diff --git a/modules/t/test-genome-DBs/circ/core/alt_allele_attrib.txt b/modules/t/test-genome-DBs/circ/core/alt_allele_attrib.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/modules/t/test-genome-DBs/circ/core/alt_allele_group.txt b/modules/t/test-genome-DBs/circ/core/alt_allele_group.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/modules/t/test-genome-DBs/circ/core/meta.txt b/modules/t/test-genome-DBs/circ/core/meta.txt
index 08741d133e001f164ba8ae10cb577cced27dc293..6602ae93aed26efb7f1a9b558750ff90060b2c3c 100644
--- a/modules/t/test-genome-DBs/circ/core/meta.txt
+++ b/modules/t/test-genome-DBs/circ/core/meta.txt
@@ -1,7 +1,10 @@
3 \N patch patch_71_72_a.sql|schema_version
4 \N patch patch_71_72_b.sql|associated_xref
+58 \N patch patch_72_73_a.sql|schema_version
+59 \N patch patch_72_73_b.sql|alt_allele_type
+60 \N patch patch_72_73_c.sql|add_object_type_marker
1 \N schema_type core
-2 \N schema_version 72
+2 \N schema_version 73
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
diff --git a/modules/t/test-genome-DBs/circ/core/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql
index 9eae740d39ad8448b6aa6650b01f773f07ad6867..66a64f23950e521044bf9eef83d8dac784ca42e9 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
@@ -1,26 +1,22 @@
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `alt_allele` (
`alt_allele_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `alt_allele_group_id` int(10) unsigned NOT NULL,
`gene_id` int(10) unsigned NOT NULL,
- `is_ref` tinyint(1) NOT NULL DEFAULT '0',
- UNIQUE KEY `gene_idx` (`gene_id`),
- UNIQUE KEY `allele_idx` (`alt_allele_id`,`gene_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `analysis_description` (
- `analysis_id` smallint(5) unsigned NOT NULL,
- `description` text,
- `display_label` varchar(255) NOT NULL,
- `displayable` tinyint(1) NOT NULL DEFAULT '1',
- `web_data` text,
- UNIQUE KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+ PRIMARY KEY (`alt_allele_id`),
+ KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `alt_allele_attrib` (
+ `alt_allele_id` int(10) unsigned DEFAULT NULL,
+ `attrib` enum('IS_REPRESENTATIVE','IS_MOST_COMMON_ALLELE','IN_CORRECTED_ASSEMBLY','HAS_CODING_POTENTIAL','IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY','IN_SYNTENIC_REGION','HAS_SAME_UNDERLYING_DNA_SEQUENCE','IN_BROKEN_ASSEMBLY_REGION','IS_VALID_ALTERNATE','SAME_AS_REPRESENTATIVE','SAME_AS_ANOTHER_ALLELE','MANUALLY_ASSIGNED','AUTOMATICALLY_ASSIGNED') DEFAULT NULL,
+ KEY `aa_idx` (`alt_allele_id`,`attrib`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `alt_allele_group` (
+ `alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ PRIMARY KEY (`alt_allele_group_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
CREATE TABLE `analysis` (
`analysis_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
@@ -39,9 +35,29 @@ CREATE TABLE `analysis` (
PRIMARY KEY (`analysis_id`),
UNIQUE KEY `logic_name_idx` (`logic_name`)
) ENGINE=InnoDB AUTO_INCREMENT=39 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `analysis_description` (
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `description` text,
+ `display_label` varchar(255) NOT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text,
+ UNIQUE KEY `analysis_idx` (`analysis_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
+CREATE TABLE `assembly` (
+ `asm_seq_region_id` int(10) unsigned NOT NULL,
+ `cmp_seq_region_id` int(10) unsigned NOT NULL,
+ `asm_start` int(10) NOT NULL,
+ `asm_end` int(10) NOT NULL,
+ `cmp_start` int(10) NOT NULL,
+ `cmp_end` int(10) NOT NULL,
+ `ori` tinyint(4) NOT NULL,
+ UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
+ KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -56,32 +72,13 @@ CREATE TABLE `assembly_exception` (
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL,
- `cmp_seq_region_id` int(10) unsigned NOT NULL,
- `asm_start` int(10) NOT NULL,
- `asm_end` int(10) NOT NULL,
- `cmp_start` int(10) NOT NULL,
- `cmp_end` int(10) NOT NULL,
- `ori` tinyint(4) NOT NULL,
- UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
- KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
- KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`description` varchar(128) DEFAULT NULL,
PRIMARY KEY (`associated_group_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -97,9 +94,7 @@ CREATE TABLE `associated_xref` (
KEY `associated_idx` (`xref_id`),
KEY `associated_group_idx` (`associated_group_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(50) DEFAULT NULL,
@@ -108,9 +103,7 @@ CREATE TABLE `attrib_type` (
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=InnoDB AUTO_INCREMENT=14078 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned NOT NULL DEFAULT '1',
@@ -123,9 +116,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`coord_system_id` int(10) unsigned NOT NULL,
@@ -140,9 +131,7 @@ CREATE TABLE `data_file` (
KEY `df_name_idx` (`name`),
KEY `df_analysis_idx` (`analysis_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `density_feature` (
`density_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`density_type_id` int(10) unsigned NOT NULL,
@@ -154,9 +143,7 @@ CREATE TABLE `density_feature` (
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
) ENGINE=InnoDB AUTO_INCREMENT=1051 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `density_type` (
`density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`analysis_id` smallint(5) unsigned NOT NULL,
@@ -166,9 +153,7 @@ CREATE TABLE `density_type` (
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
) ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
`master_xref_id` int(10) unsigned NOT NULL,
@@ -177,9 +162,16 @@ CREATE TABLE `dependent_xref` (
KEY `dependent` (`dependent_xref_id`),
KEY `master_idx` (`master_xref_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `ditag` (
+ `ditag_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `name` varchar(30) NOT NULL,
+ `type` varchar(30) NOT NULL,
+ `tag_count` smallint(6) unsigned NOT NULL DEFAULT '1',
+ `sequence` tinytext NOT NULL,
+ PRIMARY KEY (`ditag_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -199,20 +191,13 @@ CREATE TABLE `ditag_feature` (
KEY `ditag_pair_idx` (`ditag_pair_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `ditag` (
- `ditag_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(30) NOT NULL,
- `type` varchar(30) NOT NULL,
- `tag_count` smallint(6) unsigned NOT NULL DEFAULT '1',
- `sequence` tinytext NOT NULL,
- PRIMARY KEY (`ditag_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `dna` (
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `sequence` longtext NOT NULL,
+ PRIMARY KEY (`seq_region_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -240,26 +225,14 @@ CREATE TABLE `dna_align_feature` (
KEY `external_db_idx` (`external_db_id`),
KEY `pair_idx` (`pair_dna_align_feature_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `dnac` (
`seq_region_id` int(10) unsigned NOT NULL,
`sequence` mediumblob NOT NULL,
`n_line` text,
PRIMARY KEY (`seq_region_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL,
- `sequence` longtext NOT NULL,
- PRIMARY KEY (`seq_region_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -278,9 +251,7 @@ CREATE TABLE `exon` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=InnoDB AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `exon_transcript` (
`exon_id` int(10) unsigned NOT NULL,
`transcript_id` int(10) unsigned NOT NULL,
@@ -289,9 +260,7 @@ CREATE TABLE `exon_transcript` (
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `external_db` (
`external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`db_name` varchar(100) NOT NULL,
@@ -306,46 +275,14 @@ CREATE TABLE `external_db` (
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_idx` (`db_name`,`db_release`)
) ENGINE=InnoDB AUTO_INCREMENT=50745 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `external_synonym` (
`xref_id` int(10) unsigned NOT NULL,
`synonym` varchar(100) NOT NULL,
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) NOT NULL,
- `gene_version` smallint(6) NOT NULL DEFAULT '1',
- `transcript_stable_id` varchar(128) NOT NULL,
- `transcript_version` smallint(6) NOT NULL DEFAULT '1',
- `translation_stable_id` varchar(128) DEFAULT NULL,
- `translation_version` smallint(6) NOT NULL DEFAULT '1',
- `peptide_archive_id` int(10) unsigned DEFAULT NULL,
- `mapping_session_id` int(10) unsigned NOT NULL,
- KEY `gene_idx` (`gene_stable_id`,`gene_version`),
- KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
- KEY `translation_idx` (`translation_stable_id`,`translation_version`),
- KEY `peptide_archive_id_idx` (`peptide_archive_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `gene_attrib` (
- `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` text NOT NULL,
- KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
- KEY `gene_idx` (`gene_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`biotype` varchar(40) NOT NULL,
@@ -372,9 +309,31 @@ CREATE TABLE `gene` (
KEY `stable_id_idx` (`stable_id`,`version`),
KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
) ENGINE=InnoDB AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `gene_archive` (
+ `gene_stable_id` varchar(128) NOT NULL,
+ `gene_version` smallint(6) NOT NULL DEFAULT '1',
+ `transcript_stable_id` varchar(128) NOT NULL,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '1',
+ `translation_stable_id` varchar(128) DEFAULT NULL,
+ `translation_version` smallint(6) NOT NULL DEFAULT '1',
+ `peptide_archive_id` int(10) unsigned DEFAULT NULL,
+ `mapping_session_id` int(10) unsigned NOT NULL,
+ KEY `gene_idx` (`gene_stable_id`,`gene_version`),
+ KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
+ KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+ KEY `peptide_archive_id_idx` (`peptide_archive_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
+CREATE TABLE `gene_attrib` (
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `gene_idx` (`gene_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `identity_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
`xref_identity` int(5) DEFAULT NULL,
@@ -388,18 +347,14 @@ CREATE TABLE `identity_xref` (
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `interpro` (
`interpro_ac` varchar(40) NOT NULL,
`id` varchar(40) NOT NULL,
UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
KEY `id_idx` (`id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`analysis_id` smallint(5) unsigned NOT NULL,
@@ -415,9 +370,7 @@ CREATE TABLE `intron_supporting_evidence` (
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -428,9 +381,13 @@ CREATE TABLE `karyotype` (
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `map` (
+ `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `map_name` varchar(30) NOT NULL,
+ PRIMARY KEY (`map_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `mapping_session` (
`mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`old_db_name` varchar(80) NOT NULL DEFAULT '',
@@ -443,9 +400,7 @@ CREATE TABLE `mapping_session` (
`species_id` int(10) NOT NULL,
PRIMARY KEY (`mapping_session_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
`internal_schema_build` varchar(20) NOT NULL,
@@ -453,17 +408,21 @@ CREATE TABLE `mapping_set` (
PRIMARY KEY (`mapping_set_id`),
UNIQUE KEY `mapping_idx` (`internal_schema_build`,`external_schema_build`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `map` (
- `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `map_name` varchar(30) NOT NULL,
- PRIMARY KEY (`map_id`)
+
+CREATE TABLE `marker` (
+ `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
+ `left_primer` varchar(100) NOT NULL,
+ `right_primer` varchar(100) NOT NULL,
+ `min_primer_dist` int(10) unsigned NOT NULL,
+ `max_primer_dist` int(10) unsigned NOT NULL,
+ `priority` int(11) DEFAULT NULL,
+ `type` enum('est','microsatellite') DEFAULT NULL,
+ PRIMARY KEY (`marker_id`),
+ KEY `marker_idx` (`marker_id`,`priority`),
+ KEY `display_idx` (`display_marker_synonym_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`marker_id` int(10) unsigned NOT NULL,
@@ -476,9 +435,7 @@ CREATE TABLE `marker_feature` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `marker_map_location` (
`marker_id` int(10) unsigned NOT NULL,
`map_id` int(10) unsigned NOT NULL,
@@ -489,25 +446,7 @@ CREATE TABLE `marker_map_location` (
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `marker` (
- `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
- `left_primer` varchar(100) NOT NULL,
- `right_primer` varchar(100) NOT NULL,
- `min_primer_dist` int(10) unsigned NOT NULL,
- `max_primer_dist` int(10) unsigned NOT NULL,
- `priority` int(11) DEFAULT NULL,
- `type` enum('est','microsatellite') DEFAULT NULL,
- PRIMARY KEY (`marker_id`),
- KEY `marker_idx` (`marker_id`,`priority`),
- KEY `display_idx` (`display_marker_synonym_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`marker_id` int(10) unsigned NOT NULL,
@@ -517,18 +456,7 @@ CREATE TABLE `marker_synonym` (
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `meta_coord` (
- `table_name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
- `max_length` int(11) DEFAULT NULL,
- UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1',
@@ -537,10 +465,15 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=InnoDB AUTO_INCREMENT=58 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+) ENGINE=InnoDB AUTO_INCREMENT=61 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `meta_coord` (
+ `table_name` varchar(40) NOT NULL,
+ `coord_system_id` int(10) unsigned NOT NULL,
+ `max_length` int(11) DEFAULT NULL,
+ UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
@@ -549,18 +482,7 @@ CREATE TABLE `misc_attrib` (
KEY `val_only_idx` (`value`(40)),
KEY `misc_feature_idx` (`misc_feature_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `misc_feature_misc_set` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
- `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
- KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -570,9 +492,14 @@ CREATE TABLE `misc_feature` (
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `misc_feature_misc_set` (
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
+ KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(25) NOT NULL DEFAULT '',
@@ -582,13 +509,11 @@ CREATE TABLE `misc_set` (
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `object_xref` (
`object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`ensembl_id` int(10) unsigned NOT NULL,
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript') NOT NULL,
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
@@ -597,9 +522,7 @@ CREATE TABLE `object_xref` (
KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=InnoDB AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`source_xref_id` int(10) unsigned DEFAULT NULL,
@@ -608,9 +531,7 @@ CREATE TABLE `ontology_xref` (
KEY `source_idx` (`source_xref_id`),
KEY `object_idx` (`object_xref_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `operon` (
`operon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -628,17 +549,7 @@ CREATE TABLE `operon` (
KEY `name_idx` (`display_label`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `operon_transcript_gene` (
- `operon_transcript_id` int(10) unsigned DEFAULT NULL,
- `gene_id` int(10) unsigned DEFAULT NULL,
- KEY `operon_transcript_gene_idx` (`operon_transcript_id`,`gene_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -657,9 +568,13 @@ CREATE TABLE `operon_transcript` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `operon_transcript_gene` (
+ `operon_transcript_id` int(10) unsigned DEFAULT NULL,
+ `gene_id` int(10) unsigned DEFAULT NULL,
+ KEY `operon_transcript_gene_idx` (`operon_transcript_id`,`gene_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `peptide_archive` (
`peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`md5_checksum` varchar(32) DEFAULT NULL,
@@ -667,9 +582,7 @@ CREATE TABLE `peptide_archive` (
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`prediction_transcript_id` int(10) unsigned NOT NULL,
@@ -685,9 +598,7 @@ CREATE TABLE `prediction_exon` (
KEY `transcript_idx` (`prediction_transcript_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -700,9 +611,7 @@ CREATE TABLE `prediction_transcript` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -726,9 +635,7 @@ CREATE TABLE `protein_align_feature` (
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`translation_id` int(10) unsigned NOT NULL,
@@ -748,22 +655,7 @@ CREATE TABLE `protein_feature` (
KEY `hitname_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=InnoDB AUTO_INCREMENT=24117 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `qtl_feature` (
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `qtl_id` int(10) unsigned NOT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- KEY `qtl_idx` (`qtl_id`),
- KEY `loc_idx` (`seq_region_id`,`seq_region_start`),
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `qtl` (
`qtl_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`trait` varchar(255) NOT NULL,
@@ -774,9 +666,18 @@ CREATE TABLE `qtl` (
PRIMARY KEY (`qtl_id`),
KEY `trait_idx` (`trait`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `qtl_feature` (
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `qtl_id` int(10) unsigned NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ KEY `qtl_idx` (`qtl_id`),
+ KEY `loc_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `qtl_synonym` (
`qtl_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`qtl_id` int(10) unsigned NOT NULL,
@@ -785,9 +686,7 @@ CREATE TABLE `qtl_synonym` (
PRIMARY KEY (`qtl_synonym_id`),
KEY `qtl_idx` (`qtl_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`repeat_name` varchar(255) NOT NULL,
@@ -800,9 +699,7 @@ CREATE TABLE `repeat_consensus` (
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -819,9 +716,17 @@ CREATE TABLE `repeat_feature` (
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `seq_region` (
+ `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `name` varchar(40) NOT NULL,
+ `coord_system_id` int(10) unsigned NOT NULL,
+ `length` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`seq_region_id`),
+ UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+ KEY `cs_idx` (`coord_system_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=15 DEFAULT CHARSET=latin1;
+
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
@@ -830,30 +735,14 @@ CREATE TABLE `seq_region_attrib` (
KEY `val_only_idx` (`value`(40)),
KEY `seq_region_idx` (`seq_region_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `seq_region_mapping` (
`external_seq_region_id` int(10) unsigned NOT NULL,
`internal_seq_region_id` int(10) unsigned NOT NULL,
`mapping_set_id` int(10) unsigned NOT NULL,
KEY `mapping_set_idx` (`mapping_set_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `seq_region` (
- `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(40) NOT NULL,
- `coord_system_id` int(10) unsigned NOT NULL,
- `length` int(10) unsigned NOT NULL,
- PRIMARY KEY (`seq_region_id`),
- UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
- KEY `cs_idx` (`coord_system_id`)
-) ENGINE=InnoDB AUTO_INCREMENT=15 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -863,9 +752,7 @@ CREATE TABLE `seq_region_synonym` (
UNIQUE KEY `syn_idx` (`synonym`),
KEY `seq_region_idx` (`seq_region_id`)
) ENGINE=InnoDB AUTO_INCREMENT=15 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
@@ -880,9 +767,21 @@ CREATE TABLE `simple_feature` (
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
) ENGINE=InnoDB AUTO_INCREMENT=37 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `splicing_event` (
+ `splicing_event_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `name` varchar(134) DEFAULT NULL,
+ `gene_id` int(10) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ PRIMARY KEY (`splicing_event_id`),
+ KEY `gene_idx` (`gene_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `splicing_event_feature` (
`splicing_event_feature_id` int(10) unsigned NOT NULL,
`splicing_event_id` int(10) unsigned NOT NULL,
@@ -897,25 +796,7 @@ CREATE TABLE `splicing_event_feature` (
KEY `se_idx` (`splicing_event_id`),
KEY `transcript_idx` (`transcript_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `splicing_event` (
- `splicing_event_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(134) DEFAULT NULL,
- `gene_id` int(10) unsigned NOT NULL,
- `seq_region_id` int(10) unsigned NOT NULL,
- `seq_region_start` int(10) unsigned NOT NULL,
- `seq_region_end` int(10) unsigned NOT NULL,
- `seq_region_strand` tinyint(2) NOT NULL,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- PRIMARY KEY (`splicing_event_id`),
- KEY `gene_idx` (`gene_id`),
- KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `splicing_transcript_pair` (
`splicing_transcript_pair_id` int(10) unsigned NOT NULL,
`splicing_event_id` int(10) unsigned NOT NULL,
@@ -924,9 +805,7 @@ CREATE TABLE `splicing_transcript_pair` (
PRIMARY KEY (`splicing_transcript_pair_id`),
KEY `se_idx` (`splicing_event_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `stable_id_event` (
`old_stable_id` varchar(128) DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
@@ -939,9 +818,7 @@ CREATE TABLE `stable_id_event` (
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `supporting_feature` (
`exon_id` int(10) unsigned NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
@@ -949,30 +826,7 @@ CREATE TABLE `supporting_feature` (
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `transcript_attrib` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` text NOT NULL,
- KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
- KEY `transcript_idx` (`transcript_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `transcript_intron_supporting_evidence` (
- `transcript_id` int(10) unsigned NOT NULL,
- `intron_supporting_evidence_id` int(10) unsigned NOT NULL,
- `previous_exon_id` int(10) unsigned NOT NULL,
- `next_exon_id` int(10) unsigned NOT NULL,
- PRIMARY KEY (`intron_supporting_evidence_id`,`transcript_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`gene_id` int(10) unsigned DEFAULT NULL,
@@ -999,9 +853,24 @@ CREATE TABLE `transcript` (
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=InnoDB AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `transcript_attrib` (
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `transcript_idx` (`transcript_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
+CREATE TABLE `transcript_intron_supporting_evidence` (
+ `transcript_id` int(10) unsigned NOT NULL,
+ `intron_supporting_evidence_id` int(10) unsigned NOT NULL,
+ `previous_exon_id` int(10) unsigned NOT NULL,
+ `next_exon_id` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`intron_supporting_evidence_id`,`transcript_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `transcript_supporting_feature` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
@@ -1009,20 +878,7 @@ CREATE TABLE `transcript_supporting_feature` (
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `translation_attrib` (
- `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` text NOT NULL,
- KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
- KEY `val_only_idx` (`value`(40)),
- KEY `translation_idx` (`translation_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`transcript_id` int(10) unsigned NOT NULL,
@@ -1038,9 +894,16 @@ CREATE TABLE `translation` (
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=InnoDB AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
+CREATE TABLE `translation_attrib` (
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `translation_idx` (`translation_id`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
CREATE TABLE `unconventional_transcript_association` (
`transcript_id` int(10) unsigned NOT NULL,
`gene_id` int(10) unsigned NOT NULL,
@@ -1048,9 +911,7 @@ CREATE TABLE `unconventional_transcript_association` (
KEY `transcript_idx` (`transcript_id`),
KEY `gene_idx` (`gene_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('xref','cDNA','Marker') NOT NULL,
@@ -1069,18 +930,14 @@ CREATE TABLE `unmapped_object` (
KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`),
KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`summary_description` varchar(255) DEFAULT NULL,
`full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
+
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`external_db_id` int(10) unsigned NOT NULL,
@@ -1095,4 +952,4 @@ CREATE TABLE `xref` (
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
) ENGINE=InnoDB AUTO_INCREMENT=91703 DEFAULT CHARSET=latin1;
-/*!40101 SET character_set_client = @saved_cs_client */;
+
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index 04704245c1937c862ba772b01b255bf7488fdb34..689363ad8ea330eb3b1652b7ab0d92c72d64ea34 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -34,4 +34,6 @@
79 \N patch patch_70_71_b.sql|mapping_set_index
80 \N patch patch_71_72_a.sql|schema_version
81 \N patch patch_71_72_b.sql|associated_xref
-82 \N patch patch_72_73_a.sql|schema_version
+82 \N patch patch_72_73_a.sql|schema_version
+83 \N patch patch_72_73_b.sql|alt_allele_type
+84 \N patch patch_72_73_c.sql|add_object_type_marker
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
index 3781edc504d6fec08de42e6e48635ca93013576e..29e014d7cb007b07eb0f1948a25faf48d12256bd 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -515,7 +515,7 @@ CREATE TABLE `misc_set` (
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
`ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+ `ensembl_object_type` enum('RawContig', 'Transcript', 'Gene', 'Translation', 'Operon', 'OperonTranscript', 'Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/alt_allele_attrib.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/alt_allele_attrib.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/alt_allele_group.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/alt_allele_group.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
index 7744759edf66d58c59eda0bcc62f0a862bc80be0..742131718645b0b79f1733966d30b07b5b777709 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -1,4 +1,4 @@
-1 \N schema_version 72
+1 \N schema_version 73
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
@@ -34,3 +34,6 @@
83 \N patch patch_70_71_b.sql|mapping_set_index
84 \N patch patch_71_72_a.sql|schema_version
85 \N patch patch_71_72_b.sql|associated_xref
+86 \N patch patch_72_73_a.sql|schema_version
+87 \N patch patch_72_73_b.sql|alt_allele_type
+88 \N patch patch_72_73_c.sql|add_object_type_marker
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
index 38f23d93215d17f6b6dea4689c9ec0f42d3301f4..9a1857195429e1c176b042055d1a76a2ccc899de 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -1,9 +1,20 @@
CREATE TABLE `alt_allele` (
- `alt_allele_id` int(11) NOT NULL AUTO_INCREMENT,
- `gene_id` int(11) NOT NULL DEFAULT '0',
- `is_ref` tinyint(1) NOT NULL DEFAULT '0',
- UNIQUE KEY `gene_idx` (`gene_id`),
- UNIQUE KEY `allele_idx` (`alt_allele_id`,`gene_id`)
+ `alt_allele_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `alt_allele_group_id` int(10) unsigned NOT NULL,
+ `gene_id` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`alt_allele_id`),
+ KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `alt_allele_attrib` (
+ `alt_allele_id` int(10) unsigned DEFAULT NULL,
+ `attrib` enum('IS_REPRESENTATIVE','IS_MOST_COMMON_ALLELE','IN_CORRECTED_ASSEMBLY','HAS_CODING_POTENTIAL','IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY','IN_SYNTENIC_REGION','HAS_SAME_UNDERLYING_DNA_SEQUENCE','IN_BROKEN_ASSEMBLY_REGION','IS_VALID_ALTERNATE','SAME_AS_REPRESENTATIVE','SAME_AS_ANOTHER_ALLELE','MANUALLY_ASSIGNED','AUTOMATICALLY_ASSIGNED') DEFAULT NULL,
+ KEY `aa_idx` (`alt_allele_id`,`attrib`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `alt_allele_group` (
+ `alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ PRIMARY KEY (`alt_allele_group_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
@@ -447,7 +458,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=86 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=89 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -494,7 +505,7 @@ CREATE TABLE `misc_set` (
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
`ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature') CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,