/*
* 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.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.collections.ListUtils;
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.Priority;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;
/**
* Check that all chromosomes have at least some genes with certain analyses.
*/
public class SourceTypes extends SingleDatabaseTestCase {
/**
* Creates a new instance of AnalysisTypes
*/
public SourceTypes() {
setDescription("Check that all chromsosomes have at least some genes with certain sources.");
setPriority(Priority.AMBER);
setEffect("Some genes may have only Ensembl or Havana annotation.");
setFix("Possibly indicates a problem with the Havana/Ensembl merge pipeline");
setTeamResponsible(Team.GENEBUILD);
}
/**
* This only applies to core databases.
*/
public void types() {
removeAppliesToType(DatabaseType.ESTGENE);
removeAppliesToType(DatabaseType.CDNA);
removeAppliesToType(DatabaseType.VEGA);
removeAppliesToType(DatabaseType.SANGER_VEGA);
removeAppliesToType(DatabaseType.OTHERFEATURES);
removeAppliesToType(DatabaseType.RNASEQ);
}
/**
* Run the test.
*
* @param dbre
* The database registry containing all the specified databases.
*/
public boolean run(DatabaseRegistryEntry dbre) {
// only applies to human, mouse and zebrafish at the moment
Species species = dbre.getSpecies();
boolean is_merged = isMerged(species);
if (!is_merged) {
return true;
}
boolean result = true;
Connection con = dbre.getConnection();
result &= geneSources(con);
result &= transcriptSources(con);
result &= geneTranscriptSources(con);
return result;
} // run
public boolean geneSources(Connection con) {
boolean result = true;
String[] sources = { "ensembl", "havana", "ensembl_havana" };
// get all chromosomes, ignore LRG and MT
String[] seqRegionNames = DBUtils.getColumnValues(con,
"SELECT s.name FROM seq_region s, seq_region_attrib sa, attrib_type at WHERE s.seq_region_id = sa.seq_region_id AND sa.attrib_type_id = at.attrib_type_id AND code = 'karyotype_rank' AND s.name NOT LIKE 'MT'");
// loop over each seq region, check that each logic name is represented
try {
PreparedStatement stmt = con
.prepareStatement("SELECT COUNT(*) FROM gene g, seq_region sr WHERE g.seq_region_id=sr.seq_region_id AND sr.name=? AND g.source=?");
for (String seqRegion : seqRegionNames) {
for (String source : sources) {
stmt.setString(1, seqRegion);
stmt.setString(2, source);
ResultSet rs = stmt.executeQuery();
rs.first();
int rows = rs.getInt(1);
if (rows == 0) {
result = false;
ReportManager.problem(this, con, String.format("Chromosome %s has no genes with source %s", seqRegion, source));
}
rs.close();
}
}
stmt.close();
} catch (SQLException e) {
System.err.println("Error executing SQL");
e.printStackTrace();
}
return result;
} // geneSources
public boolean transcriptSources(Connection con) {
boolean result = true;
String sql = "SELECT COUNT(*) FROM transcript WHERE isnull(source)";
int rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Some transcripts have no source");
}
sql = "SELECT COUNT(*) FROM transcript t, analysis a WHERE t.analysis_id = a.analysis_id AND source not in ('ensembl') AND (logic_name LIKE '%ensembl%' OR logic_name LIKE '%nrcna%') AND logic_name NOT LIKE '%havana%'";
String useful_sql = "SELECT t.stable_id, t.source, a.logic_name FROM transcript t, analysis a WHERE t.analysis_id = a.analysis_id AND source not in ('ensembl') AND (logic_name LIKE '%ensembl%' OR logic_name LIKE '%nrcna%') AND logic_name NOT LIKE '%havana%'";
rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Some transcripts of %ensembl% and/or %ncrna% analyses do not have ensembl source. Try " + useful_sql + " to find those transcripts");
}
sql = "SELECT COUNT(*) FROM transcript t, analysis a WHERE t.analysis_id = a.analysis_id AND source not in ('havana') AND logic_name LIKE '%havana%' AND logic_name NOT LIKE '%ensembl_havana%'";
useful_sql = "SELECT t.stable_id, t.source, a.logic_name FROM transcript t, analysis a WHERE t.analysis_id = a.analysis_id AND source not in ('havana') AND logic_name LIKE '%havana%' AND logic_name NOT LIKE '%ensembl_havana%'";
rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Some transcripts of %havana% analysis do not have havana source. Try " + useful_sql + " to find those transcripts");
}
sql = "SELECT COUNT(*) FROM transcript t, analysis a WHERE t.analysis_id = a.analysis_id AND source not in ('ensembl_havana') AND logic_name LIKE '%ensembl_havana%'";
useful_sql = "SELECT t.stable_id, t.source, a.logic_name FROM transcript t, analysis a WHERE t.analysis_id = a.analysis_id AND source not in ('ensembl_havana') AND logic_name LIKE '%ensembl_havana%'";
rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Some transcripts of analysis %ensembl_havana% do not have ensembl_havana source. Try " + useful_sql + " to find those transcripts");
}
return result;
}
public boolean geneTranscriptSources(Connection con) {
boolean result = true;
String sql = "SELECT COUNT(*) FROM gene g, transcript t where g.gene_id = t.gene_id and g.source = 'ensembl' and t.source not in ('ensembl')";
String useful_sql = "SELECT g.stable_id, g.source, t.stable_id, t.source FROM gene g, transcript t where g.gene_id = t.gene_id and g.source = 'ensembl' and t.source not in ('ensembl')";
int rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Some ensembl genes have transcripts which are not ensembl. Try " + useful_sql + " to find those genes");
}
sql = "SELECT COUNT(*) FROM gene g, transcript t where g.gene_id = t.gene_id and g.source = 'havana' and t.source not in ('havana')";
useful_sql = "SELECT g.stable_id, g.source, t.stable_id, t.source FROM gene g, transcript t where g.gene_id = t.gene_id and g.source = 'havana' and t.source not in ('havana')";
rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Some havana genes have transcripts which are not havana. Try " + useful_sql + " to find those genes");
}
sql = "SELECT COUNT(*) FROM gene g, transcript t where g.gene_id = t.gene_id and g.source not in ('ensembl_havana') and t.source = 'ensembl_havana'";
useful_sql = "SELECT g.stable_id, g.source, t.stable_id, t.source FROM gene g, transcript t where g.gene_id = t.gene_id and g.source not in ('ensembl_havana') and t.source = 'ensembl_havana'";
rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Some transcripts with ensembl_havana source belong to genes whose source is not ensembl_havana. Try " + useful_sql + " to find those transcripts");
}
// Check source and analysis are consistent in the gene table
sql = "SELECT COUNT(*) FROM gene g, analysis a where g.analysis_id = a.analysis_id and source not in ('ensembl') AND (logic_name LIKE '%ensembl%' OR logic_name LIKE '%nrcna%') AND logic_name NOT LIKE '%havana%'";
useful_sql = "SELECT g.stable_id, g.source, a.logic_name FROM gene g, analysis a where g.analysis_id = a.analysis_id and source not in ('ensembl') AND (logic_name LIKE '%ensembl%' OR logic_name LIKE '%nrcna%') AND logic_name NOT LIKE '%havana%'";
rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Some genes of %ensembl% and/or %ncrna% analyses do not have ensembl source. Try " + useful_sql + " to find those genes");
}
sql = "SELECT COUNT(*) FROM gene g, analysis a WHERE g.analysis_id = a.analysis_id AND source not in ('havana') AND logic_name LIKE '%havana%' AND logic_name NOT LIKE '%ensembl_havana%'";
useful_sql = "SELECT g.stable_id, g.source, a.logic_name FROM gene g, analysis a WHERE g.analysis_id = a.analysis_id AND source not in ('havana') AND logic_name LIKE '%havana%' AND logic_name NOT LIKE '%ensembl_havana%'";
rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Some genes of %havana% analysis do not have havana source. Try " + useful_sql + " to find those genes");
}
sql = "SELECT COUNT(*) FROM gene g, analysis a WHERE g.analysis_id = a.analysis_id AND source not in ('ensembl_havana') AND logic_name LIKE '%ensembl_havana%'";
useful_sql = "SELECT g.stable_id, g.source, a.logic_name FROM gene g, analysis a WHERE g.analysis_id = a.analysis_id AND source not in ('ensembl_havana') AND logic_name LIKE '%ensembl_havana%'";
rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "Some genes of analysis %ensembl_havana% do not have ensembl_havana source. Try " + useful_sql + " to find those genes");
}
return result;
}
// --------------------------------------------------------------------------
} // AnalysisTypes