my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $species_name = $ref_arg->{species};
my $file = $ref_arg->{file};
my $verbose = $ref_arg->{verbose};
my $db = $ref_arg->{dba};
my $dbi = $ref_arg->{dbi};
$dbi = $self->dbi unless defined $dbi;
if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
croak "Need to pass source_id, species_id and file as pairs";
}
$verbose |=0;
my $project;
my $user ="ensro";
my $host;
my $port = 3306;
my $dbname;
my $pass;
if($file =~ /project[=][>](\S+?)[,]/){
$project = $1;
}
if($file =~ /host[=][>](\S+?)[,]/){
$host = $1;
}
if($file =~ /port[=][>](\S+?)[,]/){
$port = $1;
}
if($file =~ /dbname[=][>](\S+?)[,]/){
$dbname = $1;
}
if($file =~ /pass[=][>](\S+?)[,]/){
$pass = $1;
}
if($file =~ /user[=][>](\S+?)[,]/){
$user = $1;
}
my %species_id_to_names = $self->species_id2name($dbi);
if (defined $species_name) { push @{$species_id_to_names{$species_id}}, $species_name; }
if (!defined $species_id_to_names{$species_id}) { next; }
my $species_id_to_names = \%species_id_to_names;
my $names = $species_id_to_names->{$species_id};
my $species_lookup = $self->_get_species($verbose);
my $active = $self->_is_active($species_lookup, $names, $verbose);
if (!$active) {
return;
}
$species_name = $species_id_to_names{$species_id}[0];
#get stable_ids from core and create xrefs
my $registry = "Bio::EnsEMBL::Registry";
my ($gene_adaptor);
if ($host) {
'-host' => $host,
'-port' => $port,
'-user' => $user,
'-pass' => $pass,
'-dbname' => $dbname,
'-species' => $species_name,
'-group' => 'core',
);
$gene_adaptor = $db->get_GeneAdaptor();
} elsif (defined $project && $project eq 'ensembl') {
print "Loading the Registry\n" if $verbose;
$registry->load_registry_from_multiple_dbs(
{
'-host' => 'mysql-ens-sta-1',
'-port' => 4519,
'-user' => 'ensro',
},
);
$gene_adaptor = $registry->
get_adaptor($species_name,
'core',
'Gene');
} elsif (defined $project && $project eq 'ensemblgenomes') {
$registry->load_registry_from_multiple_dbs(
{
'-host' => 'mysql-eg-staging-1.ebi.ac.uk',
'-port' => 4160,
'-user' => 'ensro',
},
{
'-host' => 'mysql-eg-staging-2.ebi.ac.uk',
'-port' => 4275,
'-user' => 'ensro',
},
);
$gene_adaptor = $registry->get_adaptor($species_name, 'core', 'Gene');
} elsif (defined $db) {
$gene_adaptor = $db->get_GeneAdaptor();
} else {
die("Missing or unsupported project value. Supported values: ensembl, ensemblgenomes");
}
print "Finished loading the registry\n" if $verbose;
my @stable_ids =
map { $_->stable_id } @{$gene_adaptor->fetch_all()};
my $xref_count = 0;
foreach my $gene_stable_id (@stable_ids) {
my $xref_id = $self->add_xref({ acc => $gene_stable_id,
label => $gene_stable_id,
source_id => $source_id,
species_id => $species_id,
dbi => $dbi,
info_type => "DIRECT"} );
$self->add_direct_xref( $xref_id, $gene_stable_id, 'gene', '', $dbi);
if ($xref_id) {
$xref_count++;
}
}
print "Added $xref_count DIRECT xrefs\n" if($verbose);
if ( !$xref_count ) {
return 1; # 1 error
}
return 0; # successfull
}
Code:
