * i;
string data = master.ConvertToString().Substring(pos, ReadLength);
bool revcomp = randGen.Next(2) > 0;
bool reverse = randGen.Next(2) > 0 && !AssumeOrientedReads;
ISequence read;
if (reverse && revcomp)
{
Sequence tmp = new Sequence(Alphabets.DNA, data);
read = new Sequence(Alphabets.DNA, tmp.GetReversedSequence().ConvertToString());
}
else if (revcomp)
{
Sequence tmp = new Sequence(Alphabets.DNA, data);
read = new Sequence(Alphabets.DNA, tmp.GetReverseComplementedSequence().ConvertToString());
}
else
{
read = new Sequence(Alphabets.DNA, data);
}
inputs.Add(read);
}
OverlapDeNovoAssembler assembler = new OverlapDeNovoAssembler();
assembler.MergeThreshold = mergeThreshold;
assembler.OverlapAlgorithm = new PairwiseOverlapAligner();
((IPairwiseSequenceAligner)assembler.OverlapAlgorithm).SimilarityMatrix = new DiagonalSimilarityMatrix(matchScore, mismatchScore);
((IPairwiseSequenceAligner)assembler.OverlapAlgorithm).GapOpenCost = gapCost;
assembler.ConsensusResolver = new SimpleConsensusResolver(consensusThreshold);
assembler.AssumeStandardOrientation = AssumeOrientedReads;
IOverlapDeNovoAssembly seqAssembly = (IOverlapDeNovoAssembly)assembler.Assemble(inputs);
Assert.AreEqual(0, seqAssembly.UnmergedSequences.Count);
Assert.AreEqual(1, seqAssembly.Contigs.Count);
Contig contig0 = seqAssembly.Contigs[0];
ApplicationLog.WriteLine("master sequence and contig 0 consensus:");
ApplicationLog.WriteLine(master.ConvertToString());
ApplicationLog.WriteLine(contig0.Consensus.ConvertToString());
// note that this is tricky, esp. without oriented reads - consensus
// could be reversed and/or complemented relative to original
Assert.AreEqual(master.ConvertToString(), contig0.Consensus.ConvertToString());
}
/// <summary>
/// Do a simple sequence assembly.
/// This sample uses NeedlemanWunschAligner.
/// </summary>
/// <param name="sequences">List of sequences to assemble.</param>
/// <returns>IDeNovoAssembly which has the assembled result.</returns>
public static IDeNovoAssembly DoSimpleSequenceAssemble(List<ISequence> sequences)
{
// Create an assembler
OverlapDeNovoAssembler assembler = new OverlapDeNovoAssembler();
// Setup the parameters
assembler.OverlapAlgorithm = new NeedlemanWunschAligner();
assembler.OverlapAlgorithm.SimilarityMatrix = new DiagonalSimilarityMatrix(5, -4);
assembler.OverlapAlgorithm.GapOpenCost = -10;
assembler.ConsensusResolver = new SimpleConsensusResolver(66);
assembler.AssumeStandardOrientation = false;
return assembler.Assemble(sequences);
}
public void TestOverlapDenovoAssemblyToString()
{
const int matchScore = 5;
const int mismatchScore = -4;
const int gapCost = -10;
const double mergeThreshold = 4;
const double consensusThreshold = 66;
ISequence seq2 = new Sequence(Alphabets.DNA, "ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGAGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATATAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATATACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCGAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAA");
ISequence seq1 = new Sequence(Alphabets.DNA, "ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAATTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA");
IOverlapDeNovoAssembler assembler = new OverlapDeNovoAssembler
{
MergeThreshold = mergeThreshold,
OverlapAlgorithm = new NeedlemanWunschAligner
{
SimilarityMatrix = new DiagonalSimilarityMatrix(matchScore, mismatchScore),
GapOpenCost = gapCost
},
ConsensusResolver = new SimpleConsensusResolver(consensusThreshold),
AssumeStandardOrientation = false
};
var inputs = new List<ISequence> {seq1, seq2};
var seqAssembly = (IOverlapDeNovoAssembly) assembler.Assemble(inputs);
Assert.AreEqual(0, seqAssembly.UnmergedSequences.Count);
Assert.AreEqual(1, seqAssembly.Contigs.Count);
assembler.OverlapAlgorithm = new SmithWatermanAligner();
seqAssembly = (IOverlapDeNovoAssembly) assembler.Assemble(inputs);
string expectedString = "ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATG... +[1678]\r\n".Replace("\r\n",Environment.NewLine);
string actualString = seqAssembly.ToString();
Assert.AreEqual(expectedString, actualString);
}
public void TestContigToString()
{
// test parameters
const int matchScore = 5;
const int mismatchScore = -4;
const int gapCost = -10;
const double mergeThreshold = 4;
const double consensusThreshold = 66;
Sequence seq2 = new Sequence(Alphabets.DNA, "ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGAGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATATAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATATACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCGAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAA");
Sequence seq1 = new Sequence(Alphabets.DNA, "ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAATTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA");
OverlapDeNovoAssembler assembler = new OverlapDeNovoAssembler
{
MergeThreshold = mergeThreshold,
OverlapAlgorithm = new NeedlemanWunschAligner
{
SimilarityMatrix = new DiagonalSimilarityMatrix(matchScore, mismatchScore),
GapOpenCost = gapCost
},
ConsensusResolver = new SimpleConsensusResolver(consensusThreshold),
AssumeStandardOrientation = false,
};
IOverlapDeNovoAssembly seqAssembly = (IOverlapDeNovoAssembly) assembler.Assemble(new List<ISequence> {seq1, seq2});
Contig contig0 = seqAssembly.Contigs[0];
string actualString = contig0.ToString();
//string expectedString = "ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATG... +[1678]";
string expectedString = "AYRAARGCAAYAMWARTRRWKSYRMTAYWWRYAKTTSYRMYMKMWAMWKYWGMMACMKYAWRTR... +[1678]";
Assert.AreEqual(actualString, expectedString);
}
