public void MapContigToReverseComplementOfRead()
{
IList <ISequence> contigs = new List <ISequence>();
IList <ISequence> reads = new List <ISequence>();
Sequence seq = new Sequence(Alphabets.DNA, "TCTGATAAGG".Select(a => (byte)a).ToArray());
seq.ID = "1";
contigs.Add(seq);
Sequence read = new Sequence(Alphabets.DNA, "CCTTATCAG".Select(a => (byte)a).ToArray());
read.ID = "2";
reads.Add(read);
const int kmerLength = 6;
IList <Contig> alignment = ReadAlignment.ReadContigAlignment(contigs, reads, kmerLength);
Assert.AreEqual(alignment.Count, contigs.Count);
Contig contig = alignment.First();
Contig.AssembledSequence sequence = contig.Sequences.First();
Assert.AreEqual(sequence.Length, 9);
Assert.AreEqual(sequence.Position, 1);
Assert.AreEqual(sequence.ReadPosition, 0);
Assert.AreEqual(sequence.Sequence, reads.First());
Assert.AreEqual(sequence.IsComplemented, true);
Assert.AreEqual(sequence.IsReversed, true);
}
public void MapReadToContig()
{
IList <ISequence> contigs = new List <ISequence>();
IList <ISequence> reads = new List <ISequence>();
Sequence seq = new Sequence(Alphabets.DNA, "TCTGATAAGG");
seq.DisplayID = "1";
contigs.Add(seq);
Sequence read = new Sequence(Alphabets.DNA, "CTGATAAGG");
read.DisplayID = "2";
reads.Add(read);
const int kmerLength = 6;
IList <Contig> alignment = ReadAlignment.ReadContigAlignment(contigs, reads, kmerLength);
Assert.AreEqual(alignment.Count, contigs.Count);
Contig contig = alignment.First();
Contig.AssembledSequence sequence = contig.Sequences.First();
Assert.AreEqual(sequence.Length, 9);
Assert.AreEqual(sequence.Position, 1);
Assert.AreEqual(sequence.ReadPosition, 0);
Assert.AreEqual(sequence.Sequence, reads.First());
Assert.AreEqual(sequence.IsComplemented, false);
Assert.AreEqual(sequence.IsReversed, false);
}
public void MapReadsToSingleContig()
{
const int kmerLength = 6;
IList <ISequence> readSeqs = new List <ISequence>();
Sequence read = new Sequence(Alphabets.DNA, "GATGCCTC".Select(a => (byte)a).ToArray());
read.ID = "0";
readSeqs.Add(read);
read = new Sequence(Alphabets.DNA, "CCTCCTAT".Select(a => (byte)a).ToArray());
read.ID = "1";
readSeqs.Add(read);
read = new Sequence(Alphabets.DNA, "TCCTATC".Select(a => (byte)a).ToArray());
read.ID = "2";
readSeqs.Add(read);
read = new Sequence(Alphabets.DNA, "GCCTCCTAT".Select(a => (byte)a).ToArray());
read.ID = "3";
readSeqs.Add(read);
read = new Sequence(Alphabets.DNA, "TGCCTCCT".Select(a => (byte)a).ToArray());
read.ID = "4";
readSeqs.Add(read);
IList <ISequence> contigs = new List <ISequence> {
new Sequence(Alphabets.DNA,
"GATGCCTCCTATC".Select(a => (byte)a).ToArray())
};
IList <Contig> maps = ReadAlignment.ReadContigAlignment(contigs, readSeqs, kmerLength);
Contig contig = maps.First();
Assert.AreEqual(contig.Consensus, contigs.First());
IList <Contig.AssembledSequence> readMap = Sort(contig.Sequences);
Assert.AreEqual(readMap[0].Length, 8);
Assert.AreEqual(readMap[0].Position, 4);
Assert.AreEqual(readMap[0].ReadPosition, 0);
Assert.AreEqual(readMap[0].IsComplemented, false);
Assert.AreEqual(readMap[0].IsReversed, false);
Assert.AreEqual(readMap[1].Length, 8);
Assert.AreEqual(readMap[1].Position, 0);
Assert.AreEqual(readMap[1].ReadPosition, 0);
Assert.AreEqual(readMap[1].IsComplemented, false);
Assert.AreEqual(readMap[1].IsReversed, false);
Assert.AreEqual(readMap[2].Length, 9);
Assert.AreEqual(readMap[2].Position, 3);
Assert.AreEqual(readMap[2].ReadPosition, 0);
Assert.AreEqual(readMap[2].IsComplemented, false);
Assert.AreEqual(readMap[2].IsReversed, false);
Assert.AreEqual(readMap[3].Length, 7);
Assert.AreEqual(readMap[3].Position, 6);
Assert.AreEqual(readMap[3].ReadPosition, 0);
Assert.AreEqual(readMap[3].IsComplemented, false);
Assert.AreEqual(readMap[3].IsReversed, false);
Assert.AreEqual(readMap[4].Length, 8);
Assert.AreEqual(readMap[4].Position, 2);
Assert.AreEqual(readMap[4].ReadPosition, 0);
Assert.AreEqual(readMap[3].IsComplemented, false);
Assert.AreEqual(readMap[3].IsReversed, false);
}
public void MapReadsWithTwoContig()
{
const int kmerLength = 6;
IList <ISequence> readSeqs = new List <ISequence>();
Sequence read = new Sequence(Alphabets.DNA, "GATCTGATAA".Select(a => (byte)a).ToArray());
read.ID = "0";
readSeqs.Add(read);
read = new Sequence(Alphabets.DNA, "ATCTGATAAG".Select(a => (byte)a).ToArray());
read.ID = "1";
readSeqs.Add(read);
read = new Sequence(Alphabets.DNA, "TCTGATAAGG".Select(a => (byte)a).ToArray());
read.ID = "2";
readSeqs.Add(read);
read = new Sequence(Alphabets.DNA, "TTTTTGATGG".Select(a => (byte)a).ToArray());
read.ID = "3";
readSeqs.Add(read);
read = new Sequence(Alphabets.DNA, "TTTTGATGGC".Select(a => (byte)a).ToArray());
read.ID = "4";
readSeqs.Add(read);
read = new Sequence(Alphabets.DNA, "TTTGATGGCA".Select(a => (byte)a).ToArray());
read.ID = "5";
readSeqs.Add(read);
IList <ISequence> contigs = new List <ISequence> {
new Sequence(Alphabets.DNA, "GATCTGATAAGG".Select(a => (byte)a).ToArray()),
new Sequence(Alphabets.DNA, "TTTTTGATGGCA".Select(a => (byte)a).ToArray())
};
IList <Contig> maps =
ReadAlignment.ReadContigAlignment(contigs, readSeqs, kmerLength).OrderBy(t => t.Consensus.ToString()).ToList();
Assert.AreEqual(maps.Count, contigs.Count);
IList <Contig.AssembledSequence> readMap = Sort(maps.First().Sequences);
Assert.AreEqual(readMap[0].Length, 10);
Assert.AreEqual(readMap[0].Position, 1);
Assert.AreEqual(readMap[0].ReadPosition, 0);
Assert.AreEqual(readMap[0].IsComplemented, false);
Assert.AreEqual(readMap[0].IsReversed, false);
Assert.AreEqual(readMap[1].Length, 10);
Assert.AreEqual(readMap[1].Position, 0);
Assert.AreEqual(readMap[1].ReadPosition, 0);
Assert.AreEqual(readMap[1].IsComplemented, false);
Assert.AreEqual(readMap[1].IsReversed, false);
Assert.AreEqual(readMap[2].Length, 10);
Assert.AreEqual(readMap[2].Position, 2);
Assert.AreEqual(readMap[2].ReadPosition, 0);
Assert.AreEqual(readMap[2].IsComplemented, false);
Assert.AreEqual(readMap[2].IsReversed, false);
readMap = Sort(maps[1].Sequences);
Assert.AreEqual(readMap[0].Length, 10);
Assert.AreEqual(readMap[0].Position, 2);
Assert.AreEqual(readMap[0].ReadPosition, 0);
Assert.AreEqual(readMap[0].IsComplemented, false);
Assert.AreEqual(readMap[0].IsReversed, false);
Assert.AreEqual(readMap[1].Length, 10);
Assert.AreEqual(readMap[1].Position, 1);
Assert.AreEqual(readMap[1].ReadPosition, 0);
Assert.AreEqual(readMap[1].IsComplemented, false);
Assert.AreEqual(readMap[1].IsReversed, false);
Assert.AreEqual(readMap[2].Length, 10);
Assert.AreEqual(readMap[2].Position, 0);
Assert.AreEqual(readMap[2].ReadPosition, 0);
Assert.AreEqual(readMap[2].IsComplemented, false);
Assert.AreEqual(readMap[2].IsReversed, false);
}