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Commit 221e14bd authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Corrected parsing of the names of the single species core databases from 

the Ensembl Genomes project.

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parent 1a88db2b
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modules/Bio/EnsEMBL/Registry.pm
+ 115
− 92
View file @ 221e14bd
......@@ -1294,7 +1294,7 @@ sub load_registry_from_db {
$temp{$1} = $2;
}
} elsif (
$db =~ /^([a-z]+_[a-z]+_[a-z]+)_(?:\d+_)?(\d+)_(\d+[a-z]*)/ )
$db =~ /^([a-z]+_[a-z]+_[a-z]+(?:_\d+)?)_(\d+)_(\d+[a-z]*)/ )
{
if ( $2 eq $software_version ) {
$temp{$1} = $2 . "_" . $3;
......@@ -1324,7 +1324,7 @@ sub load_registry_from_db {
# Register Core databases
my @core_dbs = grep { /^[a-z]+_[a-z]+_core_(?:\d+)?\d+_/ } @dbnames;
my @core_dbs = grep { /^[a-z]+_[a-z]+_core_(?:\d+_)?\d+_/ } @dbnames;
foreach my $coredb (@core_dbs) {
next if ($coredb =~ /collection/); # Skip multi-species databases
......@@ -1333,16 +1333,16 @@ sub load_registry_from_db {
( $coredb =~ /(^[a-z]+_[a-z]+)_core_(?:\d+_)?(\d+)/ );
my $dba =
Bio::EnsEMBL::DBSQL::DBAdaptor->new(-group => "core",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-dbname => $coredb,
-wait_timeout => $wait_timeout,
-no_cache => $no_cache
);
Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => "core",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-dbname => $coredb,
-wait_timeout => $wait_timeout,
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
......@@ -1401,19 +1401,22 @@ sub load_registry_from_db {
my ( $species, $num ) =
( $cdnadb =~ /(^[a-z]+_[a-z]+)_cdna_(\d+)/ );
my $dba =
Bio::EnsEMBL::DBSQL::DBAdaptor->new(-group => "cdna",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-dbname => $cdnadb,
-wait_timeout => $wait_timeout,
-no_cache => $no_cache
);
Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => "cdna",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-dbname => $cdnadb,
-wait_timeout => $wait_timeout,
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
print $cdnadb. " loaded\n" if ($verbose);
if ($verbose) {
printf( "%s loaded\n", $cdnadb );
}
}
my @vega_dbs = grep { /^[a-z]+_[a-z]+_vega_\d+_/ } @dbnames;
......@@ -1431,10 +1434,13 @@ sub load_registry_from_db {
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $vegadb,
-no_cache => $no_cache);
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
print $vegadb. " loaded\n" if ($verbose);
if ($verbose) {
printf( "%s loaded\n", $vegadb );
}
}
# Otherfeatures
......@@ -1454,31 +1460,37 @@ sub load_registry_from_db {
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $other_db,
-no_cache => $no_cache );
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
print $other_db. " loaded\n" if ($verbose);
if ($verbose) {
printf( "%s loaded\n", $other_db );
}
}
# User upload DBs
my @userupload_dbs = grep { /_userdata$/ } @dbnames;
for my $userupload_db ( @userupload_dbs ) {
for my $userupload_db (@userupload_dbs) {
my ($species) = ( $userupload_db =~ /(^.+)_userdata$/ );
my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
( -group => "userupload",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $userupload_db,
-no_cache => $no_cache
);
(my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
print $userupload_db." loaded\n" if ($verbose);
my $dba =
Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => "userupload",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $userupload_db,
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
if ($verbose) {
printf( "%s loaded\n", $userupload_db );
}
}
# Variation
......@@ -1486,9 +1498,11 @@ sub load_registry_from_db {
eval "require Bio::EnsEMBL::Variation::DBSQL::DBAdaptor";
if ($@) {
# Ignore variations as code required not there for this
print
"Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found so variation databases will be ignored if found\n"
if ($verbose);
if ($verbose) {
print(
"Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found "
. "so variation databases will be ignored if found\n" );
}
} else {
my @variation_dbs =
grep { /^[a-z]+_[a-z]+_variation_\d+_/ } @dbnames;
......@@ -1506,18 +1520,22 @@ sub load_registry_from_db {
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $variation_db,
-no_cache => $no_cache
);
print $variation_db. " loaded\n" if ($verbose);
-no_cache => $no_cache );
if ($verbose) {
printf( "%s loaded\n", $variation_db );
}
}
}
eval "require Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor";
if ($@) {
#ignore funcgen DBs as code required not there for this
print
"Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor module not found so functional genomics databases will be ignored if found\n"
if ($verbose);
if ($verbose) {
# Ignore funcgen DBs as code required not there for this
print( "Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor module not found "
. "so functional genomics databases will be ignored if found\n"
);
}
} else {
my @funcgen_dbs = grep { /^[a-z]+_[a-z]+_funcgen_\d+_/ } @dbnames;
......@@ -1534,8 +1552,11 @@ sub load_registry_from_db {
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $funcgen_db,
-no_cache => $no_cache );
print $funcgen_db. " loaded\n" if ($verbose);
-no_cache => $no_cache );
if ($verbose) {
printf( "%s loaded\n", $funcgen_db );
}
}
}
......@@ -1564,7 +1585,8 @@ sub load_registry_from_db {
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $compara_db,
-no_cache => $no_cache );
-no_cache => $no_cache );
if ($verbose) {
printf( "%s loaded\n", $compara_db );
}
......@@ -1587,10 +1609,13 @@ sub load_registry_from_db {
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $ancestral_db,
-no_cache => $no_cache);
print $ancestral_db. " loaded\n" if ($verbose);
} else {
print "No Ancestral database found" if ($verbose);
-no_cache => $no_cache );
if ($verbose) {
printf( "%s loaded\n", $ancestral_db );
}
} elsif ($verbose) {
print("No Ancestral database found");
}
# GO
......@@ -1608,16 +1633,19 @@ sub load_registry_from_db {
my $go_db = "ensembl_go_" . $go_version;
my $dba =
Bio::EnsEMBL::ExternalData::GO::GOAdaptor->new(
-group => "go",
-species => "multi",
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-dbname => $go_db,
-no_cache => $no_cache
-group => "go",
-species => "multi",
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-dbname => $go_db,
-no_cache => $no_cache
);
print $go_db. " loaded\n" if ($verbose);
if ($verbose) {
printf( "%s loaded\n", $go_db );
}
}
} elsif ($verbose) {
print("No GO database found\n");
......@@ -1854,46 +1882,41 @@ sub load_registry_from_db {
-alias => [ 'horse', 'Equuscaballus' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Tursiops_truncatus",
-alias => [ 'dolphin', 'Tursiopstruncatus' ]
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Tursiops_truncatus",
-alias => [ 'dolphin', 'Tursiopstruncatus' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Procavia_capensis",
-alias => [ 'rock_hyrax', 'hyrax', 'Procaviacapensis' ]
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Procavia_capensis",
-alias => [ 'rock_hyrax', 'hyrax', 'Procaviacapensis' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Dipodomys_ordii",
-alias => [ 'kangaroo_rat', 'Dipodomysordii' ]
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Dipodomys_ordii",
-alias => [ 'kangaroo_rat', 'Dipodomysordii' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Pteropus_vampyrus",
-alias => [ 'megabat', 'Pteropusvampyrus' ]
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Pteropus_vampyrus",
-alias => [ 'megabat', 'Pteropusvampyrus' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Tarsius_syrichta",
-alias => [ 'philippine tarsier', 'tarsier', 'Tarsiussyrichta' ]
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Tarsius_syrichta",
-alias => [ 'philippine tarsier', 'tarsier', 'Tarsiussyrichta' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Vicugna_pacos",
-alias => [ 'alpaca', 'vicugnapacos' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Gorilla_gorilla",
-alias => [ 'gorilla', 'gorillagorilla' ]
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Gorilla_gorilla",
-alias => [ 'gorilla', 'gorillagorilla' ]
);
@aliases = ('compara');
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias( -species => "multi",
-alias => \@aliases
......
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