Examples with RScriptExecutor org.broadinstitute.hellbender.utils.R.RScriptExecutor used on opensource projects

Example 11 with RScriptExecutor

use of org.broadinstitute.hellbender.utils.R.RScriptExecutor in project gatk by broadinstitute.

the class CollectRrbsMetrics method doWork.

@Override
protected Object doWork() {
    if (!METRICS_FILE_PREFIX.endsWith(".")) {
        METRICS_FILE_PREFIX = METRICS_FILE_PREFIX + ".";
    }
    final File SUMMARY_OUT = new File(METRICS_FILE_PREFIX + SUMMARY_FILE_EXTENSION);
    final File DETAILS_OUT = new File(METRICS_FILE_PREFIX + DETAIL_FILE_EXTENSION);
    final File PLOTS_OUT = new File(METRICS_FILE_PREFIX + PDF_FILE_EXTENSION);
    assertIoFiles(SUMMARY_OUT, DETAILS_OUT, PLOTS_OUT);
    final SamReader samReader = SamReaderFactory.makeDefault().open(INPUT);
    if (!ASSUME_SORTED && samReader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
        throw new UserException("The input file " + INPUT.getAbsolutePath() + " does not appear to be coordinate sorted");
    }
    final ReferenceSequenceFileWalker refWalker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
    final ProgressLogger progressLogger = new ProgressLogger(logger);
    final RrbsMetricsCollector metricsCollector = new RrbsMetricsCollector(METRIC_ACCUMULATION_LEVEL, samReader.getFileHeader().getReadGroups(), C_QUALITY_THRESHOLD, NEXT_BASE_QUALITY_THRESHOLD, MINIMUM_READ_LENGTH, MAX_MISMATCH_RATE);
    for (final SAMRecord samRecord : samReader) {
        progressLogger.record(samRecord);
        if (!samRecord.getReadUnmappedFlag() && !isSequenceFiltered(samRecord.getReferenceName())) {
            final ReferenceSequence referenceSequence = refWalker.get(samRecord.getReferenceIndex());
            metricsCollector.acceptRecord(samRecord, referenceSequence);
        }
    }
    metricsCollector.finish();
    final MetricsFile<RrbsMetrics, Long> rrbsMetrics = getMetricsFile();
    metricsCollector.addAllLevelsToFile(rrbsMetrics);
    // Using RrbsMetrics as a way to get both of the metrics objects through the MultiLevelCollector. Once
    // we get it out split it apart to the two separate MetricsFiles and write them to file
    final MetricsFile<RrbsSummaryMetrics, ?> summaryFile = getMetricsFile();
    final MetricsFile<RrbsCpgDetailMetrics, ?> detailsFile = getMetricsFile();
    for (final RrbsMetrics rrbsMetric : rrbsMetrics.getMetrics()) {
        summaryFile.addMetric(rrbsMetric.getSummaryMetrics());
        for (final RrbsCpgDetailMetrics detailMetric : rrbsMetric.getDetailMetrics()) {
            detailsFile.addMetric(detailMetric);
        }
    }
    summaryFile.write(SUMMARY_OUT);
    detailsFile.write(DETAILS_OUT);
    if (PRODUCE_PLOT) {
        final RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(new Resource(R_SCRIPT, CollectRrbsMetrics.class));
        executor.addArgs(DETAILS_OUT.getAbsolutePath(), SUMMARY_OUT.getAbsolutePath(), PLOTS_OUT.getAbsolutePath());
        executor.exec();
    }
    CloserUtil.close(samReader);
    return null;
}

Example 12 with RScriptExecutor

use of org.broadinstitute.hellbender.utils.R.RScriptExecutor in project gatk by broadinstitute.

the class MeanQualityByCycle method finish.

@Override
protected void finish() {
    // Generate a "Histogram" of mean quality and write it to the file
    final MetricsFile<?, Integer> metrics = getMetricsFile();
    metrics.addHistogram(q.getMeanQualityHistogram());
    if (!oq.isEmpty())
        metrics.addHistogram(oq.getMeanQualityHistogram());
    metrics.write(OUTPUT);
    if (q.isEmpty() && oq.isEmpty()) {
        logger.warn("No valid bases found in input file. No plot will be produced.");
    } else if (PRODUCE_PLOT) {
        // Now run R to generate a chart
        final RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(new Resource(R_SCRIPT, MeanQualityByCycle.class));
        executor.addArgs(OUTPUT.getAbsolutePath(), CHART_OUTPUT.getAbsolutePath(), INPUT.getName(), plotSubtitle);
        executor.exec();
    }
}

Example 13 with RScriptExecutor

use of org.broadinstitute.hellbender.utils.R.RScriptExecutor in project gatk by broadinstitute.

the class QualityScoreDistribution method finish.

@Override
protected void finish() {
    // Built the Histograms out of the long[]s
    final Histogram<Byte> qHisto = new Histogram<>("QUALITY", "COUNT_OF_Q");
    final Histogram<Byte> oqHisto = new Histogram<>("QUALITY", "COUNT_OF_OQ");
    for (int i = 0; i < qCounts.length; ++i) {
        if (qCounts[i] > 0)
            qHisto.increment((byte) i, (double) qCounts[i]);
        if (oqCounts[i] > 0)
            oqHisto.increment((byte) i, (double) oqCounts[i]);
    }
    final MetricsFile<?, Byte> metrics = getMetricsFile();
    metrics.addHistogram(qHisto);
    if (!oqHisto.isEmpty())
        metrics.addHistogram(oqHisto);
    metrics.write(OUTPUT);
    if (qHisto.isEmpty() && oqHisto.isEmpty()) {
        log.warn("No valid bases found in input file. No plot will be produced.");
    } else if (PRODUCE_PLOT) {
        // Now run R to generate a chart
        final RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(new Resource(R_SCRIPT, QualityScoreDistribution.class));
        executor.addArgs(OUTPUT.getAbsolutePath(), CHART_OUTPUT.getAbsolutePath(), INPUT.getName(), plotSubtitle);
        executor.exec();
    }
}

Example 14 with RScriptExecutor

use of org.broadinstitute.hellbender.utils.R.RScriptExecutor in project gatk-protected by broadinstitute.

the class PlotACNVResults method writeSegmentedAlleleFractionPlot.

/**
     * @param sampleName Sample name derived from input files
     * @param contigNames List containing contig names
     * @param contigLengths List containing contig lengths (same order as contigNames)
     */
private void writeSegmentedAlleleFractionPlot(final String sampleName, final List<String> contigNames, final List<Integer> contigLengths) {
    //names separated by delimiter
    final String contigNamesArg = contigNames.stream().collect(Collectors.joining(CONTIG_DELIMITER));
    //lengths separated by delimiter
    final String contigLengthsArg = contigLengths.stream().map(Object::toString).collect(Collectors.joining(CONTIG_DELIMITER));
    final String outputDirArg = addTrailingSlashIfNecessary(outputDir);
    final RScriptExecutor executor = new RScriptExecutor();
    //this runs the R statement "source("CNVPlottingLibrary.R")" before the main script runs
    executor.addScript(new Resource(CNV_PLOTTING_R_LIBRARY, PlotSegmentedCopyRatio.class));
    executor.addScript(new Resource(ACNV_PLOTTING_R_SCRIPT, PlotACNVResults.class));
    //--args is needed for Rscript to recognize other arguments properly
    executor.addArgs("--args", "--sample_name=" + sampleName, "--snp_counts_file=" + snpCountsFile, "--tangent_file=" + tangentFile, "--segments_file=" + segmentsFile, "--contig_names=" + contigNamesArg, "--contig_lengths=" + contigLengthsArg, "--output_dir=" + outputDirArg, "--output_prefix=" + outputPrefix);
    executor.exec();
}

Example 15 with RScriptExecutor

use of org.broadinstitute.hellbender.utils.R.RScriptExecutor in project gatk-protected by broadinstitute.

the class PlotSegmentedCopyRatio method writeSegmentedCopyRatioPlots.

/**
     * @param sampleName Sample name derived from input files
     * @param contigNames List containing contig names
     * @param contigLengths List containing contig lengths (same order as contigNames)
     */
private void writeSegmentedCopyRatioPlots(final String sampleName, final List<String> contigNames, final List<Integer> contigLengths) {
    //names separated by delimiter
    final String contigNamesArg = contigNames.stream().collect(Collectors.joining(CONTIG_DELIMITER));
    //names separated by delimiter
    final String contigLengthsArg = contigLengths.stream().map(Object::toString).collect(Collectors.joining(CONTIG_DELIMITER));
    final String outputDirArg = addTrailingSlashIfNecessary(outputDir);
    final String isLog2InputArg = isLog2Input ? "TRUE" : "FALSE";
    final RScriptExecutor executor = new RScriptExecutor();
    //this runs the R statement "source("CNVPlottingLibrary.R")" before the main script runs
    executor.addScript(new Resource(CNV_PLOTTING_R_LIBRARY, PlotSegmentedCopyRatio.class));
    executor.addScript(new Resource(COPY_RATIO_PLOTTING_R_SCRIPT, PlotSegmentedCopyRatio.class));
    //--args is needed for Rscript to recognize other arguments properly
    executor.addArgs("--args", "--sample_name=" + sampleName, "--tangent_file=" + tangentFile, "--pre_tangent_file=" + preTangentFile, "--segments_file=" + segmentsFile, "--contig_names=" + contigNamesArg, "--contig_lengths=" + contigLengthsArg, "--output_dir=" + outputDirArg, "--output_prefix=" + outputPrefix, "--is_log2_input=" + isLog2InputArg);
    executor.exec();
}