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Removed other features from ProcessGCA.pm #499

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Merged
merged 1 commit into from
Jul 16, 2025
Merged

Removed other features from ProcessGCA.pm #499

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21 changes: 3 additions & 18 deletions modules/Bio/EnsEMBL/Analysis/Hive/RunnableDB/ProcessGCA.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -296,9 +296,6 @@ sub fetch_input {
my $core_dbname = $self->param('dbowner') . '_' . $production_gca . '_core_' . $ensembl_release . '_1';
$core_db_details->{'-dbname'} = $core_dbname;

my $otherfeatures_db_details = $self->param('otherfeatures_db');
my $otherfeatures_dbname = $self->param('dbowner') . '_' . $production_gca . '_otherfeatures_' . $ensembl_release . '_1';
$otherfeatures_db_details->{'-dbname'} = $otherfeatures_dbname;

my $rnaseq_summary_file = catfile( $short_read_dir, $production_name . '.csv' );
my $rnaseq_summary_file_genus = catfile( $short_read_dir, $production_name . '_gen.csv' );
Expand Down Expand Up @@ -388,10 +385,10 @@ sub fetch_input {
}

if ( -e $new_registry_file ) {
$self->create_registry_entry( $new_registry_file, $core_db_details, $otherfeatures_db_details, $production_name );
$self->create_registry_entry( $new_registry_file, $core_db_details, $production_name );
} else {
system( 'cp ' . $registry_file . ' ' . $new_registry_file );
$self->create_registry_entry( $new_registry_file, $core_db_details, $otherfeatures_db_details, $production_name );
$self->create_registry_entry( $new_registry_file, $core_db_details, $production_name );
}

#Check genebuild status of assembly unless custom loading no need to check registry
Expand All @@ -410,8 +407,6 @@ sub fetch_input {
#Output
$output_params->{'core_db'} = $core_db_details;
$output_params->{'core_dbname'} = $core_dbname;
$output_params->{'otherfeatures_db'} = $otherfeatures_db_details;
$output_params->{'otherfeatures_dbname'} = $otherfeatures_dbname;
$output_params->{'stable_id_start'} = $stable_id_start;
$output_params->{'stable_id_prefix'} = $stable_id_prefix;
$output_params->{'clade'} = $clade;
Expand Down Expand Up @@ -681,7 +676,7 @@ sub get_clade_params {
}

sub create_registry_entry {
my ( $self, $registry_path, $core_db_details, $otherfeatures_db_details, $production_name ) = @_;
my ( $self, $registry_path, $core_db_details, $production_name ) = @_;

unless ( -e $registry_path ) {
$self->throw( "A registry file was not found on the path provided. Path:\n" . $registry_path );
Expand All @@ -696,15 +691,6 @@ sub create_registry_entry {
"-species => '" . $production_name . "',\n" .
"-group => 'core',\n" .
");\n";
my $otherfeatures_string = "Bio::EnsEMBL::DBSQL::DBAdaptor->new(\n" .
"-host => '" . $otherfeatures_db_details->{'-host'} . "',\n" .
"-port => '" . $otherfeatures_db_details->{'-port'} . "',\n" .
"-dbname => '" . $otherfeatures_db_details->{'-dbname'} . "',\n" .
"-user => '" . $otherfeatures_db_details->{'-user'} . "',\n" .
"-pass => '" . $otherfeatures_db_details->{'-pass'} . "',\n" .
"-species => '" . $production_name . "',\n" .
"-group => 'otherfeatures',\n" .
");\n";

open( my $in, '<', $registry_path )
or die "Can't open " . $registry_path . " for reading.\n";
Expand All @@ -717,7 +703,6 @@ sub create_registry_entry {
print $out $line;
if ( $line =~ /\{/ ) {
print $out $core_string;
print $out $otherfeatures_string;
}
}
close $out;
Expand Down