MetaUtils.java

package org.seqcode.viz.metaprofile;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.Iterator;
import java.util.Vector;

import org.seqcode.genome.Genome;
import org.seqcode.genome.location.Gene;
import org.seqcode.genome.location.Point;
import org.seqcode.genome.location.StrandedPoint;
import org.seqcode.gsebricks.verbs.Mapper;
import org.seqcode.gsebricks.verbs.MapperIterator;
import org.seqcode.gsebricks.verbs.location.GenomeExpander;
import org.seqcode.gsebricks.verbs.location.RefGeneGenerator;


/**
 * MetaUtils: loaders from various sources
 * 
 * @author tdanford
 * @author mahony
 *
 */
public class MetaUtils {

	private Genome genome;
	
	public MetaUtils(Genome g){
		genome = g;
	}
	
	/**
	 * Load TSSs from the named table (e.g. refGene)
	 * @param geneTable
	 * @return
	 */
	public Iterator<Point> loadTSSs(String geneTable) { 
		System.err.println("Loading gene TSSs");
		RefGeneGenerator gen = new RefGeneGenerator(genome, geneTable);
		Mapper<Gene,Point> tssMapper = new Mapper<Gene,Point>() { 
			public Point execute(Gene g) { 
				if(g.getStrand() == '+') { 
					return new StrandedPoint(g.getGenome(), g.getChrom(), g.getStart(), '+');
				} else { 
					return new StrandedPoint(g.getGenome(), g.getChrom(), g.getEnd(), '-');
				}
			}
		};
		GenomeExpander<Gene> gexp = new GenomeExpander<Gene>(gen);
		Iterator<Gene> genes = gexp.execute(genome);
		Iterator<Point> points = new MapperIterator<Gene,Point>(tssMapper, genes);
		return points;
	}
	
	/**
	 * Load a set of (stranded) points from a file
	 * @param f
	 * @return
	 * @throws IOException
	 */
	public Vector<Point> loadPoints(File f) throws IOException {
		System.err.println("Loading points");
		Vector<Point> pts = new Vector<Point>();
		BufferedReader br = new BufferedReader(new FileReader(f));
		String line;
		while((line = br.readLine()) != null) {
			String [] curr = line.split("\\s+");
			String coord = curr[0];
			if(curr.length>=3 && curr[2].contains(":")){coord = curr[2];}
			
			if(coord.contains(":")) {
				String [] currB = coord.split(":");
				String chrom = currB[0].replaceAll("chr", "");
				char strand = '?';
				if(currB.length==3)
					strand = currB[2].charAt(0);
				Point pt = null;
				int location=-1;
				if(currB[1].contains("-")){
					String [] currC = currB[1].split("-");
					int start = new Integer(currC[0]);
					int stop = new Integer(currC[1]);
					location = (start+stop)/2;
					if(strand=='-' && (stop-start)%2==1)
						location+=1;
				}else{
					location = new Integer(currB[1]);
				}
				if(strand!='?')
					pt = new StrandedPoint(genome, chrom, location, strand);
				else
					pt = new Point(genome, chrom, location);
			
				pts.add(pt);
			} else { 
				System.err.println(String.format("Couldn't find point in line \"%s\"", line));
			}
		}
		br.close();
		System.err.println(pts.size()+" points loaded");
		return pts;
	}
}