001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 * Created on Mar 19, 2014
021 * Author: andreas
022 *
023 */
024
025package demo;
026
027import org.biojava.nbio.ontology.Ontology;
028import org.biojava.nbio.ontology.Term;
029import org.biojava.nbio.ontology.io.OboParser;
030import org.slf4j.Logger;
031import org.slf4j.LoggerFactory;
032
033import java.io.BufferedReader;
034import java.io.InputStream;
035import java.io.InputStreamReader;
036
037import java.util.Iterator;
038import java.util.Set;
039
040public class ParseGO {
041
042        static final Logger logger = LoggerFactory.getLogger(ParseGO.class);
043
044        /**
045         * Parses Biosapiens OBO file and logs name/description at INFO level
046         * 
047         * @param args
048         */
049        public static void main(String[] args) {
050
051                OboParser parser = new OboParser();
052                try (InputStream inStream = OboParser.class.getResourceAsStream("/ontology/bio sapiens.obo");
053                                BufferedReader oboFile = new BufferedReader(new InputStreamReader(inStream))) {
054                        Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology");
055                        Set<Term> keys = ontology.getTerms();
056                        Iterator<Term> iter = keys.iterator();
057                        while (iter.hasNext()) {
058                                Term t = iter.next();
059                                logger.info("{} [{}]", t.getName(), t.getDescription());
060                        }
061
062                } catch (Exception e) {
063                        logger.error("Exception: " + e);
064                        System.exit(1);
065                }
066        }
067}