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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 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.nio.file.Paths;
import java.util.concurrent.Callable;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.io.SeqIOTools;
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.StringArgument;
/**
* Split sequences in FASTA format and write to separate files in FASTA format.
*/
@SuppressWarnings("deprecation")
public final class SplitFasta implements Callable {
private final File fastaFile;
private final String outputFilePrefix;
private final String outputFileExtension;
private final File outputDirectory;
private static final int LINE_WIDTH = 60;
private static final String DEFAULT_OUTPUT_FILE_PREFIX = "";
private static final String DEFAULT_OUTPUT_FILE_EXTENSION = "fq.gz";
private static final File DEFAULT_OUTPUT_DIRECTORY = Paths.get(".").toFile();
private static final String USAGE = "ngs-split-fasta [args]";
/**
* Split sequences in FASTA format and write to separate files in FASTA format.
*
* @param fastaFile input FASTA file, if any
* @param outputFilePrefix output file prefix, must not be null
* @param outputFileExtension output file extension, must not be null
* @param outputDirectory output directory, must not be null
*/
public SplitFasta(final File fastaFile, final String outputFilePrefix, final String outputFileExtension, final File outputDirectory) {
checkNotNull(outputFilePrefix);
checkNotNull(outputFileExtension);
checkNotNull(outputDirectory);
this.fastaFile = fastaFile;
this.outputFilePrefix = outputFilePrefix;
this.outputFileExtension = outputFileExtension;
this.outputDirectory = outputDirectory;
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
try {
reader = reader(fastaFile);
for (SequenceIterator sequences = SeqIOTools.readFastaDNA(reader); sequences.hasNext(); ) {
Sequence sequence = sequences.nextSequence();
PrintWriter writer = null;
try {
// special case for IMGT/HLA _gen.fasta reference sequences; remove HLA: from HLA:HLA00001
String accession = sequence.getName().replace("HLA:", "");
writer = writer(new File(outputDirectory, outputFilePrefix + accession + "." + outputFileExtension));
// adapted from biojava FastaFormat since using Writer requires bending over backward
writer.print(">");
writer.println(describeSequence(sequence));
int length = sequence.length();
for (int position = 1; position < length; position += LINE_WIDTH) {
int end = Math.min(position + LINE_WIDTH - 1, length);
writer.println(sequence.subStr(position, end));
}
}
finally {
try {
writer.close();
}
catch (Exception e) {
// ignore
}
}
}
return 0;
}
finally {
try {
reader.close();
}
catch (Exception e) {
// ignore
}
}
}
private static String describeSequence(final Sequence sequence) {
return (sequence.getAnnotation().containsProperty("description_line")) ? (String) sequence.getAnnotation().getProperty("description_line") : sequence.getName();
}
/**
* 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", "fasta-file", "input FASTA file, default stdin", false);
StringArgument outputFilePrefix = new StringArgument("p", "output-file-prefix", "output file prefix, default \"\"", false);
StringArgument outputFileExtension = new StringArgument("x", "output-file-extension", "output file extension, default " + DEFAULT_OUTPUT_FILE_EXTENSION, false);
FileArgument outputDirectory = new FileArgument("d", "output-directory", "output directory, default .", false);
ArgumentList arguments = new ArgumentList(about, help, fastaFile, outputFilePrefix, outputFileExtension, outputDirectory);
CommandLine commandLine = new CommandLine(args);
SplitFasta splitFasta = 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);
}
splitFasta = new SplitFasta(fastaFile.getValue(), outputFilePrefix.getValue(DEFAULT_OUTPUT_FILE_PREFIX), outputFileExtension.getValue(DEFAULT_OUTPUT_FILE_EXTENSION), outputDirectory.getValue(DEFAULT_OUTPUT_DIRECTORY));
}
catch (CommandLineParseException e) {
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
try {
System.exit(splitFasta.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}