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Support specHLA
1 parent 6889e4d commit 6cba97b

2 files changed

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

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@@ -127,6 +127,7 @@
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import org.labkey.sequenceanalysis.run.analysis.SawfishJointCallingHandler;
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import org.labkey.sequenceanalysis.run.analysis.SequenceBasedTypingAnalysis;
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import org.labkey.sequenceanalysis.run.analysis.SnpCountAnalysis;
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import org.labkey.sequenceanalysis.run.analysis.SpecHlaAnalysis;
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import org.labkey.sequenceanalysis.run.analysis.SubreadAnalysis;
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import org.labkey.sequenceanalysis.run.analysis.UnmappedReadExportHandler;
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import org.labkey.sequenceanalysis.run.analysis.ViralAnalysis;
@@ -343,6 +344,7 @@ public static void registerPipelineSteps()
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SequencePipelineService.get().registerPipelineStep(new PindelAnalysis.Provider());
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SequencePipelineService.get().registerPipelineStep(new PbsvAnalysis.Provider());
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SequencePipelineService.get().registerPipelineStep(new GenrichStep.Provider());
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SequencePipelineService.get().registerPipelineStep(new SpecHlaAnalysis.Provider());
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SequencePipelineService.get().registerPipelineStep(new SawfishAnalysis.Provider());
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SequencePipelineService.get().registerPipelineStep(new PARalyzerAnalysis.Provider());

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SpecHlaAnalysis.java‎

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package org.labkey.sequenceanalysis.run.analysis;
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import htsjdk.samtools.SAMFileHeader;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.sequenceanalysis.model.AnalysisModel;
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import org.labkey.api.sequenceanalysis.model.Readset;
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import org.labkey.api.sequenceanalysis.pipeline.AbstractAnalysisStepProvider;
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import org.labkey.api.sequenceanalysis.pipeline.AnalysisOutputImpl;
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import org.labkey.api.sequenceanalysis.pipeline.AnalysisStep;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
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import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
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import org.labkey.api.sequenceanalysis.pipeline.SamSorter;
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import org.labkey.api.sequenceanalysis.pipeline.SamtoolsRunner;
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import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
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import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
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import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
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import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
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import org.labkey.api.util.FileUtil;
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import org.labkey.api.util.Path;
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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.List;
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public class SpecHlaAnalysis extends AbstractCommandPipelineStep<SimpleScriptWrapper> implements AnalysisStep
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{
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public SpecHlaAnalysis(PipelineStepProvider<?> provider, PipelineContext ctx)
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{
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super(provider, ctx, new SimpleScriptWrapper(ctx.getLogger()));
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}
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public static class Provider extends AbstractAnalysisStepProvider<SpecHlaAnalysis>
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{
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public Provider()
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{
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super("SpecHlaStep", "SpecHLA", null, "This will run SpecHLA for HLA genotyping from WGS/WXS data. This should use a BAM aligned to a custom HLA DB, rather than aligned to the full genome", Arrays.asList(
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), null, "https://github.com/deepomicslab/SpecHLA/");
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}
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@Override
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public SpecHlaAnalysis create(PipelineContext ctx)
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{
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return new SpecHlaAnalysis(this, ctx);
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}
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}
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@Override
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public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, ReferenceGenome referenceGenome, File outputDir) throws PipelineJobException
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{
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AnalysisOutputImpl output = new AnalysisOutputImpl();
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File subsetBam = FileUtil.appendName(outputDir, FileUtil.getBaseName(inputBam) + ".subset.bam");
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SamtoolsRunner sr = new SamtoolsRunner(getWrapper().getLogger());
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sr.execute(Arrays.asList(
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sr.getSamtoolsPath().getPath(),
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"view",
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"-h",
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"-F", "12", //This selects pairs where either mate is mapped
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"-o", subsetBam.getPath(),
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inputBam.getPath()
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));
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output.addIntermediateFile(subsetBam);
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File queryNameSortBam = new SamSorter(getPipelineCtx().getLogger()).execute(subsetBam, FileUtil.appendName(outputDir, FileUtil.getBaseName(inputBam) + ".querySort.bam"), SAMFileHeader.SortOrder.queryname);
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output.addIntermediateFile(queryNameSortBam);
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File fq1 = FileUtil.appendName(outputDir, FileUtil.getBaseName(inputBam) + ".R1.fastq.gz");
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File fq2 = FileUtil.appendName(outputDir, FileUtil.getBaseName(inputBam) + ".R2.fastq.gz");
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sr.execute(Arrays.asList(
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sr.getSamtoolsPath().getPath(),
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"fastq",
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"-1",
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fq1.getPath(),
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"-2",
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fq2.getPath(),
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queryNameSortBam.getPath()
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));
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output.addIntermediateFile(fq1);
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output.addIntermediateFile(fq2);
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File specHlaExe = AbstractCommandWrapper.resolveFileInPath("spechla", null, true);
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List<String> toRun = new ArrayList<>(Arrays.asList(
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specHlaExe.getPath(),
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"-n",
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"specHLA",
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"-u",
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"1", // 1 = exon. 0 = full-length
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"-1",
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fq1.getPath(),
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"-2",
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fq2.getPath(),
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"-o",
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outputDir.getPath()
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));
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Integer maxThreads = SequencePipelineService.get().getMaxThreads(getWrapper().getLogger());
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if (maxThreads != null)
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{
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toRun.add("-j");
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toRun.add(maxThreads.toString());
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}
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getWrapper().execute(toRun);
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File outFile = FileUtil.appendPath(outputDir, Path.parse("specHLA/hla.result.txt"));
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if (!outFile.exists())
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{
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throw new PipelineJobException("SpecHLA result file does not exist: " + outFile.getPath());
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}
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output.addSequenceOutput(outFile, FileUtil.getBaseName(inputBam) + ": HLA Typing", "specHLA Genotyping", rs.getReadsetId(), null, referenceGenome.getGenomeId(), null);
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return output;
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}
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@Override
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public Output performAnalysisPerSampleLocal(AnalysisModel model, File inputBam, File referenceFasta, File outDir) throws PipelineJobException
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{
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return null;
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}
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}

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