From 3f118be49f414d6e0af93119d10eddd43e299515 Mon Sep 17 00:00:00 2001
From: Maurice Hendrix <mh18@sanger.ac.uk>
Date: Mon, 20 Sep 2010 09:54:32 +0000
Subject: [PATCH] No longer in use, deleted
---
sql/vega_latest_schema.sql | 147 --------------------
sql/vega_specific_tables.sql | 251 -----------------------------------
2 files changed, 398 deletions(-)
delete mode 100644 sql/vega_latest_schema.sql
delete mode 100644 sql/vega_specific_tables.sql
diff --git a/sql/vega_latest_schema.sql b/sql/vega_latest_schema.sql
deleted file mode 100644
index 2887ed6030..0000000000
--- a/sql/vega_latest_schema.sql
+++ /dev/null
@@ -1,147 +0,0 @@
-###################################################################
-# FROM patch_23_24.sql
-
-# Adds a display_label column to the prediction_transcript table and
-# populates it.
-# This is done by creating a temporary table and renaming it rather than just
-# using an alter table statement followed by an update statement. This
-# is because in mysql 3 it is not possible to use a join in an update
-# statement.
-
-
-# create the temporary table
-
-CREATE TABLE tmp_prediction_transcript (
- prediction_transcript_id int unsigned not null auto_increment,
- seq_region_id int unsigned not null,
- seq_region_start int unsigned not null,
- seq_region_end int unsigned not null,
- seq_region_strand tinyint not null,
- analysis_id int,
- display_label varchar(255),
-
- PRIMARY KEY( prediction_transcript_id ),
- KEY ( seq_region_id, seq_region_start ),
- KEY analysis_idx( analysis_id )
-);
-
-
-# populate the tmp table from the original table, and generate display_labels
-# at the same time. The display label generated looks like GENSCAN00000018082
-# or SNAP00000018082, etc.
-
-INSERT INTO tmp_prediction_transcript
-SELECT pt.prediction_transcript_id, pt.seq_region_id, pt.seq_region_start,
- pt.seq_region_end, pt.seq_region_strand, pt.analysis_id,
- CONCAT(UPPER(a.logic_name), LPAD(pt.prediction_transcript_id, 11, '0'))
-FROM prediction_transcript pt, analysis a
-WHERE a.analysis_id = pt.analysis_id;
-
-
-# drop the original table and rename the temp table
-
-DROP TABLE prediction_transcript;
-ALTER TABLE tmp_prediction_transcript RENAME prediction_transcript;
-
-
-
-###################################################################
-# FROM patch_30_31.sql
-
-
-# gene table changes
-
-ALTER TABLE gene CHANGE type biotype VARCHAR(40) NOT NULL default 'protein_coding';
-ALTER TABLE gene ADD source VARCHAR(20) NOT NULL default 'ensembl';
-ALTER TABLE gene ADD confidence ENUM( 'KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED' ) default 'NOVEL';
-ALTER TABLE gene ADD description text;
-
-UPDATE gene g, gene_description gd SET g.description = gd.description WHERE gd.gene_id = g.gene_id;
-
-DROP TABLE gene_description;
-
-# transcript related changes
-
-ALTER TABLE transcript ADD biotype VARCHAR(40) NOT NULL DEFAULT 'protein_coding';
-ALTER TABLE transcript ADD confidence ENUM( 'KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED' ) default 'NOVEL';
-ALTER TABLE transcript ADD description text;
-
-# reasonable default for transcript description
-# it might be questionable whether a separate transcript description is necessary
-
-UPDATE transcript t, xref x SET t.description = x.description WHERE t.display_xref_id = x.xref_id;
-UPDATE transcript SET description=NULL WHERE description="";
-
-# usefull settings for the new tables
-
-UPDATE gene SET source = 'vega';
-
-#########################################################################################################
-# may well want to update confidence for genes and transcripts based on source of the xref, but not yet #
-
-#UPDATE gene g, xref x, external_db ed SET g.confidence='KNOWN' WHERE g.display_xref_id = x.xref_id and x.external_db_id = ed.external_db_id and g.display_xref_id != 0 and ed.status like 'KNOWN%';
-#UPDATE transcript t, xref x, external_db ed SET t.confidence='KNOWN' WHERE t.display_xref_id = x.xref_id and x.external_db_id = ed.external_db_id and t.display_xref_id != 0 and ed.status like 'KNOWN%';
-
-# HAWK -> biotype conversions
-
-UPDATE gene SET biotype='processed_transcript' WHERE biotype = 'Transcript';
-UPDATE gene SET biotype='pseudogene', confidence='NOVEL' WHERE biotype = 'Pseudogene';
-UPDATE gene SET biotype='protein_coding', confidence='NOVEL' WHERE biotype = 'Novel_CDS';
-UPDATE gene SET biotype='processed_transcript', confidence='NOVEL' WHERE biotype = 'Novel_Transcript';
-UPDATE gene SET biotype='processed_transcript',confidence='PUTATIVE' WHERE biotype = 'Putative';
-UPDATE gene SET biotype='protein_coding', confidence='KNOWN' WHERE biotype = 'Known';
-
-UPDATE gene SET biotype='processed_pseudogene', confidence=NULL WHERE biotype = 'Processed_pseudogene';
-UPDATE gene SET biotype='unprocessed_pseudogene', confidence=NULL WHERE biotype = 'Unprocessed_pseudogene';
-UPDATE gene SET biotype='protein_coding',confidence='PREDICTED' WHERE biotype = 'Predicted_Gene';
-UPDATE gene SET biotype='Ig_segment', confidence=NULL WHERE biotype = 'Ig_Segment';
-UPDATE gene SET biotype='Ig_pseudogene_segment', confidence=NULL WHERE biotype = 'Ig_Pseudogene_Segment';
-
-UPDATE gene SET biotype=replace( biotype, '-','_' );
-
-# reasonable biotypes for the transcripts, take the one from the gene
-
-UPDATE transcript t, gene g SET t.biotype = g.biotype, t.confidence = g.confidence WHERE g.gene_id = t.gene_id;
-
-
-########################
-# FROM patch_31_32.sql #
-########################
-
-
-# Add linkable & priority columns to external_db
-ALTER TABLE external_db ADD COLUMN dbprimary_acc_linkable BOOLEAN DEFAULT 1 NOT NULL;
-ALTER TABLE external_db ADD COLUMN display_label_linkable BOOLEAN DEFAULT 0 NOT NULL;
-ALTER TABLE external_db ADD COLUMN priority INT NOT NULL;
-
-
-########################
-# FROM patch_32_33.sql #
-########################
-
-# Add db_display_name column to external_db
-ALTER TABLE external_db ADD COLUMN db_display_name VARCHAR(255);
-
-########################
-# FROM patch_33_34.sql #
-########################
-
-ALTER table object_xref MODIFY ensembl_object_type ENUM( 'RawContig', 'Transcript', 'Gene', 'Translation', 'regulatory_factor', 'regulatory_feature' ) not null;
-
-alter table transcript change confidence status enum( 'KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED' );
-alter table gene change confidence status enum( 'KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED' );
-
-########################
-# FROM patch_36_37.sql #
-########################
-
-#manipulations of peptide and gene archive tables are in ensembl patch scripts
-#but are not used for vega since tables are empty
-
-
-
-
-###########################
-#set latest schema version#
-###########################
-update meta set meta_value = '37' where meta_key = 'schema_version';
diff --git a/sql/vega_specific_tables.sql b/sql/vega_specific_tables.sql
deleted file mode 100644
index 6e14342e53..0000000000
--- a/sql/vega_specific_tables.sql
+++ /dev/null
@@ -1,251 +0,0 @@
-
-# Script to create Vega specific database tables - this is used in
-# conjunction with table.sql (creates Ensembl Schema) to create a
-# Vega new schema database.
-#
-# Conventions are the same as for Ensmebl:
-# - use lower case and underscores
-# - internal ids are integers named tablename_id
-# - same name is given in foreign key relations
-#
-# Steve Trevanion (st3@sanger.ac.uk) created 2/7/04
-
-
-################################################################################
-#
-# Table structure for table 'gene_synonym'
-#
-
-CREATE TABLE gene_synonym (
- synonym_id int(10) unsigned NOT NULL auto_increment,
- name varchar(100) default NULL,
- gene_info_id int(10) unsigned NOT NULL default '0',
- PRIMARY KEY (synonym_id),
- KEY gene_info_id_idx (gene_info_id)
-) TYPE=MyISAM;
-
-
-################################################################################
-#
-# Table structure for table 'transcript_info'
-#
-
-CREATE TABLE transcript_info (
- transcript_info_id int(10) unsigned NOT NULL auto_increment,
- transcript_stable_id varchar(40) default NULL,
- name varchar(40) default NULL,
- transcript_class_id int(10) unsigned default NULL,
- cds_start_not_found enum('true','false') NOT NULL default 'true',
- cds_end_not_found enum('true','false') NOT NULL default 'true',
- mRNA_start_not_found enum('true','false') NOT NULL default 'true',
- mRNA_end_not_found enum('true','false') NOT NULL default 'true',
- author_id int(10) unsigned NOT NULL default '0',
- timestamp datetime NOT NULL default '0000-00-00 00:00:00',
- PRIMARY KEY (transcript_info_id),
- KEY transcript_stable_id_idx (transcript_stable_id)
-) TYPE=MyISAM;
-
-################################################################################
-#
-# Table structure for table 'current_gene_info'
-#
-
-CREATE TABLE current_gene_info (
- gene_info_id int(10) unsigned NOT NULL default '0',
- gene_stable_id varchar(40) default NULL,
- PRIMARY KEY (gene_info_id),
- UNIQUE KEY gene_stable_id (gene_stable_id)
-) TYPE=MyISAM;
-
-################################################################################
-#
-# Table structure for table 'current_transcript_info'
-#
-
-CREATE TABLE current_transcript_info (
- transcript_info_id int(10) unsigned NOT NULL default '0',
- transcript_stable_id varchar(40) default NULL,
- PRIMARY KEY (transcript_info_id),
- UNIQUE KEY transcript_stable_id (transcript_stable_id)
-) TYPE=MyISAM;
-
-################################################################################
-#
-# Table structure for table 'author'
-#
-
-CREATE TABLE author (
- author_id int(10) unsigned NOT NULL auto_increment,
- author_email varchar(50) default NULL,
- author_name varchar(50) default NULL,
- PRIMARY KEY (author_id)
-) TYPE=MyISAM;
-
-################################################################################
-#
-# Table structure for table 'gene_name'
-#
-
-CREATE TABLE gene_name (
- gene_name_id int(10) unsigned NOT NULL auto_increment,
- name varchar(100) default NULL,
- gene_info_id int(10) unsigned NOT NULL default '0',
- PRIMARY KEY (gene_name_id),
- KEY gene_info_id_idx (gene_info_id)
-) TYPE=MyISAM;
-
-
-################################################################################
-#
-# Table structure for table 'transcript_class'
-#
-
-CREATE TABLE transcript_class (
- transcript_class_id int(10) unsigned NOT NULL auto_increment,
- name varchar(40) default NULL,
- description varchar(255) default NULL,
- PRIMARY KEY (transcript_class_id),
- UNIQUE KEY name (name)
-) TYPE=MyISAM;
-
-################################################################################
-#
-# Table structure for table 'gene_remark'
-#
-
-CREATE TABLE gene_remark (
- gene_remark_id int(10) unsigned NOT NULL auto_increment,
- remark text,
- gene_info_id int(10) unsigned NOT NULL default '0',
- PRIMARY KEY (gene_remark_id),
- KEY gene_info_id_idx (gene_info_id)
-) TYPE=MyISAM;
-
-
-################################################################################
-#
-# Table structure for table 'gene_info'
-#
-
-CREATE TABLE gene_info (
- gene_info_id int(10) unsigned NOT NULL auto_increment,
- gene_stable_id varchar(40) default NULL,
- author_id int(10) unsigned NOT NULL default '0',
- is_known enum('true','false') default 'false',
- timestamp datetime NOT NULL default '0000-00-00 00:00:00',
- PRIMARY KEY (gene_info_id),
- KEY gene_stable_id_idx (gene_stable_id)
-) TYPE=MyISAM;
-
-
-################################################################################
-#
-# Table structure for table 'evidence'
-#
-
-CREATE TABLE evidence (
- evidence_id int(10) unsigned NOT NULL auto_increment,
- evidence_name varchar(40) default NULL,
- transcript_info_id int(10) unsigned default NULL,
- type enum('EST','cDNA','Protein','Genomic','UNKNOWN') default NULL,
- PRIMARY KEY (evidence_id),
- KEY transcript_info_id_idx (transcript_info_id)
-) TYPE=MyISAM;
-
-################################################################################
-#
-# Table structure for table 'transcript_remark'
-#
-
-CREATE TABLE transcript_remark (
- transcript_remark_id int(10) unsigned NOT NULL auto_increment,
- remark text,
- transcript_info_id int(10) unsigned NOT NULL default '0',
- PRIMARY KEY (transcript_remark_id),
- KEY transcript_info_id_idx (transcript_info_id)
-) TYPE=MyISAM;
-
-################################################################################
-#
-# Table structure for table 'clone_info'
-
-
-CREATE TABLE clone_info (
- clone_info_id int(10) unsigned NOT NULL auto_increment,
- seq_region_id int(10) unsigned NOT NULL default '0',
- author_id int(10) default NULL,
- timestamp datetime NOT NULL default '0000-00-00 00:00:00',
- PRIMARY KEY (clone_info_id),
- UNIQUE clone_id_idx (clone_id )
-) TYPE=MyISAM;
-
-
-
-################################################################################
-#
-# Table structure for table 'clone_remark'
-
-
-CREATE TABLE clone_remark (
- clone_remark_id int(10) unsigned NOT NULL auto_increment,
- remark text,
- clone_info_id int(10) unsigned NOT NULL default '0',
- PRIMARY KEY (clone_remark_id),
- KEY clone_info_id_idx (clone_info_id)
-) TYPE=MyISAM;
-
-
-################################################################################
-#
-# Table structure for table 'current_clone_info'
-
-
-CREATE TABLE current_clone_info (
- seq_region_id int(10) unsigned NOT NULL default '0',
- clone_info_id int(10) unsigned NOT NULL default '0',
- clone_version int(10) default NULL,
- PRIMARY KEY (clone_id)
-) TYPE=MyISAM;
-
-
-################################################################################
-#
-# Table structure for table 'assembly_tag'
-
-CREATE TABLE assembly_tag (
- tag_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
- contig_id INT(10) UNSIGNED NOT NULL,
- contig_start INT(10) NOT NULL,
- contig_end INT(10) NULL,
- contig_strand TINYINT(1) NOT NULL DEFAULT '0',
- tag_type ENUM('Unsure', 'Clone_left_end', 'Clone_right_end', 'Misc') NOT NULL DEFAULT 'Misc',
- tag_info TEXT NULL,
-
- PRIMARY KEY (tag_id),
- UNIQUE KEY (contig_id, contig_start, contig_end, contig_strand, tag_type)
-) TYPE=MyISAM;
-
-
-################################################################################
-#
-# Table structure for table 'keyword'
-
-CREATE TABLE keyword (
- keyword_id int(10) unsigned NOT NULL auto_increment,
- keyword_name varchar(50) default NULL,
- PRIMARY KEY (keyword_id)
-) TYPE=MyISAM;
-
-
-################################################################################
-#
-# Table structure for table 'clone_info_keyword'
-
-
-CREATE TABLE clone_info_keyword (
- keyword_id int(10) unsigned NOT NULL default '0',
- clone_info_id int(10) unsigned NOT NULL default '0',
- PRIMARY KEY (keyword_id,clone_info_id),
- KEY clone_info_id_idx (clone_info_id)
-) TYPE=MyISAM;
-
--
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