public void TracePathTestWithPalindromicContig()
{
const int kmerLengthConst = 5;
const int dangleThreshold = 3;
const int redundantThreshold = 6;
var sequences = new List<ISequence>()
{
new Sequence(Alphabets.DNA, "ATGCCTC") {ID = "0"},
new Sequence(Alphabets.DNA, "CCTCCTAT") {ID = "1"},
new Sequence(Alphabets.DNA, "TCCTATC") {ID = "2"},
new Sequence(Alphabets.DNA, "TGCCTCCT") {ID = "3"},
new Sequence(Alphabets.DNA, "ATCTTAGC") {ID = "4"},
new Sequence(Alphabets.DNA, "CTATCTTAG") {ID = "5"},
new Sequence(Alphabets.DNA, "CTTAGCG") {ID = "6"},
new Sequence(Alphabets.DNA, "GCCTCCTAT") {ID = "7"},
new Sequence(Alphabets.DNA, "TAGCGCGCTA") {ID = "8"},
new Sequence(Alphabets.DNA, "AGCGCGC") {ID = "9"},
new Sequence(Alphabets.DNA, "TTTTTT") {ID = "10"},
new Sequence(Alphabets.DNA, "TTTTTAAA") {ID = "11"},
new Sequence(Alphabets.DNA, "TAAAAA") {ID = "12"},
new Sequence(Alphabets.DNA, "TTTTAG") {ID = "13"},
new Sequence(Alphabets.DNA, "TTTAGC") {ID = "14"},
new Sequence(Alphabets.DNA, "GCGCGCCGCGCG") {ID = "15"},
};
KmerLength = kmerLengthConst;
SequenceReads.Clear();
SetSequenceReads(sequences);
CreateGraph();
DanglingLinksThreshold = dangleThreshold;
DanglingLinksPurger = new DanglingLinksPurger(dangleThreshold);
RedundantPathLengthThreshold = redundantThreshold;
RedundantPathsPurger = new RedundantPathsPurger(redundantThreshold);
UnDangleGraph();
RemoveRedundancy();
IList<ISequence> contigs = BuildContigs().ToList();
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(contigs, sequences, kmerLengthConst);
MatePairMapper builder = new MatePairMapper();
CloneLibrary.Instance.AddLibrary("abc", 5, 15);
ContigMatePairs pairedReads = builder.MapContigToMatePairs(sequences, maps);
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs overlap = filter.FilterPairedReads(pairedReads, 0);
DistanceCalculator dist = new DistanceCalculator(overlap);
overlap = dist.CalculateDistance();
ContigGraph graph = new ContigGraph();
graph.BuildContigGraph(contigs, this.KmerLength);
TracePath path = new TracePath();
IList<ScaffoldPath> paths = path.FindPaths(graph, overlap, kmerLengthConst, 3);
Assert.AreEqual(paths.Count, 3);
Assert.AreEqual(paths.First().Count, 3);
ScaffoldPath scaffold = paths.First();
Assert.AreEqual("ATGCCTCCTATCTTAGC", graph.GetNodeSequence(scaffold[0].Key).ConvertToString());
Assert.AreEqual("TTAGCGCG", graph.GetNodeSequence(scaffold[1].Key).ConvertToString());
Assert.AreEqual("GCGCGC", graph.GetNodeSequence(scaffold[2].Key).ConvertToString());
}
/// <summary>
/// Validate scaffold paths for a given input reads.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateScaffoldPath(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
string daglingThreshold = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.DanglingLinkThresholdNode);
string redundantThreshold = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.RedundantThreshold);
string[] expectedScaffoldNodes = utilityObj.xmlUtil.GetTextValues(nodeName,Constants.ScaffoldNodes);
string libraray = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.LibraryName);
string stdDeviation = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.StdDeviation);
string mean = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.Mean);
string expectedDepth = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.DepthNode);
// Get the input reads and build kmers
using (FastAParser parser = new FastAParser(filePath))
{
IEnumerable<ISequence> sequenceReads = parser.Parse();
// Build kmers from step1,graph in step2
// Remove the dangling links from graph in step3
// Remove bubbles form the graph in step4
// Pass the graph and build contigs
// Validate contig reads
this.KmerLength = Int32.Parse(kmerLength, null);
this.DanglingLinksThreshold = Int32.Parse(daglingThreshold, null);
this.DanglingLinksPurger = new DanglingLinksPurger(Int32.Parse(daglingThreshold, null));
this.RedundantPathsPurger = new RedundantPathsPurger(Int32.Parse(redundantThreshold, null));
this.RedundantPathLengthThreshold = Int32.Parse(redundantThreshold, null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
this.CreateGraph();
ContigGraph graph = new ContigGraph();
this.UnDangleGraph();
// Build contig.
this.ContigBuilder = new SimplePathContigBuilder();
this.RemoveRedundancy();
IEnumerable<ISequence> contigs = this.BuildContigs();
IList<ISequence> sortedContigs = SortContigsData(contigs.ToList());
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(sortedContigs, sequenceReads, this.KmerLength);
// Find map paired reads.
CloneLibrary.Instance.AddLibrary(libraray, float.Parse(mean, null), float.Parse(stdDeviation, null));
MatePairMapper mapPairedReads = new MatePairMapper();
ContigMatePairs pairedReads = mapPairedReads.MapContigToMatePairs(sequenceReads, maps);
// Filter contigs based on the orientation.
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairedReads, 0);
DistanceCalculator dist = new DistanceCalculator(contigpairedReads);
dist.CalculateDistance();
graph.BuildContigGraph(contigs.ToList(), this.KmerLength);
// Validate ScaffoldPath using BFS.
TracePath trace = new TracePath();
IList<ScaffoldPath> paths = trace.FindPaths(graph, contigpairedReads, Int32.Parse(kmerLength, null),
Int32.Parse(expectedDepth, null));
ScaffoldPath scaffold = paths.First();
foreach (KeyValuePair<Node, Edge> kvp in scaffold)
{
ISequence seq = graph.GetNodeSequence(kvp.Key);
string sequence = seq.ConvertToString();
string reversedSequence = seq.GetReverseComplementedSequence().ConvertToString();
Assert.IsTrue(expectedScaffoldNodes.Contains(sequence)
|| expectedScaffoldNodes.Contains(reversedSequence),
"Failed to find " + sequence + ", or " + reversedSequence);
}
}
ApplicationLog.WriteLine("PADENA P1 : FindPaths() validation for Padena step6:step6 completed successfully");
}
/// <summary>
/// Validate Filter contig nodes.
/// </summary>
/// <param name="nodeName">xml node name used for a differnt testcase.</param>
/// <param name="isFirstContig">Is First Contig?</param>
internal void ValidateFilterPaired(string nodeName, bool isFirstContig)
{
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.KmerLengthNode);
string daglingThreshold = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DanglingLinkThresholdNode);
string redundantThreshold = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.RedundantThreshold);
string expectedContigPairedReadsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ContigPairedReadsCount);
string forwardReadStartPos = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ForwardReadStartPos);
string reverseReadStartPos = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ReverseReadStartPos);
string reverseComplementStartPos = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.RerverseReadReverseCompPos);
string[] expectedForwardReadStartPos = forwardReadStartPos.Split(',');
string[] expectedReverseReadStartPos = reverseReadStartPos.Split(',');
string[] expectedReverseComplementStartPos = reverseComplementStartPos.Split(',');
// Get the input reads and build kmers
IEnumerable<ISequence> sequenceReads = null;
using (FastAParser parser = new FastAParser(filePath))
{
sequenceReads = parser.Parse();
// Build kmers from step1,graph in step2
// Remove the dangling links from graph in step3
// Remove bubbles form the graph in step4
// Pass the graph and build contigs
// Validate contig reads
this.KmerLength = Int32.Parse(kmerLength, (IFormatProvider)null);
this.DanglingLinksThreshold = Int32.Parse(daglingThreshold, (IFormatProvider)null);
this.DanglingLinksPurger = new DanglingLinksPurger(Int32.Parse(daglingThreshold, (IFormatProvider)null));
this.RedundantPathsPurger =
new RedundantPathsPurger(Int32.Parse(redundantThreshold, (IFormatProvider)null));
this.RedundantPathLengthThreshold = Int32.Parse(redundantThreshold, (IFormatProvider)null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
this.CreateGraph();
this.UnDangleGraph();
// Build contig.
this.ContigBuilder = new SimplePathContigBuilder();
this.RemoveRedundancy();
IEnumerable<ISequence> contigs = this.BuildContigs();
IList<ISequence> sortedContigs = SortContigsData(contigs.ToList());
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(
sortedContigs, sequenceReads, this.KmerLength);
// Find map paired reads.
MatePairMapper mapPairedReads = new MatePairMapper();
ContigMatePairs pairedReads = mapPairedReads.MapContigToMatePairs(sequenceReads, maps);
// Filter contigs based on the orientation.
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairedReads, 0);
Assert.AreEqual(expectedContigPairedReadsCount,
contigpairedReads.Values.Count.ToString((IFormatProvider)null));
Dictionary<ISequence, IList<ValidMatePair>> map = null;
IList<ValidMatePair> valid = null;
ISequence firstSeq = sortedContigs[0];
ISequence secondSeq = sortedContigs[1];
// Validate Contig paired reads after filtering contig sequences.
if (isFirstContig)
{
map = contigpairedReads[firstSeq];
valid = SortPairedReads(map[secondSeq], sequenceReads);
}
else
{
map = contigpairedReads[secondSeq];
valid = SortPairedReads(map[firstSeq], sequenceReads);
}
for (int index = 0; index < valid.Count; index++)
{
Assert.IsTrue((expectedForwardReadStartPos[index] ==
valid[index].ForwardReadStartPosition[0].ToString((IFormatProvider)null)
|| (expectedForwardReadStartPos[index] ==
valid[index].ForwardReadStartPosition[1].ToString((IFormatProvider)null))));
if (valid[index].ReverseReadReverseComplementStartPosition.Count > 1)
{
Assert.IsTrue((expectedReverseReadStartPos[index] ==
valid[index].ReverseReadReverseComplementStartPosition[0].ToString((IFormatProvider)null)
|| (expectedReverseReadStartPos[index] ==
valid[index].ReverseReadReverseComplementStartPosition[1].ToString((IFormatProvider)null))));
}
if (valid[index].ReverseReadStartPosition.Count > 1)
{
Assert.IsTrue((expectedReverseComplementStartPos[index] ==
valid[index].ReverseReadStartPosition[0].ToString((IFormatProvider)null)
|| (expectedReverseComplementStartPos[index] ==
valid[index].ReverseReadStartPosition[1].ToString((IFormatProvider)null))));
}
}
}
ApplicationLog.WriteLine("PADENA P1 : FilterPairedReads() validation for Padena step6:step4 completed successfully");
}
/// <summary>
/// Validate FilterPairedRead.FilterPairedRead() by passing graph object
/// </summary>
/// <param name="nodeName">xml node name used for a differnt testcase.</param>
internal void ValidateContigDistance(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.KmerLengthNode);
string daglingThreshold = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DanglingLinkThresholdNode);
string redundantThreshold = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.RedundantThreshold);
string expectedContigPairedReadsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ContigPairedReadsCount);
string distanceBetweenFirstContigs = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DistanceBetweenFirstContig);
string distanceBetweenSecondContigs = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DistanceBetweenSecondContig);
string firstStandardDeviation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstContigStandardDeviation);
string secondStandardDeviation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondContigStandardDeviation);
// Get the input reads and build kmers
IEnumerable<ISequence> sequenceReads = null;
using (FastAParser parser = new FastAParser(filePath))
{
sequenceReads = parser.Parse();
// Build kmers from step1,graph in step2
// Remove the dangling links from graph in step3
// Remove bubbles form the graph in step4
// Pass the graph and build contigs
// Validate contig reads
this.KmerLength = Int32.Parse(kmerLength, (IFormatProvider)null);
this.DanglingLinksThreshold = Int32.Parse(daglingThreshold, (IFormatProvider)null);
this.DanglingLinksPurger =
new DanglingLinksPurger(Int32.Parse(daglingThreshold, (IFormatProvider)null));
this.RedundantPathsPurger =
new RedundantPathsPurger(Int32.Parse(redundantThreshold, (IFormatProvider)null));
this.RedundantPathLengthThreshold = Int32.Parse(redundantThreshold, (IFormatProvider)null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
this.CreateGraph();
this.UnDangleGraph();
// Build contig.
this.ContigBuilder = new SimplePathContigBuilder();
this.RemoveRedundancy();
IEnumerable<ISequence> contigs = this.BuildContigs();
IList<ISequence> sortedContigs = SortContigsData(contigs.ToList());
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(sortedContigs, sequenceReads, this.KmerLength);
// Find map paired reads.
MatePairMapper mapPairedReads = new MatePairMapper();
ContigMatePairs pairedReads = mapPairedReads.MapContigToMatePairs(sequenceReads, maps);
// Filter contigs based on the orientation.
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairedReads, 0);
// Calculate the distance between contigs.
DistanceCalculator calc = new DistanceCalculator(contigpairedReads);
calc.CalculateDistance();
Assert.AreEqual(expectedContigPairedReadsCount,
contigpairedReads.Values.Count.ToString((IFormatProvider)null));
Dictionary<ISequence, IList<ValidMatePair>> map;
IList<ValidMatePair> valid;
ISequence firstSeq = sortedContigs[0];
ISequence secondSeq = sortedContigs[1];
if (contigpairedReads.ContainsKey(firstSeq))
{
map = contigpairedReads[firstSeq];
}
else
{
map = contigpairedReads[secondSeq];
}
if (map.ContainsKey(firstSeq))
{
valid = map[firstSeq];
}
else
{
valid = map[secondSeq];
}
// Validate distance and standard deviation between contigs.
Assert.AreEqual(float.Parse(distanceBetweenFirstContigs, (IFormatProvider)null),
valid.First().DistanceBetweenContigs[0]);
Assert.AreEqual(float.Parse(distanceBetweenSecondContigs, (IFormatProvider)null),
valid.First().DistanceBetweenContigs[1]);
Assert.AreEqual(float.Parse(firstStandardDeviation, (IFormatProvider)null),
valid.First().StandardDeviation[0]);
Assert.AreEqual(float.Parse(secondStandardDeviation, (IFormatProvider)null),
valid.First().StandardDeviation[1]);
}
ApplicationLog.WriteLine("PADENA P1 : DistanceCalculator() validation for Padena step6:step5 completed successfully");
}
/// <summary>
/// Validate Assembled paths for a given input reads.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateAssembledPath(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
string daglingThreshold = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.DanglingLinkThresholdNode);
string redundantThreshold = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.RedundantThreshold);
string library = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.LibraryName);
string StdDeviation = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.StdDeviation);
string mean = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Mean);
string expectedDepth = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.DepthNode);
string[] assembledPath = utilityObj.xmlUtil.GetTextValues(nodeName, Constants.SequencePathNode);
// Get the input reads and build kmers
FastAParser parser = new FastAParser();
parser.Open(filePath);
IEnumerable<ISequence> sequenceReads = parser.Parse().ToList();
parser.Close ();
// Build kmers from step1,graph in step2
// Remove the dangling links from graph in step3
// Remove bubbles form the graph in step4
// Pass the graph and build contigs
// Validate contig reads
this.KmerLength = Int32.Parse(kmerLength, null);
this.DanglingLinksThreshold = Int32.Parse(daglingThreshold, null);
this.DanglingLinksPurger = new DanglingLinksPurger(Int32.Parse(daglingThreshold, null));
this.RedundantPathsPurger = new RedundantPathsPurger(Int32.Parse(redundantThreshold, null));
this.RedundantPathLengthThreshold = Int32.Parse(redundantThreshold, null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
this.CreateGraph();
ContigGraph graph = new ContigGraph();
this.UnDangleGraph();
// Build contig.
this.ContigBuilder = new SimplePathContigBuilder();
this.RemoveRedundancy();
IEnumerable<ISequence> contigs = this.BuildContigs();
IList<ISequence> sortedContigs = SortContigsData(contigs.ToList());
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(sortedContigs, sequenceReads, this.KmerLength);
// Find map paired reads.
CloneLibrary.Instance.AddLibrary(library, float.Parse(mean, null), float.Parse(StdDeviation, null));
MatePairMapper mapPairedReads = new MatePairMapper();
ContigMatePairs pairedReads = mapPairedReads.MapContigToMatePairs(sequenceReads, maps);
// Filter contigs based on the orientation.
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairedReads, 0);
DistanceCalculator dist = new DistanceCalculator(contigpairedReads);
dist.CalculateDistance();
graph.BuildContigGraph(contigs.ToList(), this.KmerLength);
// Validate ScaffoldPath using BFS.
TracePath trace = new TracePath();
IList<ScaffoldPath> paths = trace.FindPaths(graph, contigpairedReads, Int32.Parse(kmerLength, null),
Int32.Parse(expectedDepth, null));
// Assemble paths.
PathPurger pathsAssembler = new PathPurger();
pathsAssembler.PurgePath(paths);
// Get sequences from assembled path.
IList<ISequence> seqList = paths.Select(temp => temp.BuildSequenceFromPath(graph, Int32.Parse(kmerLength, null))).ToList();
//Validate assembled sequence paths.
foreach (string sequence in seqList.Select(t => t.ConvertToString()))
{
Assert.IsTrue(assembledPath.Contains(sequence), "Failed to locate " + sequence);
}
ApplicationLog.WriteLine("PADENA P1 : AssemblePath() validation for Padena step6:step7 completed successfully");
}