text: -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
  -- Copyright [2016-2018] 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.
  
  
  # update to the new protein function prediction schema
  
  DROP TABLE protein_info;
  DROP TABLE protein_position;
  DROP TABLE polyphen_prediction;
  DROP TABLE sift_prediction;
  
  CREATE TABLE protein_function_predictions (
  
      translation_stable_id   VARCHAR(128) NOT NULL,
      transcript_stable_id    VARCHAR(128) NOT NULL,
      translation_md5         CHAR(32) NOT NULL,
      polyphen_predictions    MEDIUMBLOB,
      sift_predictions        MEDIUMBLOB,
      
      PRIMARY KEY (translation_stable_id),
      KEY transcript_idx (transcript_stable_id)
  );
  
  # add sift and polyphen scores to the transcript_variation table for biomart
  
  ALTER TABLE transcript_variation ADD COLUMN polyphen_score FLOAT DEFAULT NULL; 
  ALTER TABLE transcript_variation ADD COLUMN sift_score FLOAT DEFAULT NULL; 
  
  # patch identifier
  INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL,'patch', 'patch_63_64_c.sql|update to new protein function prediction schema');
  