org.nmdp.ngs.tools.DownsampleInterleavedFastq Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of ngs-tools Show documentation
Show all versions of ngs-tools Show documentation
Next generation sequencing (NGS/HTS) command line tools.
/*
ngs-tools Next generation sequencing (NGS/HTS) command line tools.
Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.gnu.org/licenses/lgpl.html
*/
package org.nmdp.ngs.tools;
import static com.google.common.base.Preconditions.checkNotNull;
import static org.dishevelled.compress.Readers.reader;
import static org.dishevelled.compress.Writers.writer;
import java.io.BufferedReader;
import java.io.File;
import java.io.PrintWriter;
import java.io.IOException;
import java.util.concurrent.Callable;
import org.apache.commons.math3.distribution.BinomialDistribution;
import org.apache.commons.math3.random.MersenneTwister;
import org.apache.commons.math3.random.RandomGenerator;
import org.biojava.bio.program.fastq.Fastq;
import org.biojava.bio.program.fastq.FastqWriter;
import org.biojava.bio.program.fastq.SangerFastqWriter;
import org.dishevelled.commandline.ArgumentList;
import org.dishevelled.commandline.CommandLine;
import org.dishevelled.commandline.CommandLineParseException;
import org.dishevelled.commandline.CommandLineParser;
import org.dishevelled.commandline.Switch;
import org.dishevelled.commandline.Usage;
import org.dishevelled.commandline.argument.DoubleArgument;
import org.dishevelled.commandline.argument.FileArgument;
import org.dishevelled.commandline.argument.IntegerArgument;
import org.nmdp.ngs.reads.paired.PairedEndAdapter;
import org.nmdp.ngs.reads.paired.PairedEndFastqReader;
/**
* Downsample sequences from a file in interleaved FASTQ format.
*/
public final class DownsampleInterleavedFastq implements Callable {
private final File inputFastqFile;
private final File outputFastqFile;
private final BinomialDistribution distribution;
private final FastqWriter fastqWriter = new SangerFastqWriter();
private static final String USAGE = "ngs-downsample-interleaved-fastq -p 0.5 [args]";
/**
* Downsample sequences from a file in interleaved FASTQ format.
*
* @param inputFastqFile input interleaved FASTQ file, if any
* @param outputFastqFile output interleaved FASTQ file, if any
* @param distribution binomial distribution, must not be null
*/
public DownsampleInterleavedFastq(final File inputFastqFile, final File outputFastqFile, final BinomialDistribution distribution) {
checkNotNull(distribution);
this.inputFastqFile = inputFastqFile;
this.outputFastqFile = outputFastqFile;
this.distribution = distribution;
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
PrintWriter writer = null;
try {
reader = reader(inputFastqFile);
writer = writer(outputFastqFile);
final PrintWriter w = writer;
PairedEndFastqReader.streamInterleaved(reader, new PairedEndAdapter() {
@Override
public void paired(final Fastq left, final Fastq right) {
if (distribution.sample() > 0) {
try {
fastqWriter.append(w, left);
fastqWriter.append(w, right);
}
catch (IOException e) {
throw new RuntimeException("could not write FASTQ", e);
}
}
}
});
return 0;
}
finally {
try {
reader.close();
}
catch (Exception e) {
// ignore
}
try {
writer.close();
}
catch (Exception e) {
// ignore
}
}
}
/**
* Main.
*
* @param args command line args
*/
public static void main(final String[] args) {
Switch about = new Switch("a", "about", "display about message");
Switch help = new Switch("h", "help", "display help message");
FileArgument inputFastqFile = new FileArgument("i", "input-fastq-file", "input interleaved FASTQ file, default stdin", false);
FileArgument outputFastqFile = new FileArgument("o", "output-fastq-file", "output interleaved FASTQ file, default stdout", false);
DoubleArgument probability = new DoubleArgument("p", "probability", "probability a FASTQ record will be removed, [0.0-1.0]", true);
IntegerArgument seed = new IntegerArgument("z", "seed", "random number seed, default relates to current time", false);
ArgumentList arguments = new ArgumentList(about, help, inputFastqFile, outputFastqFile, probability, seed);
CommandLine commandLine = new CommandLine(args);
DownsampleInterleavedFastq downsampleInterleavedFastq = null;
try
{
CommandLineParser.parse(commandLine, arguments);
if (about.wasFound()) {
About.about(System.out);
System.exit(0);
}
if (help.wasFound()) {
Usage.usage(USAGE, null, commandLine, arguments, System.out);
System.exit(0);
}
RandomGenerator random = seed.wasFound() ? new MersenneTwister(seed.getValue()) : new MersenneTwister();
BinomialDistribution distribution = new BinomialDistribution(random, 1, probability.getValue());
downsampleInterleavedFastq = new DownsampleInterleavedFastq(inputFastqFile.getValue(), outputFastqFile.getValue(), distribution);
}
catch (CommandLineParseException e) {
if (about.wasFound()) {
About.about(System.out);
System.exit(0);
}
if (help.wasFound()) {
Usage.usage(USAGE, null, commandLine, arguments, System.out);
System.exit(0);
}
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
catch (IllegalArgumentException e) {
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
try {
System.exit(downsampleInterleavedFastq.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}