Patched Compara and Variation test databases to schema version 95

modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt

 1	\N	schema_type	variation
-2	\N	schema_version	94
+2	\N	schema_version	95
 3	\N	patch	patch_84_85_a.sql|schema version
 4	\N	patch	patch_84_85_b.sql|create sample_synonym
 5	\N	patch	patch_84_85_c.sql|drop column moltype from variation_synonym
@@ -32,3 +32,5 @@
 32	\N	patch	patch_92_93_b.sql|Extend phenotype_ontology_accession mapped_by_attrib predefined set
 33	\N	patch	patch_92_93_c.sql|Add new evidence attribs to the variation and variation_feature tables
 34	\N	patch	patch_93_94_a.sql|schema version
+35	\N	patch	patch_94_95_a.sql|schema version
+36	\N	patch	patch_94_95_b.sql|create table to store allele synonyms

modules/t/test-genome-DBs/homo_sapiens/variation/table.sql

@@ -20,6 +20,16 @@ CREATE TABLE `allele_code` (
   UNIQUE KEY `allele_idx` (`allele`(1000))
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
+CREATE TABLE `allele_synonym` (
+  `allele_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `variation_id` int(10) unsigned NOT NULL,
+  `hgvs_genomic` varchar(600) NOT NULL,
+  `name` varchar(255) NOT NULL,
+  PRIMARY KEY (`allele_synonym_id`),
+  UNIQUE KEY `variation_name_idx` (`variation_id`,`name`),
+  KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `associate_study` (
   `study1_id` int(10) unsigned NOT NULL,
   `study2_id` int(10) unsigned NOT NULL,
@@ -168,7 +178,7 @@ 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=35 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=37 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

modules/t/test-genome-DBs/multi/compara/genome_db.txt

-4	31033	takifugu_rubripes	FUGU4	2007-11-Ensembl	0	1	\N	\N	\N	\N	24	\N
-27	51511	ciona_savignyi	CSAV2.0	2006-04-Ensembl	0	1	\N	\N	\N	\N	39	\N
-31	9544	macaca_mulatta	MMUL_1	2006-01-Ensembl	1	1	\N	\N	\N	\N	40	\N
+4	31033	takifugu_rubripes	FUGU4	2007-11-Ensembl	0	0	\N	\N	\N	\N	24	\N
+27	51511	ciona_savignyi	CSAV2.0	2006-04-Ensembl	0	0	\N	\N	\N	\N	39	\N
+31	9544	macaca_mulatta	MMUL_1	2006-01-Ensembl	1	0	\N	\N	\N	\N	40	\N
 33	9371	echinops_telfairi	TENREC	2006-01-Ensembl	0	0	\N	\N	\N	\N	40	\N
 36	69293	gasterosteus_aculeatus	BROADS1	2006-06-Ensembl	1	1	\N	\N	\N	\N	40	\N
-37	8090	oryzias_latipes	MEDAKA1	2006-05-Ensembl	1	1	\N	\N	\N	\N	41	\N
+37	8090	oryzias_latipes	MEDAKA1	2006-05-Ensembl	1	0	\N	\N	\N	\N	41	\N
 43	9258	ornithorhynchus_anatinus	OANA5	2007-01-Ensembl	1	1	\N	\N	\N	\N	42	\N
-46	13616	monodelphis_domestica	BROADO5	2007-02-Ensembl	1	1	\N	\N	\N	\N	44	\N
+46	13616	monodelphis_domestica	BROADO5	2007-02-Ensembl	1	0	\N	\N	\N	\N	44	\N
 48	37347	tupaia_belangeri	TREESHREW	2006-10-Ensembl	0	0	\N	\N	\N	\N	43	\N
 49	9365	erinaceus_europaeus	HEDGEHOG	2006-10-Ensembl	0	0	\N	\N	\N	\N	43	\N
 55	42254	sorex_araneus	COMMON_SHREW1	2007-04-Ensembl	0	0	\N	\N	\N	\N	45	\N
@@ -14,7 +14,7 @@
 61	9796	equus_caballus	EquCab2	2007-09-Ensembl	1	1	\N	\N	\N	\N	49	\N
 65	99883	tetraodon_nigroviridis	TETRAODON8	2007-11-Ensembl	1	1	\N	\N	\N	\N	50	\N
 67	9978	ochotona_princeps	pika	2008-01-Ensembl	0	0	\N	\N	\N	\N	50	\N
-69	10141	cavia_porcellus	cavPor3	2008-03-Ensembl	0	1	\N	\N	\N	\N	51	\N
+69	10141	cavia_porcellus	cavPor3	2008-03-Ensembl	0	0	\N	\N	\N	\N	51	\N
 78	9358	choloepus_hoffmanni	choHof1	2008-11-Ensembl	0	0	\N	\N	\N	\N	53	\N
 79	9813	procavia_capensis	proCap1	2008-11-Ensembl	0	0	\N	\N	\N	\N	53	\N
 80	9739	tursiops_truncatus	turTru1	2008-11-Ensembl	0	0	\N	\N	\N	\N	53	\N
@@ -24,46 +24,46 @@
 85	132908	pteropus_vampyrus	pteVam1	2008-11-Ensembl	0	0	\N	\N	\N	\N	53	\N
 87	59729	taeniopygia_guttata	taeGut3.2.4	2008-08-Ensembl	1	1	\N	\N	\N	\N	53	\N
 91	9315	macropus_eugenii	Meug_1.0	2009-02-Ensembl	0	0	\N	\N	\N	\N	55	\N
-98	9785	loxodonta_africana	loxAfr3	2009-07-Ensembl	0	1	\N	\N	\N	\N	57	\N
+98	9785	loxodonta_africana	loxAfr3	2009-07-Ensembl	0	0	\N	\N	\N	\N	57	\N
 108	9986	oryctolagus_cuniculus	OryCun2.0	2009-11-Ensembl	1	1	\N	\N	\N	\N	60	\N
-109	9646	ailuropoda_melanoleuca	ailMel1	2010-01-Ensembl	0	1	\N	\N	\N	\N	60	\N
-111	28377	anolis_carolinensis	AnoCar2.0	2010-09-Ensembl	1	1	\N	\N	\N	\N	61	\N
+109	9646	ailuropoda_melanoleuca	ailMel1	2010-01-Ensembl	0	0	\N	\N	\N	\N	60	\N
+111	28377	anolis_carolinensis	AnoCar2.0	2010-09-Ensembl	1	0	\N	\N	\N	\N	61	\N
 112	9103	meleagris_gallopavo	UMD2	2010-09-Ensembl	1	1	\N	\N	\N	\N	61	\N
-115	61853	nomascus_leucogenys	Nleu1.0	2010-10-Ensembl	0	1	\N	\N	\N	\N	62	\N
-116	8364	xenopus_tropicalis	JGI_4.2	2010-09-Ensembl	0	1	\N	\N	\N	\N	62	\N
-117	9483	callithrix_jacchus	C_jacchus3.2.1	2010-02-Ensembl	1	1	\N	\N	\N	\N	63	\N
-118	59463	myotis_lucifugus	Myoluc2.0	2010-12-Ensembl	0	1	\N	\N	\N	\N	63	\N
-120	7757	petromyzon_marinus	Pmarinus_7.0	2011-02-Ensembl	0	1	\N	\N	\N	\N	64	\N
-121	9305	sarcophilus_harrisii	DEVIL7.0	2011-03-Ensembl	0	1	\N	\N	\N	\N	64	\N
+115	61853	nomascus_leucogenys	Nleu1.0	2010-10-Ensembl	0	0	\N	\N	\N	\N	62	\N
+116	8364	xenopus_tropicalis	JGI_4.2	2010-09-Ensembl	0	0	\N	\N	\N	\N	62	\N
+117	9483	callithrix_jacchus	C_jacchus3.2.1	2010-02-Ensembl	1	0	\N	\N	\N	\N	63	\N
+118	59463	myotis_lucifugus	Myoluc2.0	2010-12-Ensembl	0	0	\N	\N	\N	\N	63	\N
+120	7757	petromyzon_marinus	Pmarinus_7.0	2011-02-Ensembl	0	0	\N	\N	\N	\N	64	\N
+121	9305	sarcophilus_harrisii	DEVIL7.0	2011-03-Ensembl	0	0	\N	\N	\N	\N	64	\N
 122	9913	bos_taurus	UMD3.1	2011-04-Ensembl	1	1	\N	\N	\N	\N	64	\N
 123	9595	gorilla_gorilla	gorGor3.1	2009-08-Ensembl	1	0	\N	\N	\N	\N	64	\N
-124	30611	otolemur_garnettii	OtoGar3	2011-06-Ensembl	0	1	\N	\N	\N	\N	65	\N
-125	9598	pan_troglodytes	CHIMP2.1.4	2011-05-Ensembl	1	1	\N	\N	\N	\N	65	\N
+124	30611	otolemur_garnettii	OtoGar3	2011-06-Ensembl	0	0	\N	\N	\N	\N	65	\N
+125	9598	pan_troglodytes	CHIMP2.1.4	2011-05-Ensembl	1	0	\N	\N	\N	\N	65	\N
 126	8049	gadus_morhua	gadMor1	2010-01-Ensembl	0	0	\N	\N	\N	\N	65	\N
 127	4932	saccharomyces_cerevisiae	R64-1-1	2011-09-SGD	1	1	\N	\N	\N	\N	65	\N
-128	7719	ciona_intestinalis	KH	2011-08-Ensembl	1	1	\N	\N	\N	\N	66	\N
-129	7897	latimeria_chalumnae	LatCha1	2011-09-Ensembl	0	1	\N	\N	\N	\N	66	\N
-130	8128	oreochromis_niloticus	Orenil1.0	2011-05-Ensembl	0	1	\N	\N	\N	\N	67	\N
-131	43179	ictidomys_tridecemlineatus	spetri2	2011-12-Ensembl	0	1	\N	\N	\N	\N	67	\N
-132	9823	sus_scrofa	Sscrofa10.2	2011-09-Ensembl	1	1	\N	\N	\N	\N	67	\N
-134	10090	mus_musculus	GRCm38	2012-01-Ensembl	1	1	\N	\N	\N	\N	68	\N
+128	7719	ciona_intestinalis	KH	2011-08-Ensembl	1	0	\N	\N	\N	\N	66	\N
+129	7897	latimeria_chalumnae	LatCha1	2011-09-Ensembl	0	0	\N	\N	\N	\N	66	\N
+130	8128	oreochromis_niloticus	Orenil1.0	2011-05-Ensembl	0	0	\N	\N	\N	\N	67	\N
+131	43179	ictidomys_tridecemlineatus	spetri2	2011-12-Ensembl	0	0	\N	\N	\N	\N	67	\N
+132	9823	sus_scrofa	Sscrofa10.2	2011-09-Ensembl	1	0	\N	\N	\N	\N	67	\N
+134	10090	mus_musculus	GRCm38	2012-01-Ensembl	1	0	\N	\N	\N	\N	68	\N
 135	9615	canis_familiaris	CanFam3.1	2011-11-Ensembl	1	1	\N	\N	\N	\N	68	\N
-136	13735	pelodiscus_sinensis	PelSin_1.0	2011-11-Ensembl	0	1	\N	\N	\N	\N	68	\N
-137	8083	xiphophorus_maculatus	Xipmac4.4.2	2012-01-Ensembl	0	1	\N	\N	\N	\N	69	\N
-138	9669	mustela_putorius_furo	MusPutFur1.0	2012-04-Ensembl	0	1	\N	\N	\N	\N	69	\N
-139	9685	felis_catus	Felis_catus_6.2	2011-12-Ensembl	1	1	\N	\N	\N	\N	70	\N
-142	9031	gallus_gallus	Galgal4	2011-12-Ensembl	1	1	\N	\N	\N	\N	71	\N
+136	13735	pelodiscus_sinensis	PelSin_1.0	2011-11-Ensembl	0	0	\N	\N	\N	\N	68	\N
+137	8083	xiphophorus_maculatus	Xipmac4.4.2	2012-01-Ensembl	0	0	\N	\N	\N	\N	69	\N
+138	9669	mustela_putorius_furo	MusPutFur1.0	2012-04-Ensembl	0	0	\N	\N	\N	\N	69	\N
+139	9685	felis_catus	Felis_catus_6.2	2011-12-Ensembl	1	0	\N	\N	\N	\N	70	\N
+142	9031	gallus_gallus	Galgal4	2011-12-Ensembl	1	0	\N	\N	\N	\N	71	\N
 143	6239	caenorhabditis_elegans	WBcel235	2014-09-WormBase	1	1	\N	\N	\N	\N	71	\N
-144	8839	anas_platyrhynchos	BGI_duck_1.0	2009-09-Ensembl	0	1	\N	\N	\N	\N	73	\N
-145	59894	ficedula_albicollis	FicAlb_1.4	2012-05-Ensembl	0	1	\N	\N	\N	\N	73	\N
-146	7994	astyanax_mexicanus	AstMex102	2013-04-Ensembl	0	1	\N	\N	\N	\N	74	\N
+144	8839	anas_platyrhynchos	BGI_duck_1.0	2009-09-Ensembl	0	0	\N	\N	\N	\N	73	\N
+145	59894	ficedula_albicollis	FicAlb_1.4	2012-05-Ensembl	0	0	\N	\N	\N	\N	73	\N
+146	7994	astyanax_mexicanus	AstMex102	2013-04-Ensembl	0	0	\N	\N	\N	\N	74	\N
 147	9940	ovis_aries	Oar_v3.1	2012-12-Ensembl	1	1	\N	\N	\N	\N	74	\N
 148	7918	lepisosteus_oculatus	LepOcu1	2012-01-Ensembl	1	1	\N	\N	\N	\N	74	\N
-149	9361	dasypus_novemcinctus	Dasnov3.0	2013-06-Ensembl	0	1	\N	\N	\N	\N	74	\N
-150	9606	homo_sapiens	NCBI33	2014-01-Ensembl	1	1	\N	\N	\N	\N	76	\N
-151	9555	papio_anubis	PapAnu2.0	2013-01-Ensembl	1	1	\N	\N	\N	\N	76	\N
-152	48698	poecilia_formosa	PoeFor_5.1.2	2013-11-Ensembl	0	1	\N	\N	\N	\N	76	\N
+149	9361	dasypus_novemcinctus	Dasnov3.0	2013-06-Ensembl	0	0	\N	\N	\N	\N	74	\N
+150	9606	homo_sapiens	NCBI33	2014-01-Ensembl	1	0	\N	\N	\N	\N	76	\N
+151	9555	papio_anubis	PapAnu2.0	2013-01-Ensembl	1	0	\N	\N	\N	\N	76	\N
+152	48698	poecilia_formosa	PoeFor_5.1.2	2013-11-Ensembl	0	0	\N	\N	\N	\N	76	\N
 153	60711	chlorocebus_sabaeus	ChlSab1.1	2014-03-Ensembl	1	1	\N	\N	\N	\N	77	\N
-154	7955	danio_rerio	GRCz10	2014-09-Ensembl	1	1	\N	\N	\N	\N	80	\N
+154	7955	danio_rerio	GRCz10	2014-09-Ensembl	1	0	\N	\N	\N	\N	80	\N
 155	10116	rattus_norvegicus	Rnor_6.0	2014-09-Ensembl	1	1	\N	\N	\N	\N	80	\N
 156	7227	drosophila_melanogaster	BDGP6	2014-05-FlyBase	1	1	\N	\N	\N	\N	79	\N

modules/t/test-genome-DBs/multi/compara/meta.txt

-53	\N	schema_version	94
+57	\N	schema_version	95
 2	\N	schema_type	compara
 3	\N	patch	patch_84_85_a.sql|schema_version
 4	\N	patch	patch_84_85_b.sql|gene_tree_root_attr
@@ -45,3 +45,7 @@
 54	\N	patch	patch_93_94_a.sql|schema_version
 55	\N	patch	patch_93_94_b.sql|homology_description_not_null
 56	\N	patch	patch_93_94_c.sql|method_link_display_name
+58	\N	patch	patch_94_95_a.sql|schema_version
+59	\N	patch	patch_94_95_b.sql|remove_unused_indices
+60	\N	patch	patch_94_95_c.sql|genome_db_is_good_for_alignment
+61	\N	patch	patch_94_95_d.sql|node_type_within_species_speciation

modules/t/test-genome-DBs/multi/compara/table.sql

@@ -40,9 +40,7 @@ CREATE TABLE `constrained_element` (
   `score` double NOT NULL DEFAULT '0',
   KEY `dnafrag_id` (`dnafrag_id`),
   KEY `constrained_element_id_idx` (`constrained_element_id`),
-  KEY `mlssid_idx` (`method_link_species_set_id`),
-  KEY `mlssid_dfId_dfStart_dfEnd_idx` (`method_link_species_set_id`,`dnafrag_id`,`dnafrag_start`,`dnafrag_end`),
-  KEY `mlssid_dfId_idx` (`method_link_species_set_id`,`dnafrag_id`)
+  KEY `mlssid_dfId_dfStart_dfEnd_idx` (`method_link_species_set_id`,`dnafrag_id`,`dnafrag_start`,`dnafrag_end`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dnafrag` (
@@ -112,7 +110,6 @@ CREATE TABLE `family_member` (
   `seq_member_id` int(10) unsigned NOT NULL,
   `cigar_line` mediumtext,
   PRIMARY KEY (`family_id`,`seq_member_id`),
-  KEY `family_id` (`family_id`),
   KEY `seq_member_id` (`seq_member_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
@@ -194,13 +191,12 @@ CREATE TABLE `gene_tree_node` (
   PRIMARY KEY (`node_id`),
   KEY `parent_id` (`parent_id`),
   KEY `seq_member_id` (`seq_member_id`),
-  KEY `root_id` (`root_id`),
   KEY `root_id_left_index` (`root_id`,`left_index`)
 ) ENGINE=MyISAM AUTO_INCREMENT=100462681 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_tree_node_attr` (
   `node_id` int(10) unsigned NOT NULL,
-  `node_type` enum('duplication','dubious','speciation','gene_split') DEFAULT NULL,
+  `node_type` enum('duplication','dubious','speciation','sub-speciation','gene_split') DEFAULT NULL,
   `species_tree_node_id` int(10) unsigned DEFAULT NULL,
   `bootstrap` tinyint(3) unsigned DEFAULT NULL,
   `duplication_confidence_score` double(5,4) DEFAULT NULL,
@@ -277,7 +273,6 @@ CREATE TABLE `gene_tree_root_tag` (
   `tag` varchar(255) DEFAULT NULL,
   `value` mediumtext NOT NULL,
   KEY `root_id_tag` (`root_id`,`tag`),
-  KEY `root_id` (`root_id`),
   KEY `tag` (`tag`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
@@ -288,7 +283,7 @@ CREATE TABLE `genome_db` (
   `assembly` varchar(100) NOT NULL DEFAULT '',
   `genebuild` varchar(100) NOT NULL DEFAULT '',
   `has_karyotype` tinyint(1) NOT NULL DEFAULT '0',
-  `is_high_coverage` tinyint(1) NOT NULL DEFAULT '0',
+  `is_good_for_alignment` tinyint(1) NOT NULL DEFAULT '0',
   `genome_component` varchar(5) DEFAULT NULL,
   `strain_name` varchar(40) DEFAULT NULL,
   `display_name` varchar(255) DEFAULT NULL,
@@ -341,7 +336,6 @@ CREATE TABLE `genomic_align_tree` (
   `distance_to_parent` double NOT NULL DEFAULT '1',
   PRIMARY KEY (`node_id`),
   KEY `parent_id` (`parent_id`),
-  KEY `root_id` (`root_id`),
   KEY `left_index` (`root_id`,`left_index`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
@@ -404,7 +398,6 @@ CREATE TABLE `homology_member` (
   `perc_id` float unsigned DEFAULT '0',
   `perc_pos` float unsigned DEFAULT '0',
   PRIMARY KEY (`homology_id`,`gene_member_id`),
-  KEY `homology_id` (`homology_id`),
   KEY `gene_member_id` (`gene_member_id`),
   KEY `seq_member_id` (`seq_member_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=300000000;
@@ -436,7 +429,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
   KEY `species_value_idx` (`species_id`,`meta_value`(255))
-) ENGINE=MyISAM AUTO_INCREMENT=57 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=62 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `method_link` (
   `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,

modules/t/test-genome-DBs/mus_musculus/variation/meta.txt

 1	\N	schema_type	variation
-2	\N	schema_version	94
+2	\N	schema_version	95
 6	1	species.production_name	mus_musculus
 15	1	web_config	sv_study#Keane 2011 (DGVa study estd118)#Keane 2011#estd118
 14	1	web_config	set#All failed variants#All failed variants#variation_set_fail_all#failed
@@ -59,3 +59,5 @@
 65	\N	patch	patch_92_93_b.sql|Extend phenotype_ontology_accession mapped_by_attrib predefined set
 66	\N	patch	patch_92_93_c.sql|Add new evidence attribs to the variation and variation_feature tables
 67	\N	patch	patch_93_94_a.sql|schema version
+68	\N	patch	patch_94_95_a.sql|schema version
+69	\N	patch	patch_94_95_b.sql|create table to store allele synonyms

modules/t/test-genome-DBs/mus_musculus/variation/table.sql

@@ -20,6 +20,16 @@ CREATE TABLE `allele_code` (
   UNIQUE KEY `allele_idx` (`allele`)
 ) ENGINE=MyISAM AUTO_INCREMENT=685956 DEFAULT CHARSET=latin1;
 
+CREATE TABLE `allele_synonym` (
+  `allele_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `variation_id` int(10) unsigned NOT NULL,
+  `hgvs_genomic` varchar(600) NOT NULL,
+  `name` varchar(255) NOT NULL,
+  PRIMARY KEY (`allele_synonym_id`),
+  UNIQUE KEY `variation_name_idx` (`variation_id`,`name`),
+  KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `associate_study` (
   `study1_id` int(10) unsigned NOT NULL,
   `study2_id` int(10) unsigned NOT NULL,
@@ -168,7 +178,7 @@ 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=68 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=70 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,