/*
* 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.
*/
/*
* Copyright (C) 2004 EBI, GRL
*
* This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation,
* Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package org.ensembl.healthcheck.testcase.generic;
import java.sql.Connection;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;
/**
* Check that there are no translations for pseudogenes.
*/
public class Pseudogene extends SingleDatabaseTestCase {
/**
* Check the assembly_exception table.
*/
public Pseudogene() {
setDescription("Check that there are no translations for pseudogenes");
setTeamResponsible(Team.GENEBUILD);
}
/**
* Check the data in the assembly_exception table. Note referential integrity checks are done in CoreForeignKeys.
*
* @param dbre
* The database to use.
* @return Result.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
String qry = "select count(*) from gene,transcript,translation " + "where gene.biotype like '%pseudogene%'" + " and transcript.gene_id=gene.gene_id "
+ " and translation.transcript_id=transcript.transcript_id and gene.biotype!= 'polymorphic_pseudogene' ";
if (dbre.getType() == DatabaseType.SANGER_VEGA) {// for sangervega ignore genes that do not have source havana or WU and allow
// polymorphic_pseudogene to have translations
qry += " and (gene.source='havana' or gene.source='WU')";
}
if (dbre.getType() == DatabaseType.SANGER_VEGA ||
dbre.getType() == DatabaseType.VEGA) {
// Vega allows translations on translated_processed_pseudogene-s
qry += " and gene.biotype != 'translated_processed_pseudogene'";
}
int rows = DBUtils.getRowCount(con, qry);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Translation table contains " + rows + " rows for pseudogene types - should contain none");
}
if (result) {
ReportManager.correct(this, con, "No pseudogenes have translations");
}
return result;
}
/**
* This applies to 'core and 'vega' core schema databases
*/
public void types() {
removeAppliesToType(DatabaseType.OTHERFEATURES);
removeAppliesToType(DatabaseType.ESTGENE);
removeAppliesToType(DatabaseType.VEGA);
removeAppliesToType(DatabaseType.RNASEQ);
}
} // Pseudogene