From 4f1437a0258ceba00d40127a51f77d371f510922 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 12 Sep 2011 10:38:20 +0000
Subject: [PATCH] Correctly pick up Ensembl Genomes ontology database.
---
modules/Bio/EnsEMBL/Registry.pm | 73 +++++++++++++++++----------------
1 file changed, 38 insertions(+), 35 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 67c3bd2a4d..c88888d6b9 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -257,7 +257,7 @@ sub load_all {
}
if ( defined $cfg ) {
- my %default_adaptor_args = ();
+ my %default_adaptor_args = ();
if ( $cfg->SectionExists('default') ) {
# The 'default' section is special. It contain default
@@ -1291,8 +1291,8 @@ sub change_access{
(((!defined($user)) or ($user eq $dbc->username))) and
((!defined($dbname)) or ($dbname eq $dbc->dbname))){
if($dbc->connected()){
- $dbc->db_handle->disconnect();
- $dbc->connected(undef);
+ $dbc->db_handle->disconnect();
+ $dbc->connected(undef);
}
# over write the username and password
$dbc->username($new_user);
@@ -1471,7 +1471,8 @@ sub load_registry_from_db {
$species_suffix = "";
}
- my $ontology_version = 0;
+ my $ontology_db;
+ my $ontology_version;
$user ||= "ensro";
if ( !defined($port) ) {
@@ -1513,10 +1514,12 @@ sub load_registry_from_db {
}
} elsif ( $db =~ /^(.+)_(userdata)$/x ) {
$temp{$1} = $2;
- } elsif ( $db =~ /^(ensembl_compara # compara database
+ } elsif (
+ $db =~ /^(ensembl_compara # compara database
(?:_\w+)*?) # optional ensembl genomes bit
_
- (\d+)$/x ) { # db version
+ (\d+)$/x )
+ { # db version
if ( $2 eq $software_version ) {
$temp{$1} = $2;
}
@@ -1524,20 +1527,23 @@ sub load_registry_from_db {
if ( $2 eq $software_version ) {
$temp{$1} = $2;
}
- } elsif ( $db =~ /^(ensembl(?:genomes)_ontology)_(\d+)/x ) {
- if ( $2 eq $software_version ) {
- $ontology_version = $2;
+ } elsif ( $db =~ /^ensembl(?:genomes)?_ontology_(?:\d+_)?(\d+)/x ) {
+ if ( $1 eq $software_version ) {
+ $ontology_db = $db;
+ $ontology_version = $1;
}
- } elsif ( $db =~ /^([a-z]+_[a-z0-9]+ # species name e.g. homo_sapiens
- _
- [a-z]+ # db type
- (?:_\d+)?) # optional end bit for ensembl genomes databases
- _
- (\d+) # database release
- _
- (\w+) # assembly number can have letters too e.g 37c
- /x
- ) {
+ } elsif (
+ $db =~ /^([a-z]+_[a-z0-9]+ # species name e.g. homo_sapiens
+ _
+ [a-z]+ # db type
+ (?:_\d+)?) # optional end bit for ensembl genomes databases
+ _
+ (\d+) # database release
+ _
+ (\w+) # assembly number can have letters too e.g 37c
+ /x
+ )
+ {
# Species specific databases (core, cdna, vega etc.)
@@ -1566,7 +1572,7 @@ sub load_registry_from_db {
my @dbs = grep { /^[a-z]+_[a-z0-9]+ # species name
_
$type # the database type
- _
+ _
(?:\d+_)? # optional end bit for ensembl genomes
\d+ # database release
_
@@ -1574,13 +1580,13 @@ sub load_registry_from_db {
foreach my $database (@dbs) {
if ( index( $database, 'collection' ) != -1 ) {
- # Skip multi-species databases.
- next;
+ # Skip multi-species databases.
+ next;
}
my ( $species, $num ) =
- ( $database =~ /(^[a-z]+_[a-z0-9]+) # species name
+ ( $database =~ /(^[a-z]+_[a-z0-9]+) # species name
_
$type # type
_
@@ -1594,7 +1600,7 @@ sub load_registry_from_db {
}
my $dba =
- Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+ Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => $type,
-species => $species.$species_suffix,
-host => $host,
@@ -1606,8 +1612,8 @@ sub load_registry_from_db {
-no_cache => $no_cache );
if ($verbose) {
- printf( "Species '%s' loaded from database '%s'\n",
- $species, $database );
+ printf( "Species '%s' loaded from database '%s'\n",
+ $species, $database );
}
}
}
@@ -1916,9 +1922,6 @@ sub load_registry_from_db {
if ( $ontology_version != 0 ) {
require Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
- my $ontology_db =
- sprintf( "ensembl_ontology_%d", $ontology_version );
-
my $dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
'-species' => 'multi'.$species_suffix,
'-group' => 'ontology',
@@ -2079,7 +2082,7 @@ sub find_and_add_aliases {
} elsif (
$lc_species ne $class->get_alias( $alias_suffix ) )
{
- $class->remove_alias( $species, $alias_suffix );
+ $class->remove_alias( $species, $alias_suffix );
}
}
@@ -2272,11 +2275,11 @@ sub add_new_tracks{
if(defined($species_reg)){
foreach my $dba (@{$reg->get_all_DBAdaptors()}){
if(!$reg->default_track($dba->species,$dba->group)){
- $pars{'available'} = "species ".$reg->get_alias($dba->species());
- $pars{'db_alias'} = $dba->group();
-# print STDERR "Adding new track for ".$dba->species."\t".$dba->group."\n";
- $conf->add_new_track_generictranscript('',$dba->group(), "black",$pos,%pars);
- $pos++;
+ $pars{'available'} = "species ".$reg->get_alias($dba->species());
+ $pars{'db_alias'} = $dba->group();
+# print STDERR "Adding new track for ".$dba->species."\t".$dba->group."\n";
+ $conf->add_new_track_generictranscript('',$dba->group(), "black",$pos,%pars);
+ $pos++;
}
}
}
--
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