view variant_effect_predictor/Bio/EnsEMBL/Variation/Pipeline/FinishVariationClass.pm @ 0:1f6dce3d34e0

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package Bio::EnsEMBL::Variation::Pipeline::FinishVariationClass;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Variation::Pipeline::BaseVariationProcess);

my $DEBUG = 0;

sub run {
    my $self = shift;
    
    my $temp_var_table = $self->required_param('temp_var_table');
    
    my $temp_var_feat_table = $self->required_param('temp_var_feat_table');
  
    my $var_dba = $self->get_species_adaptor('variation');
    
    my $dbc = $var_dba->dbc;
    
    # copy the attribs across to the real tables

    $dbc->do(qq{
        UPDATE  variation_feature vf, $temp_var_feat_table tvf
        SET     vf.class_attrib_id = tvf.class_attrib_id
        WHERE   vf.variation_feature_id = tvf.variation_feature_id
    });

    $dbc->do(qq{
        UPDATE  variation v, $temp_var_table tv
        SET     v.class_attrib_id = tv.class_attrib_id
        WHERE   v.variation_id = tv.variation_id
    });
    
    # and get rid of the temp tables
    $dbc->do(qq{DROP TABLE $temp_var_table});
    $dbc->do(qq{DROP TABLE $temp_var_feat_table});
    
    return;
}

1;