Adding depth of coverage features to firehose summary tools
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2860 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl
parent
71f18e941f
commit
0e05a3acb0
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@ -0,0 +1,369 @@
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package org.broadinstitute.sting.oneoffprojects.firehosesummary;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
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import java.io.*;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
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*
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* @Author chartl
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* @Date Feb 18, 2010
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*/
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class AnalyzeDepthCLP extends CommandLineProgram {
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@Argument(fullName = "depthOfCoverageFile", shortName = "df", doc = "The Depth of Coverage output file", required = true)
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public File docFile = null;
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@Argument(fullName = "summaryFile", shortName = "sf", doc = "The summary file to which to output", required = true)
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public File summaryFile = null;
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@Argument(fullName = "plotBaseName", shortName = "bn", doc = "The base name for the plot files (e.g. 'foo' yields plots 'foo_DoC_by_sample.pdf'). Please ensure this name contains no spaces.", required = false)
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public String plotBaseName = "DepthAnalysis";
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@Argument(fullName = "pathToRScript", 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 = "./";
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private boolean containsByLocus = false;
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private boolean containsByTarget = false;
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///////////////////////////////////////////////////////////////////////////////////
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// CONSTANT VALUES: SUMMARY STRING FOR NO INFORMATION, R-SCRIPT ARGUMENTS, ETC
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///////////////////////////////////////////////////////////////////////////////////
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private final String DEFAULT_SUMMARY_STRING = "No Summary Information";
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private final String PER_LOCUS_R_ARGUMENTS = "PlotInterleavedRows depth_of_coverage\\;proportion_of_bases_above\\;Per_Sample_Depth_of_Coverage\\;"+plotBaseName+"_per_locus";
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private final String PER_TARGET_R_ARGUMENTS = "PlotInterleavedRows depth_of_coverage\\;proportion_of_targets_with_mean_coverage_above\\;Per_Sample_Average_DoC_Over_Targets\\;"+plotBaseName+"_per_target";
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///////////////////////////////////////////////////////////////////////////////////
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// ANALYSIS START: CALCULATE STATISTICS, WRITE IN R-READABLE FORMAT, MAKE PLOTS
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///////////////////////////////////////////////////////////////////////////////////
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protected int execute() {
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List<DepthStatisticsCalculator> depthStats = calculateDepthStatistics(docFile);
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String perLocusSummary = DEFAULT_SUMMARY_STRING;
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String perTargetSummary = DEFAULT_SUMMARY_STRING;
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if ( containsByLocus ) {
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File baseSummaryTable = writeBaseSummaryFile(depthStats);
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perLocusSummary = generatePerLocusSummary(baseSummaryTable,depthStats);
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}
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if ( containsByTarget ) {
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File targetSummaryTable = writeTargetSumamryFile(depthStats);
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perTargetSummary = generatePerTargetSummary(targetSummaryTable, depthStats);
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}
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writeSummaryInfoFile(summaryFile,perLocusSummary,perTargetSummary);
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return 1;
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}
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///////////////////////////////////////////////////////////////////////////////////
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// OPEN AND WRITE FINAL SUMMARY DOC FILE
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///////////////////////////////////////////////////////////////////////////////////
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private void writeSummaryInfoFile(File sFile, String locusSummary, String targetSummary) {
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PrintWriter writer;
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try {
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writer = new PrintWriter(sFile);
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writer.printf("%s%n","##Depth of coverage summary file");
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writer.printf("%s%n","##Well_Covered_Samples_By_Base - % of samples with >80% bases covered to 10x");
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writer.printf("%s%n","##Well_Covered_Samples_By_Mean - % of samples with mean coverage > 10x");
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writer.printf("%s%n%n","##Well_Covered_Samples_By_Target - % of samples with >80% targets covered to 10x");
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if ( containsByLocus )
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writer.printf("%s%n",locusSummary);
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if ( containsByTarget )
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writer.printf("%s",targetSummary);
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writer.close();
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} catch (IOException e) {
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throw new StingException("Error writing final depth of coverage summary file",e);
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}
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}
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///////////////////////////////////////////////////////////////////////////////////
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// CALL R-SCRIPTS AND GENERATE OVERALL SUMMARY FILES
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///////////////////////////////////////////////////////////////////////////////////
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private String generatePerLocusSummary(File rReadablePlotFile, List<DepthStatisticsCalculator> calcs) {
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String rCommand = PATH_TO_RSCRIPT+" "+PATH_TO_RESOURCES+" "+rReadablePlotFile.getAbsolutePath()+" "+PER_LOCUS_R_ARGUMENTS;
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try {
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Process p = Runtime.getRuntime().exec(rCommand);
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} catch ( IOException e ) {
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throw new StingException("Error executing r command for per locus plot generation",e);
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}
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StringBuilder summary = new StringBuilder();
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summary.append(String.format("%s%n","PER_LOCUS_SUMMARY"));
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int numSamples = calcs.size()-2;
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int numGoodSamples = 0;
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int numGoodSamplesByMeanCvg = 0;
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double totalAvgCoverage = -1;
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double totalStdevCoverage = -1;
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for ( DepthStatisticsCalculator calc : calcs ) {
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if ( calc.getName().equalsIgnoreCase("total_coverage")) {
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totalAvgCoverage = calc.getMean();
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totalStdevCoverage = Math.sqrt(calc.getVar());
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} else if ( ! calc.getName().equalsIgnoreCase("coverage_without_deletions") ) {
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if ( calc.getPercentWellCoveredLoci() > 0.8 ) {
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numGoodSamples++;
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}
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if ( calc.getMean() > 10 ) {
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numGoodSamplesByMeanCvg++;
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}
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}
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}
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summary.append(String.format("%s\t%f%n","Average_Coverage:",totalAvgCoverage));
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summary.append(String.format("%s\t%f%n","Stdev_Coverage:",totalStdevCoverage));
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summary.append(String.format("%s\t%.2f%n","%Well_Covered_Samples_By_Base", ( (double) numGoodSamples*100 )/( (double) numSamples)));
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summary.append(String.format("%s\t%.2f%n","%Well_Covered_Samples_By_Mean", ( (double) numGoodSamplesByMeanCvg*100) / ( (double) numSamples )));
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return summary.toString();
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}
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private String generatePerTargetSummary(File rReadablePlotFile, List<DepthStatisticsCalculator> calcs) {
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String rCommand = PATH_TO_RSCRIPT+" "+PATH_TO_RESOURCES+" "+rReadablePlotFile.getAbsolutePath()+" "+PER_TARGET_R_ARGUMENTS;
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try {
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Process p = Runtime.getRuntime().exec(rCommand);
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} catch ( IOException e ) {
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throw new StingException("Error executing r command for per locus plot generation",e);
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}
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StringBuilder summary = new StringBuilder();
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summary.append(String.format("%s%n","PER_TARGET_SUMMARY"));
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int numSamples = calcs.size()-2;
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int numGoodSamples = 0;
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for ( DepthStatisticsCalculator calc : calcs ) {
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if ( calc.getName().equalsIgnoreCase("total_coverage")) {
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// do nothing
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} else if ( ! calc.getName().equalsIgnoreCase("coverage_without_deletions") ) {
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if ( calc.getPercentWellCoveredTargets() > 0.8 ) {
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numGoodSamples++;
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}
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}
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}
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summary.append(String.format("%s\t%.2f%n","%Well_Covered_Samples_By_Target", ( (double) numGoodSamples*100) / ( (double) numSamples )));
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return summary.toString();
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}
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///////////////////////////////////////////////////////////////////////////////////
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// R-READABLE TEMPORARY FILE CREATION
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///////////////////////////////////////////////////////////////////////////////////
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private File writeBaseSummaryFile(List<DepthStatisticsCalculator> calcs) {
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File perLocusSummaryFile;
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try {
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perLocusSummaryFile = File.createTempFile(plotBaseName+"_per_locus_summary",".txt");
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} catch ( IOException e ) {
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throw new StingException("Could not create a temporary file. Please check the permissions of the directory you are running in, and that the base name is not a filepath.",e);
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}
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PrintWriter locusWriter;
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try {
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locusWriter = new PrintWriter(perLocusSummaryFile);
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} catch ( IOException e ) {
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throw new StingException("Locus summary temporary file was created but could not be opened.",e);
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}
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for ( DepthStatisticsCalculator calc : calcs ) {
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if ( ! calc.getName().equalsIgnoreCase("total_coverage") && ! calc.getName().equalsIgnoreCase("coverage_without_deletions") ) {
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locusWriter.printf("%s\t%f\t%f\t%f\t%f\t%f\t%f",calc.getName(),calc.getLocusProportions());
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locusWriter.printf("%s\t%d\t%d\t%d\t%d\t%d\t%d",calc.getName(),calc.getEvalPoints());
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}
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}
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locusWriter.close();
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return perLocusSummaryFile;
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}
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private File writeTargetSumamryFile(List<DepthStatisticsCalculator> calcs) {
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File perTargetSummaryFile;
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try {
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perTargetSummaryFile = File.createTempFile(plotBaseName+"_per_target_summary",".txt");
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} catch ( IOException e ) {
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throw new StingException("Could not create a temporary file. Please check the permissions of the directory you are running in, and that the base name is not a filepath.",e);
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}
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PrintWriter targetWriter;
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try {
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targetWriter = new PrintWriter(perTargetSummaryFile);
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} catch ( IOException e ) {
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throw new StingException("Target summary temporary file was created but could not be opened.",e);
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}
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for ( DepthStatisticsCalculator calc : calcs ) {
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if ( ! calc.getName().equalsIgnoreCase("total_coverage") && ! calc.getName().equalsIgnoreCase("coverage_without_deletions") ) {
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targetWriter.printf("%s\t%f\t%f\t%f\t%f\t%f\t%f",calc.getName(),calc.getTargetProportions());
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targetWriter.printf("%s\t%d\t%d\t%d\t%d\t%d\t%d",calc.getName(),calc.getEvalPoints());
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}
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}
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targetWriter.close();
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return perTargetSummaryFile;
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}
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///////////////////////////////////////////////////////////////////////////////////
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// READING THE DEPTH OF COVERAGE FILE INTO CALCULATOR OBJECTS
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///////////////////////////////////////////////////////////////////////////////////
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private List<DepthStatisticsCalculator> calculateDepthStatistics(File docFile) {
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BufferedReader docReader;
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try {
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docReader = new BufferedReader( new FileReader(docFile) );
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} catch ( IOException e) {
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throw new StingException("The file "+docFile.getAbsolutePath()+" could not be opened...",e);
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}
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String locusHeader = getDOCSectionHeader(docReader); // this will read to the first section header
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List<DepthStatisticsCalculator> docCalculators;
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if ( locusHeader != null && locusHeader.equalsIgnoreCase("PER_LOCUS_COVERAGE_SECTION")) {
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containsByLocus = true;
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docCalculators = instantiateDOCCalculators(docReader);
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updateLocusInfo(docCalculators,docReader);
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String targetHeader = getDOCSectionHeader(docReader);
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if ( targetHeader != null && targetHeader.equalsIgnoreCase("PER_TARGET_COVERAGE_SECTION") ) {
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containsByTarget = true;
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updateTargetInfo(docCalculators,docReader);
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} else {
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containsByTarget = false;
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}
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} else if ( locusHeader != null && locusHeader.equalsIgnoreCase("PER_TARGET_COVERAGE_SECTION") ) {
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containsByTarget = true;
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containsByLocus = false;
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docCalculators = instantiateDOCCalculators(docReader);
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updateTargetInfo(docCalculators,docReader);
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} else {
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containsByLocus = false;
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containsByTarget = false;
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docCalculators = null;
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}
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return docCalculators;
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}
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private List<DepthStatisticsCalculator> instantiateDOCCalculators(BufferedReader reader) {
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String header;
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try {
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header = reader.readLine();
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} catch (IOException e) {
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throw new StingException("Unable to read the section header",e);
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}
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List<DepthStatisticsCalculator> calcs = new ArrayList<DepthStatisticsCalculator>();
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int offset = -1;
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for ( String entry : header.split("\t") ) {
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if ( offset > -1 ) {
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calcs.add(new DepthStatisticsCalculator(entry));
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}
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offset++;
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}
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return calcs;
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}
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private void updateLocusInfo(List<DepthStatisticsCalculator> calcs, BufferedReader reader) {
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String docLocLine;
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try {
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docLocLine = reader.readLine();
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while ( ! isEndOfSection(docLocLine) ) {
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int offset = -1;
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for ( String entry : docLocLine.split("\t") ) {
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if ( offset > -1 ) {
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calcs.get(offset).updateLocus(Integer.parseInt(entry));
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}
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offset++;
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}
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}
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} catch ( IOException e) {
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throw new StingException("Error reading locus depth of coverage information",e);
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}
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}
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private void updateTargetInfo(List<DepthStatisticsCalculator> calcs, BufferedReader reader) {
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String docLocLine;
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try {
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docLocLine = reader.readLine();
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while ( ! isEndOfSection(docLocLine) ) {
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int offset = -1;
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int targetSize = 0;
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for ( String entry : docLocLine.split("\t") ) {
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if ( offset == -1 ) {
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targetSize = parseInterval(entry);
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} else {
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calcs.get(offset).updateTargets(targetSize,Integer.parseInt(entry));
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}
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offset++;
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}
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}
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} catch ( IOException e ) {
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throw new StingException("Error reading target depth of coverage information",e);
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}
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}
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///////////////////////////////////////////////////////////////////////////////////
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// FILE IO METHODS -- DEPEND ON DEPTH OF COVERAGE FILE FORMAT
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///////////////////////////////////////////////////////////////////////////////////
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private boolean isEndOfSection( String line ) {
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// sections delimited by empty line
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return line.equalsIgnoreCase("");
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}
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private String getDOCSectionHeader(BufferedReader reader) {
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String header;
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try {
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do {
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header = reader.readLine();
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} while ( ! isDOCSectionSeparator(header) && header != null);
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} catch (IOException e) {
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throw new StingException("Error reading depth of coverage file",e);
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}
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return header;
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}
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private boolean isDOCSectionSeparator( String line ) {
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return line.contains("_COVERAGE_SECTION");
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}
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private int parseInterval(String interval) {
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String startstop = interval.split(":")[1];
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int start = Integer.parseInt(startstop.split("-")[0]);
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int stop = Integer.parseInt(startstop.split("-")[1]);
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return stop - start;
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}
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}
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///////////////////////////////////////////////////////////////////////////////////
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// PROGRAM START -- THE MAIN() METHOD AND WRAPPER CLASS
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///////////////////////////////////////////////////////////////////////////////////
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public class AnalyzeDepthOfCoverage {
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public static void main(String[] args) {
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AnalyzeDepthCLP depthAnalysis = new AnalyzeDepthCLP();
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CommandLineProgram.start(depthAnalysis,args);
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System.exit(0);
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}
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}
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@ -25,7 +25,7 @@ public class DepthStatisticsCalculator extends SummaryStatisticsCalculator {
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private int targetsAbove99x;
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private int numTargets;
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public static double[] DEPTH_CUTOFFS = {1,4,10,25,50,100};
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public static int[] DEPTH_CUTOFFS = {1,4,10,25,50,100};
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public DepthStatisticsCalculator(String name) {
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super(name);
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@ -125,4 +125,8 @@ public class DepthStatisticsCalculator extends SummaryStatisticsCalculator {
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public double getPercentWellCoveredTargets() {
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return 10*( (double) targetsAbove9x )/( (double) numTargets );
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}
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public int[] getEvalPoints() {
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return DepthStatisticsCalculator.DEPTH_CUTOFFS;
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}
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}
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@ -17,18 +17,18 @@ import java.util.*;
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class FirehoseSummaryCLP extends CommandLineProgram {
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@Argument(fullName = "depthOfCoverageFile", shortName = "doc", doc="Path to the depth of coverage file", required=true)
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private File depthOfCoverage = null;
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@Argument(fullName = "contaminationFile", shortName = "con", doc="Path to the contamination file", required=true)
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private File contamination = null;
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@Argument(fullName = "errorRateFile", shortName = "err", doc="Path to the error rate file", required=true)
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private File errorRate = null;
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@Argument(fullName = "zipFiles", shortName = "zip", doc="List of paths to zip files which contain summary metrics files", required=false)
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private String zipFiles = null;
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// @Argument(fullName = "contaminationFile", shortName = "con", doc="Path to the contamination file", required=true)
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// private File contamination = null;
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// @Argument(fullName = "errorRateFile", shortName = "err", doc="Path to the error rate file", required=true)
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// private File errorRate = null;
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// @Argument(fullName = "zipFiles", shortName = "zip", doc="List of paths to zip files which contain summary metrics files", required=false)
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// private String zipFiles = null;
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private static String R_SCRIPT = "plotFirehoseDataQCMetrics.R";
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private static String SCRIPT_DOC_FLAG = "DOC";
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protected int execute() {
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SummaryFileCollection metricsFiles = getFileHandles();
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// SummaryFileCollection metricsFiles = getFileHandles();
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List<DepthStatisticsCalculator> depthStats = calculateDepthStatistics(depthOfCoverage);
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String docSummary = makeDOCPlots(depthStats);
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return 1;
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@ -85,18 +85,18 @@ class FirehoseSummaryCLP extends CommandLineProgram {
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return "temporary";
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}
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private SummaryFileCollection getFileHandles() {
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if ( zipFiles == null ) {
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return null;
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}
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SummaryFileCollection summaryFiles = new SummaryFileCollection();
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for ( String zipFile : zipFiles.split(",") ) {
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summaryFiles.process(zipFile);
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}
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return summaryFiles;
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}
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// private SummaryFileCollection getFileHandles() {
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// if ( zipFiles == null ) {
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// return null;
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// }
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//
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// SummaryFileCollection summaryFiles = new SummaryFileCollection();
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// for ( String zipFile : zipFiles.split(",") ) {
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// summaryFiles.process(zipFile);
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// }
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//
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// return summaryFiles;
|
||||
// }
|
||||
|
||||
private List<DepthStatisticsCalculator> calculateDepthStatistics(File docFile) {
|
||||
BufferedReader docReader;
|
||||
|
|
@ -219,39 +219,39 @@ public class GenerateFirehoseSummary {
|
|||
}
|
||||
}
|
||||
|
||||
class SummaryFileCollection {
|
||||
|
||||
// container class for files we'll be summarizing
|
||||
|
||||
public Map<String,File> fingerprintSummaryFiles;
|
||||
public Map<String,File> hybridSelectionMetricsFiles;
|
||||
public Map<String,File> insertSizeDistributionFiles;
|
||||
public Map<String,File> alignmentMetricsFiles;
|
||||
|
||||
public SummaryFileCollection() {
|
||||
fingerprintSummaryFiles = new HashMap<String,File>();
|
||||
hybridSelectionMetricsFiles = new HashMap<String, File>();
|
||||
insertSizeDistributionFiles = new HashMap<String,File>();
|
||||
alignmentMetricsFiles = new HashMap<String,File>();
|
||||
}
|
||||
|
||||
public void process(String zipFilePath) {
|
||||
String sampleName = zipFilePath.split("_sequencing_metrics.zip")[0].split("_")[1];
|
||||
File fingerprintSummaryFile = new File(sampleName+".summary_fingerprint_metrics");
|
||||
File hybridSelectionFile = new File(sampleName+".hybrid_selection_metrics");
|
||||
File insertSizeFile = new File(sampleName+".insert_size_metrics");
|
||||
File alignmentFile = new File(sampleName+".alignment_metrics");
|
||||
|
||||
String command = "unzip "+zipFilePath;
|
||||
try {
|
||||
Process p = Runtime.getRuntime().exec(command);
|
||||
} catch (IOException e) {
|
||||
throw new RuntimeException("Could not unzip the file "+zipFilePath);
|
||||
}
|
||||
|
||||
fingerprintSummaryFiles.put(sampleName,fingerprintSummaryFile);
|
||||
hybridSelectionMetricsFiles.put(sampleName,hybridSelectionFile);
|
||||
insertSizeDistributionFiles.put(sampleName,insertSizeFile);
|
||||
alignmentMetricsFiles.put(sampleName,alignmentFile);
|
||||
}
|
||||
}
|
||||
//class SummaryFileCollection {
|
||||
//
|
||||
// // container class for files we'll be summarizing
|
||||
//
|
||||
// public Map<String,File> fingerprintSummaryFiles;
|
||||
// public Map<String,File> hybridSelectionMetricsFiles;
|
||||
// public Map<String,File> insertSizeDistributionFiles;
|
||||
// public Map<String,File> alignmentMetricsFiles;
|
||||
//
|
||||
// public SummaryFileCollection() {
|
||||
// fingerprintSummaryFiles = new HashMap<String,File>();
|
||||
// hybridSelectionMetricsFiles = new HashMap<String, File>();
|
||||
// insertSizeDistributionFiles = new HashMap<String,File>();
|
||||
// alignmentMetricsFiles = new HashMap<String,File>();
|
||||
// }
|
||||
//
|
||||
// public void process(String zipFilePath) {
|
||||
// String sampleName = zipFilePath.split("_sequencing_metrics.zip")[0].split("_")[1];
|
||||
// File fingerprintSummaryFile = new File(sampleName+".summary_fingerprint_metrics");
|
||||
// File hybridSelectionFile = new File(sampleName+".hybrid_selection_metrics");
|
||||
// File insertSizeFile = new File(sampleName+".insert_size_metrics");
|
||||
// File alignmentFile = new File(sampleName+".alignment_metrics");
|
||||
//
|
||||
// String command = "unzip "+zipFilePath;
|
||||
// try {
|
||||
// Process p = Runtime.getRuntime().exec(command);
|
||||
// } catch (IOException e) {
|
||||
// throw new RuntimeException("Could not unzip the file "+zipFilePath);
|
||||
// }
|
||||
//
|
||||
// fingerprintSummaryFiles.put(sampleName,fingerprintSummaryFile);
|
||||
// hybridSelectionMetricsFiles.put(sampleName,hybridSelectionFile);
|
||||
// insertSizeDistributionFiles.put(sampleName,insertSizeFile);
|
||||
// alignmentMetricsFiles.put(sampleName,alignmentFile);
|
||||
// }
|
||||
//}
|
||||
Loading…
Reference in New Issue