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bbimberbbimber
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Preliminary support for PrintReadBackedHaplotypes
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4 files changed

+230
-28
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4 files changed

+230
-28
lines changed

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java‎

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@@ -52,6 +52,7 @@
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import org.labkey.sequenceanalysis.analysis.MultiQCBamHandler;
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import org.labkey.sequenceanalysis.analysis.MultiQCHandler;
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import org.labkey.sequenceanalysis.analysis.PicardAlignmentMetricsHandler;
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import org.labkey.sequenceanalysis.analysis.PrintReadBackedHaplotypesHandler;
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import org.labkey.sequenceanalysis.analysis.RecalculateSequenceMetricsHandler;
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import org.labkey.sequenceanalysis.analysis.RnaSeqcHandler;
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import org.labkey.sequenceanalysis.analysis.SbtGeneCountHandler;
@@ -338,6 +339,7 @@ public static void registerPipelineSteps()
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SequenceAnalysisService.get().registerFileHandler(new PicardAlignmentMetricsHandler());
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SequenceAnalysisService.get().registerFileHandler(new BamHaplotypeHandler());
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SequenceAnalysisService.get().registerFileHandler(new BamCleanupHandler());
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SequenceAnalysisService.get().registerFileHandler(new PrintReadBackedHaplotypesHandler());
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SequenceAnalysisService.get().registerFileHandler(new HaplotypeCallerHandler());
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SequenceAnalysisService.get().registerFileHandler(new RnaSeqcHandler());
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SequenceAnalysisService.get().registerFileHandler(new CombineStarGeneCountsHandler());

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PrintReadBackedHaplotypesHandler.java‎

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package org.labkey.sequenceanalysis.analysis;
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import htsjdk.samtools.util.Interval;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.logging.log4j.Logger;
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import org.json.JSONObject;
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import org.labkey.api.module.ModuleLoader;
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import org.labkey.api.pipeline.PipelineJob;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.pipeline.RecordedAction;
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import org.labkey.api.sequenceanalysis.SequenceOutputFile;
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import org.labkey.api.sequenceanalysis.pipeline.AbstractParameterizedOutputHandler;
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import org.labkey.api.sequenceanalysis.pipeline.CommandLineParam;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
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import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
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import org.labkey.api.sequenceanalysis.run.DISCVRSeqRunner;
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import org.labkey.api.util.FileType;
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import org.labkey.api.util.FileUtil;
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import org.labkey.api.util.PageFlowUtil;
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import org.labkey.sequenceanalysis.SequenceAnalysisModule;
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import org.labkey.sequenceanalysis.util.SequenceUtil;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.LinkedHashSet;
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import java.util.List;
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/**
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* Created by bimber on 2/3/2016.
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*/
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public class PrintReadBackedHaplotypesHandler extends AbstractParameterizedOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>
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{
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private FileType _bamFileType = new FileType("bam", false);
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public PrintReadBackedHaplotypesHandler()
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{
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super(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.class), "Print Read-Backed Haplotypes", "This scans the alignments over the provided interval(s), and reports all unique haplotypes.", new LinkedHashSet<>(PageFlowUtil.set("/sequenceanalysis/field/IntervalField.js")), Arrays.asList(
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ToolParameterDescriptor.create("intervals", "Intervals", "The intervals over which to merge the data. They should be in the form: chr01:102-20394", "sequenceanalysis-intervalfield", new JSONObject(){{
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put("allowBlank", false);
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}}, null),
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ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("-mq"), "minQual", "Min Base Quality", "Nucleotides with quality scores below this value will be converted to N", "ldk-integerfield", new JSONObject(){{
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put("minValue", 0);
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}}, 10),
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ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("-rc"), "requiredCoverageFraction", "Required Coverage Fraction", "A haplotype must have coverage over this fraction of the interval to be reported", "ldk-numberfield", new JSONObject(){{
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put("minValue", 0);
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put("maxValue", 0);
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put("decimalPrecision", 2);
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}}, null)
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));
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}
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@Override
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public boolean canProcess(SequenceOutputFile o)
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{
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return o.getFile() != null && _bamFileType.isType(o.getFile());
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}
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@Override
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public boolean doRunRemote()
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{
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return true;
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}
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@Override
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public boolean doRunLocal()
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{
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return false;
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}
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@Override
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public SequenceOutputProcessor getProcessor()
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{
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return new Processor();
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}
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@Override
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public boolean doSplitJobs()
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{
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return true;
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}
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public class Processor implements SequenceOutputProcessor
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{
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@Override
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public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
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{
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for (SequenceOutputFile so : inputFiles)
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{
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if (so.getReadset() != null)
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{
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ctx.getSequenceSupport().cacheReadset(so.getReadset(), ctx.getJob().getUser());
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}
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else
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{
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ctx.getJob().getLogger().error("Output file lacks a readset and will be skipped: " + so.getRowid());
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}
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}
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}
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@Override
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public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext ctx) throws UnsupportedOperationException, PipelineJobException
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{
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PipelineJob job = ctx.getJob();
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if (inputFiles.isEmpty())
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{
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job.getLogger().warn("no input files");
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}
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for (SequenceOutputFile so : inputFiles)
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{
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RecordedAction action = new RecordedAction(getName());
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action.setStartTime(new Date());
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action.addInput(so.getFile(), "Input BAM");
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File input = so.getFile();
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String intervalText = StringUtils.trimToNull(ctx.getParams().optString("intervals"));
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if (intervalText == null)
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{
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throw new PipelineJobException("Must provide a list of intervals");
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}
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List<String> args = new ArrayList<>();
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List<Interval> il = SequenceUtil.parseAndSortIntervals(intervalText);
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if (il != null)
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{
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for (Interval i : il)
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{
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args.add("-L");
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args.add(i.getContig() + ":" + i.getStart() + "-" + i.getEnd());
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}
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}
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List<String> extraArgs = getClientCommandArgs(ctx.getParams());
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if (extraArgs != null)
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{
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args.addAll(extraArgs);
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}
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File output = new File(ctx.getWorkingDirectory(), FileUtil.getBaseName(input) + ".txt");
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Wrapper wrapper = new Wrapper(ctx.getLogger());
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wrapper.execute(input, ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id()).getWorkingFastaFile(), output, args);
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action.addOutput(output, "Local Haplotypes", false);
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ctx.addActions(action);
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SequenceOutputFile o = new SequenceOutputFile();
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o.setName(output.getName());
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o.setFile(output);
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o.setLibrary_id(so.getLibrary_id());
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o.setCategory("Local Haplotypes");
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o.setReadset(so.getReadset());
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ctx.addSequenceOutput(o);
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}
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}
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@Override
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public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List<SequenceOutputFile> inputFiles, JSONObject params, File outputDir, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
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{
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}
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}
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public static class Wrapper extends DISCVRSeqRunner
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{
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public Wrapper(Logger log)
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{
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super(log);
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}
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public File execute(File bam, File fasta, File output, List<String> extraArgs) throws PipelineJobException
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{
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List<String> args = getBaseArgs("PrintReadBackedHaplotypes");
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args.add("-I");
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args.add(bam.getPath());
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args.add("-R");
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args.add(fasta.getPath());
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args.add("-O");
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args.add(output.getPath());
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args.addAll(extraArgs);
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execute(args);
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if (!output.exists())
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{
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throw new PipelineJobException("Unable to find file: " + output.getPath());
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}
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return output;
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}
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}
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}

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/VariantsToTableStep.java‎

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@@ -23,6 +23,7 @@
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import org.labkey.api.util.PageFlowUtil;
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import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
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import org.labkey.sequenceanalysis.pipeline.VariantProcessingJob;
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import org.labkey.sequenceanalysis.util.SequenceUtil;
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import javax.annotation.Nullable;
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import java.io.File;
@@ -142,7 +143,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
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}
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String intervalText = StringUtils.trimToNull(getProvider().getParameterByName("intervals").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class));
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List<Interval> il = parseAndSortIntervals(intervalText);
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List<Interval> il = SequenceUtil.parseAndSortIntervals(intervalText);
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if (il != null)
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{
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for (Interval i : il)
@@ -223,31 +224,4 @@ public void generateTable(File inputVcf, File outputFile, File referenceFasta, L
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}
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}
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}
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private List<Interval> parseAndSortIntervals(String intervalString) throws PipelineJobException
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{
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intervalString = StringUtils.trimToNull(intervalString);
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if (intervalString == null)
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{
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return null;
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}
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intervalString = intervalString.replaceAll("(\\n|\\r|;)+", ";");
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List<Interval> intervals = new ArrayList<>();
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for (String i : intervalString.split(";"))
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{
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String[] tokens = i.split(":|-");
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if (tokens.length != 3)
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{
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throw new PipelineJobException("Invalid interval: " + i);
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}
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intervals.add(new Interval(tokens[0], Integer.parseInt(tokens[1]), Integer.parseInt(tokens[2])));
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}
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Collections.sort(intervals);
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return intervals;
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}
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}

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java‎

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@@ -23,6 +23,7 @@
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import htsjdk.variant.vcf.VCFHeader;
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import htsjdk.variant.vcf.VCFUtils;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.SystemUtils;
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import org.apache.logging.log4j.Logger;
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import org.jetbrains.annotations.Nullable;
@@ -594,4 +595,31 @@ public static void deleteFolderWithRm(Logger log, File directory) throws Pipelin
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new SimpleScriptWrapper(log).execute(Arrays.asList("rm", "-Rf", directory.getPath()));
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}
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}
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public static List<Interval> parseAndSortIntervals(String intervalString) throws PipelineJobException
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{
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intervalString = StringUtils.trimToNull(intervalString);
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if (intervalString == null)
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{
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return null;
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}
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intervalString = intervalString.replaceAll("(\\n|\\r|;)+", ";");
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List<Interval> intervals = new ArrayList<>();
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for (String i : intervalString.split(";"))
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{
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String[] tokens = i.split(":|-");
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if (tokens.length != 3)
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{
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throw new PipelineJobException("Invalid interval: " + i);
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}
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intervals.add(new Interval(tokens[0], Integer.parseInt(tokens[1]), Integer.parseInt(tokens[2])));
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}
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Collections.sort(intervals);
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return intervals;
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}
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}

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