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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 2011-08-27 12:54:13 -04:00
parent 810a71c631
commit ccec0b4d73
2 changed files with 32 additions and 37 deletions
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33
public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
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@ -31,6 +31,7 @@ import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate; import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum; import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection; import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.R.RScriptExecutor;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
@ -38,6 +39,7 @@ import org.broadinstitute.sting.utils.text.XReadLines;
import java.io.*; import java.io.*;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection; import java.util.Collection;
import java.util.Map; import java.util.Map;
import java.util.regex.Pattern; import java.util.regex.Pattern;
@ -323,13 +325,14 @@ public class AnalyzeCovariates extends CommandLineProgram {
} }
private void callRScripts() { private void callRScripts() {
RScriptExecutor.RScriptArgumentCollection argumentCollection =
new RScriptExecutor.RScriptArgumentCollection(PATH_TO_RSCRIPT, Arrays.asList(PATH_TO_RESOURCES));
RScriptExecutor executor = new RScriptExecutor(argumentCollection, true);
int numReadGroups = 0; int numReadGroups = 0;
// for each read group // for each read group
for( Object readGroupKey : dataManager.getCollapsedTable(0).data.keySet() ) { for( Object readGroupKey : dataManager.getCollapsedTable(0).data.keySet() ) {
Process p;
if(++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS || NUM_READ_GROUPS_TO_PROCESS == -1) { if(++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS || NUM_READ_GROUPS_TO_PROCESS == -1) {
String readGroup = readGroupKey.toString(); String readGroup = readGroupKey.toString();
@ -338,36 +341,20 @@ public class AnalyzeCovariates extends CommandLineProgram {
// for each covariate // for each covariate
for( int iii = 1; iii < requestedCovariates.size(); iii++ ) { for( int iii = 1; iii < requestedCovariates.size(); iii++ ) {
Covariate cov = requestedCovariates.get(iii); Covariate cov = requestedCovariates.get(iii);
try { final String outputFilename = OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat";
if (DO_INDEL_QUALITY) { if (DO_INDEL_QUALITY) {
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_indelQuality.R" + " " + executor.callRScripts("plot_indelQuality.R", outputFilename,
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
p.waitFor();
} else { } else {
if( iii == 1 ) { if( iii == 1 ) {
// Analyze reported quality // Analyze reported quality
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_QualityScoreCovariate.R" + " " + executor.callRScripts("plot_residualError_QualityScoreCovariate.R", outputFilename,
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " + 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
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
p.waitFor();
} else { // Analyze all other covariates } else { // Analyze all other covariates
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_OtherCovariate.R" + " " + executor.callRScripts("plot_residualError_OtherCovariate.R", outputFilename,
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
p.waitFor();
} }
} }
} catch (InterruptedException e) {
e.printStackTrace();
System.exit(-1);
} catch (IOException e) {
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.");
e.printStackTrace();
System.exit(-1);
}
} }
} else { // at the maximum number of read groups so break out } else { // at the maximum number of read groups so break out
break; break;

14
public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java
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@ -57,8 +57,16 @@ public class RScriptExecutor {
public String PATH_TO_RSCRIPT = "Rscript"; public String PATH_TO_RSCRIPT = "Rscript";
@Advanced @Advanced
@Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required = false) @Argument(fullName = "path_to_Rresources", shortName = "Rresources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
public List<String> PATH_TO_RESOURCES = Arrays.asList("public/R/", "private/R/"); public List<String> PATH_TO_RESOURCES = Arrays.asList("public/R/", "private/R/");
public RScriptArgumentCollection() {}
/** For testing and convenience */
public RScriptArgumentCollection(final String PATH_TO_RSCRIPT, final List<String> PATH_TO_RESOURCES) {
this.PATH_TO_RSCRIPT = PATH_TO_RSCRIPT;
this.PATH_TO_RESOURCES = PATH_TO_RESOURCES;
}
} }
final RScriptArgumentCollection myArgs; final RScriptArgumentCollection myArgs;
@ -69,11 +77,11 @@ public class RScriptExecutor {
this.exceptOnError = exceptOnError; this.exceptOnError = exceptOnError;
} }
public void callRScripts(String scriptName, String... scriptArgs) { public void callRScripts(String scriptName, Object... scriptArgs) {
callRScripts(scriptName, Arrays.asList(scriptArgs)); callRScripts(scriptName, Arrays.asList(scriptArgs));
} }
public void callRScripts(String scriptName, List<String> scriptArgs) { public void callRScripts(String scriptName, List<Object> scriptArgs) {
try { try {
final File pathToScript = findScript(scriptName); final File pathToScript = findScript(scriptName);
if ( pathToScript == null ) return; // we failed but shouldn't exception out if ( pathToScript == null ) return; // we failed but shouldn't exception out