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/*
dsh-bio-tools Command line tools.
Copyright (c) 2013-2024 held jointly by the individual authors.
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.fsf.org/licensing/licenses/lgpl.html
> http://www.opensource.org/licenses/lgpl-license.php
*/
package org.dishevelled.bio.tools;
import static com.google.common.base.Preconditions.checkNotNull;
import static org.dishevelled.bio.read.PairedEndFastqReader.isLeft;
import static org.dishevelled.bio.read.PairedEndFastqReader.isRight;
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.nio.file.Path;
import java.util.concurrent.Callable;
import org.biojava.bio.program.fastq.Fastq;
import org.biojava.bio.program.fastq.FastqWriter;
import org.biojava.bio.program.fastq.SangerFastqReader;
import org.biojava.bio.program.fastq.SangerFastqWriter;
import org.biojava.bio.program.fastq.StreamListener;
import org.dishevelled.bio.read.PairedEndAdapter;
import org.dishevelled.bio.read.PairedEndFastqReader;
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.FileArgument;
import org.dishevelled.commandline.argument.PathArgument;
/**
* Convert interleaved FASTQ format into first and second DNA sequence files in FASTQ format.
*
* @author Michael Heuer
*/
public final class DisinterleaveFastq implements Callable {
private final Path pairedPath;
private final Path unpairedPath;
private final File firstFastqFile;
private final File secondFastqFile;
private static final String USAGE = "dsh-disinterleave-fastq -p foo.paired.fq.gz [-u foo.unpaired.fq.gz] -1 foo_1.fq.gz -2 foo_2.fq.gz";
/**
* Convert interleaved FASTQ format into first and second DNA sequence files in FASTQ format.
*
* @deprecated will be removed in version 3.0
* @param pairedFile input interleaved paired FASTQ file, must not be null
* @param unpairedFile input unpaired FASTQ file, if any
* @param firstFastqFile first FASTQ output file, must not be null
* @param secondFastqFile second FASTQ output file, must not be null
*/
public DisinterleaveFastq(final File pairedFile, final File unpairedFile, final File firstFastqFile, final File secondFastqFile) {
this(pairedFile == null ? null : pairedFile.toPath(),
unpairedFile == null ? null : unpairedFile.toPath(),
firstFastqFile,
secondFastqFile);
}
/**
* Convert interleaved FASTQ format into first and second DNA sequence files in FASTQ format.
*
* @since 2.1
* @param pairedPath input interleaved paired FASTQ path, must not be null
* @param unpairedPath input unpaired FASTQ file, if any
* @param firstFastqFile first FASTQ output file, must not be null
* @param secondFastqFile second FASTQ output file, must not be null
*/
public DisinterleaveFastq(final Path pairedPath, final Path unpairedPath, final File firstFastqFile, final File secondFastqFile) {
checkNotNull(pairedPath);
checkNotNull(firstFastqFile);
checkNotNull(secondFastqFile);
this.pairedPath = pairedPath;
this.unpairedPath = unpairedPath;
this.firstFastqFile = firstFastqFile;
this.secondFastqFile = secondFastqFile;
}
@Override
public Integer call() throws Exception {
BufferedReader pairedReader = null;
BufferedReader unpairedReader = null;
PrintWriter firstWriter = null;
PrintWriter secondWriter = null;
try {
pairedReader = reader(pairedPath);
firstWriter = writer(firstFastqFile);
secondWriter = writer(secondFastqFile);
final PrintWriter fw = firstWriter;
final PrintWriter sw = secondWriter;
final FastqWriter firstFastqWriter = new SangerFastqWriter();
final FastqWriter secondFastqWriter = new SangerFastqWriter();
PairedEndFastqReader.streamInterleaved(pairedReader, new PairedEndAdapter() {
@Override
public void paired(final Fastq left, final Fastq right) {
try {
firstFastqWriter.append(fw, left);
secondFastqWriter.append(sw, right);
}
catch (IOException e) {
throw new RuntimeException("could not write paired end reads", e);
}
}
@Override
public void unpaired(final Fastq unpaired) {
throw new IllegalArgumentException("interleaved paired file contained unpaired read " + unpaired.getDescription());
}
});
if (unpairedPath != null) {
unpairedReader = reader(unpairedPath);
new SangerFastqReader().stream(unpairedReader, new StreamListener() {
@Override
public void fastq(final Fastq fastq) {
try {
if (isLeft(fastq)) {
firstFastqWriter.append(fw, fastq);
}
else if (isRight(fastq)) {
secondFastqWriter.append(sw, fastq);
}
}
catch (IOException e) {
throw new RuntimeException("could not write unpaired read", e);
}
}
});
}
return 0;
}
finally {
try {
pairedReader.close();
}
catch (Exception e) {
// ignore
}
try {
unpairedReader.close();
}
catch (Exception e) {
// ignore
}
try {
firstWriter.close();
}
catch (Exception e) {
// ignore
}
try {
secondWriter.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");
PathArgument pairedPath = new PathArgument("p", "paired-path", "interleaved paired FASTQ input path", true);
PathArgument unpairedPath = new PathArgument("u", "unpaired-path", "unpaired FASTQ input path", false);
FileArgument firstFastqFile = new FileArgument("1", "first-fastq-file", "first FASTQ output file", true);
FileArgument secondFastqFile = new FileArgument("2", "second-fastq-file", "second FASTQ output file", true);
ArgumentList arguments = new ArgumentList(about, help, pairedPath, unpairedPath, firstFastqFile, secondFastqFile);
CommandLine commandLine = new CommandLine(args);
DisinterleaveFastq disinterleaveFastq = 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);
}
disinterleaveFastq = new DisinterleaveFastq(pairedPath.getValue(), unpairedPath.getValue(), firstFastqFile.getValue(), secondFastqFile.getValue());
}
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);
}
try {
System.exit(disinterleaveFastq.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
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