From 97775d4671f8f86e5bd48eede1f52fe0d220fd7b Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 16 Jun 2005 12:44:46 +0000
Subject: [PATCH] Created; drop & re-create regulatory feature tables.
---
sql/patch_31_32.sql | 83 +++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 83 insertions(+)
create mode 100644 sql/patch_31_32.sql
diff --git a/sql/patch_31_32.sql b/sql/patch_31_32.sql
new file mode 100644
index 0000000000..b4e33ac4c2
--- /dev/null
+++ b/sql/patch_31_32.sql
@@ -0,0 +1,83 @@
+# Many changes to regulatory-feature-related tables
+# Since these tables are empty it is easier to drop the existing
+# tables and re-create the new ones
+
+DROP TABLE regulatory_feature;
+DROP TABLE regulatory_motif;
+DROP TABLE regulatory_feature_object;
+DROP TABLE peptide_regulatory_feature;
+
+################################################################################
+#
+# Table structure for table 'regulatory_feature'
+#
+# Describes instances of regulatory_factor binding to the genome.
+
+CREATE TABLE regulatory_feature (
+
+ regulatory_feature_id INT NOT NULL auto_increment,
+ name VARCHAR(255) NOT NULL,
+ seq_region_id INT NOT NULL, # FK refs seq_region
+ seq_region_start INT NOT NULL,
+ seq_region_end INT NOT NULL,
+ seq_region_strand TINYINT NOT NULL,
+ analysis_id INT NOT NULL, # FK refs analysis
+ regulatory_factor_id INT, # FK refs regulatory_motif
+
+
+ PRIMARY KEY(regulatory_feature_id)
+
+) COLLATE=latin1_swedish_ci TYPE=MyISAM;
+
+################################################################################
+#
+# Table structure for table 'regulatory_factor'
+#
+
+CREATE TABLE regulatory_factor (
+
+ regulatory_factor_id INT NOT NULL auto_increment,
+ name VARCHAR(255) NOT NULL,
+ type ENUM('miRNA_target', 'transcription_factor', 'transcription_factor_complex'),
+
+ PRIMARY KEY(regulatory_factor_id)
+
+) COLLATE=latin1_swedish_ci TYPE=MyISAM;
+
+################################################################################
+#
+# Table structure for table 'regulatory_feature_object'
+#
+# Relates regulatory regions to the Ensembl objects they influence. Many-many.
+
+CREATE TABLE regulatory_feature_object (
+
+ regulatory_feature_id INT NOT NULL, # FK to regulatory_feature
+ ensembl_object_type ENUM( 'Transcript', 'Translation', 'Gene') NOT NULL,
+ ensembl_object_id INT NOT NULL, # FK to transcript,gene etc
+ influence ENUM('positive', 'negative', 'mixed', 'unknown'),
+ evidence VARCHAR(255),
+
+ KEY regulatory_feature_idx (regulatory_feature_id),
+ KEY ensembl_object_idx (ensembl_object_type, ensembl_object_id)
+
+) COLLATE=latin1_swedish_ci TYPE=MyISAM;
+
+
+################################################################################
+#
+# Table structure for table 'regulatory_factor_transcript'
+#
+# Describes which transcripts code for particular regulatory factors.
+
+CREATE TABLE regulatory_factor_transcript (
+
+ transcript_id INT NOT NULL, # FK to transcript
+ regulatory_factor_id INT NOT NULL, # FK to regulatory_feature
+
+ KEY translation_idx (transcript_id),
+ KEY regulatory_factor_idx (regulatory_factor_id)
+
+) COLLATE=latin1_swedish_ci TYPE=MyISAM;
+
+
--
GitLab