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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 static org.dishevelled.compress.Writers.writer;
import java.io.BufferedReader;
import java.io.File;
import java.io.PrintWriter;
import java.nio.file.Path;
import java.util.concurrent.Callable;
import java.util.regex.Pattern;
import org.dishevelled.bio.feature.gff3.Gff3Listener;
import org.dishevelled.bio.feature.gff3.Gff3Reader;
import org.dishevelled.bio.feature.gff3.Gff3Record;
import org.dishevelled.bio.feature.gff3.Gff3Writer;
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.PathArgument;
/**
* Rename references in GFF3 files.
*
* @deprecated by RenameGff3References in version 2.1, to be removed in 3.0
* @author Michael Heuer
*/
public final class RenameReferences implements Callable {
private final boolean chr;
private final Path inputGff3Path;
private final File outputGff3File;
private static final String USAGE = "dsh-rename-references [--chr] -i input.gff3.gz -o output.gff3.gz";
/**
* Rename references in GFF3 files.
*
* @param chr true to add "chr" to chromosome names
* @param inputGff3File input GFF3 file, if any
* @param outputGff3File output GFF3 file, if any
*/
public RenameReferences(final boolean chr, final File inputGff3File, final File outputGff3File) {
this(chr, inputGff3File == null ? null : inputGff3File.toPath(), outputGff3File);
}
/**
* Rename references in GFF3 files.
*
* @since 2.1
* @param chr true to add "chr" to chromosome names
* @param inputGff3Path input GFF3 path, if any
* @param outputGff3File output GFF3 file, if any
*/
public RenameReferences(final boolean chr, final Path inputGff3Path, final File outputGff3File) {
this.chr = chr;
this.inputGff3Path = inputGff3Path;
this.outputGff3File = outputGff3File;
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
PrintWriter writer = null;
try {
reader = reader(inputGff3Path);
writer = writer(outputGff3File);
final PrintWriter w = writer;
Gff3Reader.stream(reader, new Gff3Listener() {
@Override
public boolean record(final Gff3Record record) {
Gff3Record renamed = new Gff3Record(rename(record.getSeqid()),
record.getSource(),
record.getFeatureType(),
record.getStart(),
record.getEnd(),
record.getScore(),
record.getStrand(),
record.getPhase(),
record.getAttributes());
Gff3Writer.write(renamed, w);
return true;
}
});
return 0;
}
finally {
try {
reader.close();
}
catch (Exception e) {
// empty
}
try {
writer.close();
}
catch (Exception e) {
// empty
}
}
}
private static final Pattern AUTOSOMAL = Pattern.compile("^([0-9]+)$");
private static final Pattern SEX = Pattern.compile("^([XYZW])$");
private static final Pattern MITOCHONDRIAL = Pattern.compile("^[chrM,MT]$");
private static final Pattern CHR = Pattern.compile("^chr(.+)$");
private static final Pattern CHRUN_ = Pattern.compile("^chrUn_(.+)$");
private static final Pattern V = Pattern.compile("([0-9]+)v([0-9]+)");
static String addChr(final String seqid) {
String result = seqid;
// 1 --> chr1
result = AUTOSOMAL.matcher(result).replaceAll("chr$1");
// X --> chrX
result = SEX.matcher(result).replaceAll("chr$1");
// MT --> chrM
result = MITOCHONDRIAL.matcher(result).replaceAll("chrM");
return result;
}
static String removeChr(final String seqid) {
String result = seqid;
// 123v1 --> 123.1
result = V.matcher(result).replaceAll("$1.$2");
// chrUn_GL00 --> GL00
result = CHRUN_.matcher(result).replaceAll("$1");
// chrM --> MT
result = MITOCHONDRIAL.matcher(result).replaceAll("MT");
// chr1 --> 1
result = CHR.matcher(result).replaceAll("$1");
return result;
}
String rename(final String seqid) {
return chr ? addChr(seqid) : removeChr(seqid);
}
/**
* 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");
Switch chr = new Switch("c", "chr", "add \"chr\" to chromosome names");
PathArgument inputGff3Path = new PathArgument("i", "input-gff3-path", "input GFF3 path, default stdin", false);
FileArgument outputGff3File = new FileArgument("o", "output-gff3-file", "output GFF3 file, default stdout", false);
ArgumentList arguments = new ArgumentList(about, help, chr, inputGff3Path, outputGff3File);
CommandLine commandLine = new CommandLine(args);
RenameReferences renameReferences = 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);
}
renameReferences = new RenameReferences(chr.wasFound(), inputGff3Path.getValue(), outputGff3File.getValue());
}
catch (CommandLineParseException 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);
}
catch (NullPointerException | IllegalArgumentException e) {
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
try {
System.exit(renameReferences.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
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