public void TestLISWithCrossAndOverlap()
{
// Create a list of Mum classes.
List <Match> MUM = new List <Match>();
Match mum;
mum = new Match();
mum.ReferenceSequenceOffset = 0;
mum.Length = 5;
mum.QuerySequenceOffset = 5;
MUM.Add(mum);
mum = new Match();
mum.ReferenceSequenceOffset = 3;
mum.Length = 5;
mum.QuerySequenceOffset = 0;
MUM.Add(mum);
// ILongestIncreasingSubsequence lis = new LongestIncreasingSubsequence();
LongestIncreasingSubsequence lis = new LongestIncreasingSubsequence();
IList <Match> lisList = lis.SortMum(MUM);
IList <Match> lisList1 = lis.GetLongestSequence(lisList);
List <Match> expectedOutput = new List <Match>();
mum = new Match();
mum.ReferenceSequenceOffset = 0;
mum.Length = 5;
mum.QuerySequenceOffset = 5;
expectedOutput.Add(mum);
Assert.IsTrue(CompareMumList(lisList1, expectedOutput));
}
public void TestSortMum()
{
// Create a list of Mum classes.
List <Match> MUM = new List <Match>();
Match mum;
mum = new Match();
mum.ReferenceSequenceOffset = 4;
mum.Length = 3;
mum.QuerySequenceOffset = 0;
MUM.Add(mum);
mum = new Match();
mum.ReferenceSequenceOffset = 0;
mum.Length = 3;
mum.QuerySequenceOffset = 3;
MUM.Add(mum);
LongestIncreasingSubsequence lis = new LongestIncreasingSubsequence();
IList <Match> lisList = lis.SortMum(MUM);
List <Match> expectedOutput = new List <Match>();
mum = new Match();
mum.ReferenceSequenceOffset = 0;
mum.Length = 3;
mum.QuerySequenceOffset = 3;
expectedOutput.Add(mum);
mum = new Match();
mum.ReferenceSequenceOffset = 4;
mum.Length = 3;
mum.QuerySequenceOffset = 0;
expectedOutput.Add(mum);
Assert.IsTrue(CompareMumList(lisList, expectedOutput));
}
private static void Main(string[] args)
{
try
{
Stopwatch stopWatchMumUtil = Stopwatch.StartNew();
Stopwatch stopWatchInterval = new Stopwatch();
Console.Error.WriteLine(SplashString());
if (args.Length > 0)
{
CommandLineOptions myArgs = ProcessCommandLine(args);
TimeSpan writetime = new TimeSpan();
LongestIncreasingSubsequence lis = new LongestIncreasingSubsequence();
IEnumerable <Match> mums;
if (myArgs.PerformLISOnly)
{
stopWatchInterval.Restart();
IList <Match> parsedMUMs = ParseMums(myArgs.FileList[0]);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed MUM file: {0}", Path.GetFullPath(myArgs.FileList[0]));
Console.Error.WriteLine(" Total MUMs: {0:#,000}", parsedMUMs.Count);
Console.Error.WriteLine(" Read/Processing time: {0}", stopWatchInterval.Elapsed);
}
stopWatchInterval.Restart();
IList <Match> sortedMUMs = lis.SortMum(parsedMUMs);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Sort MUM time: {0}", stopWatchInterval.Elapsed);
}
stopWatchInterval.Restart();
if (sortedMUMs.Count != 0)
{
mums = lis.GetLongestSequence(sortedMUMs);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Perform LIS time: {0}", stopWatchInterval.Elapsed);
}
stopWatchInterval.Restart();
WriteMums(mums);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Write MUM time: {0}", stopWatchInterval.Elapsed);
}
stopWatchMumUtil.Stop();
}
else
{
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Perform LIS time: {0}", stopWatchInterval.Elapsed);
}
stopWatchInterval.Restart();
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Write MUM time: {0}", stopWatchInterval.Elapsed);
}
stopWatchMumUtil.Stop();
}
}
else
{
FileInfo refFileinfo = new FileInfo(myArgs.FileList[0]);
long refFileLength = refFileinfo.Length;
refFileinfo = null;
stopWatchInterval.Restart();
IEnumerable <ISequence> referenceSequences = ParseFastA(myArgs.FileList[0]);
ISequence referenceSequence = referenceSequences.First();
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed Reference FastA file: {0}", Path.GetFullPath(myArgs.FileList[0]));
Console.Error.WriteLine(" Length of first Sequence: {0:#,000}", referenceSequence.Count);
Console.Error.WriteLine(" Read/Processing time: {0}", stopWatchInterval.Elapsed);
Console.Error.WriteLine(" File Size : {0}", refFileLength);
}
FileInfo queryFileinfo = new FileInfo(myArgs.FileList[1]);
long queryFileLength = queryFileinfo.Length;
refFileinfo = null;
stopWatchInterval.Restart();
IEnumerable <ISequence> querySequences = ParseFastA(myArgs.FileList[1]);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed Query FastA file: {0}", Path.GetFullPath(myArgs.FileList[1]));
Console.Error.WriteLine(" Read/Processing time: {0}", stopWatchInterval.Elapsed);
Console.Error.WriteLine(" File Size : {0}", queryFileLength);
}
if (myArgs.ReverseOnly)
{
stopWatchInterval.Restart();
querySequences = ReverseComplementSequenceList(querySequences);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Reverse Complement time: {0}", stopWatchInterval.Elapsed);
}
}
else if (myArgs.Both)
{ // add the reverse complement sequences to the query list too
stopWatchInterval.Restart();
querySequences = AddReverseComplementsToSequenceList(querySequences);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Add Reverse Complement time: {0}", stopWatchInterval.Elapsed);
}
}
TimeSpan mummerTime = new TimeSpan(0, 0, 0);
stopWatchInterval.Restart();
Sequence seq = referenceSequence as Sequence;
if (seq == null)
{
throw new ArgumentException("MUMmer supports only Sequence class");
}
MUMmer mummer = new MUMmer(seq);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine("Suffix tree construction time: {0}", stopWatchInterval.Elapsed);
}
mummer.LengthOfMUM = myArgs.Length;
mummer.NoAmbiguity = myArgs.NoAmbiguity;
long querySeqCount = 0;
double sumofSeqLength = 0;
if (myArgs.MaxMatch)
{
foreach (ISequence querySeq in querySequences)
{
stopWatchInterval.Restart();
IList <Match> mumList = GetMumsForLIS(mummer.GetMatchesUniqueInReference(querySeq));
if (mumList.Count != 0)
{
mums = lis.GetLongestSequence(lis.SortMum(mumList));
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
WriteMums(mums, referenceSequence, querySeq, myArgs);
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
else
{
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
}
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Number of query Sequences: {0}", querySeqCount);
Console.Error.WriteLine(" Average length of query Sequences: {0}", sumofSeqLength / querySeqCount);
Console.Error.WriteLine(" Compute GetMumsMaxMatch() with LIS time: {0}", mummerTime);
}
}
else if (myArgs.Mum)
{
foreach (ISequence querySeq in querySequences)
{
stopWatchInterval.Restart();
IList <Match> mumList = GetMumsForLIS(mummer.GetMatchesUniqueInReference(querySeq));
if (mumList.Count != 0)
{
mums = lis.GetLongestSequence(lis.SortMum(mumList));
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
WriteMums(mums, referenceSequence, querySeq, myArgs);
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
else
{
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
}
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Number of query Sequences: {0}", querySeqCount);
Console.Error.WriteLine(" Average length of query Sequences: {0}", sumofSeqLength / querySeqCount);
Console.Error.WriteLine(" Compute GetMumsMum() with LIS time: {0}", mummerTime);
}
}
else if (myArgs.Mumreference)
{
// NOTE:
// mum3.GetMUMs() this really implements the GetMumReference() functionality
// mums = mum3.GetMumsReference( referenceSequences[0], querySequences); // should be
foreach (ISequence querySeq in querySequences)
{
stopWatchInterval.Restart();
IList <Match> mumList = GetMumsForLIS(mummer.GetMatchesUniqueInReference(querySeq));
if (mumList.Count != 0)
{
mums = lis.GetLongestSequence(lis.SortMum(mumList));
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
// do sort
// WriteLongestIncreasingSubsequences
WriteMums(mums, referenceSequence, querySeq, myArgs);
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
else
{
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
}
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Number of query Sequences: {0}", querySeqCount);
Console.Error.WriteLine(" Average length of query Sequences: {0}", sumofSeqLength / querySeqCount);
Console.Error.WriteLine(" Compute GetMumsReference() time: {0}", mummerTime);
}
}
else
{
// cannot happen as argument processing already asserted one of the three options must be specified
Console.Error.WriteLine("\nError: one of /maxmatch, /mum, /mumreference options must be specified.");
Environment.Exit(-1);
// kill the error about unitialized use of 'mums' in the next block...the compiler does not recognize
// Environment.Exit() as a no-return function
throw new Exception("Never hit this");
}
}
if (myArgs.Verbose)
{
Console.Error.WriteLine(" WriteMums() time: {0}", writetime);
}
stopWatchMumUtil.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Total LisUtil Runtime: {0}", stopWatchMumUtil.Elapsed);
}
}
else
{
Console.WriteLine(Resources.LisUtilHelp);
}
}
catch (Exception ex)
{
DisplayException(ex);
}
}
/// <summary>
/// This method is considered as main execute method which defines the
/// step by step algorithm. Derived class flows the defined flow by this
/// method. Store generated MUMs in properties MUMs, SortedMUMs.
/// Alignment first finds MUMs for all the query sequence, and then
/// runs pairwise algorithm on gaps to produce alignments.
/// </summary>
/// <param name="referenceSequence">Reference sequence.</param>
/// <param name="querySequenceList">List of input sequences.</param>
/// <returns>A list of sequence alignments.</returns>
private IList <IPairwiseSequenceAlignment> AlignmentWithAccumulatedMUMs(
ISequence referenceSequence,
IEnumerable <ISequence> querySequenceList)
{
// Get MUMs
this.mums = new Dictionary <ISequence, IEnumerable <Match> >();
IList <IPairwiseSequenceAlignment> results = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment alignment = null;
IEnumerable <Match> mum;
if (this.Validate(referenceSequence, querySequenceList))
{
// Safety check for public methods to ensure that null
// inputs are handled.
if (referenceSequence == null || querySequenceList == null)
{
return(null);
}
Sequence seq = referenceSequence as Sequence;
if (seq == null)
{
throw new ArgumentException(Properties.Resource.OnlySequenceClassSupported);
}
MUMmer mummer = new MUMmer(seq);
mummer.LengthOfMUM = this.LengthOfMUM;
mummer.NoAmbiguity = this.AmbigiousMatchesAllowed;
foreach (ISequence sequence in querySequenceList)
{
if (sequence.Equals(referenceSequence))
{
continue;
}
alignment = new PairwiseSequenceAlignment(referenceSequence, sequence);
// Step2 : streaming process is performed with the query sequence
if (this.MaximumMatchEnabled)
{
mum = mummer.GetMatches(sequence);
}
else
{
mum = mummer.GetMatchesUniqueInReference(sequence);
}
this.mums.Add(sequence, mum);
// Step3(a) : sorted mum list based on reference sequence
LongestIncreasingSubsequence lis = new LongestIncreasingSubsequence();
IList <Match> sortedMumList = lis.SortMum(GetMumsForLIS(mum));
if (sortedMumList.Count > 0)
{
// Step3(b) : LIS using greedy cover algorithm
IList <Match> finalMumList = lis.GetLongestSequence(sortedMumList);
if (finalMumList.Count > 0)
{
// Step 4 : get all the gaps in each sequence and call
// pairwise alignment
alignment.PairwiseAlignedSequences.Add(
this.ProcessGaps(referenceSequence, sequence, finalMumList));
}
results.Add(alignment);
}
else
{
IList <IPairwiseSequenceAlignment> sequenceAlignment = this.RunPairWise(
referenceSequence,
sequence);
foreach (IPairwiseSequenceAlignment pairwiseAlignment in sequenceAlignment)
{
results.Add(pairwiseAlignment);
}
}
}
}
return(results);
}