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SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java
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| @@ -0,0 +1,172 @@ | ||
| package org.labkey.sequenceanalysis.run.alignment; | ||
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| 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.SequenceAnalysisService; | ||
| import org.labkey.api.sequenceanalysis.SequenceOutputFile; | ||
| import org.labkey.api.sequenceanalysis.pipeline.AbstractParameterizedOutputHandler; | ||
| import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport; | ||
| import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler; | ||
| import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; | ||
| import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; | ||
| import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper; | ||
| import org.labkey.api.util.FileUtil; | ||
| import org.labkey.sequenceanalysis.SequenceAnalysisModule; | ||
| import org.labkey.sequenceanalysis.run.variant.DepthOfCoverageHandler; | ||
| import org.labkey.sequenceanalysis.util.SequenceUtil; | ||
|
|
||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
|
|
||
| public class ParagraphStep extends AbstractParameterizedOutputHandler<SequenceOutputHandler.SequenceOutputProcessor> | ||
| { | ||
| public ParagraphStep() | ||
| { | ||
| super(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.class), "Paragraph SV Genotyping", "This will run paraGRAPH on one or more BAM files to genotype SVs", null, Arrays.asList( | ||
| ToolParameterDescriptor.createExpDataParam("svVCF", "Input VCF", "This is the DataId of the VCF containing the SVs to genotype", "ldk-expdatafield", new JSONObject() | ||
| {{ | ||
| put("allowBlank", false); | ||
| }}, null) | ||
| )); | ||
| } | ||
|
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| @Override | ||
| public boolean canProcess(SequenceOutputFile o) | ||
| { | ||
| return o.getFile() != null && o.getFile().exists() && SequenceUtil.FILETYPE.bamOrCram.getFileType().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 DepthOfCoverageHandler.Processor(); | ||
| } | ||
|
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| public static class Processor implements SequenceOutputProcessor | ||
| { | ||
| @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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| @Override | ||
| public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext ctx) throws UnsupportedOperationException, PipelineJobException | ||
| { | ||
| File inputVCF = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("svVCF")); | ||
| if (!inputVCF.exists()) | ||
| { | ||
| throw new PipelineJobException("Unable to find file: " + inputVCF.getPath()); | ||
| } | ||
|
|
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| for (SequenceOutputFile so : inputFiles) | ||
| { | ||
| List<String> depthArgs = new ArrayList<>(); | ||
| depthArgs.add("idxdepth"); | ||
| depthArgs.add("-d"); | ||
| depthArgs.add(so.getFile().getPath()); | ||
|
|
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| File coverageFile = new File(ctx.getWorkingDirectory(), "coverage.txt"); | ||
| depthArgs.add("-o"); | ||
| depthArgs.add(coverageFile.getPath()); | ||
|
|
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| depthArgs.add("-r"); | ||
| depthArgs.add(ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id()).getWorkingFastaFile().getPath()); | ||
|
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| new SimpleScriptWrapper(ctx.getLogger()).execute(depthArgs); | ||
|
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| if (!coverageFile.exists()) | ||
| { | ||
| throw new PipelineJobException("Missing file: " + coverageFile.getPath()); | ||
| } | ||
|
|
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| // Should produce a simple text file: | ||
| // id path depth read length | ||
| // TNPRC-IB18 ../IB18.cram 29.77 150 | ||
|
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| List<String> paragraphArgs = new ArrayList<>(); | ||
| paragraphArgs.add("multigrmpy.py"); | ||
| paragraphArgs.add("--verbose"); | ||
|
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| File paragraphOut = new File(ctx.getWorkingDirectory(), FileUtil.getBaseName(so.getFile()) + ".paragraph.txt"); | ||
| paragraphArgs.add("-o"); | ||
| paragraphArgs.add(paragraphOut.getPath()); | ||
|
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| int svVcfId = ctx.getParams().optInt("svVCF"); | ||
| if (svVcfId == 0) | ||
| { | ||
| throw new PipelineJobException("Missing svVCF ID"); | ||
| } | ||
|
|
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| File svVcf = ctx.getSequenceSupport().getCachedData(svVcfId); | ||
| if (svVcf == null) | ||
| { | ||
| throw new PipelineJobException("File not found for ID: " + svVcfId); | ||
| } | ||
| else if (!svVcf.exists()) | ||
| { | ||
| throw new PipelineJobException("Missing file: " + svVcf.getPath()); | ||
| } | ||
|
|
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| paragraphArgs.add("-i"); | ||
| paragraphArgs.add(svVcf.getPath()); | ||
|
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| paragraphArgs.add("-m"); | ||
| paragraphArgs.add(coverageFile.getPath()); | ||
|
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| paragraphArgs.add("-r"); | ||
| paragraphArgs.add(ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id()).getWorkingFastaFile().getPath()); | ||
|
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| paragraphArgs.add("--scratch-dir"); | ||
| paragraphArgs.add(SequencePipelineService.get().getJavaTempDir()); | ||
|
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| Integer threads = SequencePipelineService.get().getMaxThreads(ctx.getLogger()); | ||
| if (threads != null) | ||
| { | ||
| paragraphArgs.add("--threads"); | ||
| paragraphArgs.add(threads.toString()); | ||
| } | ||
|
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| paragraphArgs.add("--logfile"); | ||
| paragraphArgs.add(new File(ctx.getWorkingDirectory(), "paragraph.log").getPath()); | ||
|
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| new SimpleScriptWrapper(ctx.getLogger()).execute(paragraphArgs); | ||
|
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| File genotypes = new File(ctx.getWorkingDirectory(), "genotypes.vcf.gz"); | ||
| if (!genotypes.exists()) | ||
| { | ||
| throw new PipelineJobException("Missing file: " + genotypes.getPath()); | ||
| } | ||
|
|
||
| try | ||
| { | ||
| SequenceAnalysisService.get().ensureVcfIndex(genotypes, ctx.getLogger()); | ||
| } | ||
| catch (IOException e) | ||
| { | ||
| throw new PipelineJobException(e); | ||
| } | ||
|
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| ctx.getFileManager().addSequenceOutput(genotypes, "paraGRAPH Genotypes: " + so.getName(), "paraGRAPH Genoypes", so.getReadset(), null, so.getLibrary_id(), "Input VCF: " + svVcf.getName() + " (" + svVcfId + ")"); | ||
| } | ||
| } | ||
| } | ||
| } |