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162
SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/DeepVariantHandler.java
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|---|---|---|
| @@ -0,0 +1,162 @@ | ||
| package org.labkey.sequenceanalysis.analysis; | ||
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| import org.apache.commons.lang3.StringUtils; | ||
| import org.json.JSONObject; | ||
| import org.labkey.api.module.ModuleLoader; | ||
| import org.labkey.api.pipeline.PipelineJob; | ||
| import org.labkey.api.pipeline.PipelineJobException; | ||
| import org.labkey.api.pipeline.RecordedAction; | ||
| import org.labkey.api.sequenceanalysis.SequenceOutputFile; | ||
| import org.labkey.api.sequenceanalysis.pipeline.AbstractParameterizedOutputHandler; | ||
| import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome; | ||
| import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport; | ||
| import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler; | ||
| import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; | ||
| import org.labkey.api.util.FileType; | ||
| import org.labkey.api.util.FileUtil; | ||
| import org.labkey.sequenceanalysis.SequenceAnalysisModule; | ||
| import org.labkey.sequenceanalysis.run.analysis.DeepVariantAnalysis; | ||
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|
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| import java.io.File; | ||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.Date; | ||
| import java.util.List; | ||
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|
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| /** | ||
| * Created by bimber on 2/3/2016. | ||
| */ | ||
| public class DeepVariantHandler extends AbstractParameterizedOutputHandler<SequenceOutputHandler.SequenceOutputProcessor> | ||
| { | ||
| private final FileType _bamOrCramFileType = new FileType(Arrays.asList("bam", "cram"), "bam"); | ||
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| public DeepVariantHandler() | ||
| { | ||
| super(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.class), "Run DeepVariant", "This will run DeepVariant on the selected BAMs to generate gVCF files.", null, DeepVariantAnalysis.getToolDescriptors()); | ||
| } | ||
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| @Override | ||
| public boolean canProcess(SequenceOutputFile o) | ||
| { | ||
| return o.getFile() != null && _bamOrCramFileType.isType(o.getFile()); | ||
| } | ||
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| @Override | ||
| public boolean doRunRemote() | ||
| { | ||
| return true; | ||
| } | ||
|
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| @Override | ||
| public boolean doRunLocal() | ||
| { | ||
| return false; | ||
| } | ||
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| @Override | ||
| public SequenceOutputProcessor getProcessor() | ||
| { | ||
| return new Processor(); | ||
| } | ||
|
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| @Override | ||
| public boolean doSplitJobs() | ||
| { | ||
| return true; | ||
| } | ||
|
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| public class Processor implements SequenceOutputProcessor | ||
| { | ||
| @Override | ||
| public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException | ||
| { | ||
| String modelType = ctx.getParams().optString("modelType"); | ||
| DeepVariantAnalysis.inferModelType(modelType, ctx); | ||
| } | ||
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| @Override | ||
| public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext ctx) throws UnsupportedOperationException, PipelineJobException | ||
| { | ||
| PipelineJob job = ctx.getJob(); | ||
| if (inputFiles.size() != 1) | ||
| { | ||
| throw new PipelineJobException("Expected a single input file"); | ||
| } | ||
|
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| SequenceOutputFile so = inputFiles.get(0); | ||
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| RecordedAction action = new RecordedAction(getName()); | ||
| action.setStartTime(new Date()); | ||
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| action.addInput(so.getFile(), "Input BAM File"); | ||
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| File outputFile = new File(ctx.getOutputDir(), FileUtil.getBaseName(so.getFile()) + ".g.vcf.gz"); | ||
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| DeepVariantAnalysis.DeepVariantWrapper wrapper = new DeepVariantAnalysis.DeepVariantWrapper(job.getLogger()); | ||
| wrapper.setOutputDir(ctx.getOutputDir()); | ||
|
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| ReferenceGenome referenceGenome = ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id()); | ||
| if (referenceGenome == null) | ||
| { | ||
| throw new PipelineJobException("No reference genome found for output: " + so.getRowid()); | ||
| } | ||
|
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| String inferredModelType = ctx.getSequenceSupport().getCachedObject("modelType", String.class); | ||
| String modelType = inferredModelType == null ? ctx.getParams().optString("modelType") : inferredModelType; | ||
| if (modelType == null) | ||
| { | ||
| throw new PipelineJobException("Missing model type"); | ||
| } | ||
|
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| List<String> args = new ArrayList<>(getClientCommandArgs(ctx.getParams())); | ||
| args.add("--model_type=" + modelType); | ||
|
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| String binVersion = ctx.getParams().optString("binVersion"); | ||
| if (binVersion == null) | ||
| { | ||
| throw new PipelineJobException("Missing binVersion"); | ||
| } | ||
|
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| wrapper.execute(so.getFile(), referenceGenome.getWorkingFastaFile(), outputFile, ctx.getFileManager(), binVersion, args); | ||
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| action.addOutput(outputFile, "gVCF File", false); | ||
|
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| SequenceOutputFile o = new SequenceOutputFile(); | ||
| o.setName(outputFile.getName()); | ||
| o.setFile(outputFile); | ||
| o.setLibrary_id(so.getLibrary_id()); | ||
| o.setCategory("DeepVariant gVCF File"); | ||
| o.setReadset(so.getReadset()); | ||
| o.setDescription("DeepVariant Version: " + binVersion); | ||
|
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| ctx.addSequenceOutput(o); | ||
|
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| ctx.addActions(action); | ||
| } | ||
|
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| private List<String> getClientCommandArgs(JSONObject params) | ||
| { | ||
| List<String> ret = new ArrayList<>(); | ||
|
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| for (ToolParameterDescriptor desc : getParameters()) | ||
| { | ||
| if (desc.getCommandLineParam() != null) | ||
| { | ||
| String val = params.optString(desc.getName(), null); | ||
| if (StringUtils.trimToNull(val) != null) | ||
| { | ||
| ret.addAll(desc.getCommandLineParam().getArguments(" ", val)); | ||
| } | ||
| } | ||
| } | ||
|
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| return ret; | ||
| } | ||
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| @Override | ||
| 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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