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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.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.FileArgument;
import org.nmdp.ngs.reads.paired.PairedEndAdapter;
import org.nmdp.ngs.reads.paired.PairedEndFastqReader;
/**
* Convert first and second sequence files in FASTQ format to interleaved FASTQ format.
*/
public final class InterleaveFastq implements Callable {
private final File firstFastqFile;
private final File secondFastqFile;
private final File pairedFile;
private final File unpairedFile;
private static final String USAGE = "ngs-interleave-fastq -1 foo_1.fq.gz -2 foo_2.fq.gz --paired foo.paired.fq.gz --unpaired foo.unpaired.fq.gz";
/**
* Convert first and second sequence files in FASTQ format to interleaved FASTQ format.
*
* @param firstFastqFile first FASTQ input file, must not be null
* @param secondFastqFile second FASTQ input file, must not be null
* @param pairedFile output interleaved paired FASTQ file, must not be null
* @param unpairedFile output unpaired FASTQ file, must not be null
*/
public InterleaveFastq(final File firstFastqFile, final File secondFastqFile, final File pairedFile, final File unpairedFile) {
checkNotNull(firstFastqFile);
checkNotNull(secondFastqFile);
checkNotNull(pairedFile);
checkNotNull(unpairedFile);
this.firstFastqFile = firstFastqFile;
this.secondFastqFile = secondFastqFile;
this.pairedFile = pairedFile;
this.unpairedFile = unpairedFile;
}
@Override
public Integer call() throws Exception {
BufferedReader firstReader = null;
BufferedReader secondReader = null;
PrintWriter pairedWriter = null;
PrintWriter unpairedWriter = null;
try {
firstReader = reader(firstFastqFile);
secondReader = reader(secondFastqFile);
pairedWriter = writer(pairedFile);
unpairedWriter = writer(unpairedFile);
final PrintWriter pw = pairedWriter;
final PrintWriter uw = unpairedWriter;
final FastqWriter pairedFastqWriter = new SangerFastqWriter();
final FastqWriter unpairedFastqWriter = new SangerFastqWriter();
PairedEndFastqReader.streamPaired(firstReader, secondReader, new PairedEndAdapter() {
@Override
public void paired(final Fastq left, final Fastq right) {
try {
pairedFastqWriter.append(pw, left);
pairedFastqWriter.append(pw, right);
}
catch (IOException e) {
throw new RuntimeException("could not write paired end reads", e);
}
}
@Override
public void unpaired(final Fastq unpaired) {
try {
unpairedFastqWriter.append(uw, unpaired);
}
catch (IOException e) {
throw new RuntimeException("could not write unpaired read", e);
}
}
});
return 0;
}
finally {
try {
firstReader.close();
}
catch (Exception e) {
// ignore
}
try {
secondReader.close();
}
catch (Exception e) {
// ignore
}
try {
pairedWriter.close();
}
catch (Exception e) {
// ignore
}
try {
unpairedWriter.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 firstFastqFile = new FileArgument("1", "first-fastq-file", "first FASTQ input file", true);
FileArgument secondFastqFile = new FileArgument("2", "second-fastq-file", "second FASTQ input file", true);
FileArgument pairedFile = new FileArgument("p", "paired-file", "output interleaved paired FASTQ file", true);
FileArgument unpairedFile = new FileArgument("u", "unpaired-file", "output unpaired FASTQ file", true);
ArgumentList arguments = new ArgumentList(about, help, firstFastqFile, secondFastqFile, pairedFile, unpairedFile);
CommandLine commandLine = new CommandLine(args);
InterleaveFastq interleaveFastq = 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);
}
interleaveFastq = new InterleaveFastq(firstFastqFile.getValue(), secondFastqFile.getValue(), pairedFile.getValue(), unpairedFile.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(interleaveFastq.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}