org.snpeff.reactome.GeneIds 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.reactome;

import org.snpeff.fileIterator.LineFileIterator;
import org.snpeff.gtex.IdMap;
import org.snpeff.util.Gpr;

/**
 * Maps different Gene IDs:
 * 		- ENSEMBL Gene ID to transcript ID
 * 		- ENSEMBL Gene ID to Gene Name
 * 		- ENSEMBL Gene ID to Refseq Gene ID
 * 		- ENSEMBL Gene ID to Refseq Protein ID
 * 
 * @author pcingola
 */
public class GeneIds {

	IdMap id2tr = new IdMap();
	IdMap id2geneName = new IdMap();
	IdMap id2refseqId = new IdMap();
	IdMap id2refseqProtId = new IdMap();

	public GeneIds(String fileName) {
		load(fileName);
	}

	public IdMap getId2geneName() {
		return id2geneName;
	}

	public IdMap getId2refseqId() {
		return id2refseqId;
	}

	public IdMap getId2refseqProtId() {
		return id2refseqProtId;
	}

	public IdMap getId2tr() {
		return id2tr;
	}

	/**
	 * Load data from file
	 * @param fileName
	 */
	protected void load(String fileName) {
		if (!Gpr.canRead(fileName)) throw new RuntimeException("Cannot read file '" + fileName + "'");

		LineFileIterator lfi = new LineFileIterator(fileName);
		for (String line : lfi) {
			if (lfi.getLineNum() <= 1) continue;
			String fields[] = line.split("\t", -1); // Split , don't trim trailing entries

			// Parse field
			String geneId = fields[0];
			String trId = fields[1];
			String geneName = fields[2];
			String refseqId = fields[3];
			String refseqProId = fields[4];

			// Add mappings
			id2tr.add(geneId, trId);
			id2geneName.add(geneId, geneName);
			id2refseqId.add(geneId, refseqId);
			id2refseqProtId.add(geneId, refseqProId);
		}
	}

}