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Commit 628e5121 authored by Andy Yates's avatar Andy Yates
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Test schema now matches live. Any future patching should be done using the... 

Test schema now matches live. Any future patching should be done using the ensembl-test/scripts/patch_test_databases.pl script.
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Showing with 554 additions and 714 deletions
modules/t/test-genome-DBs/circ/core/meta.txt
View file @ 628e5121
1 \N schema_version 68
1 \N schema_version 70
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
......@@ -22,4 +22,11 @@
64 1 assembly.mapping chromosome:NCBI33#chunk
65 1 assembly.mapping alt_chrom#chromosome:NCBI33
66 1 assembly.mapping alt_chrom|chromosome:NCBI33|contig
67 1 species.production_name homo_sapiens
67 1 species.production_name circ
75 \N schema_type core
76 \N patch patch_68_69_a.sql|schema_version
77 \N patch patch_69_70_a.sql|schema_version
78 \N patch patch_69_70_b.sql|add_mapping_set_history
79 \N patch patch_69_70_c.sql|column_datatype_consistency
80 \N patch patch_69_70_d.sql|data_file_id_auto_increment
81 \N patch patch_69_70_e.sql|protein_feature_hit_description
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @ 628e5121
......@@ -29,3 +29,4 @@
74 \N patch patch_69_70_c.sql|column_datatype_consistency
75 \N patch patch_69_70_d.sql|data_file_id_auto_increment
76 \N patch patch_69_70_e.sql|protein_feature_hit_description
77 \N schema_type core
modules/t/test-genome-DBs/homo_sapiens/core/oligo_array.sql deleted 100644 → 0
View file @ 0dfcf9d9
-- MySQL dump 10.13 Distrib 5.1.61, for redhat-linux-gnu (x86_64)
--
-- Host: mysql-eg-devel-1.ebi.ac.uk Database: homo_sapiens_core_test_db
-- ------------------------------------------------------
-- Server version 5.1.49-log
/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
/*!40101 SET NAMES utf8 */;
/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
/*!40103 SET TIME_ZONE='+00:00' */;
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='' */;
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
--
-- Table structure for table `oligo_array`
--
DROP TABLE IF EXISTS `oligo_array`;
/*!40101 SET @saved_cs_client = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `oligo_array` (
`oligo_array_id` int(11) NOT NULL AUTO_INCREMENT,
`parent_array_id` int(11) DEFAULT NULL,
`probe_setsize` tinyint(4) NOT NULL DEFAULT '0',
`name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`type` enum('AFFY','OLIGO') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`oligo_array_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
/*!40101 SET character_set_client = @saved_cs_client */;
/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
-- Dump completed on 2012-11-05 10:52:11
modules/t/test-genome-DBs/homo_sapiens/core/oligo_feature.sql deleted 100644 → 0
View file @ 0dfcf9d9
-- MySQL dump 10.13 Distrib 5.1.61, for redhat-linux-gnu (x86_64)
--
-- Host: mysql-eg-devel-1.ebi.ac.uk Database: homo_sapiens_core_test_db
-- ------------------------------------------------------
-- Server version 5.1.49-log
/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
/*!40101 SET NAMES utf8 */;
/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
/*!40103 SET TIME_ZONE='+00:00' */;
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='' */;
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
--
-- Table structure for table `oligo_feature`
--
DROP TABLE IF EXISTS `oligo_feature`;
/*!40101 SET @saved_cs_client = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `oligo_feature` (
`oligo_feature_id` int(11) NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_start` int(11) NOT NULL DEFAULT '0',
`seq_region_end` int(11) NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`mismatches` tinyint(4) DEFAULT NULL,
`oligo_probe_id` int(11) NOT NULL DEFAULT '0',
`analysis_id` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`oligo_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `probe_idx` (`oligo_probe_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
/*!40101 SET character_set_client = @saved_cs_client */;
/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
-- Dump completed on 2012-11-05 10:52:11
modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.sql deleted 100644 → 0
View file @ 0dfcf9d9
-- MySQL dump 10.13 Distrib 5.1.61, for redhat-linux-gnu (x86_64)
--
-- Host: mysql-eg-devel-1.ebi.ac.uk Database: homo_sapiens_core_test_db
-- ------------------------------------------------------
-- Server version 5.1.49-log
/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
/*!40101 SET NAMES utf8 */;
/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
/*!40103 SET TIME_ZONE='+00:00' */;
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='' */;
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
--
-- Table structure for table `oligo_probe`
--
DROP TABLE IF EXISTS `oligo_probe`;
/*!40101 SET @saved_cs_client = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `oligo_probe` (
`oligo_probe_id` int(11) NOT NULL AUTO_INCREMENT,
`oligo_array_id` int(11) NOT NULL DEFAULT '0',
`probeset` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`name` varchar(20) COLLATE latin1_bin DEFAULT NULL,
`description` text COLLATE latin1_bin,
`length` smallint(5) NOT NULL DEFAULT '0',
PRIMARY KEY (`oligo_probe_id`,`oligo_array_id`),
KEY `probeset_idx` (`probeset`),
KEY `array_idx` (`oligo_array_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
/*!40101 SET character_set_client = @saved_cs_client */;
/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
-- Dump completed on 2012-11-05 10:52:11
modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.sql
View file @ 628e5121
......@@ -32,6 +32,7 @@ CREATE TABLE `protein_feature` (
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
`external_data` text COLLATE latin1_bin,
`hit_description` text COLLATE latin1_bin,
PRIMARY KEY (`protein_feature_id`),
KEY `translation_id` (`translation_id`),
......
modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt
View file @ 628e5121
27374 21716 76 99 45 75 0 41 0 0 0 \N
217249 21716 47 151 49 79 PF000001 41 87.1 8.2e-25 0 \N
242732 21716 80 160 71 101 0 41 0 3.2e-11 0 \N
217179 21717 1 94 49 79 PF000019 41 99.1 3.3e-28 0 \N
242734 21717 3 91 71 101 0 41 0 1.7e-15 0 \N
217309 21718 76 201 49 79 PF000019 41 118.9 8.9e-34 0 \N
242735 21718 1 185 71 101 0 41 0 3e-14 0 \N
27378 21719 90 117 45 75 0 41 0 0 0 \N
83043 21719 21 41 44 74 0 41 2.37 0 0 \N
242736 21719 76 124 71 101 0 41 0 0.0017 0 \N
24545 21720 79 101 46 76 0 41 0 0 0 \N
24546 21720 106 123 46 76 0 41 0 0 0 \N
24547 21720 138 155 46 76 0 41 0 0 0 \N
24548 21720 192 214 46 76 0 41 0 0 0 \N
83044 21720 37 59 44 74 0 41 2.67 0 0 \N
116148 21720 93 100 42 72 0 41 0 0 0 \N
83051 21721 24 37 44 74 0 41 2.3 0 0 \N
83052 21721 170 184 44 74 0 41 1.97 0 0 \N
83053 21721 212 235 44 74 0 41 2.47 0 0 \N
242779 21721 47 146 71 101 0 41 0 0.002 0 \N
83045 21722 135 149 44 74 0 41 1.97 0 0 \N
83046 21722 171 187 44 74 PF000001 41 1.66 0 0 \N
83047 21722 217 230 44 74 0 41 1.09 0 0 \N
83048 21722 361 376 44 74 0 41 2.44 0 0 \N
83049 21722 470 482 44 74 0 41 2.2 0 0 \N
83050 21722 512 520 44 74 0 41 0.76 0 0 \N
116149 21722 347 358 42 72 0 41 0 0 0 \N
116150 21723 268 290 42 72 0 41 1 0 0 \N
116151 21723 377 389 42 72 0 41 1 0 0 \N
130095 21723 144 241 41 71 0 41 26.88 0 0 \N
130097 21723 78 138 41 71 0 41 19.623 0 0 \N
161506 21723 144 158 40 70 0 41 394 9.81e-06 0 \N
161508 21723 165 175 40 70 0 41 321 2.59e-05 0 \N
161510 21723 177 188 40 70 0 41 288 1.03e-06 0 \N
161512 21723 194 204 40 70 0 41 295 4.86e-05 0 \N
161514 21723 215 229 40 70 0 41 349 7e-07 0 \N
161516 21723 81 91 40 70 0 41 266 3.18e-05 0 \N
161518 21723 95 110 40 70 0 41 334 1.38e-07 0 \N
161520 21723 111 120 40 70 0 41 225 0.0222 0 \N
161522 21723 124 136 40 70 0 41 341 1.82e-06 0 \N
161524 21723 83 103 40 70 0 41 565 7.11e-09 0 \N
161526 21723 103 119 40 70 0 41 188 0.099 0 \N
217502 21723 83 138 49 79 58 41 98.9 6.4e-27 0 \N
217503 21723 146 228 49 79 79 41 150.9 1.5e-42 0 \N
217504 21723 264 513 49 79 294 41 260.8 1.2e-75 0 \N
242780 21723 244 526 71 101 0 41 0 2.3e-79 0 \N
242781 21723 138 282 71 101 0 41 0 1.3e-33 0 \N
242782 21723 81 162 71 101 0 41 0 2.5e-22 0 \N
24549 21724 263 285 46 76 0 41 0 0 0 \N
24550 21724 329 351 46 76 0 41 0 0 0 \N
24551 21724 361 383 46 76 0 41 0 0 0 \N
24552 21724 396 418 46 76 0 41 0 0 0 \N
24553 21724 433 455 46 76 0 41 0 0 0 \N
24554 21724 483 505 46 76 0 41 0 0 0 \N
24555 21724 515 537 46 76 0 41 0 0 0 \N
24556 21724 550 572 46 76 0 41 0 0 0 \N
24557 21724 587 609 46 76 0 41 0 0 0 \N
83054 21724 270 275 44 74 0 41 0.92 0 0 \N
83055 21724 326 335 44 74 0 41 1.97 0 0 \N
83056 21724 367 378 44 74 0 41 2.05 0 0 \N
83057 21724 513 529 44 74 0 41 2.42 0 0 \N
217569 21724 37 583 49 79 600 41 1244.7 0 0 \N
242783 21724 3 576 71 101 0 41 0 0.0058 0 \N
27431 21725 113 133 45 75 0 41 0 0 0 \N
83058 21725 30 40 44 74 0 41 1.87 0 0 \N
83059 21725 109 135 44 74 0 41 2.49 0 0 \N
217397 21725 146 331 49 79 324 41 84.5 1.4e-22 0 \N
83060 21726 369 397 44 74 0 41 2.53 0 0 \N
83061 21726 417 432 44 74 0 41 2.3 0 0 \N
83062 21726 443 458 44 74 0 41 2.43 0 0 \N
116152 21726 70 92 42 72 0 41 1 0 0 \N
116153 21726 100 120 42 72 0 41 1 0 0 \N
116154 21726 129 149 42 72 0 41 1 0 0 \N
116155 21726 158 178 42 72 0 41 1 0 0 \N
116156 21726 193 213 42 72 0 41 0 0 0 \N
116157 21726 221 242 42 72 0 41 1 0 0 \N
130099 21726 68 97 41 71 0 41 14.815 0 0 \N
130101 21726 98 125 41 71 0 41 11.676 0 0 \N
130103 21726 127 154 41 71 0 41 9.556 0 0 \N
130105 21726 156 183 41 71 0 41 9.536 0 0 \N
130107 21726 191 218 41 71 0 41 12.092 0 0 \N
130109 21726 219 247 41 71 0 41 11.281 0 0 \N
217476 21726 68 94 49 79 24 41 12.8 0.29 0 \N
217477 21726 100 122 49 79 24 41 25.3 9.2e-05 0 \N
217478 21726 129 151 49 79 24 41 19.7 0.0045 0 \N
217479 21726 158 180 49 79 24 41 19.2 0.0063 0 \N
217480 21726 193 215 49 79 24 41 22.9 0.00049 0 \N
217481 21726 221 244 49 79 24 41 24 0.00023 0 \N
242784 21726 80 124 71 101 0 41 0 1.5e-09 0 \N
242785 21726 205 245 71 101 0 41 0 7.5e-09 0 \N
242786 21726 58 85 71 101 0 41 0 0.0011 0 \N
34517 21727 1 26 43 73 0 41 0 0 0 \N
83063 21727 15 22 44 74 0 41 0.81 0 0 \N
34518 21728 1 26 43 73 0 41 0 0 0 \N
83064 21728 15 22 44 74 0 41 0.81 0 0 \N
27435 21729 355 375 45 75 0 41 0 0 0 \N
27437 21729 436 473 45 75 0 41 0 0 0 \N
27440 21729 482 519 45 75 0 41 0 0 0 \N
27443 21729 541 579 45 75 0 41 0 0 0 \N
83065 21729 6 17 44 74 0 41 2.13 0 0 \N
83066 21729 370 407 44 74 0 41 2.15 0 0 \N
83067 21729 437 458 44 74 0 41 2.44 0 0 \N
83068 21729 493 514 44 74 0 41 2.5 0 0 \N
83069 21729 537 548 44 74 0 41 1.9 0 0 \N
83070 21729 685 697 44 74 0 41 2.26 0 0 \N
83071 21729 711 735 44 74 0 41 2.42 0 0 \N
116158 21729 96 103 42 72 0 41 0 0 0 \N
116159 21729 239 250 42 72 0 41 1 0 0 \N
130111 21729 6 256 41 71 0 41 55.446 0 0 \N
161528 21729 87 108 40 70 0 41 911 4.44e-16 0 \N
161530 21729 206 223 40 70 0 41 585 2.63e-10 0 \N
161532 21729 240 258 40 70 0 41 576 8.36e-12 0 \N
161534 21729 290 311 40 70 0 41 833 4.44e-16 0 \N
217672 21729 55 341 49 79 373 41 576.3 1.3e-170 0 \N
242791 21729 4 365 71 101 0 41 0 8.4e-131 0 \N
83072 21730 3 16 44 74 0 41 1.78 0 0 \N
83073 21730 140 153 44 74 0 41 2.15 0 0 \N
83074 21730 442 469 44 74 0 41 1.89 0 0 \N
83075 21730 644 654 44 74 0 41 1.87 0 0 \N
83076 21730 1221 1235 44 74 0 41 2.15 0 0 \N
83077 21730 1250 1264 44 74 0 41 2.2 0 0 \N
83078 21731 194 211 44 74 0 41 1.95 0 0 \N
83079 21731 335 348 44 74 0 41 2.15 0 0 \N
83080 21731 637 664 44 74 0 41 1.89 0 0 \N
83081 21731 839 849 44 74 0 41 1.87 0 0 \N
83082 21732 33 61 44 74 0 41 2.68 0 0 \N
83083 21732 161 178 44 74 0 41 1.83 0 0 \N
83084 21732 375 396 44 74 0 41 1.93 0 0 \N
116160 21732 92 102 42 72 0 41 0 0 0 \N
130113 21732 235 252 41 71 0 41 3 0 0 \N
83085 21735 76 95 44 74 0 41 2.54 0 0 \N
83086 21735 104 122 44 74 0 41 2.65 0 0 \N
83087 21736 5 20 44 74 0 41 1.92 0 0 \N
83088 21737 47 65 44 74 0 41 2.35 0 0 \N
83089 21737 72 83 44 74 0 41 1.65 0 0 \N
83090 21737 110 125 44 74 0 41 2.42 0 0 \N
83091 21737 142 154 44 74 0 41 2.16 0 0 \N
83092 21737 166 177 44 74 0 41 2.08 0 0 \N
83093 21737 565 576 44 74 0 41 1.96 0 0 \N
116161 21737 309 316 42 72 0 41 0 0 0 \N
116162 21737 643 655 42 72 0 41 0 0 0 \N
217810 21737 223 296 49 79 87 41 121 1.5e-33 0 \N
217811 21737 576 849 49 79 418 41 -74 8.5e-06 0 \N
242841 21737 573 848 71 101 0 41 0 3e-50 0 \N
242842 21737 216 351 71 101 0 41 0 1.2e-41 0 \N
27455 21738 193 213 45 75 0 41 0 0 0 \N
83094 21738 256 267 44 74 0 41 2.12 0 0 \N
130115 21738 14 116 41 71 0 41 8.924 0 0 \N
217326 21738 15 117 49 79 106 41 28 1.5e-05 0 \N
217327 21738 210 257 49 79 56 41 106 4.7e-29 0 \N
242845 21738 13 115 71 101 0 41 0 3e-17 0 \N
83095 21739 44 56 44 74 0 41 2.19 0 0 \N
130117 21739 144 201 41 71 0 41 9.695 0 0 \N
217297 21739 141 168 49 79 29 41 4.4 1.7 0 \N
217298 21739 176 204 49 79 29 41 12.7 0.15 0 \N
242846 21739 117 207 71 101 0 41 0 4e-10 0 \N
27374 21716 76 99 45 75 0 41 0 0 0 \N \N
217249 21716 47 151 49 79 PF000001 41 87.1 8.2e-25 0 \N \N
242732 21716 80 160 71 101 0 41 0 3.2e-11 0 \N \N
217179 21717 1 94 49 79 PF000019 41 99.1 3.3e-28 0 \N \N
242734 21717 3 91 71 101 0 41 0 1.7e-15 0 \N \N
217309 21718 76 201 49 79 PF000019 41 118.9 8.9e-34 0 \N \N
242735 21718 1 185 71 101 0 41 0 3e-14 0 \N \N
27378 21719 90 117 45 75 0 41 0 0 0 \N \N
83043 21719 21 41 44 74 0 41 2.37 0 0 \N \N
242736 21719 76 124 71 101 0 41 0 0.0017 0 \N \N
24545 21720 79 101 46 76 0 41 0 0 0 \N \N
24546 21720 106 123 46 76 0 41 0 0 0 \N \N
24547 21720 138 155 46 76 0 41 0 0 0 \N \N
24548 21720 192 214 46 76 0 41 0 0 0 \N \N
83044 21720 37 59 44 74 0 41 2.67 0 0 \N \N
116148 21720 93 100 42 72 0 41 0 0 0 \N \N
83051 21721 24 37 44 74 0 41 2.3 0 0 \N \N
83052 21721 170 184 44 74 0 41 1.97 0 0 \N \N
83053 21721 212 235 44 74 0 41 2.47 0 0 \N \N
242779 21721 47 146 71 101 0 41 0 0.002 0 \N \N
83045 21722 135 149 44 74 0 41 1.97 0 0 \N \N
83046 21722 171 187 44 74 PF000001 41 1.66 0 0 \N \N
83047 21722 217 230 44 74 0 41 1.09 0 0 \N \N
83048 21722 361 376 44 74 0 41 2.44 0 0 \N \N
83049 21722 470 482 44 74 0 41 2.2 0 0 \N \N
83050 21722 512 520 44 74 0 41 0.76 0 0 \N \N
116149 21722 347 358 42 72 0 41 0 0 0 \N \N
116150 21723 268 290 42 72 0 41 1 0 0 \N \N
116151 21723 377 389 42 72 0 41 1 0 0 \N \N
130095 21723 144 241 41 71 0 41 26.88 0 0 \N \N
130097 21723 78 138 41 71 0 41 19.623 0 0 \N \N
161506 21723 144 158 40 70 0 41 394 9.81e-06 0 \N \N
161508 21723 165 175 40 70 0 41 321 2.59e-05 0 \N \N
161510 21723 177 188 40 70 0 41 288 1.03e-06 0 \N \N
161512 21723 194 204 40 70 0 41 295 4.86e-05 0 \N \N
161514 21723 215 229 40 70 0 41 349 7e-07 0 \N \N
161516 21723 81 91 40 70 0 41 266 3.18e-05 0 \N \N
161518 21723 95 110 40 70 0 41 334 1.38e-07 0 \N \N
161520 21723 111 120 40 70 0 41 225 0.0222 0 \N \N
161522 21723 124 136 40 70 0 41 341 1.82e-06 0 \N \N
161524 21723 83 103 40 70 0 41 565 7.11e-09 0 \N \N
161526 21723 103 119 40 70 0 41 188 0.099 0 \N \N
217502 21723 83 138 49 79 58 41 98.9 6.4e-27 0 \N \N
217503 21723 146 228 49 79 79 41 150.9 1.5e-42 0 \N \N
217504 21723 264 513 49 79 294 41 260.8 1.2e-75 0 \N \N
242780 21723 244 526 71 101 0 41 0 2.3e-79 0 \N \N
242781 21723 138 282 71 101 0 41 0 1.3e-33 0 \N \N
242782 21723 81 162 71 101 0 41 0 2.5e-22 0 \N \N
24549 21724 263 285 46 76 0 41 0 0 0 \N \N
24550 21724 329 351 46 76 0 41 0 0 0 \N \N
24551 21724 361 383 46 76 0 41 0 0 0 \N \N
24552 21724 396 418 46 76 0 41 0 0 0 \N \N
24553 21724 433 455 46 76 0 41 0 0 0 \N \N
24554 21724 483 505 46 76 0 41 0 0 0 \N \N
24555 21724 515 537 46 76 0 41 0 0 0 \N \N
24556 21724 550 572 46 76 0 41 0 0 0 \N \N
24557 21724 587 609 46 76 0 41 0 0 0 \N \N
83054 21724 270 275 44 74 0 41 0.92 0 0 \N \N
83055 21724 326 335 44 74 0 41 1.97 0 0 \N \N
83056 21724 367 378 44 74 0 41 2.05 0 0 \N \N
83057 21724 513 529 44 74 0 41 2.42 0 0 \N \N
217569 21724 37 583 49 79 600 41 1244.7 0 0 \N \N
242783 21724 3 576 71 101 0 41 0 0.0058 0 \N \N
27431 21725 113 133 45 75 0 41 0 0 0 \N \N
83058 21725 30 40 44 74 0 41 1.87 0 0 \N \N
83059 21725 109 135 44 74 0 41 2.49 0 0 \N \N
217397 21725 146 331 49 79 324 41 84.5 1.4e-22 0 \N \N
83060 21726 369 397 44 74 0 41 2.53 0 0 \N \N
83061 21726 417 432 44 74 0 41 2.3 0 0 \N \N
83062 21726 443 458 44 74 0 41 2.43 0 0 \N \N
116152 21726 70 92 42 72 0 41 1 0 0 \N \N
116153 21726 100 120 42 72 0 41 1 0 0 \N \N
116154 21726 129 149 42 72 0 41 1 0 0 \N \N
116155 21726 158 178 42 72 0 41 1 0 0 \N \N
116156 21726 193 213 42 72 0 41 0 0 0 \N \N
116157 21726 221 242 42 72 0 41 1 0 0 \N \N
130099 21726 68 97 41 71 0 41 14.815 0 0 \N \N
130101 21726 98 125 41 71 0 41 11.676 0 0 \N \N
130103 21726 127 154 41 71 0 41 9.556 0 0 \N \N
130105 21726 156 183 41 71 0 41 9.536 0 0 \N \N
130107 21726 191 218 41 71 0 41 12.092 0 0 \N \N
130109 21726 219 247 41 71 0 41 11.281 0 0 \N \N
217476 21726 68 94 49 79 24 41 12.8 0.29 0 \N \N
217477 21726 100 122 49 79 24 41 25.3 9.2e-05 0 \N \N
217478 21726 129 151 49 79 24 41 19.7 0.0045 0 \N \N
217479 21726 158 180 49 79 24 41 19.2 0.0063 0 \N \N
217480 21726 193 215 49 79 24 41 22.9 0.00049 0 \N \N
217481 21726 221 244 49 79 24 41 24 0.00023 0 \N \N
242784 21726 80 124 71 101 0 41 0 1.5e-09 0 \N \N
242785 21726 205 245 71 101 0 41 0 7.5e-09 0 \N \N
242786 21726 58 85 71 101 0 41 0 0.0011 0 \N \N
34517 21727 1 26 43 73 0 41 0 0 0 \N \N
83063 21727 15 22 44 74 0 41 0.81 0 0 \N \N
34518 21728 1 26 43 73 0 41 0 0 0 \N \N
83064 21728 15 22 44 74 0 41 0.81 0 0 \N \N
27435 21729 355 375 45 75 0 41 0 0 0 \N \N
27437 21729 436 473 45 75 0 41 0 0 0 \N \N
27440 21729 482 519 45 75 0 41 0 0 0 \N \N
27443 21729 541 579 45 75 0 41 0 0 0 \N \N
83065 21729 6 17 44 74 0 41 2.13 0 0 \N \N
83066 21729 370 407 44 74 0 41 2.15 0 0 \N \N
83067 21729 437 458 44 74 0 41 2.44 0 0 \N \N
83068 21729 493 514 44 74 0 41 2.5 0 0 \N \N
83069 21729 537 548 44 74 0 41 1.9 0 0 \N \N
83070 21729 685 697 44 74 0 41 2.26 0 0 \N \N
83071 21729 711 735 44 74 0 41 2.42 0 0 \N \N
116158 21729 96 103 42 72 0 41 0 0 0 \N \N
116159 21729 239 250 42 72 0 41 1 0 0 \N \N
130111 21729 6 256 41 71 0 41 55.446 0 0 \N \N
161528 21729 87 108 40 70 0 41 911 4.44e-16 0 \N \N
161530 21729 206 223 40 70 0 41 585 2.63e-10 0 \N \N
161532 21729 240 258 40 70 0 41 576 8.36e-12 0 \N \N
161534 21729 290 311 40 70 0 41 833 4.44e-16 0 \N \N
217672 21729 55 341 49 79 373 41 576.3 1.3e-170 0 \N \N
242791 21729 4 365 71 101 0 41 0 8.4e-131 0 \N \N
83072 21730 3 16 44 74 0 41 1.78 0 0 \N \N
83073 21730 140 153 44 74 0 41 2.15 0 0 \N \N
83074 21730 442 469 44 74 0 41 1.89 0 0 \N \N
83075 21730 644 654 44 74 0 41 1.87 0 0 \N \N
83076 21730 1221 1235 44 74 0 41 2.15 0 0 \N \N
83077 21730 1250 1264 44 74 0 41 2.2 0 0 \N \N
83078 21731 194 211 44 74 0 41 1.95 0 0 \N \N
83079 21731 335 348 44 74 0 41 2.15 0 0 \N \N
83080 21731 637 664 44 74 0 41 1.89 0 0 \N \N
83081 21731 839 849 44 74 0 41 1.87 0 0 \N \N
83082 21732 33 61 44 74 0 41 2.68 0 0 \N \N
83083 21732 161 178 44 74 0 41 1.83 0 0 \N \N
83084 21732 375 396 44 74 0 41 1.93 0 0 \N \N
116160 21732 92 102 42 72 0 41 0 0 0 \N \N
130113 21732 235 252 41 71 0 41 3 0 0 \N \N
83085 21735 76 95 44 74 0 41 2.54 0 0 \N \N
83086 21735 104 122 44 74 0 41 2.65 0 0 \N \N
83087 21736 5 20 44 74 0 41 1.92 0 0 \N \N
83088 21737 47 65 44 74 0 41 2.35 0 0 \N \N
83089 21737 72 83 44 74 0 41 1.65 0 0 \N \N
83090 21737 110 125 44 74 0 41 2.42 0 0 \N \N
83091 21737 142 154 44 74 0 41 2.16 0 0 \N \N
83092 21737 166 177 44 74 0 41 2.08 0 0 \N \N
83093 21737 565 576 44 74 0 41 1.96 0 0 \N \N
116161 21737 309 316 42 72 0 41 0 0 0 \N \N
116162 21737 643 655 42 72 0 41 0 0 0 \N \N
217810 21737 223 296 49 79 87 41 121 1.5e-33 0 \N \N
217811 21737 576 849 49 79 418 41 -74 8.5e-06 0 \N \N
242841 21737 573 848 71 101 0 41 0 3e-50 0 \N \N
242842 21737 216 351 71 101 0 41 0 1.2e-41 0 \N \N
27455 21738 193 213 45 75 0 41 0 0 0 \N \N
83094 21738 256 267 44 74 0 41 2.12 0 0 \N \N
130115 21738 14 116 41 71 0 41 8.924 0 0 \N \N
217326 21738 15 117 49 79 106 41 28 1.5e-05 0 \N \N
217327 21738 210 257 49 79 56 41 106 4.7e-29 0 \N \N
242845 21738 13 115 71 101 0 41 0 3e-17 0 \N \N
83095 21739 44 56 44 74 0 41 2.19 0 0 \N \N
130117 21739 144 201 41 71 0 41 9.695 0 0 \N \N
217297 21739 141 168 49 79 29 41 4.4 1.7 0 \N \N
217298 21739 176 204 49 79 29 41 12.7 0.15 0 \N \N
242846 21739 117 207 71 101 0 41 0 4e-10 0 \N \N
modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.sql
View file @ 628e5121
......@@ -31,6 +31,7 @@ CREATE TABLE `unmapped_object` (
`target_score` double DEFAULT NULL,
`ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` VARCHAR(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
KEY `id_idx` (`identifier`),
KEY `anal_idx` (`analysis_id`),
......
modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.txt
View file @ 628e5121
1 xref 9 4100 X1234 1 70.5 60.2 21716 Translation
2 xref 9 4100 X5678 1 75 50.1 21717 Transcript
3 cDNA 1290 4200 cDNA12 2 80 40 21718 Translation
4 cDNA 1290 4200 cDNA34 2 60.5 30.9 21719 Transcript
1 xref 9 4100 X1234 1 70.5 60.2 21716 Translation \N
2 xref 9 4100 X5678 1 75 50.1 21717 Transcript \N
3 cDNA 1290 4200 cDNA12 2 80 40 21718 Translation \N
4 cDNA 1290 4200 cDNA34 2 60.5 30.9 21719 Transcript \N
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
View file @ 628e5121
1 \N schema_version 68
1 \N schema_version 70
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
......@@ -23,3 +23,10 @@
65 1 assembly.mapping alt_chrom#chromosome:NCBI33
66 1 assembly.mapping alt_chrom|chromosome:NCBI33|contig
67 1 species.production_name homo_sapiens
75 \N schema_type core
76 \N patch patch_68_69_a.sql|schema_version
77 \N patch patch_69_70_a.sql|schema_version
78 \N patch patch_69_70_b.sql|add_mapping_set_history
79 \N patch patch_69_70_c.sql|column_datatype_consistency
80 \N patch patch_69_70_d.sql|data_file_id_auto_increment
81 \N patch patch_69_70_e.sql|protein_feature_hit_description
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