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Next generation sequencing (NGS/HTS) command line tools.
/*
ngs-tools Next generation sequencing (NGS/HTS) command line tools.
Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
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.gnu.org/licenses/lgpl.html
*/
package org.nmdp.ngs.tools;
import static com.google.common.base.Preconditions.checkNotNull;
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.io.IOException;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.Callable;
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.nmdp.ngs.align.BedListener;
import org.nmdp.ngs.align.BedReader;
import org.nmdp.ngs.align.BedRecord;
import org.nmdp.ngs.align.BedWriter;
/**
* Liftover BED file.
*/
public final class LiftoverBed implements Callable {
private final File refBedFile;
private final File sourceBedFile;
private final File targetBedFile;
private static final String USAGE = "ngs-liftover-bed -r ref.bed.gz [args]";
/**
* Liftover BED file.
*
* @param refBedFile reference BED file, must not be null
* @param sourceBedFile source BED file, if any
* @param targetBedFile target BED file, if any
*/
public LiftoverBed(final File refBedFile, final File sourceBedFile, final File targetBedFile) {
checkNotNull(refBedFile);
this.refBedFile = refBedFile;
this.sourceBedFile = sourceBedFile;
this.targetBedFile = targetBedFile;
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
PrintWriter writer = null;
try {
reader = reader(sourceBedFile);
writer = writer(targetBedFile);
final PrintWriter w = writer;
final Map ref = readRefFile();
BedReader.stream(reader, new BedListener() {
@Override
public boolean record(final BedRecord source) {
BedRecord target = ref.get(source.chrom());
if (target != null) {
BedRecord lifted = new BedRecord(target.chrom(),
target.start() + source.start(),
target.start() + source.start() + (source.end() - source.start()),
source.name());
BedWriter.write(lifted, w);
}
return true;
}
});
return 0;
}
finally {
try {
reader.close();
}
catch (Exception e) {
// empty
}
try {
writer.close();
}
catch (Exception e) {
// empty
}
}
}
private Map readRefFile() throws IOException {
BufferedReader reader = null;
final Map ref = new HashMap(10000);
try {
reader = reader(refBedFile);
BedReader.stream(reader, new BedListener() {
@Override
public boolean record(final BedRecord rec) {
BedRecord prev = ref.put(rec.name(), rec);
if (prev != null) {
// warn non-unique mapping
}
return true;
}
});
}
finally {
try {
reader.close();
}
catch (Exception e) {
// empty
}
}
return ref;
}
/**
* 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 refBedFile = new FileArgument("r", "ref-bed-file", "reference BED file", true);
FileArgument sourceBedFile = new FileArgument("i", "source-bed-file", "input BED file, default stdin", false);
FileArgument targetBedFile = new FileArgument("o", "target-bed-file", "output BED file, default stdout", false);
ArgumentList arguments = new ArgumentList(about, help, refBedFile, sourceBedFile, targetBedFile);
CommandLine commandLine = new CommandLine(args);
LiftoverBed liftoverBed = 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);
}
liftoverBed = new LiftoverBed(refBedFile.getValue(), sourceBedFile.getValue(), targetBedFile.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);
}
try {
System.exit(liftoverBed.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}