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ParseGO.java
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67 lines (58 loc) · 1.79 KB
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on Mar 19, 2014
* Author: andreas
*
*/
package demo;
import org.biojava.nbio.ontology.Ontology;
import org.biojava.nbio.ontology.Term;
import org.biojava.nbio.ontology.io.OboParser;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Iterator;
import java.util.Set;
public class ParseGO {
static final Logger logger = LoggerFactory.getLogger(ParseGO.class);
/**
* Parses Biosapiens OBO file and logs name/description at INFO level
*
* @param args
*/
public static void main(String[] args) {
OboParser parser = new OboParser();
try (InputStream inStream = OboParser.class.getResourceAsStream("/ontology/biosapiens.obo");
BufferedReader oboFile = new BufferedReader(new InputStreamReader(inStream))) {
Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology");
Set<Term> keys = ontology.getTerms();
Iterator<Term> iter = keys.iterator();
while (iter.hasNext()) {
Term t = iter.next();
logger.info("{} [{}]", t.getName(), t.getDescription());
}
} catch (Exception e) {
logger.error("Exception: " + e);
System.exit(1);
}
}
}