org.dishevelled.bio.tools.RenameBedReferences Maven / Gradle / Ivy
The newest version!
/*
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 org.dishevelled.bio.feature.bed.BedListener;
import org.dishevelled.bio.feature.bed.BedReader;
import org.dishevelled.bio.feature.bed.BedRecord;
import org.dishevelled.bio.feature.bed.BedWriter;
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 BED files.
*
* @since 2.1
* @author Michael Heuer
*/
public final class RenameBedReferences extends AbstractRenameReferences {
private static final String USAGE = "dsh-rename-bed-references [--chr] -i input.bed.gz -o output.bed.gz";
/**
* Rename references in BED files.
*
* @deprecated will be removed in version 3.0
* @param chr true to add "chr" to chromosome names
* @param inputBedFile input BED file, if any
* @param outputBedFile output BED file, if any
*/
public RenameBedReferences(final boolean chr, final File inputBedFile, final File outputBedFile) {
this(chr, inputBedFile == null ? null : inputBedFile.toPath(), outputBedFile);
}
/**
* Rename references in BED files.
*
* @since 2.1
* @param chr true to add "chr" to chromosome names
* @param inputBedPath input BED path, if any
* @param outputBedFile output BED file, if any
*/
public RenameBedReferences(final boolean chr, final Path inputBedPath, final File outputBedFile) {
super(chr, inputBedPath, outputBedFile);
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
PrintWriter writer = null;
try {
reader = reader(inputPath);
writer = writer(outputFile);
final PrintWriter w = writer;
BedReader.stream(reader, new BedListener() {
@Override
public boolean record(final BedRecord record) {
BedRecord renamed = null;
switch (record.getFormat()) {
case BED3:
renamed = new BedRecord(rename(record.getChrom()),
record.getStart(),
record.getEnd());
break;
case BED4:
renamed = new BedRecord(rename(record.getChrom()),
record.getStart(),
record.getEnd(),
record.getName());
break;
case BED5:
renamed = new BedRecord(rename(record.getChrom()),
record.getStart(),
record.getEnd(),
record.getName(),
record.getScore());
break;
case BED6:
renamed = new BedRecord(rename(record.getChrom()),
record.getStart(),
record.getEnd(),
record.getName(),
record.getScore(),
record.getStrand());
break;
case BED12:
renamed = new BedRecord(rename(record.getChrom()),
record.getStart(),
record.getEnd(),
record.getName(),
record.getScore(),
record.getStrand(),
record.getThickStart(),
record.getThickEnd(),
record.getItemRgb(),
record.getBlockCount(),
record.getBlockSizes(),
record.getBlockStarts());
break;
default:
break;
}
if (renamed != null) {
BedWriter.write(renamed, w);
}
return true;
}
});
return 0;
}
finally {
try {
reader.close();
}
catch (Exception e) {
// empty
}
try {
writer.close();
}
catch (Exception e) {
// empty
}
}
}
/**
* 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 reference names");
PathArgument inputBedPath = new PathArgument("i", "input-bed-path", "input BED path, default stdin", false);
FileArgument outputBedFile = new FileArgument("o", "output-bed-file", "output BED file, default stdout", false);
ArgumentList arguments = new ArgumentList(about, help, chr, inputBedPath, outputBedFile);
CommandLine commandLine = new CommandLine(args);
RenameBedReferences renameBedReferences = 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);
}
renameBedReferences = new RenameBedReferences(chr.wasFound(), inputBedPath.getValue(), outputBedFile.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(renameBedReferences.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy