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patch_61_62_i.sql
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-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-- Copyright [2016-2022] EMBL-European Bioinformatics Institute
--
-- Licensed under the Apache License, Version 2.0 (the "License");
-- you may not use this file except in compliance with the License.
-- You may obtain a copy of the License at
--
-- http://www.apache.org/licenses/LICENSE-2.0
--
-- Unless required by applicable law or agreed to in writing, software
-- distributed under the License is distributed on an "AS IS" BASIS,
-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-- See the License for the specific language governing permissions and
-- limitations under the License.
# change the consequence_type column in variation_feature to use SO accessions
ALTER TABLE variation_feature MODIFY consequence_type SET (
'intergenic_variant',
'splice_acceptor_variant',
'splice_donor_variant',
'complex_change_in_transcript',
'stop_lost',
'coding_sequence_variant',
'non_synonymous_codon',
'stop_gained',
'synonymous_codon',
'frameshift_variant',
'nc_transcript_variant',
'mature_miRNA_variant',
'NMD_transcript_variant',
'5_prime_UTR_variant',
'3_prime_UTR_variant',
'incomplete_terminal_codon_variant',
'intron_variant',
'splice_region_variant',
'5KB_downstream_variant',
'500B_downstream_variant',
'5KB_upstream_variant',
'2KB_upstream_variant',
'initiator_codon_change',
'stop_retained_variant',
'inframe_codon_gain',
'inframe_codon_loss',
'miRNA_target_site_variant',
'pre_miRNA_variant',
'regulatory_region_variant',
'increased_binding_affinity',
'decreased_binding_affinity',
'binding_site_variant'
) DEFAULT 'intergenic_variant' NOT NULL;
# patch identifier
INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL,'patch', 'patch_61_62_i.sql|change the consequence_type column in variation_feature to use SO terms');