diff variant_effect_predictor/Bio/EnsEMBL/Variation/Pipeline/UpdateVariationFeature.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/Pipeline/UpdateVariationFeature.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,58 @@
+package Bio::EnsEMBL::Variation::Pipeline::UpdateVariationFeature;
+
+use strict;
+use warnings;
+
+use base qw(Bio::EnsEMBL::Variation::Pipeline::BaseVariationProcess);
+
+sub run {
+
+    my $self = shift;
+
+    my $var_dba = $self->get_species_adaptor('variation');
+    
+    my $dbc = $var_dba->dbc;
+    
+    # first set the default consequence type
+
+    $dbc->do(qq{
+        UPDATE  variation_feature
+        SET     consequence_types = 'intergenic_variant'
+    }) or die "Failed to reset consequence_types on variation_feature";
+
+    # create a temp table (dropping it if it exists)
+
+    my $temp_table = 'variation_feature_with_tv';
+
+    $dbc->do(qq{DROP TABLE IF EXISTS $temp_table})
+        or die "Failed to drop pre-existing temp table";
+    
+    $dbc->do(qq{CREATE TABLE $temp_table LIKE variation_feature})
+        or die "Failed to create temp table";
+
+    # concatenate the consequence types from transcript_variation 
+
+    $dbc->do(qq{
+        INSERT INTO $temp_table (variation_feature_id, consequence_types)
+        SELECT  variation_feature_id, GROUP_CONCAT(DISTINCT(consequence_types)) 
+        FROM    transcript_variation 
+        GROUP BY variation_feature_id
+    }) or die "Populating temp table failed";
+
+    # update variation_feature
+    
+    $dbc->do(qq{
+        UPDATE  variation_feature vf, $temp_table tvf
+        SET     vf.consequence_types = tvf.consequence_types
+        WHERE   vf.variation_feature_id = tvf.variation_feature_id
+    }) or die "Failed to update vf table";
+
+    # and get rid of our temp table
+
+    $dbc->do(qq{DROP TABLE $temp_table})
+        or die "Failed to drop temp table";
+
+}
+
+1;
+