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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.checkArgument;
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.util.Iterator;
import java.util.concurrent.Callable;
import org.biojava.bio.program.fastq.Fastq;
import org.biojava.bio.program.fastq.FastqBuilder;
import org.biojava.bio.program.fastq.FastqVariant;
import org.biojava.bio.program.fastq.FastqWriter;
import org.biojava.bio.program.fastq.SangerFastqWriter;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.io.SeqIOTools;
import org.biojava.bio.symbol.Symbol;
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.IntegerArgument;
/**
* Convert sequences in FASTA format to FASTQ format.
*/
@SuppressWarnings("deprecation")
public final class FastaToFastq implements Callable {
private final int quality;
private final File fastaFile;
private final File fastqFile;
public static final int DEFAULT_QUALITY = 40;
private static final String USAGE = "ngs-fasta-to-fastq [args]";
/**
* Convert sequences in FASTA format to FASTQ format.
*
* @param fastaFile input FASTA file, if any
* @param fastqFile output FASTQ file, if any
* @param quality quality, must be in the range [0..93]
*/
public FastaToFastq(final File fastaFile, final File fastqFile, final int quality) {
checkArgument((quality > -1) && (quality < 94), "quality must be in the range [0..93]");
this.quality = quality;
this.fastaFile = fastaFile;
this.fastqFile = fastqFile;
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
PrintWriter writer = null;
try {
reader = reader(fastaFile);
writer = writer(fastqFile);
FastqWriter fastqWriter = new SangerFastqWriter();
for (SequenceIterator sequences = SeqIOTools.readFastaDNA(reader); sequences.hasNext(); ) {
Sequence sequence = sequences.nextSequence();
StringBuilder seq = new StringBuilder();
StringBuilder qual = new StringBuilder();
for (Iterator i = sequence.iterator(); i.hasNext(); ) {
Symbol symbol = i.next();
seq.append(DNATools.dnaToken(symbol));
qual.append(FastqVariant.FASTQ_SANGER.quality(quality));
}
Fastq fastq = new FastqBuilder()
.withVariant(FastqVariant.FASTQ_SANGER)
.withDescription(sequence.getName())
.withSequence(seq.toString())
.withQuality(qual.toString())
.build();
fastqWriter.append(writer, fastq);
}
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 fastaFile = new FileArgument("i", "input-fasta-file", "input FASTA file, default stdin", false);
FileArgument fastqFile = new FileArgument("o", "output-fastq-file", "output FASTQ file, default stdout", false);
IntegerArgument quality = new IntegerArgument("q", "quality", "quality score for FASTQ, [0..93], default " + DEFAULT_QUALITY, false);
ArgumentList arguments = new ArgumentList(about, help, fastaFile, fastqFile, quality);
CommandLine commandLine = new CommandLine(args);
FastaToFastq fastaToFastq = 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);
}
fastaToFastq = new FastaToFastq(fastaFile.getValue(), fastqFile.getValue(), quality.getValue(DEFAULT_QUALITY));
}
catch (CommandLineParseException e) {
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
try {
System.exit(fastaToFastq.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}