org.dishevelled.bio.tools.SplitInterleavedFastq Maven / Gradle / Ivy
/*
dsh-bio-tools Command line tools.
Copyright (c) 2013-2022 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 com.google.common.io.Files;
import org.biojava.bio.program.fastq.Fastq;
import org.biojava.bio.program.fastq.FastqWriter;
import org.biojava.bio.program.fastq.SangerFastqWriter;
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.IntegerArgument;
import org.dishevelled.commandline.argument.LongArgument;
import org.dishevelled.commandline.argument.StringArgument;
import org.dishevelled.compress.Compress;
/**
* Split interleaved FASTQ files.
*
* @author Michael Heuer
*/
public final class SplitInterleavedFastq extends AbstractSplit {
private final FastqWriter fastqWriter = new SangerFastqWriter();
private static final String USAGE = "dsh-split-interleaved-fastq -r 100 -i foo.ifq.gz";
/**
* Split interleaved FASTQ files.
*
* @param inputFile input file, if any
* @param bytes split the input file at next pair of records after each n bytes, if any
* @param records split the input file after each n records, respecting pairs, if any
* @param prefix output file prefix, must not be null
* @param suffix output file suffix, must not be null
*/
public SplitInterleavedFastq(final File inputFile, final Long bytes, final Long records, final String prefix, final String suffix) {
this(inputFile, bytes, records, prefix, -1, suffix);
}
/**
* Split interleaved FASTQ files.
*
* @since 1.3.2
* @param inputFile input file, if any
* @param bytes split the input file at next pair of records after each n bytes, if any
* @param records split the input file after each n records, respecting pairs, 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 SplitInterleavedFastq(final File inputFile, final Long bytes, final Long records, final String prefix, final int leftPad, final String suffix) {
super(inputFile, bytes, records, prefix, leftPad, suffix);
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
try {
reader = reader(inputFile);
PairedEndFastqReader.streamInterleaved(reader, new PairedEndAdapter() {
private long r = 0L;
private int files = 0;
private CountingWriter writer;
@Override
public void paired(final Fastq left, final Fastq right) {
if (writer == null) {
writer = createCountingWriter(files);
}
try {
fastqWriter.append(writer, left);
fastqWriter.append(writer, right);
writer.flush();
}
catch (IOException e) {
// ignore
}
r += 2;
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 File file) {
String baseName = Files.getNameWithoutExtension(file.getName());
// trim trailing .ifq if present
return baseName.endsWith(".ifq") ? baseName.substring(0, baseName.length() - 4) : baseName;
}
static String getFileExtensions(final File file) {
String baseName = Files.getNameWithoutExtension(file.getName());
String extension = Files.getFileExtension(file.getName());
// add .ifq to extension if present
return baseName.endsWith(".ifq") ? ".ifq." + extension : "." + 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");
FileArgument inputFile = new FileArgument("i", "input-file", "input interleaved FASTQ file, default stdin", false);
StringArgument bytes = new StringArgument("b", "bytes", "split input file at next pair of records after each n bytes", false);
LongArgument records = new LongArgument("r", "records", "split input file after each n records, respecting pairs", 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. .ifq.gz", false);
ArgumentList arguments = new ArgumentList(about, help, inputFile, bytes, records, prefix, leftPad, suffix);
CommandLine commandLine = new CommandLine(args);
SplitInterleavedFastq splitInterleavedFastq = 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 (inputFile.wasFound()) {
p = getBaseName(inputFile.getValue());
}
else {
p = "x";
}
}
String s = suffix.getValue();
if (!suffix.wasFound()) {
if (inputFile.wasFound()) {
s = getFileExtensions(inputFile.getValue());
}
else {
if (Compress.isBgzfInputStream(System.in)) {
s = ".ifq.bgz";
}
else if (Compress.isGzipInputStream(System.in)) {
s = ".ifq.gz";
}
else if (Compress.isBzip2InputStream(System.in)) {
s = ".ifq.bz2";
}
else {
s = ".ifq";
}
}
}
splitInterleavedFastq = new SplitInterleavedFastq(inputFile.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(splitInterleavedFastq.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
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