new schema patch

sql/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 biotype='protein_coding' WHERE biotype = 'ensembl';
+ 
+UPDATE gene SET confidence='KNOWN' WHERE display_xref_id != 0;
+UPDATE transcript SET confidence='KNOWN' WHERE display_xref_id != 0;
+
+# some vega specific stuff, shouldnt harm anybody else
+UPDATE gene SET biotype='unclassified' WHERE biotype = 'Transcript';
+UPDATE gene SET biotype='pseudogene' WHERE biotype = 'Pseudogene';
+UPDATE gene SET biotype='protein_coding', confidence='NOVEL' WHERE biotype = 'Novel_CDS';
+UPDATE gene SET biotype='unclassified', confidence='NOVEL' WHERE biotype = 'Novel_Transcript';
+UPDATE gene SET biotype='unclassified',confidence='PUTATIVE' WHERE biotype = 'Putative';
+UPDATE gene SET biotype='protein_coding', confidence='KNOWN' WHERE biotype = 'Known';
+
+UPDATE gene SET biotype='processed_pseudogene' WHERE biotype = 'Processed_pseudogene';
+UPDATE gene SET biotype='unprocessed_pseudogene' WHERE biotype = 'Unprocessed_pseudogene';
+UPDATE gene SET biotype='protein_coding',confidence='PREDICTED' WHERE biotype = 'Predicted_Gene';
+UPDATE gene SET biotype='Ig_segment' WHERE biotype = 'Ig_Segment';
+UPDATE gene SET biotype='Ig_pseudogene_segment' 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 WHERE g.gene_id = t.gene_id;
+
+
+# new tables regulatory stuff and transcript supporting features
+
+
+################################################################################
+#
+# Table structure for table 'regulatory_feature'
+#
+
+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_motif_id   INT,                           # FK refs regulatory_motif
+  influence             ENUM('positive', 'negative', 'mixed', 'unknown'),
+
+  PRIMARY KEY(regulatory_feature_id)
+
+) TYPE=MyISAM;
+
+################################################################################
+#
+# Table structure for table 'regulatory_motif'
+#
+
+CREATE TABLE regulatory_motif (
+
+  regulatory_motif_id   INT NOT NULL auto_increment,
+  name                  VARCHAR(255) NOT NULL,
+  type                  ENUM('miRNA_target', 'promoter'),
+
+  PRIMARY KEY(regulatory_motif_id)
+
+) 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
+
+  KEY regulatory_feature_idx (regulatory_feature_id),
+  KEY ensembl_object_idx (ensembl_object_type, ensembl_object_id)
+
+) TYPE=MyISAM;
+
+
+################################################################################
+#
+# Table structure for table 'peptide_regulatory_feature'
+#
+
+CREATE TABLE peptide_regulatory_feature (
+
+  translation_id        INT NOT NULL,               # FK to translation
+  regulatory_feature_id INT NOT NULL,               # FK to regulatory_feature
+
+  KEY translation_idx (translation_id),
+  KEY regulatory_feature_idx (regulatory_feature_id)
+
+) TYPE=MyISAM;
+
+################################################################################
+#
+# Table structure for table 'transcript_supporting_feature'
+#
+
+CREATE TABLE transcript_supporting_feature (
+
+  transcript_id 	      int(11) DEFAULT '0' NOT NULL,
+  feature_type                enum('dna_align_feature','protein_align_feature'),
+  feature_id                  int(11) DEFAULT '0' NOT NULL,
+
+  UNIQUE all_idx (transcript_id,feature_type,feature_id),
+  KEY feature_idx (feature_type,feature_id)
+
+) MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+