org.dishevelled.bio.tools.IdentifyGfa1 Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of dsh-bio-tools Show documentation
Command line tools.
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 java.util.Map;

import java.util.concurrent.Callable;

import java.util.concurrent.atomic.AtomicLong;

import com.google.common.collect.ImmutableMap;

import org.dishevelled.bio.annotation.Annotation;

import org.dishevelled.bio.assembly.gfa1.Containment;
import org.dishevelled.bio.assembly.gfa1.Gfa1Listener;
import org.dishevelled.bio.assembly.gfa1.Gfa1Reader;
import org.dishevelled.bio.assembly.gfa1.Gfa1Record;
import org.dishevelled.bio.assembly.gfa1.Gfa1Writer;
import org.dishevelled.bio.assembly.gfa1.Link;
import org.dishevelled.bio.assembly.gfa1.Traversal;

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;

/**
 * Add identifier annotation to records in GFA 1.0 format.
 *
 * @since 2.0.3
 * @author  Michael Heuer
 */
public final class IdentifyGfa1 implements Callable {
    private final Path inputGfa1Path;
    private final File outputGfa1File;
    private static final String USAGE = "dsh-identify-gfa1 [args]";


    /**
     * Add identifier annotation to records in GFA 1.0 format.
     *
     * @deprecated will be removed in version 3.0
     * @param inputGfa1File input GFA 1.0 file, if any
     * @param outputGfa1File output GFA 1.0 file, if any
     */
    public IdentifyGfa1(final File inputGfa1File, final File outputGfa1File) {
        this(inputGfa1File == null ? null : inputGfa1File.toPath(), outputGfa1File);
    }

    /**
     * Add identifier annotation to records in GFA 1.0 format.
     *
     * @since 2.1
     * @param inputGfa1Path input GFA 1.0 path, if any
     * @param outputGfa1File output GFA 1.0 file, if any
     */
    public IdentifyGfa1(final Path inputGfa1Path, final File outputGfa1File) {
        this.inputGfa1Path = inputGfa1Path;
        this.outputGfa1File = outputGfa1File;
    }


    @Override
    public Integer call() throws Exception {
        BufferedReader reader = null;
        PrintWriter writer = null;
        try {
            reader = reader(inputGfa1Path);
            writer = writer(outputGfa1File);

            final PrintWriter w = writer;
            final AtomicLong count = new AtomicLong();
            Gfa1Reader.stream(reader, new Gfa1Listener() {
                    @Override
                    public boolean record(final Gfa1Record gfa1Record) {
                        String id = String.valueOf(count.getAndIncrement());

                        if (gfa1Record instanceof Containment) {
                            Containment containment = (Containment) gfa1Record;
                            Gfa1Writer.write(new Containment(containment.getContainer(), containment.getContained(), containment.getPosition(), containment.getOverlap(), addId(id, containment.getAnnotations())), w);
                        }
                        else if (gfa1Record instanceof Link) {
                            Link link = (Link) gfa1Record;
                            Gfa1Writer.write(new Link(link.getSource(), link.getTarget(), link.getOverlap(), addId(id, link.getAnnotations())), w);
                        }
                        else if (gfa1Record instanceof Traversal) {
                            Traversal traversal = (Traversal) gfa1Record;
                            Gfa1Writer.write(new Traversal(traversal.getPathName(), traversal.getOrdinal(), traversal.getSource(), traversal.getTarget(), traversal.getOverlap(), addId(id, traversal.getAnnotations())), w);
                        }
                        else {
                            Gfa1Writer.write(gfa1Record, w);
                        }
                        return true;
                    }
                });

            return 0;
        }
        finally {
            try {
                reader.close();
            }
            catch (Exception e) {
                // ignore
            }
            try {
                writer.close();
            }
            catch (Exception e) {
                // ignore
            }
        }
    }

    /**
     * Add an annotation for the specified identifier to the specified annotations.
     *
     * @param id identifier to add
     * @param annotations annotations to add identifier annotation to
     * @return new annotations including an annotation for the specified identifier
     */
    private static Map addId(final String id, final Map annotations) {
        Annotation value = new Annotation("ID", "Z", id);
        if (annotations.isEmpty()) {
            return ImmutableMap.of("ID", value);
        }
        return ImmutableMap.builder()
            .putAll(annotations)
            .put("ID", value)
            .build();
    }


    /**
     * 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 outputGfa1File = new FileArgument("o", "output-gfa1-file", "output GFA 1.0 file, default stdout", false);

        ArgumentList arguments = new ArgumentList(about, help, inputGfa1Path, outputGfa1File);
        CommandLine commandLine = new CommandLine(args);

        IdentifyGfa1 identifyGfa1 = 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);
            }
            identifyGfa1 = new IdentifyGfa1(inputGfa1Path.getValue(), outputGfa1File.getValue());
        }
        catch (CommandLineParseException e) {
            Usage.usage(USAGE, e, commandLine, arguments, System.err);
            System.exit(-1);
        }
        try {
            System.exit(identifyGfa1.call());
        }
        catch (Exception e) {
            e.printStackTrace();
            System.exit(1);
        }
    }
}