-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-- Copyright [2016-2019] EMBL-European Bioinformatics Institute
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# patch_87_88_e.sql
#
# Title: New column in the gene_member table to record the biotype (group) of each gene
#
# Description:
#   This new column allows to distinguish between coding and non-coding genes without
#   having to look at the seq_member table

SET session sql_mode='TRADITIONAL';

ALTER TABLE gene_member ADD COLUMN biotype_group ENUM('coding', 'snoncoding', 'lnoncoding', 'mnoncoding', 'LRG') NOT NULL DEFAULT 'coding' AFTER genome_db_id;
UPDATE gene_member JOIN seq_member USING (gene_member_id) SET biotype_group = "snoncoding" WHERE seq_member.source_name LIKE "%TRANS";

# Patch identifier
INSERT INTO meta (species_id, meta_key, meta_value)
  VALUES (NULL, 'patch', 'patch_87_88_e.sql|biotype_group');
