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Commit 479110ac authored by Marek Szuba's avatar Marek Szuba
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Patched Compara and Variation test databases to schema version 95

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modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
View file @ 479110ac
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
View file @ 479110ac
......@@ -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
View file @ 479110ac
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
View file @ 479110ac
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
View file @ 479110ac
......@@ -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
View file @ 479110ac
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
View file @ 479110ac
......@@ -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,
......
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