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1 package Bio::EnsEMBL::Variation::Pipeline::UpdateVariationFeature;
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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 sub run {
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9
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10 my $self = shift;
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11
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12 my $var_dba = $self->get_species_adaptor('variation');
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13
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14 my $dbc = $var_dba->dbc;
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15
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16 # first set the default consequence type
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17
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18 $dbc->do(qq{
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19 UPDATE variation_feature
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20 SET consequence_types = 'intergenic_variant'
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21 }) or die "Failed to reset consequence_types on variation_feature";
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22
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23 # create a temp table (dropping it if it exists)
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24
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25 my $temp_table = 'variation_feature_with_tv';
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26
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27 $dbc->do(qq{DROP TABLE IF EXISTS $temp_table})
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28 or die "Failed to drop pre-existing temp table";
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29
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30 $dbc->do(qq{CREATE TABLE $temp_table LIKE variation_feature})
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31 or die "Failed to create temp table";
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32
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33 # concatenate the consequence types from transcript_variation
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34
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35 $dbc->do(qq{
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36 INSERT INTO $temp_table (variation_feature_id, consequence_types)
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37 SELECT variation_feature_id, GROUP_CONCAT(DISTINCT(consequence_types))
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38 FROM transcript_variation
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39 GROUP BY variation_feature_id
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40 }) or die "Populating temp table failed";
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41
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42 # update variation_feature
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43
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44 $dbc->do(qq{
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45 UPDATE variation_feature vf, $temp_table tvf
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46 SET vf.consequence_types = tvf.consequence_types
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47 WHERE vf.variation_feature_id = tvf.variation_feature_id
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48 }) or die "Failed to update vf table";
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49
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50 # and get rid of our temp table
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51
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52 $dbc->do(qq{DROP TABLE $temp_table})
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53 or die "Failed to drop temp table";
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54
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55 }
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56
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57 1;
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58
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