/*
* 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.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;
/**
* Check that the start and end of genes and transcripts make sense.
*/
public class ExonTranscriptStartEnd extends SingleDatabaseTestCase {
/**
* Create a new ExonTranscriptStartEnd test case.
*/
public ExonTranscriptStartEnd() {
setDescription("Checks that exon and transcript start/end agree");
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 check.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
// Check that the minimum exon seq_region_start in a transcript is the same as the
// transcript's start
// and that the maximum exon seq_region_start in a transcript it the same as the
// transcript's end
// The SQL below will return cases where this is not true
String sql = " SELECT tr.transcript_id, e.exon_id, tr.seq_region_start AS transcript_start, tr.seq_region_end AS transcript_end, "
+ "MIN(e.seq_region_start) as min_exon_start, MAX(e.seq_region_end) AS max_exon_end "
+ "FROM exon e, transcript tr, exon_transcript et "
+ "WHERE e.exon_id=et.exon_id AND et.transcript_id=tr.transcript_id "
+ "AND tr.transcript_id not in (select transcript_id from transcript_attrib inner join attrib_type using (attrib_type_id) where code='trans_spliced')"
+ "GROUP BY et.transcript_id HAVING min_exon_start != transcript_start OR max_exon_end != transcript_end ";
Connection con = dbre.getConnection();
Statement stmt = null;
ResultSet rs = null;
try {
stmt = dbre.getConnection().createStatement();
rs = stmt.executeQuery(sql);
while (rs.next()) {
ReportManager.problem(this, con, "Min/max exon start/ends do not agree with transcript start/end in transcript " + rs.getLong(1));
result = false;
}
rs.close();
stmt.close();
} catch (Exception e) {
e.printStackTrace();
}
finally {
DBUtils.closeQuietly(rs);
DBUtils.closeQuietly(stmt);
}
if (result) {
ReportManager.correct(this, con, "All exon/transcript start/ends agree");
}
return result;
}
}