edu.berkeley.compbio.ncbitaxonomy.Exporter.java Source code

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Here is the source code for edu.berkeley.compbio.ncbitaxonomy.Exporter.java

Source

/*
 * Copyright (c) 2008-2013  David Soergel  <dev@davidsoergel.com>
 * Licensed under the Apache License, Version 2.0
 * http://www.apache.org/licenses/LICENSE-2.0
 */

package edu.berkeley.compbio.ncbitaxonomy;

import org.springframework.context.ApplicationContext;

import java.io.FileWriter;
import java.util.Set;

/**
 * @author <a href="mailto:dev@davidsoergel.com">David Soergel</a>
 * @version $Id$
 */
public class Exporter {
    static String[] ranks = { "phylum", "class", "order", "family", "genus", "species" };

    public static void main(String[] argv) {
        try {
            ApplicationContext ctx = NcbiTaxonomyDbContextFactory.makeNcbiTaxonomyDbContext();
            NcbiTaxonomyPhylogeny ncbi = (NcbiTaxonomyPhylogeny) ctx.getBean("ncbiTaxonomyPhylogeny");

            FileWriter treeWriter = new FileWriter("tree.newick");
            ncbi.toNewick(treeWriter, "", "", 0, 0);
            treeWriter.close();

            FileWriter synonymWriter = new FileWriter("synonyms");
            ncbi.writeSynonyms(synonymWriter);
            synonymWriter.close();

            for (String rank : ranks) {
                FileWriter rankWriter = new FileWriter(rank);
                Set<Integer> ids = ncbi.getTaxIdsWithRank(rank);
                for (Integer id : ids) {
                    rankWriter.append(id.toString()).append("\n");
                }
                rankWriter.close();
            }
        } catch (Throwable e) {
            e.printStackTrace();
        }
    }
}