From 221e14bd280e1ae92babe277f95e5d12121e9c81 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 26 Nov 2008 11:48:32 +0000
Subject: [PATCH] Corrected parsing of the names of the single species core
databases from the Ensembl Genomes project.
Formatting.
---
modules/Bio/EnsEMBL/Registry.pm | 207 ++++++++++++++++++--------------
1 file changed, 115 insertions(+), 92 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 621477a421..855542d8be 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -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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