GeneTranscriptStartEnd.java

/*
 * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
 * Copyright [2016-2017] EMBL-European Bioinformatics Institute
 * 
 * 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 org.ensembl.healthcheck.testcase.generic;

import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.Statement;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Species;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;

/**
 * Check that the start and end of genes and transcripts make sense.
 */
public class GeneTranscriptStartEnd extends SingleDatabaseTestCase {

	/**
	 * Create a new GeneTranscriptStartEnd test case.
	 */
	public GeneTranscriptStartEnd() {

		setDescription("Checks that gene start/end agrees with transcript table");
		setTeamResponsible(Team.GENEBUILD);
	}

	/**
	 * This only applies to core and Vega databases.
	 */
	public void types() {

		removeAppliesToType(DatabaseType.OTHERFEATURES);
		removeAppliesToType(DatabaseType.RNASEQ);

	}

	/**
	 * Run the test.
	 * 
	 * @param dbre
	 *          The database to use.
	 * @return true if the test passed.
	 * 
	 */
	public boolean run(DatabaseRegistryEntry dbre) {

		boolean startEndResult = true;
		boolean strandResult = true;

		// check that the lowest transcript start of a gene's transcripts is the
		// same as the gene's
		// start
		// and that the highest transcript end of a gene's transcripts is the same
		// as the gene's
		// end
		// the SQL below will return any where this is /not/ the case
		String sql = "SELECT g.gene_id, g.stable_id, g.seq_region_start AS gene_start, g.seq_region_end AS gene_end, MIN(tr.seq_region_start) AS min_transcript_start, MAX(tr.seq_region_end) AS max_transcript_end FROM gene g, transcript tr WHERE tr.gene_id=g.gene_id GROUP BY tr.gene_id HAVING (gene_start <> min_transcript_start OR gene_end <> max_transcript_end)";

		Connection con = dbre.getConnection();

		try {

			Statement stmt = con.createStatement();
			ResultSet rs = stmt.executeQuery(sql);

			rs.beforeFirst();

			// gene GC32491 in drosophila is allowed to have all sorts of things wrong
			// with it
			if (rs != null && !rs.isAfterLast() && rs.next() && dbre.getSpecies() != Species.DROSOPHILA_MELANOGASTER && rs.getString("stable_id") != null
					&& !rs.getString("stable_id").equalsIgnoreCase("CG32491")) {

				ReportManager.problem(this, con, "Gene ID " + rs.getLong(1) + " has start/end that does not agree with transcript start/end");
				startEndResult = false;

				while (rs.next()) {
					ReportManager.problem(this, con, "Gene ID " + rs.getLong(1) + " has start/end that does not agree with transcript start/end");
					startEndResult = false;
				}
				rs.close();

				if (startEndResult) {
					ReportManager.correct(this, con, "All gene/transcript start/end agree");
				}

				// also check that all gene's transcripts have the same strand as the
				// gene
				sql = "SELECT g.gene_id FROM gene g, transcript tr WHERE tr.gene_id=g.gene_id AND tr.seq_region_strand != g.seq_region_strand";
				rs = stmt.executeQuery(sql);

				while (rs.next()) {
					ReportManager.problem(this, con, "Gene ID " + rs.getLong(1) + " has strand that does not agree with transcript strand");
					strandResult = false;
				}
				rs.close();
				stmt.close();

				if (strandResult) {
					ReportManager.correct(this, con, "All gene/transcript strands agree");
				}

			} // if drosophila gene

		} catch (Exception e) {
			e.printStackTrace();
		}

		return startEndResult && strandResult;

	}

}