Useful profiling tool that reads in a single rod and evalutes the time it takes to read the file by byte, by line, into pieces, just the sites of the vcf, and finally the full vcf. Emits a useful table for plotting with the associated R script that can be run like Rscript R/analyzeRodProfile.R table.txt table.pdf titleString
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4728 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
parent
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commit
8768e1a240
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#!/bin/env Rscript
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args <- commandArgs(TRUE)
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verbose = TRUE
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d = read.table(args[1],head=T)
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outfile = args[2]
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title = args[3]
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# -----------------------------------------------------------------------------------------------
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# plot timing
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# -----------------------------------------------------------------------------------------------
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pdf(outfile, height=5, width=8)
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boxplot(d$walltime ~ d$operation, ylab = "Elapsed wall time in seconds [Log10 Scale]", log="y", main=title, cex.axis=0.75)
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dev.off()
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@ -297,6 +297,19 @@ public class RefMetaDataTracker {
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return contexts.iterator().next();
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}
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/**
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* Very simple accessor that gets the first (and only!) VC associated with name at the current location, or
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* null if there's no binding here.
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*
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* @param ref
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* @param name
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* @param curLocation
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* @return
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*/
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public VariantContext getVariantContext(ReferenceContext ref, String name, GenomeLoc curLocation) {
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return getVariantContext(ref, name, null, curLocation, true);
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}
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private void addVariantContexts(Collection<VariantContext> contexts, RODRecordList rodList, ReferenceContext ref, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
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for ( GATKFeature rec : rodList ) {
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/*
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* Copyright (c) 2010, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.qc;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.util.ParsingUtils;
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import org.broad.tribble.vcf.VCFConstants;
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import org.broad.tribble.vcf.VCFCodec;
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import org.broad.tribble.readers.LineReader;
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import org.broad.tribble.readers.AsciiLineReader;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.utils.Utils;
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import java.io.PrintStream;
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import java.io.File;
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import java.io.FileInputStream;
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import java.util.*;
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/**
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* Emits specific fields as dictated by the user from one or more VCF files.
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*/
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@Requires(value={})
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public class ProfileRodSystem extends RodWalker<Integer, Integer> {
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@Output(doc="File to which results should be written",required=true)
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protected PrintStream out;
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@Argument(fullName="nIterations", shortName="N", doc="Number of raw reading iterations to perform", required=false)
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int nIterations = 1;
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@Argument(fullName="maxRecords", shortName="M", doc="Max. number of records to process", required=false)
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int MAX_RECORDS = -1;
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public void initialize() {
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File rodFile = getRodFile();
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out.printf("# walltime is in seconds%n");
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out.printf("# file is %s%n", rodFile);
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out.printf("# file size is %d bytes%n", rodFile.length());
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out.printf("operation\titeration\twalltime%n");
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for ( int i = 0; i < nIterations; i++ ) {
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out.printf("read.bytes\t%d\t%.2f%n", i, readFile(rodFile, ReadMode.BY_BYTE));
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out.printf("read.line\t%d\t%.2f%n", i, readFile(rodFile, ReadMode.BY_LINE));
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out.printf("line.and.parts\t%d\t%.2f%n", i, readFile(rodFile, ReadMode.BY_PARTS));
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out.printf("decode.loc\t%d\t%.2f%n", i, readFile(rodFile, ReadMode.DECODE_LOC));
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out.printf("full.decode\t%d\t%.2f%n", i, readFile(rodFile, ReadMode.DECODE));
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}
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startTimer(); // start up timer for map itself
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}
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private enum ReadMode { BY_BYTE, BY_LINE, BY_PARTS, DECODE_LOC, DECODE };
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private final double readFile(File f, ReadMode mode) {
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startTimer();
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try {
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byte[] data = new byte[100000];
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FileInputStream s = new FileInputStream(f);
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if ( mode == ReadMode.BY_BYTE ) {
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while (true) {
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if ( s.read(data) == -1 )
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break;
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}
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} else {
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int counter = 0;
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VCFCodec codec = new VCFCodec();
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String[] parts = new String[100000];
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AsciiLineReader lineReader = new AsciiLineReader(s);
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if ( mode == ReadMode.DECODE_LOC || mode == ReadMode.DECODE )
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codec.readHeader(lineReader);
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while (counter++ < MAX_RECORDS || MAX_RECORDS == -1) {
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String line = lineReader.readLine();
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if ( line == null )
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break;
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else if ( mode == ReadMode.BY_PARTS ) {
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ParsingUtils.split(line, parts, VCFConstants.FIELD_SEPARATOR_CHAR);
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}
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else if ( mode == ReadMode.DECODE_LOC ) {
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codec.decodeLoc(line);
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}
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else if ( mode == ReadMode.DECODE ) {
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processOneVC((VariantContext)codec.decode(line));
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}
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}
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}
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} catch ( Exception e ) {
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throw new RuntimeException(e);
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}
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return elapsedTime();
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}
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private long startTime = -1l;
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private void startTimer() {
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startTime = System.currentTimeMillis();
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}
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private double elapsedTime() {
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final long curTime = System.currentTimeMillis();
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return (curTime - startTime) / 1000.0;
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}
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private File getRodFile() {
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List<ReferenceOrderedDataSource> rods = this.getToolkit().getRodDataSources();
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ReferenceOrderedDataSource rod = rods.get(0);
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return rod.getReferenceOrderedData().getFile();
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null ) // RodWalkers can make funky map calls
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return 0;
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VariantContext vc = tracker.getVariantContext(ref, "rod", context.getLocation());
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processOneVC(vc);
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return 0;
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}
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private static final void processOneVC(VariantContext vc) {
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vc.getNSamples(); // force us to parse the samples
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}
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public Integer reduceInit() {
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return 0;
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}
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public Integer reduce(Integer counter, Integer sum) {
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return counter + sum;
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}
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public void onTraversalDone(Integer sum) {
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out.printf("gatk.traversal\t%d\t%.2f%n", 0, elapsedTime());
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}
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}
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