AnalyzeCovariates uses the general RScript system now
-- Convenience constructor for collection for testing -- callRScript() now accepts Objects not Strings, for convenience
This commit is contained in:
Mark DePristo
parent
810a71c631
commit
ccec0b4d73
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@ -31,6 +31,7 @@ import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
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import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
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import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection;
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import org.broadinstitute.sting.utils.R.RScriptExecutor;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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@ -38,6 +39,7 @@ import org.broadinstitute.sting.utils.text.XReadLines;
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import java.io.*;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.Map;
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import java.util.regex.Pattern;
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@ -91,12 +93,12 @@ import java.util.regex.Pattern;
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* -resources resources/ \
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* -ignoreQ 5
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* </pre>
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*
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*
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*/
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@DocumentedGATKFeature(
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groupName = "AnalyzeCovariates",
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summary = "Package to plot residual accuracy versus error covariates for the base quality score recalibrator")
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groupName = "AnalyzeCovariates",
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summary = "Package to plot residual accuracy versus error covariates for the base quality score recalibrator")
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public class AnalyzeCovariates extends CommandLineProgram {
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/////////////////////////////
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@ -118,7 +120,7 @@ public class AnalyzeCovariates extends CommandLineProgram {
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private String PATH_TO_RESOURCES = "public/R/";
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@Argument(fullName = "ignoreQ", shortName = "ignoreQ", doc = "Ignore bases with reported quality less than this number.", required = false)
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private int IGNORE_QSCORES_LESS_THAN = 5;
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@Argument(fullName = "numRG", shortName = "numRG", doc = "Only process N read groups. Default value: -1 (process all read groups)", required = false)
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@Argument(fullName = "numRG", shortName = "numRG", doc = "Only process N read groups. Default value: -1 (process all read groups)", required = false)
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private int NUM_READ_GROUPS_TO_PROCESS = -1; // -1 means process all read groups
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/**
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@ -323,13 +325,14 @@ public class AnalyzeCovariates extends CommandLineProgram {
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}
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private void callRScripts() {
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RScriptExecutor.RScriptArgumentCollection argumentCollection =
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new RScriptExecutor.RScriptArgumentCollection(PATH_TO_RSCRIPT, Arrays.asList(PATH_TO_RESOURCES));
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RScriptExecutor executor = new RScriptExecutor(argumentCollection, true);
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int numReadGroups = 0;
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// for each read group
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for( Object readGroupKey : dataManager.getCollapsedTable(0).data.keySet() ) {
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Process p;
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if(++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS || NUM_READ_GROUPS_TO_PROCESS == -1) {
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String readGroup = readGroupKey.toString();
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@ -338,35 +341,19 @@ public class AnalyzeCovariates extends CommandLineProgram {
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// for each covariate
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for( int iii = 1; iii < requestedCovariates.size(); iii++ ) {
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Covariate cov = requestedCovariates.get(iii);
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try {
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if (DO_INDEL_QUALITY) {
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p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_indelQuality.R" + " " +
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OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
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cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
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p.waitFor();
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} else {
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final String outputFilename = OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat";
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if (DO_INDEL_QUALITY) {
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executor.callRScripts("plot_indelQuality.R", outputFilename,
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cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
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} else {
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if( iii == 1 ) {
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// Analyze reported quality
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p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_QualityScoreCovariate.R" + " " +
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OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
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IGNORE_QSCORES_LESS_THAN + " " + MAX_QUALITY_SCORE + " " + MAX_HISTOGRAM_VALUE); // The third argument is the Q scores that should be turned pink in the plot because they were ignored
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p.waitFor();
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} else { // Analyze all other covariates
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p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_OtherCovariate.R" + " " +
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OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
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cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
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p.waitFor();
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}
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// Analyze reported quality
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executor.callRScripts("plot_residualError_QualityScoreCovariate.R", outputFilename,
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IGNORE_QSCORES_LESS_THAN, MAX_QUALITY_SCORE, MAX_HISTOGRAM_VALUE); // The third argument is the Q scores that should be turned pink in the plot because they were ignored
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} else { // Analyze all other covariates
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executor.callRScripts("plot_residualError_OtherCovariate.R", outputFilename,
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cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
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}
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} catch (InterruptedException e) {
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e.printStackTrace();
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System.exit(-1);
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} catch (IOException e) {
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System.out.println("Fatal Exception: Perhaps RScript jobs are being spawned too quickly? One work around is to process fewer read groups using the -numRG option.");
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e.printStackTrace();
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System.exit(-1);
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}
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}
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} else { // at the maximum number of read groups so break out
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@ -57,8 +57,16 @@ public class RScriptExecutor {
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public String PATH_TO_RSCRIPT = "Rscript";
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@Advanced
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@Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
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@Argument(fullName = "path_to_Rresources", shortName = "Rresources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
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public List<String> PATH_TO_RESOURCES = Arrays.asList("public/R/", "private/R/");
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public RScriptArgumentCollection() {}
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/** For testing and convenience */
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public RScriptArgumentCollection(final String PATH_TO_RSCRIPT, final List<String> PATH_TO_RESOURCES) {
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this.PATH_TO_RSCRIPT = PATH_TO_RSCRIPT;
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this.PATH_TO_RESOURCES = PATH_TO_RESOURCES;
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}
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}
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final RScriptArgumentCollection myArgs;
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@ -69,11 +77,11 @@ public class RScriptExecutor {
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this.exceptOnError = exceptOnError;
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}
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public void callRScripts(String scriptName, String... scriptArgs) {
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public void callRScripts(String scriptName, Object... scriptArgs) {
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callRScripts(scriptName, Arrays.asList(scriptArgs));
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}
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public void callRScripts(String scriptName, List<String> scriptArgs) {
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public void callRScripts(String scriptName, List<Object> scriptArgs) {
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try {
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final File pathToScript = findScript(scriptName);
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if ( pathToScript == null ) return; // we failed but shouldn't exception out
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