ubic.gemma.loader.genome.GffParser.java Source code

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Here is the source code for ubic.gemma.loader.genome.GffParser.java

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/*
 * The Gemma project
 * 
 * Copyright (c) 2007 University of British Columbia
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *       http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
package ubic.gemma.loader.genome;

import java.util.Collection;
import java.util.HashSet;

import org.apache.commons.lang.StringUtils;

import ubic.gemma.loader.util.parser.BasicLineParser;
import ubic.gemma.model.genome.Chromosome;
import ubic.gemma.model.genome.Gene;
import ubic.gemma.model.genome.PhysicalLocation;
import ubic.gemma.model.genome.Taxon;
import ubic.gemma.model.genome.gene.GeneProduct;
import ubic.gemma.util.SequenceBinUtils;

/**
 * Simple parser for GFF format (version 2). See http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml.
 * <p>
 * Fields are: &lt;seqname&gt; &lt;source&gt; &lt;feature&gt; &lt;start&lt; &lt;end&gt; &lt;score&gt; &lt;strand&gt;
 * &lt;frame&gt; [attributes] [comments]. A header can be present.
 * <p>
 * Implementation note: Currently each line is converted to a Gene with an associated GeneProduct; this will have to be
 * expanded/changed.
 * 
 * @author pavlidis
 * @version $Id: GffParser.java,v 1.9 2012/05/27 02:58:32 paul Exp $
 */
public class GffParser extends BasicLineParser<Gene> {
    Collection<Gene> results = new HashSet<Gene>();

    Taxon taxon;

    public Taxon getTaxon() {
        return taxon;
    }

    public void setTaxon(Taxon taxon) {
        this.taxon = taxon;
    }

    @Override
    protected void addResult(Gene obj) {
        if (results.contains(obj)) {
            log.warn("Already have " + obj);
        }
        results.add(obj);
    }

    @Override
    public Collection<Gene> getResults() {
        return results;
    }

    @Override
    public Gene parseOneLine(String line) {

        if (this.taxon == null) {
            throw new IllegalStateException("You must set the taxon first");
        }

        String[] fields = StringUtils.splitPreserveAllTokens(line, '\t');
        Gene newGene = Gene.Factory.newInstance();
        GeneProduct geneProduct = GeneProduct.Factory.newInstance();

        String seqName = fields[0]; // chromosome
        // String source = fields[1];
        String featureType = fields[2];
        long start = Long.parseLong(fields[3]);
        long end = Long.parseLong(fields[4]);
        int length = (int) (end - start);
        String strand = fields[6];

        String attributes = fields[8];

        newGene.setDescription(featureType);
        geneProduct.setDescription(featureType);

        String[] attFields = StringUtils.splitPreserveAllTokens(attributes, ';');
        for (int i = 0; i < attFields.length; i++) {

            String f = attFields[i];

            if (f == null || f.length() == 0) {
                continue;
            }

            f = StringUtils.strip(f);
            log.debug(f);
            String[] subf = StringUtils.split(f, '=');

            if (subf.length != 2) {
                throw new IllegalArgumentException("Couldn't parse '" + f + "'");
            }

            String ti = subf[0];
            String val = subf[1];

            if (ti.equals("ID")) {
                val = val.replaceAll("\"", "");
                newGene.setName(val);
                newGene.setOfficialSymbol(val);
                geneProduct.setName(val);
            } else if (ti.equals("ACC")) {
                // don't know what database!
            }
        }

        // String comments = fields[9];

        Chromosome chromosome = Chromosome.Factory.newInstance();
        chromosome.setName(seqName);
        chromosome.setTaxon(taxon);

        PhysicalLocation location = PhysicalLocation.Factory.newInstance();
        location.setChromosome(chromosome);
        location.setNucleotide(start);
        location.setNucleotideLength(length);
        location.setBin(SequenceBinUtils.binFromRange(location.getNucleotide().intValue(),
                location.getNucleotide().intValue() + location.getNucleotideLength().intValue()));
        location.setStrand(strand);

        geneProduct.setPhysicalLocation(location);
        geneProduct.setGene(newGene);

        newGene.setTaxon(taxon);
        newGene.setPhysicalLocation(location);
        newGene.getProducts().add(geneProduct);

        return newGene;

    }

}