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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.io.PrintWriter;
import java.nio.file.Path;
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.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 FASTA files.
*
* @author Michael Heuer
*/
@SuppressWarnings("deprecation")
public final class SplitFasta extends AbstractSplit {
private final String alphabet;
private final int lineWidth;
static final String DEFAULT_ALPHABET = "dna";
static final int DEFAULT_LINE_WIDTH = 70;
static final String DESCRIPTION_LINE = "description_line";
private static final String USAGE = "dsh-split-fasta -r 100 -i foo.fa.gz";
/**
* Split FASTA 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
* @param lineWidth line width
*/
public SplitFasta(final File inputFile,
final Long bytes,
final Long records,
final String prefix,
final String suffix,
final int lineWidth) {
this(inputFile == null ? null : inputFile.toPath(),
bytes,
records,
prefix,
suffix,
lineWidth);
}
/**
* Split FASTA 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
* @param lineWidth line width
*/
public SplitFasta(final Path inputPath,
final Long bytes,
final Long records,
final String prefix,
final String suffix,
final int lineWidth) {
this(inputPath, DEFAULT_ALPHABET, bytes, records, prefix, -1, suffix, lineWidth);
}
/**
* Split FASTA 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
* @param lineWidth line width
*/
public SplitFasta(final File inputFile,
final Long bytes,
final Long records,
final String prefix,
final int leftPad,
final String suffix,
final int lineWidth) {
this(inputFile == null ? null : inputFile.toPath(),
bytes,
records,
prefix,
leftPad,
suffix,
lineWidth);
}
/**
* Split FASTA 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
* @param lineWidth line width
*/
public SplitFasta(final Path inputPath,
final Long bytes,
final Long records,
final String prefix,
final int leftPad,
final String suffix,
final int lineWidth) {
this(inputPath, DEFAULT_ALPHABET, bytes, records, prefix, leftPad, suffix, lineWidth);
}
/**
* Split FASTA files.
*
* @since 2.0
* @param inputFile input file, if any
* @param alphabet input file alphabet { dna, protein }, 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
* @param lineWidth line width
*/
public SplitFasta(final File inputFile,
final String alphabet,
final Long bytes,
final Long records,
final String prefix,
final int leftPad,
final String suffix,
final int lineWidth) {
this(inputFile == null ? null : inputFile.toPath(),
alphabet,
bytes,
records,
prefix,
leftPad,
suffix,
lineWidth);
}
/**
* Split FASTA files.
*
* @since 2.1
* @param inputPath input path, if any
* @param alphabet input path alphabet { dna, protein }, 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
* @param lineWidth line width
*/
public SplitFasta(final Path inputPath,
final String alphabet,
final Long bytes,
final Long records,
final String prefix,
final int leftPad,
final String suffix,
final int lineWidth) {
super(inputPath, bytes, records, prefix, leftPad, suffix);
this.lineWidth = lineWidth;
this.alphabet = alphabet;
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
try {
reader = reader(inputPath);
long r = 0L;
int files = 0;
CountingWriter writer = null;
for (SequenceIterator sequences = isProteinAlphabet() ? SeqIOTools.readFastaProtein(reader) : SeqIOTools.readFastaDNA(reader); sequences.hasNext(); ) {
Sequence sequence = sequences.nextSequence();
if (writer == null) {
writer = createCountingWriter(files);
}
try {
writeSequence(sequence, lineWidth, writer.asPrintWriter());
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();
}
}
boolean isProteinAlphabet() {
return alphabet != null && (alphabet.equalsIgnoreCase("protein") || alphabet.equalsIgnoreCase("aa"));
}
// copied with mods from biojava-legacy FastaFormat, as it uses PrintStream not PrintWriter
static String describeSequence(final Sequence sequence) {
return sequence.getAnnotation().containsProperty(DESCRIPTION_LINE) ?
(String) sequence.getAnnotation().getProperty(DESCRIPTION_LINE) : sequence.getName();
}
static void writeSequence(final Sequence sequence, final int lineWidth, final PrintWriter writer) {
writer.print(">");
writer.println(describeSequence(sequence));
for (int i = 1, length = sequence.length(); i <= length; i += lineWidth) {
writer.println(sequence.subStr(i, Math.min(i + lineWidth - 1, length)));
}
}
static String getBaseName(final Path path) {
String baseName = getNameWithoutExtension(path);
// trim trailing .fa or .fasta if present after trimming compression extension
if (baseName.endsWith(".fa")) {
return baseName.substring(0, baseName.length() - 3);
}
else if (baseName.endsWith(".fasta")) {
return baseName.substring(0, baseName.length() - 6);
}
return baseName;
}
static String getFileExtensions(final Path path) {
String baseName = getNameWithoutExtension(path);
String extension = getFileExtension(path);
// add .fa or .fasta to extension if present
if (baseName.endsWith(".fa")) {
return ".fa." + extension;
}
else if (baseName.endsWith(".fasta")) {
return ".fasta." + 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 FASTA path, default stdin", false);
StringArgument alphabet = new StringArgument("e", "alphabet", "input FASTA alphabet { dna, protein }, default dna", 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. .fa.gz", false);
IntegerArgument lineWidth = new IntegerArgument("w", "line-width", "line width, default " + DEFAULT_LINE_WIDTH, false);
ArgumentList arguments = new ArgumentList(about, help, inputPath, alphabet, bytes, records, prefix, leftPad, suffix, lineWidth);
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);
}
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 = ".fa.bgz";
}
else if (Compress.isGzipInputStream(System.in)) {
s = ".fa.gz";
}
else if (Compress.isBzip2InputStream(System.in)) {
s = ".fa.bz2";
}
else {
s = ".fa";
}
}
}
splitFasta = new SplitFasta(inputPath.getValue(), alphabet.getValue(DEFAULT_ALPHABET), b, records.getValue(), p, leftPad.getValue(-1), s, lineWidth.getValue(DEFAULT_LINE_WIDTH));
}
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(splitFasta.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
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