/// <summary> /// Writes delta for query sequences. /// </summary> /// <param name="sorter">Sorter instance.</param> /// <param name="unsortedDeltaFilename">Unsorted Delta Filename.</param> /// <param name="queryParser">Query/read sequences parser.</param> /// <param name="outputfilename">Output file name.</param> public static void WriteSortedDelta(DeltaAlignmentSorter sorter, string unsortedDeltaFilename, FastASequencePositionParser queryParser, string outputfilename) { if (sorter == null) { throw new ArgumentNullException("sorter"); } using (DeltaAlignmentParser unsortedDeltaParser = new DeltaAlignmentParser(unsortedDeltaFilename, queryParser)) { using (StreamWriter writer = new StreamWriter(outputfilename)) { long deltaPositionInFile = 0; foreach (long id in sorter.GetSortedIds()) { DeltaAlignment deltaAlignment = unsortedDeltaParser.GetDeltaAlignmentAt(id); deltaAlignment.Id = deltaPositionInFile; string deltaString = Helper.GetString(deltaAlignment); deltaPositionInFile += deltaString.Length; writer.Write(deltaString); } writer.Flush(); } } }
/// <summary> /// Refine layout in the delta alignments. /// </summary> public void RefineLayout() { TimeSpan timeSpan = new TimeSpan(); Stopwatch runAlgorithm = new Stopwatch(); runAlgorithm.Restart(); FileInfo inputFileinfo = new FileInfo(this.FilePath[1]); long inputFileLength = inputFileinfo.Length; FastASequencePositionParser queryParser; using (var input = File.OpenRead(FilePath[1])) { queryParser = new FastASequencePositionParser(input, true); queryParser.CacheSequencesForRandomAccess(); } runAlgorithm.Stop(); if (this.Verbose) { Output.WriteLine(OutputLevel.Verbose); Output.WriteLine(OutputLevel.Verbose, "Processed Query FastA file: {0}", Path.GetFullPath(this.FilePath[1])); Output.WriteLine(OutputLevel.Verbose, " Read/Processing time : {0}", runAlgorithm.Elapsed); Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", inputFileLength); } inputFileinfo = new FileInfo(this.FilePath[0]); inputFileLength = inputFileinfo.Length; runAlgorithm.Restart(); using (var input = File.OpenRead(FilePath[0])) using (DeltaAlignmentCollection deltaCollection = new DeltaAlignmentCollection(input, queryParser)) { runAlgorithm.Stop(); if (this.Verbose) { Output.WriteLine(OutputLevel.Verbose); Output.WriteLine(OutputLevel.Verbose, "Processed DeltaAlignment file: {0}", Path.GetFullPath(this.FilePath[0])); Output.WriteLine(OutputLevel.Verbose, " Read/Processing time : {0}", runAlgorithm.Elapsed); Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", inputFileLength); } runAlgorithm.Restart(); IEnumerable <DeltaAlignment> result = LayoutRefiner.RefineLayout(deltaCollection); DeltaAlignmentSorter sorter = new DeltaAlignmentSorter(); WriteDelta(result, sorter, UnsortedLayoutRefinmentOutputFilename); runAlgorithm.Stop(); timeSpan = timeSpan.Add(runAlgorithm.Elapsed); runAlgorithm.Restart(); WriteSortedDelta(sorter, UnsortedLayoutRefinmentOutputFilename, queryParser, this.OutputFile); runAlgorithm.Stop(); } if (this.Verbose) { Output.WriteLine(OutputLevel.Verbose); Output.WriteLine(OutputLevel.Verbose, "Compute time: {0}", timeSpan); Output.WriteLine(OutputLevel.Verbose, "Write time: {0}", runAlgorithm.Elapsed); } }
/// <summary> /// Resolve ambiguity in the delta alignments. /// </summary> public void ResolveAmbiguity() { TimeSpan repeatResolutionSpan = new TimeSpan(); Stopwatch runRepeatResolution = new Stopwatch(); runRepeatResolution.Restart(); FileInfo inputFileinfo = new FileInfo(this.FilePath[1]); long inputFileLength = inputFileinfo.Length; runRepeatResolution.Stop(); if (this.Verbose) { Console.Error.WriteLine(); Console.Error.WriteLine(" Processed Query FastA file: {0}", Path.GetFullPath(this.FilePath[1])); Console.Error.WriteLine(" Read/Processing time: {0}", runRepeatResolution.Elapsed); Console.Error.WriteLine(" File Size : {0}", inputFileLength); } inputFileinfo = new FileInfo(this.FilePath[0]); inputFileLength = inputFileinfo.Length; runRepeatResolution.Restart(); DeltaAlignmentSorter sorter = null; using (var alignmentStream = File.OpenRead(this.FilePath[0])) using (var readStream = File.OpenRead(this.FilePath[1])) using (DeltaAlignmentCollection deltaCollection = new DeltaAlignmentCollection(alignmentStream, readStream)) { runRepeatResolution.Stop(); if (this.Verbose) { Console.Error.WriteLine(); Console.Error.WriteLine(" Processed DeltaAlignment file: {0}", Path.GetFullPath(this.FilePath[0])); Console.Error.WriteLine(" Read/Processing time: {0}", runRepeatResolution.Elapsed); Console.Error.WriteLine(" File Size : {0}", inputFileLength); } runRepeatResolution.Restart(); IEnumerable <DeltaAlignment> outputDeltas = RepeatResolver.ResolveAmbiguity(deltaCollection); sorter = new DeltaAlignmentSorter(); WriteUnsortedDelta(outputDeltas, sorter); } runRepeatResolution.Stop(); repeatResolutionSpan = repeatResolutionSpan.Add(runRepeatResolution.Elapsed); runRepeatResolution.Restart(); this.WriteDelta(sorter); runRepeatResolution.Stop(); if (this.Verbose) { Console.Error.WriteLine(" Compute time: {0}", repeatResolutionSpan); Console.Error.WriteLine(" Write() time: {0}", runRepeatResolution.Elapsed); } }
/// <summary> /// Writes delta for query sequences. /// </summary> /// <param name="delta">The Deltas.</param> private void WriteDelta( DeltaAlignmentSorter sorter) { FastASequencePositionParser sequenceParser = null; DeltaAlignmentParser unsortedDeltaParser = null; TextWriter textWriterConsoleOutSave = Console.Out; StreamWriter streamWriterConsoleOut = null; try { sequenceParser = new FastASequencePositionParser(this.FilePath[1], true); unsortedDeltaParser = new DeltaAlignmentParser(UnsortedDeltaFile, sequenceParser); if (!string.IsNullOrEmpty(this.OutputFile)) { streamWriterConsoleOut = new StreamWriter(this.OutputFile); Console.SetOut(streamWriterConsoleOut); } long deltaPositionInFile = 0; foreach (long id in sorter.GetSortedIds()) { DeltaAlignment deltaAlignment = unsortedDeltaParser.GetDeltaAlignmentAt(id); deltaAlignment.Id = deltaPositionInFile; string deltaString = Helper.GetString(deltaAlignment); deltaPositionInFile += deltaString.Length; Console.Write(deltaString); } Console.Out.Flush(); } finally { if (streamWriterConsoleOut != null) { streamWriterConsoleOut.Dispose(); streamWriterConsoleOut = null; } if (sequenceParser != null) { sequenceParser.Dispose(); sequenceParser = null; } if (unsortedDeltaParser != null) { unsortedDeltaParser.Dispose(); unsortedDeltaParser = null; } Console.SetOut(textWriterConsoleOutSave); } }
/// <summary> /// Writes delta for query sequences. /// </summary> /// <param name="delta">The Deltas.</param> /// <param name="sorter">Sorter instance.</param> private static void WriteUnsortedDelta(IEnumerable <DeltaAlignment> delta, DeltaAlignmentSorter sorter) { using (var writer = new StreamWriter(UnsortedDeltaFile)) { long deltaPositionInFile = 0; foreach (DeltaAlignment deltaAlignment in delta) { deltaAlignment.Id = deltaPositionInFile; string deltaString = Helper.GetString(deltaAlignment); deltaPositionInFile += deltaString.Length; writer.Write(deltaString); sorter.Add(deltaAlignment.Id, deltaAlignment.FirstSequenceStart); } } }
/// <summary> /// Writes delta for query sequences. /// </summary> /// <param name="delta">The Deltas.</param> /// <param name="sorter">Sorter instance.</param> /// <param name="outputStream">Output file name.</param> public static void WriteUnsortedDelta(IEnumerable <DeltaAlignment> delta, DeltaAlignmentSorter sorter, Stream outputStream) { using (StreamWriter writer = new StreamWriter(outputStream)) { long deltaPositionInFile = 0; foreach (DeltaAlignment deltaAlignment in delta) { deltaAlignment.Id = deltaPositionInFile; string deltaString = Helper.GetString(deltaAlignment); deltaPositionInFile += deltaString.Length; writer.Write(deltaString); sorter.Add(deltaAlignment.Id, deltaAlignment.FirstSequenceStart); } writer.Flush(); } }
/// <summary> /// Writes delta for query sequences. /// </summary> /// <param name="deltaAlignments">Delta alignments to write.</param> /// <param name="filename">File name to write.</param> private static void WriteDelta(IEnumerable <DeltaAlignment> deltaAlignments, DeltaAlignmentSorter sorter, string filename) { using (StreamWriter writer = new StreamWriter(filename)) { long deltaPositionInFile = 0; foreach (DeltaAlignment deltaAlignment in deltaAlignments) { deltaAlignment.Id = deltaPositionInFile; string deltaString = Helper.GetString(deltaAlignment); deltaPositionInFile += deltaString.Length; writer.Write(deltaString); sorter.Add(deltaAlignment.Id, deltaAlignment.FirstSequenceStart); } writer.Flush(); } }
/// <summary> /// Writes delta for query sequences. /// </summary> /// <param name="sorter">Sorter instance.</param> /// <param name="unsortedDeltaFilename">Unsorted Delta Filename.</param> /// <param name="queryFilename">Query/read sequences filename.</param> /// <param name="outputfilename">Output file name.</param> private static void WriteSortedDelta(DeltaAlignmentSorter sorter, string unsortedDeltaFilename, FastASequencePositionParser queryParser, string outputfilename) { using (DeltaAlignmentParser unsortedDeltaParser = new DeltaAlignmentParser(unsortedDeltaFilename, queryParser)) { TextWriter textWriterConsoleOutSave = Console.Out; StreamWriter streamWriterConsoleOut = null; try { if (!string.IsNullOrEmpty(outputfilename)) { streamWriterConsoleOut = new StreamWriter(outputfilename); Console.SetOut(streamWriterConsoleOut); } long deltaPositionInFile = 0; foreach (long id in sorter.GetSortedIds()) { DeltaAlignment deltaAlignment = unsortedDeltaParser.GetDeltaAlignmentAt(id); deltaAlignment.Id = deltaPositionInFile; string deltaString = Helper.GetString(deltaAlignment); deltaPositionInFile += deltaString.Length; Console.Write(deltaString); } Console.Out.Flush(); } finally { if (streamWriterConsoleOut != null) { streamWriterConsoleOut.Dispose(); streamWriterConsoleOut = null; } Console.SetOut(textWriterConsoleOutSave); } } }
/// <summary> /// Assemble the input sequences into the largest possible contigs. /// </summary> /// <param name="referenceSequence">The sequence used as backbone for assembly.</param> /// <param name="queryParser">The parser to load the sequences to assemble.</param> /// <returns>IComparativeAssembly instance which contains list of assembled sequences.</returns> public IEnumerable <ISequence> Assemble(IEnumerable <ISequence> referenceSequence, FastASequencePositionParser queryParser) { this._progressTimer = new Timer(ProgressTimerInterval); this._progressTimer.Elapsed += this.ProgressTimerElapsed; if (queryParser == null) { throw new ArgumentNullException("queryParser"); } string readAlignmentOutputFilename = null; string unsortedRepeatResolutionOutputFilename = null; string repeateResolutionOutputFilename = null; string unsortedLayoutRefinmentOutputFilename = null; string layoutRefinmentOutputFileName = null; try { // Converting to list to avoid multiple parse of the reference file if its a yield return var refSequences = referenceSequence.ToList(); // CacheSequencesForRandomAccess will ignore the call if called more than once. queryParser.CacheSequencesForRandomAccess(); IEnumerable <ISequence> reads = queryParser.Parse(); // Comparative Assembly Steps // 1) Read Alignment (Calling NUCmer for aligning reads to reference sequence) this.StatusEventStart(Properties.Resources.ReadAlignmentStarted); IEnumerable <DeltaAlignment> alignmentBetweenReferenceAndReads = this.ReadAlignment(refSequences, reads.Where(a => a.Count >= this.LengthOfMum)); readAlignmentOutputFilename = Path.GetTempFileName(); WriteDelta(alignmentBetweenReferenceAndReads, readAlignmentOutputFilename); this.StatusEventEnd(Properties.Resources.ReadAlignmentEnded); // 2) Repeat Resolution this.StatusEventStart(Properties.Resources.RepeatResolutionStarted); DeltaAlignmentSorter sorter; unsortedRepeatResolutionOutputFilename = Path.GetTempFileName(); using (DeltaAlignmentCollection deltaAlignmentFromReadAlignment = new DeltaAlignmentCollection(readAlignmentOutputFilename, queryParser)) { IEnumerable <DeltaAlignment> repeatResolvedDeltas = RepeatResolution(deltaAlignmentFromReadAlignment); sorter = new DeltaAlignmentSorter(refSequences[0].Count); WriteUnsortedDelta(repeatResolvedDeltas, sorter, unsortedRepeatResolutionOutputFilename); } this.StatusEventEnd(Properties.Resources.RepeatResolutionEnded); this.StatusEventStart(Properties.Resources.SortingResolvedDeltasStarted); repeateResolutionOutputFilename = Path.GetTempFileName(); WriteSortedDelta(sorter, unsortedRepeatResolutionOutputFilename, queryParser, repeateResolutionOutputFilename); this.StatusEventEnd(Properties.Resources.SortingResolvedDeltasEnded); // 3) Layout Refinement this.StatusEventStart(Properties.Resources.LayoutRefinementStarted); layoutRefinmentOutputFileName = Path.GetTempFileName(); using (DeltaAlignmentCollection unsortedDeltaCollectionForLayoutRefinment = new DeltaAlignmentCollection(repeateResolutionOutputFilename, queryParser)) { unsortedLayoutRefinmentOutputFilename = Path.GetTempFileName(); IEnumerable <DeltaAlignment> layoutRefinedDeltas = LayoutRefinment(unsortedDeltaCollectionForLayoutRefinment); sorter = new DeltaAlignmentSorter(refSequences[0].Count); WriteUnsortedDelta(layoutRefinedDeltas, sorter, unsortedLayoutRefinmentOutputFilename); WriteSortedDelta(sorter, unsortedLayoutRefinmentOutputFilename, queryParser, layoutRefinmentOutputFileName); } this.StatusEventEnd(Properties.Resources.LayoutRefinementEnded); // 4) Consensus Generation this.StatusEventStart(Properties.Resources.ConsensusGenerationStarted); IList <ISequence> contigs; using (var delta = new DeltaAlignmentCollection(layoutRefinmentOutputFileName, queryParser)) { contigs = this.ConsensusGenerator(delta).ToList(); } this.StatusEventEnd(Properties.Resources.ConsensusGenerationEnded); if (this.ScaffoldingEnabled) { // 5) Scaffold Generation this.StatusEventStart(Properties.Resources.ScaffoldGenerationStarted); IEnumerable <ISequence> scaffolds = this.ScaffoldsGenerator(contigs, reads); this.StatusEventEnd(Properties.Resources.ScaffoldGenerationEnded); return(scaffolds); } else { return(contigs); } } finally { this._progressTimer.Stop(); // Cleanup temp files. if (!string.IsNullOrEmpty(readAlignmentOutputFilename)) { File.Delete(readAlignmentOutputFilename); } if (!string.IsNullOrEmpty(unsortedRepeatResolutionOutputFilename)) { File.Delete(unsortedRepeatResolutionOutputFilename); } if (!string.IsNullOrEmpty(repeateResolutionOutputFilename)) { File.Delete(repeateResolutionOutputFilename); } if (!string.IsNullOrEmpty(unsortedLayoutRefinmentOutputFilename)) { File.Delete(unsortedLayoutRefinmentOutputFilename); } if (!string.IsNullOrEmpty(layoutRefinmentOutputFileName)) { File.Delete(layoutRefinmentOutputFileName); } } }
/// <summary> /// Assemble the input sequences into the largest possible contigs. /// </summary> /// <param name="referenceSequence">The sequence used as backbone for assembly.</param> /// <param name="queryParser">The parser to load the sequences to assemble.</param> /// <returns>IComparativeAssembly instance which contains list of assembled sequences.</returns> public IEnumerable <ISequence> Assemble(IEnumerable <ISequence> referenceSequence, FastASequencePositionParser queryParser) { if (referenceSequence == null) { throw new ArgumentNullException("referenceSequence"); } if (queryParser == null) { throw new ArgumentNullException("queryParser"); } Stream readAlignmentOutputStream = null; Stream unsortedRepeatResolutionOutputStream = null; Stream repeatResolutionOutputStream = null; Stream unsortedLayoutRefinmentOutputStream = null; Stream layoutRefinmentOutputStream = null; try { // Converting to list to avoid multiple parse of the reference file if its a yield return var refSequences = referenceSequence.ToList(); // CacheSequencesForRandomAccess will ignore the call if called more than once. queryParser.CacheSequencesForRandomAccess(); IEnumerable <ISequence> reads = queryParser.Parse(); // Comparative Assembly Steps // 1) Read Alignment (Calling NUCmer for aligning reads to reference sequence) this.StatusEventStart(Properties.Resource.ReadAlignmentStarted); IEnumerable <DeltaAlignment> alignmentBetweenReferenceAndReads = this.ReadAlignment(refSequences, reads.Where(a => a.Count >= this.LengthOfMum)); readAlignmentOutputStream = PlatformManager.Services.CreateTempStream(); WriteDelta(alignmentBetweenReferenceAndReads, readAlignmentOutputStream); this.StatusEventEnd(Properties.Resource.ReadAlignmentEnded); // 2) Repeat Resolution this.StatusEventStart(Properties.Resource.RepeatResolutionStarted); DeltaAlignmentSorter sorter; unsortedRepeatResolutionOutputStream = PlatformManager.Services.CreateTempStream(); using (var deltaAlignmentFromReadAlignment = new DeltaAlignmentCollection(readAlignmentOutputStream, queryParser)) { IEnumerable <DeltaAlignment> repeatResolvedDeltas = RepeatResolution(deltaAlignmentFromReadAlignment); sorter = new DeltaAlignmentSorter(refSequences[0].Count); WriteUnsortedDelta(repeatResolvedDeltas, sorter, unsortedRepeatResolutionOutputStream); } this.StatusEventEnd(Properties.Resource.RepeatResolutionEnded); this.StatusEventStart(Properties.Resource.SortingResolvedDeltasStarted); repeatResolutionOutputStream = PlatformManager.Services.CreateTempStream(); WriteSortedDelta(sorter, unsortedRepeatResolutionOutputStream, queryParser, repeatResolutionOutputStream); this.StatusEventEnd(Properties.Resource.SortingResolvedDeltasEnded); // 3) Layout Refinement this.StatusEventStart(Properties.Resource.LayoutRefinementStarted); layoutRefinmentOutputStream = PlatformManager.Services.CreateTempStream(); using (var unsortedDeltaCollectionForLayoutRefinment = new DeltaAlignmentCollection(repeatResolutionOutputStream, queryParser)) { unsortedLayoutRefinmentOutputStream = PlatformManager.Services.CreateTempStream(); IEnumerable <DeltaAlignment> layoutRefinedDeltas = LayoutRefinment(unsortedDeltaCollectionForLayoutRefinment); sorter = new DeltaAlignmentSorter(refSequences[0].Count); WriteUnsortedDelta(layoutRefinedDeltas, sorter, unsortedLayoutRefinmentOutputStream); WriteSortedDelta(sorter, unsortedLayoutRefinmentOutputStream, queryParser, layoutRefinmentOutputStream); } this.StatusEventEnd(Properties.Resource.LayoutRefinementEnded); // 4) Consensus Generation this.StatusEventStart(Properties.Resource.ConsensusGenerationStarted); IList <ISequence> contigs; using (var delta = new DeltaAlignmentCollection(layoutRefinmentOutputStream, queryParser)) { contigs = this.ConsensusGenerator(delta).ToList(); } this.StatusEventEnd(Properties.Resource.ConsensusGenerationEnded); if (this.ScaffoldingEnabled) { // 5) Scaffold Generation this.StatusEventStart(Properties.Resource.ScaffoldGenerationStarted); IEnumerable <ISequence> scaffolds = this.ScaffoldsGenerator(contigs, reads); this.StatusEventEnd(Properties.Resource.ScaffoldGenerationEnded); return(scaffolds); } else { return(contigs); } } finally { // Cleanup temp files. if (readAlignmentOutputStream != null) { readAlignmentOutputStream.Dispose(); } if (unsortedRepeatResolutionOutputStream != null) { unsortedRepeatResolutionOutputStream.Dispose(); } if (repeatResolutionOutputStream != null) { repeatResolutionOutputStream.Dispose(); } if (unsortedLayoutRefinmentOutputStream != null) { unsortedLayoutRefinmentOutputStream.Dispose(); } if (layoutRefinmentOutputStream != null) { layoutRefinmentOutputStream.Dispose(); } } }