org.snpeff.spliceSites.TranscriptSet Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation

Variant annotation and effect prediction package.

The newest version!

package org.snpeff.spliceSites;

import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;

import org.snpeff.collections.AutoHashMap;
import org.snpeff.interval.Chromosome;
import org.snpeff.interval.Gene;
import org.snpeff.interval.Genome;
import org.snpeff.interval.Transcript;
import org.snpeff.util.Timer;

/**
 * A set of transcripts
 *
 * @author pablocingolani
 */
public class TranscriptSet implements Iterable {

	public static final int MAX_TRANSCRIPTS_PER_GENE = 1000;

	boolean debug;
	boolean verbose;

	Genome genome;

	HashSet transcripts;

	AutoHashMap> transcriptsByChromo;

	public TranscriptSet(Genome genome) {
		this.genome = genome;
		transcripts = new HashSet();
		transcriptsByChromo = new AutoHashMap>(new ArrayList());
	}

	/**
	 * Filter out "bad transcripts"
	 */
	public void filter() {
		if (verbose) Timer.showStdErr("Filtering transcripts: Removing non-coding and transcripts with errors");

		int total = 0, kept = 0;
		for (Gene gene : genome.getGenes()) {
			if (gene.numChilds() > MAX_TRANSCRIPTS_PER_GENE) {
				System.err.println("Ignoring gene '" + gene.getGeneName() + "', too many transcripts (" + gene.numChilds() + ")");
				continue;
			}

			for (Transcript tr : gene) {
				total++;

				if (!tr.isProteinCoding()) {
					if (debug) System.err.println("Ignoring transcript '" + tr.getId() + "', non-coding.");
					continue;
				}
				if (tr.hasError()) {
					if (debug) System.err.println("Ignoring transcript '" + tr.getId() + "', it has errors.");
					continue;
				}

				transcripts.add(tr);
				transcriptsByChromo.getOrCreate(tr.getChromosomeName()).add(tr);
				kept++;
			}
		}

		if (verbose) Timer.showStdErr("Done. Kept / total: " + kept + " / " + total);

	}

	public List getByChromo(String chrName) {
		return transcriptsByChromo.getOrCreate(Chromosome.simpleName(chrName));
	}

	@Override
	public Iterator iterator() {
		return transcripts.iterator();
	}

	public void setDebug(boolean debug) {
		this.debug = debug;
	}

	public void setVerbose(boolean verbose) {
		this.verbose = verbose;
	}
}