RefGenePromoterGenerator.java

package org.seqcode.gsebricks.verbs.location;

import java.util.*;
import java.sql.*;

import org.seqcode.genome.Genome;
import org.seqcode.genome.location.Gene;
import org.seqcode.genome.location.Region;


/**
 * Generator that returns Gene objects from the refGene table (or
 * table with a similar structure, eg sgdGene) in a UCSC annotation
 * database.  The size parameter determines the size of the upstream
 * promoter region to use.  Any gene whose promoter region overlaps
 * the input region is returned
*/

public class RefGenePromoterGenerator extends RefGeneGenerator {
    private int up, down;

    public RefGenePromoterGenerator(Genome g, int size) {
        super(g);
        this.up = size;
        this.down = size;
    }
    public RefGenePromoterGenerator(Genome g, String t, int size) {
        super(g,t);
        this.up = size;
        this.down = size;
    }
    public RefGenePromoterGenerator(Genome g, int up, int down) {
        super(g);
        this.up = up;
        this.down = down;
    }
    public RefGenePromoterGenerator(Genome g, String t, int up, int down) {
        super(g,t);
        this.up = up;
        this.down = down;
    }
    public Iterator<Gene> execute(Region region) {
        try {
            java.sql.Connection cxn =
                getGenome().getAnnotationDBConnection();
            String query = "select name, chrom, strand, txStart, txEnd " + (isRetrievingExons() ? ",exonCount, exonStarts, exonEnds" : "") + 
                " from " + getTable() + " where chrom = ? and " +
                "((strand = '+' and ((txStart - " + up + "  <= ? and txStart + " + down + " >= ?) or (txStart - " + up + " >= ? and txStart - " + up + "<= ?))) or " + 
                " (strand = '-' and ((txEnd - " + down + "  <= ? and txEnd + " + up + " >= ?) or (txEnd - " + down + " >= ? and txEnd - " + down + "<= ?)))) " + 
                "order by txStart";
            PreparedStatement ps = cxn.prepareStatement(query);
            String chr = region.getChrom();
            if (!chr.matches("^(chr|scaffold).*")) {
                chr = "chr" + chr;
            }
            ps.setString(1,chr);
            ps.setInt(2,region.getStart());
            ps.setInt(3,region.getStart());
            ps.setInt(4,region.getStart());
            ps.setInt(5,region.getEnd());
            ps.setInt(6,region.getStart());
            ps.setInt(7,region.getStart());
            ps.setInt(8,region.getStart());
            ps.setInt(9,region.getEnd());

            Iterator<Gene> results = parseResults(ps);            
            cxn.close();
            return results;
        } catch (SQLException ex) {
            ex.printStackTrace();
            throw new org.seqcode.data.connections.DatabaseException("Couldn't get UCSC RefGenes",ex);
        }
    }
}