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1 package Bio::EnsEMBL::Variation::Pipeline::FinishVariationClass;
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2
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3 use strict;
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4 use warnings;
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5
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6 use base qw(Bio::EnsEMBL::Variation::Pipeline::BaseVariationProcess);
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7
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8 my $DEBUG = 0;
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9
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10 sub run {
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11 my $self = shift;
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12
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13 my $temp_var_table = $self->required_param('temp_var_table');
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14
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15 my $temp_var_feat_table = $self->required_param('temp_var_feat_table');
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16
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17 my $var_dba = $self->get_species_adaptor('variation');
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18
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19 my $dbc = $var_dba->dbc;
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20
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21 # copy the attribs across to the real tables
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22
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23 $dbc->do(qq{
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24 UPDATE variation_feature vf, $temp_var_feat_table tvf
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25 SET vf.class_attrib_id = tvf.class_attrib_id
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26 WHERE vf.variation_feature_id = tvf.variation_feature_id
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27 });
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28
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29 $dbc->do(qq{
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30 UPDATE variation v, $temp_var_table tv
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31 SET v.class_attrib_id = tv.class_attrib_id
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32 WHERE v.variation_id = tv.variation_id
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33 });
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34
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35 # and get rid of the temp tables
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36 $dbc->do(qq{DROP TABLE $temp_var_table});
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37 $dbc->do(qq{DROP TABLE $temp_var_feat_table});
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38
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39 return;
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40 }
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41
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42 1;
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43
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