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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
This commit is contained in:
depristo 2010-11-24 14:59:16 +00:00
parent 7a8b85dd15
commit 8768e1a240
3 changed files with 195 additions and 0 deletions
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15
R/analyzeRodProfile.R 100755
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@ -0,0 +1,15 @@
#!/bin/env Rscript
args <- commandArgs(TRUE)
verbose = TRUE
d = read.table(args[1],head=T)
outfile = args[2]
title = args[3]
# -----------------------------------------------------------------------------------------------
# plot timing
# -----------------------------------------------------------------------------------------------
pdf(outfile, height=5, width=8)
boxplot(d$walltime ~ d$operation, ylab = "Elapsed wall time in seconds [Log10 Scale]", log="y", main=title, cex.axis=0.75)
dev.off()

13
java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
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@ -297,6 +297,19 @@ public class RefMetaDataTracker {
return contexts.iterator().next(); return contexts.iterator().next();
} }
/**
* Very simple accessor that gets the first (and only!) VC associated with name at the current location, or
* null if there's no binding here.
*
* @param ref
* @param name
* @param curLocation
* @return
*/
public VariantContext getVariantContext(ReferenceContext ref, String name, GenomeLoc curLocation) {
return getVariantContext(ref, name, null, curLocation, true);
}
private void addVariantContexts(Collection<VariantContext> contexts, RODRecordList rodList, ReferenceContext ref, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) { private void addVariantContexts(Collection<VariantContext> contexts, RODRecordList rodList, ReferenceContext ref, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
for ( GATKFeature rec : rodList ) { for ( GATKFeature rec : rodList ) {

167
java/src/org/broadinstitute/sting/gatk/walkers/qc/ProfileRodSystem.java 100755
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@ -0,0 +1,167 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.qc;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.util.ParsingUtils;
import org.broad.tribble.vcf.VCFConstants;
import org.broad.tribble.vcf.VCFCodec;
import org.broad.tribble.readers.LineReader;
import org.broad.tribble.readers.AsciiLineReader;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.utils.Utils;
import java.io.PrintStream;
import java.io.File;
import java.io.FileInputStream;
import java.util.*;
/**
* Emits specific fields as dictated by the user from one or more VCF files.
*/
@Requires(value={})
public class ProfileRodSystem extends RodWalker<Integer, Integer> {
@Output(doc="File to which results should be written",required=true)
protected PrintStream out;
@Argument(fullName="nIterations", shortName="N", doc="Number of raw reading iterations to perform", required=false)
int nIterations = 1;
@Argument(fullName="maxRecords", shortName="M", doc="Max. number of records to process", required=false)
int MAX_RECORDS = -1;
public void initialize() {
File rodFile = getRodFile();
out.printf("# walltime is in seconds%n");
out.printf("# file is %s%n", rodFile);
out.printf("# file size is %d bytes%n", rodFile.length());
out.printf("operation\titeration\twalltime%n");
for ( int i = 0; i < nIterations; i++ ) {
out.printf("read.bytes\t%d\t%.2f%n", i, readFile(rodFile, ReadMode.BY_BYTE));
out.printf("read.line\t%d\t%.2f%n", i, readFile(rodFile, ReadMode.BY_LINE));
out.printf("line.and.parts\t%d\t%.2f%n", i, readFile(rodFile, ReadMode.BY_PARTS));
out.printf("decode.loc\t%d\t%.2f%n", i, readFile(rodFile, ReadMode.DECODE_LOC));
out.printf("full.decode\t%d\t%.2f%n", i, readFile(rodFile, ReadMode.DECODE));
}
startTimer(); // start up timer for map itself
}
private enum ReadMode { BY_BYTE, BY_LINE, BY_PARTS, DECODE_LOC, DECODE };
private final double readFile(File f, ReadMode mode) {
startTimer();
try {
byte[] data = new byte[100000];
FileInputStream s = new FileInputStream(f);
if ( mode == ReadMode.BY_BYTE ) {
while (true) {
if ( s.read(data) == -1 )
break;
}
} else {
int counter = 0;
VCFCodec codec = new VCFCodec();
String[] parts = new String[100000];
AsciiLineReader lineReader = new AsciiLineReader(s);
if ( mode == ReadMode.DECODE_LOC || mode == ReadMode.DECODE )
codec.readHeader(lineReader);
while (counter++ < MAX_RECORDS || MAX_RECORDS == -1) {
String line = lineReader.readLine();
if ( line == null )
break;
else if ( mode == ReadMode.BY_PARTS ) {
ParsingUtils.split(line, parts, VCFConstants.FIELD_SEPARATOR_CHAR);
}
else if ( mode == ReadMode.DECODE_LOC ) {
codec.decodeLoc(line);
}
else if ( mode == ReadMode.DECODE ) {
processOneVC((VariantContext)codec.decode(line));
}
}
}
} catch ( Exception e ) {
throw new RuntimeException(e);
}
return elapsedTime();
}
private long startTime = -1l;
private void startTimer() {
startTime = System.currentTimeMillis();
}
private double elapsedTime() {
final long curTime = System.currentTimeMillis();
return (curTime - startTime) / 1000.0;
}
private File getRodFile() {
List<ReferenceOrderedDataSource> rods = this.getToolkit().getRodDataSources();
ReferenceOrderedDataSource rod = rods.get(0);
return rod.getReferenceOrderedData().getFile();
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null ) // RodWalkers can make funky map calls
return 0;
VariantContext vc = tracker.getVariantContext(ref, "rod", context.getLocation());
processOneVC(vc);
return 0;
}
private static final void processOneVC(VariantContext vc) {
vc.getNSamples(); // force us to parse the samples
}
public Integer reduceInit() {
return 0;
}
public Integer reduce(Integer counter, Integer sum) {
return counter + sum;
}
public void onTraversalDone(Integer sum) {
out.printf("gatk.traversal\t%d\t%.2f%n", 0, elapsedTime());
}
}