org.dishevelled.bio.tools.Gfa1ToGfa2 Maven / Gradle / Ivy
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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.File;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.Callable;
import org.dishevelled.bio.annotation.Annotation;
import org.dishevelled.bio.assembly.gfa1.Containment;
import org.dishevelled.bio.assembly.gfa1.Gfa1Adapter;
import org.dishevelled.bio.assembly.gfa1.Gfa1Reader;
import org.dishevelled.bio.assembly.gfa1.Header;
import org.dishevelled.bio.assembly.gfa1.Link;
import org.dishevelled.bio.assembly.gfa1.Path;
import org.dishevelled.bio.assembly.gfa1.Segment;
import org.dishevelled.bio.assembly.gfa2.Alignment;
import org.dishevelled.bio.assembly.gfa2.Gfa2Writer;
import org.dishevelled.bio.assembly.gfa2.Position;
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;
/**
* Convert GFA 1.0 format to GFA 2.0 format.
*
* @author Michael Heuer
*/
public final class Gfa1ToGfa2 implements Callable {
private final java.nio.file.Path inputGfa1Path;
private final File outputGfa2File;
private static final String USAGE = "dsh-gfa1-to-gfa2 -i input.gfa1.gz -o output.gfa2.gz";
/**
* Convert GFA 1.0 format to GFA 2.0 format.
*
* @deprecated will be removed in version 3.0
* @param inputGfa1File input GFA 1.0 file, if any
* @param outputGfa2File output GFA 2.0 file, if any
*/
public Gfa1ToGfa2(final File inputGfa1File, final File outputGfa2File) {
this(inputGfa1File == null ? null : inputGfa1File.toPath(), outputGfa2File);
}
/**
* Convert GFA 1.0 format to GFA 2.0 format.
*
* @since 2.1
* @param inputGfa1Path input GFA 1.0 path, if any
* @param outputGfa2File output GFA 2.0 file, if any
*/
public Gfa1ToGfa2(final java.nio.file.Path inputGfa1Path, final File outputGfa2File) {
this.inputGfa1Path = inputGfa1Path;
this.outputGfa2File = outputGfa2File;
}
@Override
public Integer call() throws Exception {
PrintWriter writer = null;
try {
writer = writer(outputGfa2File);
final PrintWriter w = writer;
Gfa1Reader.stream(reader(inputGfa1Path), new Gfa1Adapter() {
@Override
public boolean header(final Header header) {
// convert VN:Z:1.0 to VN:Z:2.0 annotation if present
if (header.getAnnotations().containsKey("VN")) {
if (!"1.0".equals(header.getAnnotations().get("VN").getValue())) {
throw new RuntimeException("cannot convert input as GFA 1.0, was " + header.getAnnotations().get("VN").getValue());
}
Map annotations = new HashMap();
annotations.put("VN", new Annotation("VN", "Z", "2.0"));
for (Annotation annotation : header.getAnnotations().values()) {
if (!"VN".equals(annotation.getName())) {
annotations.put(annotation.getName(), annotation);
}
}
Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Header(annotations), w);
}
else {
Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Header(header.getAnnotations()), w);
}
return true;
}
@Override
public boolean segment(final Segment segment) {
if (segment.getSequence() != null) {
Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), segment.getSequence().length(), segment.getSequence(), segment.getAnnotations()), w);
}
else if (segment.getAnnotations().containsKey("LN")) {
Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), Integer.parseInt(segment.getAnnotations().get("LN").getValue()), segment.getSequence(), segment.getAnnotations()), w);
}
else {
Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), 0, segment.getSequence(), segment.getAnnotations()), w);
}
return true;
}
@Override
public boolean link(final Link link) {
Position unknown = new Position(0, false);
Alignment alignment = link.getOverlap() == null ? null : Alignment.valueOf(link.getOverlap());
Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Edge(null, toGfa2Reference(link.getSource()), toGfa2Reference(link.getTarget()), unknown, unknown, unknown, unknown, alignment, link.getAnnotations()), w);
return true;
}
@Override
public boolean containment(final Containment containment) {
Position unknown = new Position(0, false);
Position targetStart = new Position(containment.getPosition(), false);
Alignment alignment = containment.getOverlap() == null ? null : Alignment.valueOf(containment.getOverlap());
Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Edge(null, toGfa2Reference(containment.getContainer()), toGfa2Reference(containment.getContained()), unknown, unknown, targetStart, unknown, alignment, containment.getAnnotations()), w);
return true;
}
@Override
public boolean path(final Path path) {
Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Path(path.getName(), toGfa2References(path.getSegments()), path.getAnnotations()), w);
return true;
}
});
return 0;
}
finally {
try {
writer.close();
}
catch (Exception e) {
// empty
}
}
}
static List toGfa2References(List references) {
List gfa2References = new ArrayList(references.size());
for (org.dishevelled.bio.assembly.gfa1.Reference reference : references) {
gfa2References.add(toGfa2Reference(reference));
}
return gfa2References;
}
static org.dishevelled.bio.assembly.gfa2.Reference toGfa2Reference(org.dishevelled.bio.assembly.gfa1.Reference reference) {
return new org.dishevelled.bio.assembly.gfa2.Reference(reference.getId(), toGfa2Orientation(reference.getOrientation()));
}
static org.dishevelled.bio.assembly.gfa2.Orientation toGfa2Orientation(org.dishevelled.bio.assembly.gfa1.Orientation orientation) {
return orientation.isForward() ? org.dishevelled.bio.assembly.gfa2.Orientation.FORWARD : org.dishevelled.bio.assembly.gfa2.Orientation.REVERSE;
}
/**
* 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 inputGfa1Path = new PathArgument("i", "input-gfa1-path", "input GFA 1.0 path, default stdin", false);
FileArgument outputGfa2File = new FileArgument("o", "output-gfa2-file", "output GFA 2.0 file, default stdout", false);
ArgumentList arguments = new ArgumentList(about, help, inputGfa1Path, outputGfa2File);
CommandLine commandLine = new CommandLine(args);
Gfa1ToGfa2 gfa1ToGfa2 = 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);
}
gfa1ToGfa2 = new Gfa1ToGfa2(inputGfa1Path.getValue(), outputGfa2File.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(gfa1ToGfa2.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
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