Created; drop & re-create regulatory feature tables.

sql/patch_31_32.sql

+# 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;
+
+