Updated AnalyzeCovariates to extend org.broadinstitute.sting.utils.cmdLine.CommandLineProgram and use the standard argument parsing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2335 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin
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@ -3,6 +3,8 @@ package org.broadinstitute.sting.analyzecovariates;
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import org.broadinstitute.sting.gatk.walkers.recalibration.*;
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import org.broadinstitute.sting.utils.PackageUtils;
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import org.broadinstitute.sting.utils.xReadLines;
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import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import java.util.ArrayList;
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import java.util.List;
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@ -13,33 +15,40 @@ import java.io.*;
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* Created by IntelliJ IDEA.
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* User: rpoplin
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* Date: Dec 1, 2009
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*
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* Create collapsed versions of the recal csv file and call R scripts to plot residual error versus the various covariates.
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*/
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public class AnalyzeCovariates {
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class AnalyzeCovariatesCLP extends CommandLineProgram {
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/////////////////////////////
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// Command Line Arguments
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/////////////////////////////
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private static String RECAL_FILE = "output.recal_data.csv";
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private static String OUTPUT_DIR = "analyzeCovariates/";
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private static String PATH_TO_RSCRIPT = "/broad/tools/apps/R-2.6.0/bin/Rscript";
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private static String PATH_TO_RESOURCES = "R/";
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private static int IGNORE_QSCORES_LESS_THAN = 5;
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private static int NUM_READ_GROUPS_TO_PROCESS = -1; // -1 means process all read groups
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@Argument(fullName = "recal_file", shortName = "recalFile", doc = "The input recal csv file to analyze", required = false)
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private String RECAL_FILE = "output.recal_data.csv";
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@Argument(fullName = "output_dir", shortName = "outputDir", doc = "The directory in which to output all the plots and intermediate data files", required = false)
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private String OUTPUT_DIR = "analyzeCovariates/";
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@Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is probably /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
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private String PATH_TO_RSCRIPT = "/broad/tools/apps/R-2.6.0/bin/Rscript";
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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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private String PATH_TO_RESOURCES = "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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private int NUM_READ_GROUPS_TO_PROCESS = -1; // -1 means process all read groups
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/////////////////////////////
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// Private Member Variables
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/////////////////////////////
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private static AnalysisDataManager dataManager; // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
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private static ArrayList<Covariate> requestedCovariates; // List of covariates to be used in this calculation
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private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
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private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
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private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
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private AnalysisDataManager dataManager; // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
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private ArrayList<Covariate> requestedCovariates; // List of covariates to be used in this calculation
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private final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
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private final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
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private final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
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public static void main(String[] args) {
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protected int execute() {
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// parse command line arguments
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parseArguments( args );
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// create the output directory where all the data tables and plots will go
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try {
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Process p = Runtime.getRuntime().exec("mkdir " + OUTPUT_DIR);
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@ -64,51 +73,10 @@ public class AnalyzeCovariates {
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callRScripts();
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System.out.println("...Done!");
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return 1;
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}
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private static void parseArguments( String[] args ) {
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int iii = 0;
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String arg;
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try {
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while( iii < args.length && args[iii].startsWith("-") ) {
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arg = args[iii++];
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if( arg.equals( "-recalFile" ) ) {
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RECAL_FILE = args[iii++];
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} else if( arg.equals( "-Rscript" ) ) {
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PATH_TO_RSCRIPT = args[iii++];
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} else if( arg.equals( "-resources" ) ) {
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PATH_TO_RESOURCES = args[iii++];
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} else if( arg.equals( "-ignoreQ" ) ) {
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IGNORE_QSCORES_LESS_THAN = Integer.parseInt( args[iii++] );
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} else if (arg.equals( "-numRG" ) ) {
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NUM_READ_GROUPS_TO_PROCESS = Integer.parseInt( args[iii++] );
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} else if( arg.equals( "-outputDir" ) ) {
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OUTPUT_DIR = args[iii++];
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} else {
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iii = -1;
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break;
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}
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}
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if( iii != args.length ) {
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throw new RuntimeException( "Exception" );
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}
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} catch(Exception e) {
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System.out.println( "Usage: [-option param] \n" );
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System.out.println(" Available options:");
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System.out.println("\t-recalFile <path>\tPath to input recal csv file. Default value: output.recal_data.csv");
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System.out.println("\t-Rscript <path>\t\tPath to your implementation of Rscript. Default value: /broad/tools/apps/R-2.6.0/bin/Rscript");
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System.out.println("\t-resources <path>\tPath to resources folder holding the Sting R scripts. Default value: R/");
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System.out.println("\t-outputDir <path>\tWhere to put the output plots. Default value: analyzeCovariates/");
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System.out.println("\t-ignoreQ <int>\t\tIgnore bases with reported quality less than this number. Default value: 5");
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System.out.println("\t-numRG <int>\t\tOnly process N read groups. Default value: -1 (process all read groups)");
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System.exit(-1);
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}
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}
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private static void initializeData() {
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private void initializeData() {
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// Get a list of all available covariates
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List<Class<? extends Covariate>> classes = PackageUtils.getClassesImplementingInterface(Covariate.class);
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@ -191,7 +159,7 @@ public class AnalyzeCovariates {
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}
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}
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private static void addCSVData(String line) {
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private void addCSVData(String line) {
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String[] vals = line.split(",");
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// Check if the data line is malformed, for example if the read group string contains a comma then it won't be parsed correctly
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@ -214,7 +182,7 @@ public class AnalyzeCovariates {
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}
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private static void writeDataTables() {
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private void writeDataTables() {
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int numReadGroups = 0;
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@ -268,7 +236,7 @@ public class AnalyzeCovariates {
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}
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}
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private static void callRScripts() {
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private void callRScripts() {
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int numReadGroups = 0;
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@ -305,3 +273,11 @@ public class AnalyzeCovariates {
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}
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}
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}
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public class AnalyzeCovariates {
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public static void main(String args[]) {
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AnalyzeCovariatesCLP clp = new AnalyzeCovariatesCLP();
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CommandLineProgram.start( clp, args );
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System.exit(0);
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}
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}
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