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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 org.dishevelled.compress.Readers.reader;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.nio.file.Path;
import org.biojava.bio.program.fastq.Fastq;
import org.biojava.bio.program.fastq.FastqReader;
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.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.IntegerArgument;
import org.dishevelled.commandline.argument.LongArgument;
import org.dishevelled.commandline.argument.PathArgument;
import org.dishevelled.commandline.argument.StringArgument;
import org.dishevelled.compress.Compress;
/**
* Split FASTQ files.
*
* @author Michael Heuer
*/
public final class SplitFastq extends AbstractSplit {
private final FastqReader fastqReader = new SangerFastqReader();
private final FastqWriter fastqWriter = new SangerFastqWriter();
private static final String USAGE = "dsh-split-fastq -r 100 -i foo.fq.gz";
/**
* Split FASTQ files.
*
* @deprecated will be removed in version 3.0
* @param inputFile input file, if any
* @param bytes split the input file at next record after each n bytes, if any
* @param records split the input file after each n records, if any
* @param prefix output file prefix, must not be null
* @param suffix output file suffix, must not be null
*/
public SplitFastq(final File inputFile, final Long bytes, final Long records, final String prefix, final String suffix) {
this(inputFile == null ? null : inputFile.toPath(),
bytes,
records,
prefix,
suffix);
}
/**
* Split FASTQ files.
*
* @since 2.1
* @param inputPath input path, if any
* @param bytes split the input path at next record after each n bytes, if any
* @param records split the input path after each n records, if any
* @param prefix output file prefix, must not be null
* @param suffix output file suffix, must not be null
*/
public SplitFastq(final Path inputPath, final Long bytes, final Long records, final String prefix, final String suffix) {
this(inputPath, bytes, records, prefix, -1, suffix);
}
/**
* Split FASTQ files.
*
* @since 1.3.2
* @deprecated will be removed in version 3.0
* @param inputFile input file, if any
* @param bytes split the input file at next record after each n bytes, if any
* @param records split the input file after each n records, if any
* @param prefix output file prefix, must not be null
* @param leftPad left pad split index in output file name
* @param suffix output file suffix, must not be null
*/
public SplitFastq(final File inputFile, final Long bytes, final Long records, final String prefix, final int leftPad, final String suffix) {
this(inputFile == null ? null : inputFile.toPath(),
bytes,
records,
prefix,
leftPad,
suffix);
}
/**
* Split FASTQ files.
*
* @since 2.1
* @param inputPath input path, if any
* @param bytes split the input path at next record after each n bytes, if any
* @param records split the input path after each n records, if any
* @param prefix output file prefix, must not be null
* @param leftPad left pad split index in output file name
* @param suffix output file suffix, must not be null
*/
public SplitFastq(final Path inputPath, final Long bytes, final Long records, final String prefix, final int leftPad, final String suffix) {
super(inputPath, bytes, records, prefix, leftPad, suffix);
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
try {
reader = reader(inputPath);
fastqReader.stream(reader, new StreamListener() {
private long r = 0L;
private int files = 0;
private CountingWriter writer;
@Override
public void fastq(final Fastq fastq) {
if (writer == null) {
writer = createCountingWriter(files);
}
try {
fastqWriter.append(writer, fastq);
writer.flush();
}
catch (IOException e) {
// ignore
}
r++;
if (r >= records || writer.getCount() >= bytes) {
r = 0L;
files++;
try {
writer.close();
}
catch (Exception e) {
// ignore
}
finally {
writer = null;
}
}
}
});
return 0;
}
finally {
try {
reader.close();
}
catch (Exception e) {
// ignore
}
closeWriters();
}
}
static String getBaseName(final Path path) {
String baseName = getNameWithoutExtension(path);
// trim trailing .fq or .fastq if present after trimming compression extension
if (baseName.endsWith(".fq")) {
return baseName.substring(0, baseName.length() - 3);
}
else if (baseName.endsWith(".fastq")) {
return baseName.substring(0, baseName.length() - 6);
}
return baseName;
}
static String getFileExtensions(final Path path) {
String baseName = getNameWithoutExtension(path);
String extension = getFileExtension(path);
// add .fq or .fastq to extension if present
if (baseName.endsWith(".fq")) {
return ".fq." + extension;
}
else if (baseName.endsWith(".fastq")) {
return ".fastq." + extension;
}
return extension;
}
/**
* 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 inputPath = new PathArgument("i", "input-path", "input FASTQ path, default stdin", false);
StringArgument bytes = new StringArgument("b", "bytes", "split input path at next record after each n bytes", false);
LongArgument records = new LongArgument("r", "records", "split input path after each n records", false);
StringArgument prefix = new StringArgument("p", "prefix", "output file prefix", false);
IntegerArgument leftPad = new IntegerArgument("d", "left-pad", "left pad split index in output file name", false);
StringArgument suffix = new StringArgument("s", "suffix", "output file suffix, e.g. .fq.gz", false);
ArgumentList arguments = new ArgumentList(about, help, inputPath, bytes, records, prefix, leftPad, suffix);
CommandLine commandLine = new CommandLine(args);
SplitFastq splitFastq = 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);
}
Long b = bytes.wasFound() ? toBytes(bytes.getValue()) : null;
String p = prefix.getValue();
if (!prefix.wasFound()) {
if (inputPath.wasFound()) {
p = getBaseName(inputPath.getValue());
}
else {
p = "x";
}
}
String s = suffix.getValue();
if (!suffix.wasFound()) {
if (inputPath.wasFound()) {
s = getFileExtensions(inputPath.getValue());
}
else {
if (Compress.isBgzfInputStream(System.in)) {
s = ".fq.bgz";
}
else if (Compress.isGzipInputStream(System.in)) {
s = ".fq.gz";
}
else if (Compress.isBzip2InputStream(System.in)) {
s = ".fq.bz2";
}
else {
s = ".fq";
}
}
}
splitFastq = new SplitFastq(inputPath.getValue(), b, records.getValue(), p, leftPad.getValue(-1), s);
}
catch (CommandLineParseException | NullPointerException 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(splitFastq.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
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