/// <summary>
/// Finds contig pairs having valid mate pairs connection between them.
/// </summary>
/// <param name="reads">Input list of reads.</param>
/// <param name="alignment">Reads contig alignment.</param>
/// <returns>Contig Mate pair map.</returns>
public ContigMatePairs MapContigToMatePairs(IEnumerable <ISequence> reads, ReadContigMap alignment)
{
if (alignment == null)
{
throw new ArgumentNullException("alignment");
}
if (reads == null)
{
throw new ArgumentNullException("reads");
}
Dictionary <ISequence, IList <ReadMap> > contigs1;
Dictionary <ISequence, IList <ReadMap> > contigs2;
ContigMatePairs contigMatePairs = new ContigMatePairs();
foreach (ISequence read in reads)
{
Match match = this.readExpression.Match(read.ID);
if (match.Success)
{
string mateDisplayID = GenerateExpression(match);
if (alignment.TryGetValue(read.ID, out contigs1) && alignment.TryGetValue(mateDisplayID, out contigs2))
{
MatePair pair;
if (match.Groups[2].Value == "X1" || match.Groups[2].Value == "F" ||
match.Groups[2].Value == "1" || match.Groups[2].Value == "x1" ||
match.Groups[2].Value == "f" || match.Groups[2].Value == "a" ||
match.Groups[2].Value == "A")
{
pair = new MatePair(read.ID, mateDisplayID, match.Groups[3].Value);
ContigMatePairMapper(contigs1, contigs2, pair, contigMatePairs);
}
else
{
pair = new MatePair(mateDisplayID, read.ID, match.Groups[3].Value);
ContigMatePairMapper(contigs2, contigs1, pair, contigMatePairs);
}
alignment.Remove(read.ID);
alignment.Remove(mateDisplayID);
}
}
}
return(contigMatePairs);
}
/// <summary>
/// Creates Paired Read Contig Map.
/// </summary>
/// <param name="forwardContigs">Contigs aligning to forward read.</param>
/// <param name="reverseContigs">Contigs aligning to reverse read.</param>
/// <param name="pair">Mate Pair.</param>
/// <param name="contigMatePairs">Contig mate pair.</param>
private static void ContigMatePairMapper(
Dictionary <ISequence, IList <ReadMap> > forwardContigs,
Dictionary <ISequence, IList <ReadMap> > reverseContigs,
MatePair pair,
ContigMatePairs contigMatePairs)
{
foreach (KeyValuePair <ISequence, IList <ReadMap> > forwardContigMaps in forwardContigs)
{
Dictionary <ISequence, IList <ValidMatePair> > forwardContig;
if (!contigMatePairs.TryGetValue(forwardContigMaps.Key, out forwardContig))
{
forwardContig = new Dictionary <ISequence, IList <ValidMatePair> >();
contigMatePairs.Add(forwardContigMaps.Key, forwardContig);
}
foreach (KeyValuePair <ISequence, IList <ReadMap> > reverseContigMaps in reverseContigs)
{
IList <ValidMatePair> matePairs;
if (!forwardContig.TryGetValue(reverseContigMaps.Key, out matePairs))
{
matePairs = new List <ValidMatePair>();
forwardContig.Add(reverseContigMaps.Key, matePairs);
}
foreach (ReadMap forwardMap in forwardContigMaps.Value)
{
foreach (ReadMap reverseMap in reverseContigMaps.Value)
{
ValidMatePair validPairedRead = new ValidMatePair();
validPairedRead.PairedRead = pair;
validPairedRead.ForwardReadStartPosition.Add(forwardMap.StartPositionOfContig);
validPairedRead.ReverseReadStartPosition.Add(
reverseMap.StartPositionOfContig + reverseMap.Length - 1);
validPairedRead.ReverseReadReverseComplementStartPosition.Add(
reverseContigMaps.Key.Count - reverseMap.StartPositionOfContig - 1);
matePairs.Add(validPairedRead);
}
}
}
}
}
/// <summary>
/// Map reads to mate pairs.
/// </summary>
/// <param name="reads">List of Reads.</param>
/// <returns>List of mate pairs.</returns>
public IList<MatePair> Map(IEnumerable<ISequence> reads)
{
if (null == reads)
{
throw new ArgumentNullException("reads");
}
Dictionary<string, MatePair> pairs = new Dictionary<string, MatePair>();
MatePair mate;
string exp = string.Empty;
foreach (ISequence read in reads)
{
if (read == null)
{
throw new ArgumentException(Properties.Resource.ReadCannotBeNull);
}
if (pairs.TryGetValue(read.ID, out mate))
{
if (string.IsNullOrEmpty(mate.ForwardReadID))
{
mate.ForwardReadID = read.ID;
}
else
{
mate.ReverseReadID = read.ID;
}
}
else
{
Match match = this.readExpression.Match(read.ID);
if (match.Success)
{
mate = new MatePair(match.Groups[3].Value);
if (match.Groups[2].Value == "X1" || match.Groups[2].Value == "F" ||
match.Groups[2].Value == "1" || match.Groups[2].Value == "x1" ||
match.Groups[2].Value == "f" || match.Groups[2].Value == "a" ||
match.Groups[2].Value == "A")
{
mate.ForwardReadID = read.ID;
}
else
{
mate.ReverseReadID = read.ID;
}
exp = GenerateExpression(match);
if (!pairs.ContainsKey(exp))
{
pairs.Add(exp, mate);
}
else
{
throw new FormatException(
string.Format(CultureInfo.CurrentCulture,Properties.Resource.DuplicatingReadIds, read.ID));
}
}
}
}
return pairs.Values.Where(pair => !string.IsNullOrEmpty(pair.ForwardReadID)
&& !string.IsNullOrEmpty(pair.ReverseReadID)).ToList();
}
/// <summary>
/// Creates Paired Read Contig Map.
/// </summary>
/// <param name="forwardContigs">Contigs aligning to forward read.</param>
/// <param name="reverseContigs">Contigs aligning to reverse read.</param>
/// <param name="pair">Mate Pair.</param>
/// <param name="contigMatePairs">Contig mate pair.</param>
private static void ContigMatePairMapper(
Dictionary<ISequence, IList<ReadMap>> forwardContigs,
Dictionary<ISequence, IList<ReadMap>> reverseContigs,
MatePair pair,
ContigMatePairs contigMatePairs)
{
foreach (KeyValuePair<ISequence, IList<ReadMap>> forwardContigMaps in forwardContigs)
{
Dictionary<ISequence, IList<ValidMatePair>> forwardContig;
if (!contigMatePairs.TryGetValue(forwardContigMaps.Key, out forwardContig))
{
forwardContig = new Dictionary<ISequence, IList<ValidMatePair>>();
contigMatePairs.Add(forwardContigMaps.Key, forwardContig);
}
foreach (KeyValuePair<ISequence, IList<ReadMap>> reverseContigMaps in reverseContigs)
{
IList<ValidMatePair> matePairs;
if (!forwardContig.TryGetValue(reverseContigMaps.Key, out matePairs))
{
matePairs = new List<ValidMatePair>();
forwardContig.Add(reverseContigMaps.Key, matePairs);
}
foreach (ReadMap forwardMap in forwardContigMaps.Value)
{
foreach (ReadMap reverseMap in reverseContigMaps.Value)
{
ValidMatePair validPairedRead = new ValidMatePair();
validPairedRead.PairedRead = pair;
validPairedRead.ForwardReadStartPosition.Add(forwardMap.StartPositionOfContig);
validPairedRead.ReverseReadStartPosition.Add(
reverseMap.StartPositionOfContig + reverseMap.Length - 1);
validPairedRead.ReverseReadReverseComplementStartPosition.Add(
reverseContigMaps.Key.Count - reverseMap.StartPositionOfContig - 1);
matePairs.Add(validPairedRead);
}
}
}
}
}
/// <summary>
/// Finds contig pairs having valid mate pairs connection between them.
/// </summary>
/// <param name="reads">Input list of reads.</param>
/// <param name="alignment">Reads contig alignment.</param>
/// <returns>Contig Mate pair map.</returns>
public ContigMatePairs MapContigToMatePairs(IEnumerable<ISequence> reads, ReadContigMap alignment)
{
if (alignment == null)
{
throw new ArgumentNullException("alignment");
}
if (reads == null)
{
throw new ArgumentNullException("reads");
}
Dictionary<ISequence, IList<ReadMap>> contigs1;
Dictionary<ISequence, IList<ReadMap>> contigs2;
ContigMatePairs contigMatePairs = new ContigMatePairs();
foreach (ISequence read in reads)
{
Match match = this.readExpression.Match(read.ID);
if (match.Success)
{
string mateDisplayID = GenerateExpression(match);
if (alignment.TryGetValue(read.ID, out contigs1) && alignment.TryGetValue(mateDisplayID, out contigs2))
{
MatePair pair;
if (match.Groups[2].Value == "X1" || match.Groups[2].Value == "F" ||
match.Groups[2].Value == "1" || match.Groups[2].Value == "x1" ||
match.Groups[2].Value == "f" || match.Groups[2].Value == "a" ||
match.Groups[2].Value == "A")
{
pair = new MatePair(read.ID, mateDisplayID, match.Groups[3].Value);
ContigMatePairMapper(contigs1, contigs2, pair, contigMatePairs);
}
else
{
pair = new MatePair(mateDisplayID, read.ID, match.Groups[3].Value);
ContigMatePairMapper(contigs2, contigs1, pair, contigMatePairs);
}
alignment.Remove(read.ID);
alignment.Remove(mateDisplayID);
}
}
}
return contigMatePairs;
}
public void ValidateMatePairToString()
{
var p = new MatePair("2K") {ForwardReadID = "F", ReverseReadID = "R"};
string actualString = p.ToString();
string expectedString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.MatePairExpectedNode);
Assert.AreEqual(actualString, expectedString);
}
/// <summary>
/// Map reads to mate pairs.
/// </summary>
/// <param name="reads">List of Reads.</param>
/// <returns>List of mate pairs.</returns>
public IList <MatePair> Map(IEnumerable <ISequence> reads)
{
if (null == reads)
{
throw new ArgumentNullException("reads");
}
Dictionary <string, MatePair> pairs = new Dictionary <string, MatePair>();
MatePair mate;
string exp = string.Empty;
foreach (ISequence read in reads)
{
if (read == null)
{
throw new ArgumentException(Properties.Resource.ReadCannotBeNull);
}
if (pairs.TryGetValue(read.ID, out mate))
{
if (string.IsNullOrEmpty(mate.ForwardReadID))
{
mate.ForwardReadID = read.ID;
}
else
{
mate.ReverseReadID = read.ID;
}
}
else
{
Match match = this.readExpression.Match(read.ID);
if (match.Success)
{
mate = new MatePair(match.Groups[3].Value);
if (match.Groups[2].Value == "X1" || match.Groups[2].Value == "F" ||
match.Groups[2].Value == "1" || match.Groups[2].Value == "x1" ||
match.Groups[2].Value == "f" || match.Groups[2].Value == "a" ||
match.Groups[2].Value == "A")
{
mate.ForwardReadID = read.ID;
}
else
{
mate.ReverseReadID = read.ID;
}
exp = GenerateExpression(match);
if (!pairs.ContainsKey(exp))
{
pairs.Add(exp, mate);
}
else
{
throw new FormatException(
string.Format(CultureInfo.CurrentCulture, Properties.Resource.DuplicatingReadIds, read.ID));
}
}
}
}
return(pairs.Values.Where(pair => !string.IsNullOrEmpty(pair.ForwardReadID) &&
!string.IsNullOrEmpty(pair.ReverseReadID)).ToList());
}
public void TestMatePairToString()
{
MatePair p = new MatePair("2K") {ForwardReadID = "F", ReverseReadID = "R"};
string actualString = p.ToString();
const string expectedString = "ForwardReadID=F, ReverseReadID=R, MeanLength=2000, Standard Deviation=100";
Assert.AreEqual(actualString, expectedString);
}
