コード例 #1
0
        /// <summary>
        /// Always download reference that aren't present and set default options
        /// </summary>
        /// <param name="options"></param>
        public static void FinishSetup(Options options)
        {
            // Download ensembl references and set default paths
            EnsemblDownloadsWrapper downloadsWrapper = new EnsemblDownloadsWrapper();

            downloadsWrapper.DownloadReferences(options.SpritzDirectory, options.SpritzDirectory, options.Reference, false);
            options.GenomeFasta              = options.GenomeFasta ?? downloadsWrapper.GenomeFastaPath;
            options.GeneModelGtfOrGff        = options.GeneModelGtfOrGff ?? downloadsWrapper.Gff3GeneModelPath;
            options.GenomeStarIndexDirectory = options.GenomeStarIndexDirectory ?? STARWrapper.GetGenomeStarIndexDirectoryPath(options.GenomeFasta, options.GeneModelGtfOrGff);
            options.ProteinFastaPath         = options.ProteinFastaPath ?? downloadsWrapper.ProteinFastaPath;
        }
コード例 #2
0
        /// <summary>
        /// Runs a two-pass STAR alignment for a given set of RNA-Seq fastq files,
        /// or it performs a Bowtie2 alignment for WGS or exome sequencing files.
        /// </summary>
        public void PerformAlignment()
        {
            int starThreads = Math.Min(18, Parameters.Threads); // 18 max, otherwise it throws a segmentation fault in sorting the BAM files

            if (Parameters.ExperimentType == ExperimentType.RNASequencing)
            {
                // Alignment preparation
                WrapperUtility.GenerateAndRunScript(WrapperUtility.GetAnalysisScriptPath(Parameters.AnalysisDirectory, "GenomeGenerate.bash"),
                                                    STARWrapper.GenerateGenomeIndex(
                                                        Parameters.SpritzDirectory,
                                                        Parameters.Threads,
                                                        Parameters.GenomeStarIndexDirectory,
                                                        new string[] { Parameters.ReorderedFastaPath },
                                                        Parameters.GeneModelGtfOrGffPath,
                                                        Parameters.Fastqs))
                .WaitForExit();

                // there's trouble with the number of open files for sorting and stuff, which increases with the number of threads
                // 18 is the max that works with the default max number of open files
                TwoPassAlignment(starThreads, Parameters.OverwriteStarAlignment);
            }
            else
            {
                foreach (string[] fastq in Parameters.Fastqs)
                {
                    SkewerWrapper.Trim(Parameters.SpritzDirectory, Parameters.AnalysisDirectory, Parameters.Threads, 19, fastq, false, out string[] trimmedFastqs, out string skewerLog);
                    FastqsForAlignment.Add(trimmedFastqs);
                }
                TopHatWrapper.GenerateBowtieIndex(Parameters.SpritzDirectory, Parameters.AnalysisDirectory, Parameters.ReorderedFastaPath, out string bowtieIndexPrefix);
                List <string> alignmentCommands = new List <string> {
                    "echo \"Aligning reads with bowtie2.\""
                };
                foreach (string[] fastq in FastqsForAlignment)
                {
                    // alignment
                    alignmentCommands.AddRange(TopHatWrapper.Bowtie2Align(Parameters.SpritzDirectory, Parameters.AnalysisDirectory,
                                                                          bowtieIndexPrefix, Parameters.Threads, fastq, Parameters.StrandSpecific, out string sortedBamPath));
                    alignmentCommands.Add(SamtoolsWrapper.IndexBamCommand(sortedBamPath));

                    // mark duplicates
                    GATKWrapper gatk = new GATKWrapper(1);
                    alignmentCommands.AddRange(gatk.PrepareBamAndFasta(Parameters.SpritzDirectory, Parameters.AnalysisDirectory, Parameters.Threads, sortedBamPath, Parameters.ReorderedFastaPath, Parameters.Reference));
                    alignmentCommands.Add(SamtoolsWrapper.IndexBamCommand(gatk.PreparedBamPath));

                    SortedBamFiles.Add(sortedBamPath);
                    DedupedBamFiles.Add(gatk.PreparedBamPath);
                }
                WrapperUtility.GenerateAndRunScript(WrapperUtility.GetAnalysisScriptPath(Parameters.AnalysisDirectory, "BowtieAlignment.bash"), alignmentCommands).WaitForExit();
            }
        }
コード例 #3
0
        /// <summary>
        /// Infers the strandedness of reads based on aligning a subset.
        /// </summary>
        /// <param name="spritzDirectory"></param>
        /// <param name="analysisDirectory"></param>
        /// <param name="threads"></param>
        /// <param name="fastqPaths"></param>
        /// <param name="genomeStarIndexDirectory"></param>
        /// <param name="reorderedFasta"></param>
        /// <param name="geneModelGtfOrGff"></param>
        /// <returns></returns>
        public static BAMProperties InferStrandedness(string spritzDirectory, string analysisDirectory, int threads, string[] fastqPaths, string genomeStarIndexDirectory,
                                                      string reorderedFasta, string geneModelGtfOrGff)
        {
            // Alignment preparation
            WrapperUtility.GenerateAndRunScript(WrapperUtility.GetAnalysisScriptPath(analysisDirectory, "GenomeGenerate.bash"),
                                                STARWrapper.GenerateGenomeIndex(spritzDirectory, threads, genomeStarIndexDirectory, new string[] { reorderedFasta }, geneModelGtfOrGff, new List <string[]> {
                fastqPaths
            }))
            .WaitForExit();

            STARWrapper.SubsetFastqs(spritzDirectory, analysisDirectory, fastqPaths, 30000, analysisDirectory, out string[] subsetFastqs);

            string subsetOutPrefix = Path.Combine(Path.GetDirectoryName(subsetFastqs[0]), Path.GetFileNameWithoutExtension(subsetFastqs[0]));

            WrapperUtility.GenerateAndRunScript(WrapperUtility.GetAnalysisScriptPath(analysisDirectory, "AlignSubset.bash"),
                                                STARWrapper.BasicAlignReadCommands(spritzDirectory, threads, genomeStarIndexDirectory, subsetFastqs, subsetOutPrefix, false, STARGenomeLoadOption.LoadAndKeep))
            .WaitForExit();
            BAMProperties bamProperties = new BAMProperties(subsetOutPrefix + STARWrapper.BamFileSuffix, geneModelGtfOrGff, new Genome(reorderedFasta), 0.8);

            return(bamProperties);
        }
コード例 #4
0
        /// <summary>
        /// Performs the bulk of two-pass alignments
        /// </summary>
        private void TwoPassAlignment(int threads, bool overWriteStarAlignment)
        {
            // Trimming and strand specificity
            Genome genome = new Genome(Parameters.ReorderedFastaPath);

            foreach (string[] fq in Parameters.Fastqs)
            {
                // Infer strand specificity before trimming because trimming can change read pairings
                string[] fqForAlignment      = fq;
                bool     localStrandSpecific = Parameters.StrandSpecific;
                if (Parameters.InferStrandSpecificity || Parameters.UseReadSubset)
                {
                    STARWrapper.SubsetFastqs(Parameters.SpritzDirectory, Parameters.AnalysisDirectory, fqForAlignment,
                                             Parameters.ReadSubset, Parameters.AnalysisDirectory, out string[] subsetFastqs);
                    if (Parameters.UseReadSubset)
                    {
                        fqForAlignment = subsetFastqs;
                    }
                    if (Parameters.InferStrandSpecificity)
                    {
                        string subsetOutPrefix = Path.Combine(Path.GetDirectoryName(subsetFastqs[0]), Path.GetFileNameWithoutExtension(subsetFastqs[0]));
                        WrapperUtility.GenerateAndRunScript(WrapperUtility.GetAnalysisScriptPath(Parameters.AnalysisDirectory, "AlignSubset.bash"),
                                                            STARWrapper.BasicAlignReadCommands(Parameters.SpritzDirectory, threads, Parameters.GenomeStarIndexDirectory, subsetFastqs, subsetOutPrefix, false, STARGenomeLoadOption.LoadAndKeep))
                        .WaitForExit();
                        BAMProperties bamProperties = new BAMProperties(subsetOutPrefix + STARWrapper.BamFileSuffix, Parameters.GeneModelGtfOrGffPath, new Genome(Parameters.ReorderedFastaPath), 0.8);
                        localStrandSpecific = bamProperties.Strandedness != Strandedness.None;
                    }
                }

                SkewerWrapper.Trim(Parameters.SpritzDirectory, Parameters.AnalysisDirectory, threads, 19, fqForAlignment, false, out string[] trimmedFastqs, out string skewerLog);
                fqForAlignment = trimmedFastqs;

                StrandSpecificities.Add(localStrandSpecific);
                FastqsForAlignment.Add(fqForAlignment);
            }

            // Alignment
            List <string> alignmentCommands = new List <string>();

            foreach (string[] fq in FastqsForAlignment)
            {
                string outPrefix = Path.Combine(Path.GetDirectoryName(fq[0]), Path.GetFileNameWithoutExtension(fq[0]));
                if (!File.Exists(outPrefix + STARWrapper.SpliceJunctionFileSuffix) || overWriteStarAlignment)
                {
                    alignmentCommands.AddRange(STARWrapper.FirstPassAlignmentCommands(Parameters.SpritzDirectory, threads, Parameters.GenomeStarIndexDirectory, fq, outPrefix, StrandSpecificities[FastqsForAlignment.IndexOf(fq)], STARGenomeLoadOption.LoadAndKeep));
                }
                FirstPassSpliceJunctions.Add(outPrefix + STARWrapper.SpliceJunctionFileSuffix);
            }
            int uniqueSuffix = 1;

            foreach (string f in FastqsForAlignment.SelectMany(f => f))
            {
                uniqueSuffix = uniqueSuffix ^ f.GetHashCode();
            }
            alignmentCommands.AddRange(STARWrapper.RemoveGenome(Parameters.SpritzDirectory, Parameters.GenomeStarIndexDirectory));
            alignmentCommands.AddRange(STARWrapper.ProcessFirstPassSpliceCommands(FirstPassSpliceJunctions, uniqueSuffix, out string spliceJunctionStartDatabase));
            SecondPassGenomeDirectory = Parameters.GenomeStarIndexDirectory + "SecondPass" + uniqueSuffix.ToString();
            alignmentCommands.AddRange(STARWrapper.GenerateGenomeIndex(Parameters.SpritzDirectory, threads, SecondPassGenomeDirectory, new string[] { Parameters.ReorderedFastaPath }, Parameters.GeneModelGtfOrGffPath, Parameters.Fastqs, spliceJunctionStartDatabase));
            foreach (string[] fq in FastqsForAlignment)
            {
                string outPrefix = Path.Combine(Path.GetDirectoryName(fq[0]), Path.GetFileNameWithoutExtension(fq[0]));
                OutputPrefixes.Add(outPrefix);
                alignmentCommands.AddRange(STARWrapper.AlignRNASeqReadsForVariantCalling(Parameters.SpritzDirectory, threads, SecondPassGenomeDirectory, fq, outPrefix, overWriteStarAlignment, StrandSpecificities[FastqsForAlignment.IndexOf(fq)], STARGenomeLoadOption.LoadAndKeep));
                SortedBamFiles.Add(outPrefix + STARWrapper.SortedBamFileSuffix);
                DedupedBamFiles.Add(outPrefix + STARWrapper.DedupedBamFileSuffix);
                ChimericSamFiles.Add(outPrefix + STARWrapper.ChimericSamFileSuffix);
                ChimericJunctionFiles.Add(outPrefix + STARWrapper.ChimericJunctionsFileSuffix);
            }
            alignmentCommands.AddRange(STARWrapper.RemoveGenome(Parameters.SpritzDirectory, SecondPassGenomeDirectory));
            WrapperUtility.GenerateAndRunScript(WrapperUtility.GetAnalysisScriptPath(Parameters.AnalysisDirectory, "AlignReads.bash"), alignmentCommands).WaitForExit();
        }