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/*
* Copyright (C) 2009-2010 Institute for Computational Biomedicine,
* Weill Medical College of Cornell University
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.campagnelab.goby.modes;
import com.google.protobuf.ByteString;
import com.martiansoftware.jsap.JSAPException;
import com.martiansoftware.jsap.JSAPResult;
import org.campagnelab.goby.reads.Reads;
import org.campagnelab.goby.reads.ReadsReader;
import it.unimi.dsi.fastutil.bytes.ByteArrayList;
import it.unimi.dsi.fastutil.ints.Int2ObjectMap;
import it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap;
import it.unimi.dsi.logging.ProgressLogger;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.math.random.MersenneTwister;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintStream;
import java.util.Arrays;
import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
/**
* Evaluate statistics for read qualities.
*
* @author Fabien Campagne
*/
public class ReadQualityStatsMode extends AbstractGobyMode {
private static final Logger LOG = LoggerFactory.getLogger(ReadQualityStatsMode.class);
/**
* The mode name.
*/
private static final String MODE_NAME = "read-quality-stats";
/**
* The mode description help text.
*/
private static final String MODE_DESCRIPTION =
"Calculate statistics for quality scores in a compact reads file.";
/**
* The output file.
*/
private File outputFile;
/**
* The basename of the compact read files.
*/
private final List<File> inputFiles = new LinkedList<File>();
private double sampleFraction = 0.01;
@Override
public String getModeName() {
return MODE_NAME;
}
@Override
public String getModeDescription() {
return MODE_DESCRIPTION;
}
enum OutputFormat {
TSV,
}
private OutputFormat outputFormat = OutputFormat.TSV;
/**
* Number of samples ignored because of sampleFraction value < 1.0d.
*/
private long numberOfSkippedReads;
/**
* Number of samples observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
* this should be the total number of samples in the file.
*/
private long numberOfObservedReads;
/**
* Configure.
*
* @param args command line arguments
* @return this object for chaining
* @throws java.io.IOException error parsing
* @throws com.martiansoftware.jsap.JSAPException
* error parsing
*/
@Override
public AbstractCommandLineMode configure(final String[] args)
throws IOException, JSAPException {
final JSAPResult jsapResult = parseJsapArguments(args);
final File[] inputFilesArray = jsapResult.getFileArray("input");
inputFiles.addAll(Arrays.asList(inputFilesArray));
outputFile = jsapResult.getFile("output");
outputFormat = OutputFormat.valueOf(jsapResult.getString("format").toUpperCase());
sampleFraction = jsapResult.getDouble("sample-fraction");
return this;
}
/**
* The percentage of reads to process. 0.01 means 1% of reads,
* 1.0 means 100% of reads. The default of 0.01 should work fine
* for most files but if you are dealing with a very small file
* you should set this to 1.0.
*
* @return The percentage of reads to process
*/
public double getSampleFraction() {
return sampleFraction;
}
/**
* The precentage of reads to process. 0.01 means 1% of reads,
* 1.0 means 100% of reads. The default of 0.01 should work fine
* for most files but if you are dealing with a very small file
* you should set this to 1.0.
*
* @param sampleFraction The percentage of reads to process
*/
public void setSampleFraction(final double sampleFraction) {
this.sampleFraction = sampleFraction;
}
/**
* Get the list of files (reads/alignments) to process.
*
* @return The list of files.
*/
public List<File> getInputFiles() {
return inputFiles;
}
/**
* Add the specified file to the list of files to process.
*
* @param inputFile The file to process
*/
public void addInputFile(final File inputFile) {
inputFiles.add(inputFile);
}
/**
* Get the output file.
*
* @return the output file
*/
public File getOutputFile() {
return outputFile;
}
/**
* Set the output file.
*
* @param outputFile the output file
*/
public void setOutputFile(final File outputFile) {
this.outputFile = outputFile;
}
/**
* Number of reads skipped because of sampleFraction value < 1.0d.
* @return the number of skipped samples.
*/
public long getNumberOfSkippedReads() {
return numberOfSkippedReads;
}
/**
* Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
* this should be the total number of reads in the file.
* @return the number of observed samples
*/
public long getNumberOfObservedReads() {
return numberOfObservedReads;
}
/**
* Display the alignments as text files.
*
* @throws java.io.IOException error reading / writing
*/
@Override
public void execute() throws IOException {
PrintStream writer = null;
try {
numberOfSkippedReads = 0;
numberOfObservedReads = 0;
writer = outputFile == null ? System.out
: new PrintStream(new FileOutputStream(outputFile));
final Int2ObjectMap<ReadQualityStats> qualityStats = new Int2ObjectOpenHashMap<ReadQualityStats>();
final ProgressLogger progress = new ProgressLogger(LOG);
progress.start();
final MersenneTwister random = new MersenneTwister(37);
final boolean doSample = sampleFraction < 1.0d;
writer.println("basename\treadIndex\t25%-percentile\tmedian\taverageQuality\t75%-percentile");
for (final File filename : inputFiles) {
final ReadsReader reader = new ReadsReader(filename);
// we do getName to remove any path, that is not taken out by ReadsReader.getBasename().
final String basename = FilenameUtils.getName(ReadsReader.getBasename(filename.toString()));
for (final Reads.ReadEntry entry : reader) {
if (!doSample || random.nextDouble() < sampleFraction) {
final ByteString qualityScores = entry.getQualityScores();
final int size = qualityScores.size();
for (int readIndex = 0; readIndex < size; readIndex++) {
final byte code = qualityScores.byteAt(readIndex);
ReadQualityStats stats = qualityStats.get(readIndex);
if (stats == null) {
stats = new ReadQualityStats(1.0d);
qualityStats.put(readIndex, stats);
stats.readIndex = readIndex;
}
stats.observe(code);
}
numberOfObservedReads++;
} else {
numberOfSkippedReads++;
}
progress.lightUpdate();
}
for (final ReadQualityStats stat : qualityStats.values()) {
if (!stat.sampleIsEmpty()) {
stat.evaluatePercentiles();
writer.printf("%s\t%d\t%d\t%d\t%f\t%d%n",
basename,
stat.readIndex,
stat.percentile(25),
stat.percentile(50),
stat.averageQuality / stat.observedCount,
stat.percentile(75));
}
}
}
progress.updateAndDisplay();
progress.stop();
} finally {
if (writer != System.out) {
IOUtils.closeQuietly(writer);
}
}
}
/**
* Main method.
*
* @param args command line args.
* @throws com.martiansoftware.jsap.JSAPException
* error parsing
* @throws java.io.IOException error parsing or executing.
*/
public static void main(final String[] args) throws JSAPException, IOException {
new ReadQualityStatsMode().configure(args).execute();
}
private static class ReadQualityStats {
private final MersenneTwister random = new MersenneTwister();
private int readIndex;
// byte minValue;
// byte maxValue;
private final ByteArrayList sample = new ByteArrayList();
private double averageQuality;
private int observedCount;
private final double sampleFraction;
private final boolean doSample;
private ReadQualityStats(final double sampleFraction) {
this.sampleFraction = sampleFraction;
doSample = sampleFraction < 1.0;
}
void observe(final byte b) {
averageQuality += b;
observedCount += 1;
if (!doSample || random.nextDouble() < sampleFraction) {
sample.add(b);
}
}
public void evaluatePercentiles() {
Collections.sort(sample);
}
public byte percentile(final double percent) {
final int index = (int) ((double) sample.size() * percent / 100d);
return sample.get(index);
}
public boolean sampleIsEmpty() {
return sample.isEmpty();
}
}
}
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