From 7f47b961debd0b25452aa74165b4f53ee386afce Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Fri, 2 Mar 2012 09:14:19 +0000
Subject: [PATCH] Patches for 67. Index addition on transcript, new status on
transcript & gene and a new supporting evidence table for introns
---
sql/patch_66_67_c.sql | 24 ++++++++++++++++++++++++
sql/patch_66_67_d.sql | 16 ++++++++++++++++
sql/patch_66_67_e.sql | 13 +++++++++++++
sql/table.sql | 40 ++++++++++++++++++++++++++++++++++------
4 files changed, 87 insertions(+), 6 deletions(-)
create mode 100644 sql/patch_66_67_c.sql
create mode 100644 sql/patch_66_67_d.sql
create mode 100644 sql/patch_66_67_e.sql
diff --git a/sql/patch_66_67_c.sql b/sql/patch_66_67_c.sql
new file mode 100644
index 0000000000..b0c825664a
--- /dev/null
+++ b/sql/patch_66_67_c.sql
@@ -0,0 +1,24 @@
+# patch_66_67_c.sql
+#
+# Title: Adding intron_supporting_evidence table
+#
+# Description: Introns can be supported by an external feature. This gives a
+# weight to how much we believe the intron
+#
+
+CREATE TABLE intron_supporting_evidence (
+ intron_supporting_evidence_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ previous_exon_id INT(10) UNSIGNED NOT NULL,
+ next_exon_id INT(10) UNSIGNED NOT NULL,
+ hit_name VARCHAR(100) NOT NULL,
+ score DECIMAL(10,3),
+ score_type ENUM('NONE', 'DEPTH') DEFAULT 'NONE',
+
+ PRIMARY KEY (intron_supporting_evidence_id),
+
+ UNIQUE KEY (previous_exon_id, next_exon_id)
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+# Patch identifier:
+INSERT INTO meta (species_id, meta_key, meta_value)
+ VALUES (NULL, 'patch', 'patch_66_67_c.sql|adding_intron_supporting_evidence');
diff --git a/sql/patch_66_67_d.sql b/sql/patch_66_67_d.sql
new file mode 100644
index 0000000000..288f86bce1
--- /dev/null
+++ b/sql/patch_66_67_d.sql
@@ -0,0 +1,16 @@
+# patch_66_67_d.sql
+#
+# Title: Adding new status type ANNOTATED
+#
+# Description: Including a new status type for genes and transcript
+#
+
+ALTER TABLE gene MODIFY COLUMN status
+ ENUM('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED');
+
+ALTER TABLE transcript MODIFY COLUMN status
+ ENUM('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED');
+
+# Patch identifier:
+INSERT INTO meta (species_id, meta_key, meta_value)
+ VALUES (NULL, 'patch', 'patch_66_67_d.sql|adding_gene_transcript_annotated');
diff --git a/sql/patch_66_67_e.sql b/sql/patch_66_67_e.sql
new file mode 100644
index 0000000000..b108806097
--- /dev/null
+++ b/sql/patch_66_67_e.sql
@@ -0,0 +1,13 @@
+# patch_66_67_e.sql
+#
+# Title: Adding an index to gene canonical transcript id
+#
+# Description: This is a lookup which is normally fast but when we have a lot
+# of genes in a core schema (multispecies DBs) then these queries slow down
+#
+
+ALTER TABLE gene ADD KEY canonical_transcript_id_idx (canonical_transcript_id);
+
+# Patch identifier:
+INSERT INTO meta (species_id, meta_key, meta_value)
+ VALUES (NULL, 'patch', 'patch_66_67_e.sql|index_canonical_transcript_id');
diff --git a/sql/table.sql b/sql/table.sql
index 90489bf69e..4a489bb0ea 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -259,6 +259,32 @@ CREATE TABLE exon (
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+/**
+@table intron_supporting_evidence
+@desc Provides the evidence which we have used to declare an intronic region
+
+@column intron_supporting_evidence_id Surrogate primary key
+@column previous_exon_id Indicates the exon flanking upstream of the intron. Foreign key references to the @link exon table.
+@column next_exon_id Indicates the exon flanking downstream of the intron. Foreign key references to the @link exon table.
+@column score Score supporting the intron
+@column score_type The type of score e.g. NONE
+
+@see exon
+
+*/
+
+CREATE TABLE intron_supporting_evidence (
+ intron_supporting_evidence_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+ previous_exon_id INT(10) UNSIGNED NOT NULL,
+ next_exon_id INT(10) UNSIGNED NOT NULL,
+ hit_name VARCHAR(100) NOT NULL,
+ score DECIMAL(10,3),
+ score_type ENUM('NONE', 'DEPTH') DEFAULT 'NONE',
+
+ PRIMARY KEY (intron_supporting_evidence_id),
+
+ UNIQUE KEY (previous_exon_id, next_exon_id)
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
/**
@table exon_transcript
@@ -271,7 +297,6 @@ CREATE TABLE exon (
@see exon
@see transcript
-
*/
CREATE TABLE exon_transcript (
@@ -327,7 +352,7 @@ CREATE TABLE gene (
seq_region_strand TINYINT(2) NOT NULL,
display_xref_id INT(10) UNSIGNED,
source VARCHAR(20) NOT NULL,
- status ENUM('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN'),
+ status ENUM('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED'),
description TEXT,
is_current BOOLEAN NOT NULL DEFAULT 1,
canonical_transcript_id INT(10) UNSIGNED NOT NULL,
@@ -341,7 +366,8 @@ CREATE TABLE gene (
KEY seq_region_idx (seq_region_id, seq_region_start),
KEY xref_id_index (display_xref_id),
KEY analysis_idx (analysis_id),
- KEY stable_id_idx (stable_id, version)
+ KEY stable_id_idx (stable_id, version),
+ KEY canonical_transcript_id_idx (canonical_transcript_id)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
@@ -447,7 +473,10 @@ INSERT INTO meta (species_id, meta_key, meta_value) VALUES
# NOTE: Avoid line-breaks in values.
INSERT INTO meta (species_id, meta_key, meta_value) VALUES
(NULL, 'patch', 'patch_66_67_a.sql|schema_version'),
- (NULL, 'patch', 'patch_66_67_b.sql|drop_stable_id_views')
+ (NULL, 'patch', 'patch_66_67_b.sql|drop_stable_id_views'),
+ (NULL, 'patch', 'patch_66_67_c.sql|adding_intron_supporting_evidence'),
+ (NULL, 'patch', 'patch_66_67_d.sql|adding_gene_transcript_annotated'),
+ (NULL, 'patch', 'patch_66_67_e.sql|index_canonical_transcript_id'),
;
/**
@@ -672,7 +701,7 @@ CREATE TABLE transcript (
seq_region_strand TINYINT(2) NOT NULL,
display_xref_id INT(10) UNSIGNED,
biotype VARCHAR(40) NOT NULL,
- status ENUM('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN'),
+ status ENUM('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED'),
description TEXT,
is_current BOOLEAN NOT NULL DEFAULT 1,
canonical_translation_id INT(10) UNSIGNED,
@@ -2516,4 +2545,3 @@ CREATE TABLE data_file (
INDEX df_analysis_idx(analysis_id)
) ENGINE=MyISAM;
-
--
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