public void SimpleConsensusWithMakeConsensusMethod()
{
IOverlapDeNovoAssembly assembly = GetSequenceAssembly("consensus");
string contigConsensus = utilityObj.xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.ContigConsensusNode);
double consensusThreshold = double.Parse(utilityObj.xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.ConsensusThresholdNode), null);
IAlphabet alphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.AlphabetNameNode));
// Read the contig from Contig method.
Contig contigReadForConsensus = assembly.Contigs[0];
contigReadForConsensus.Consensus = null;
OverlapDeNovoAssembler 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((IFormatProvider)null,
"SimpleConsensusMethod BVT : Consensus read is '{0}'.",
contigReadForConsensus.Consensus.ToString()));
Console.WriteLine(string.Format((IFormatProvider)null,
"SimpleConsensusMethod BVT : Consensus read is '{0}'.",
contigReadForConsensus.Consensus.ToString()));
}
/// <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(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MatchScoreNode), null);
int mismatchScore = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MisMatchScoreNode), null);
int gapCost = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapCostNode), null);
double mergeThreshold = double.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MergeThresholdNode), null);
double consensusThreshold = double.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ConsensusThresholdNode),
null);
string[] sequences = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SequencesNode);
IAlphabet alphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
string documentation = 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 = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
(assembler.OverlapAlgorithm).SimilarityMatrix = new SimilarityMatrix(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(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ContigSequencesCountNode), null);
string contigConsensus = 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(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.UnMergedSequencesCountNode),
null);
int contigsCount = int.Parse(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>
/// Validate Sequence Assembler Test cases based on additional parameter values
/// </summary>
/// <param name="additionalParameter">Addtional parameters</param>
void ValidateSequenceAssemblerGeneral(string additionalParameter)
{
// Get the parameters from Xml
int matchScore = int.Parse(_utilityObj._xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.MatchScoreNode), null);
int mismatchScore = int.Parse(_utilityObj._xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.MisMatchScoreNode), null);
int gapCost = int.Parse(_utilityObj._xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.GapCostNode), null);
double mergeThreshold = double.Parse(_utilityObj._xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.MergeThresholdNode), null);
double consensusThreshold = double.Parse(_utilityObj._xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.ConsensusThresholdNode), null);
string sequence1 = _utilityObj._xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode1);
string sequence2 = _utilityObj._xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode2);
string sequence3 = _utilityObj._xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.SequenceNode3);
IAlphabet alphabet = Utility.GetAlphabet(_utilityObj._xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.AlphabetNameNode));
MoleculeType molType = Utility.GetMoleculeType(_utilityObj._xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.MoleculeTypeNode));
// Log based on the test cases
switch (additionalParameter)
{
case "consensus":
// Logs the sequences
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SimpleConsensusMethod BVT : Sequence 1 used is '{0}'.", sequence1));
Console.WriteLine(string.Format((IFormatProvider)null,
"SimpleConsensusMethod BVT : Sequence 1 used is '{0}'.", sequence1));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SimpleConsensusMethod BVT : Sequence 2 used is '{0}'.", sequence2));
Console.WriteLine(string.Format((IFormatProvider)null,
"SimpleConsensusMethod BVT : Sequence 2 used is '{0}'.", sequence2));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SimpleConsensusMethod BVT : Sequence 3 used is '{0}'.", sequence3));
Console.WriteLine(string.Format((IFormatProvider)null,
"SimpleConsensusMethod BVT : Sequence 3 used is '{0}'.", sequence3));
break;
default:
// Logs the sequences
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Sequence 1 used is '{0}'.", sequence1));
Console.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Sequence 1 used is '{0}'.", sequence1));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Sequence 2 used is '{0}'.", sequence2));
Console.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Sequence 2 used is '{0}'.", sequence2));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Sequence 3 used is '{0}'.", sequence3));
Console.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Sequence 3 used is '{0}'.", sequence3));
break;
}
Sequence seq1 = new Sequence(alphabet, sequence1);
Sequence seq2 = new Sequence(alphabet, sequence2);
Sequence seq3 = new Sequence(alphabet, sequence3);
// 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, molType);
((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);
// Assembles all the sequences.
IOverlapDeNovoAssembly assembly = (IOverlapDeNovoAssembly)assembler.Assemble(inputs);
// Get the parameters from Xml in general
int contigSequencesCount = int.Parse(_utilityObj._xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.ContigSequencesCountNode), null);
string contigConsensus = _utilityObj._xmlUtil.GetTextValue(Constants.AssemblyAlgorithmNodeName,
Constants.ContigConsensusNode);
switch (additionalParameter.ToLower(CultureInfo.CurrentCulture))
{
case "assemble":
// Get the parameters from Xml for Assemble() method test cases.
int unMergedCount = int.Parse(_utilityObj._xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.UnMergedSequencesCountNode), null);
int contigsCount = int.Parse(_utilityObj._xmlUtil.GetTextValue(
Constants.AssemblyAlgorithmNodeName,
Constants.ContigsCountNode), null);
Assert.AreEqual(unMergedCount, assembly.UnmergedSequences.Count);
Assert.AreEqual(contigsCount, assembly.Contigs.Count);
Contig contigRead = assembly.Contigs[0];
// Logs the concensus
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Un Merged Sequences Count is '{0}'.",
assembly.UnmergedSequences.Count.ToString((IFormatProvider)null)));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Contigs Count is '{0}'.",
assembly.Contigs.Count.ToString((IFormatProvider)null)));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Contig Sequences Count is '{0}'.",
contigRead.Sequences.Count.ToString((IFormatProvider)null)));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Consensus read is '{0}'.",
contigRead.Consensus.ToString()));
Console.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Consensus read is '{0}'.",
contigRead.Consensus.ToString()));
Assert.AreEqual(contigConsensus, contigRead.Consensus.ToString());
Assert.AreEqual(contigSequencesCount, contigRead.Sequences.Count);
break;
case "contig":
// Read the contig from Contig method.
Contig contigsRead = assembly.Contigs[0];
// Log the required info.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Consensus read is '{0}'.",
contigsRead.Consensus.ToString()));
Console.WriteLine(string.Format((IFormatProvider)null,
"SequenceAssembly BVT : Consensus read is '{0}'.",
contigsRead.Consensus.ToString()));
ApplicationLog.WriteLine("SequenceAssembly BVT : Successfully read the Contig.");
Console.WriteLine("SequenceAssembly BVT : Successfully read the Contig.");
Assert.AreEqual(contigConsensus, contigsRead.Consensus.ToString());
Assert.AreEqual(contigSequencesCount, contigsRead.Sequences.Count);
break;
case "consensus":
// Read the contig from Contig method.
Contig contigReadForConsensus = assembly.Contigs[0];
contigReadForConsensus.Consensus = null;
OverlapDeNovoAssembler simpleSeqAssembler = new OverlapDeNovoAssembler();
simpleSeqAssembler.ConsensusResolver = new SimpleConsensusResolver(consensusThreshold);
simpleSeqAssembler.MakeConsensus(alphabet, contigReadForConsensus);
// Log the required info.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SimpleConsensusMethod BVT : Consensus read is '{0}'.",
contigReadForConsensus.Consensus.ToString()));
Console.WriteLine(string.Format((IFormatProvider)null,
"SimpleConsensusMethod BVT : Consensus read is '{0}'.",
contigReadForConsensus.Consensus.ToString()));
Assert.AreEqual(contigConsensus, contigReadForConsensus.Consensus.ToString());
break;
default:
break;
}
}
