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ensembl-test
Unverified Commit a9f245b6 authored by ens-bwalts's avatar ens-bwalts Committed by GitHub
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Merge pull request #39 from Ensembl/e100_version_bump 

Bump test-database schema versions to 99/100
parents 26dafa5a 2c682439
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Showing with 37215 additions and 36885 deletions
modules/t/test-genome-DBs/homo_sapiens/core/analysis.txt
View file @ a9f245b6
......@@ -34,3 +34,4 @@
8406 2009-06-01 09:01:22 xrefexoneratedna NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL
8407 2007-09-07 12:01:22 est2genome_human_havana NULL 10-Nov-10 (105) NULL NULL NULL NULL ori_analysis => Est2genome_human_raw, mode => single ClusterDepthFilter NULL EST_Human similarity
8408 2007-09-07 12:01:22 uniprot_sw_havana NULL 2010_11 NULL NULL NULL NULL percentid_cutoff => 40, ori_analysis => Uniprot_raw, hit_db => Swissprot, mode => single DepthFilter NULL SwissProt NULL
8409 2017-11-02 10:15:53 gifts_import GIFTS NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL
\ No newline at end of file
modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt
View file @ a9f245b6
......@@ -19,3 +19,6 @@
19 karyotype_rank Rank in the karyotype For a given seq_region, if it is part of the species karyotype, will indicate its rank
20 proj_parent_g projection parent gene Stable identifier of the parent gene this gene was projected from (projection between different species and/or assemblies).
21 proj_parent_t projection parent transcript Stable identifier of the parent transcript this transcript was projected from (projection between different species and/or assemblies).
22 mirna_arm miRNA arm Hairpin arm from which this miRNA has come from
23 _stop_codon_rt Stop Codon Readthrough \N
24 appris APPRIS \N
modules/t/test-genome-DBs/homo_sapiens/core/biotype.txt 0 → 100644
View file @ a9f245b6
64 protein_coding gene core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0001217 protein_coding_gene
65 protein_coding transcript core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0000234 mRNA
87 tRNA gene core,otherfeatures,presite 76 \N snoncoding SO:0001263 ncRNA_gene
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @ a9f245b6
1 \N schema_version 90
1 \N schema_version 100
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
......@@ -89,3 +89,27 @@
156 \N patch patch_89_90_a.sql|schema_version
157 \N patch patch_89_90_b.sql|remove_status
158 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
159 \N patch patch_90_91_a.sql|schema_version
160 \N patch patch_90_91_b.sql|align_type
161 \N patch patch_90_91_c.sql|protein_align_type
162 \N patch patch_90_91_d.sql|remove_external_data
163 \N patch patch_91_92_a.sql|schema_version
164 \N patch patch_91_92_b.sql|add_cigar_line_align_type
165 \N patch patch_92_93_a.sql|schema_version
166 \N patch patch_92_93_b.sql|biotype_table
167 \N patch patch_92_93_c.sql|collate_index_interpro
168 \N patch patch_93_94_a.sql|schema_version
169 \N patch patch_93_94_b.sql|nullable_ox_analysis
170 \N patch patch_93_94_c.sql|default_aln_type
171 \N patch patch_94_95_a.sql|schema_version
172 \N patch patch_94_95_b.sql|vertebrate_division_rename
173 \N patch patch_94_95_c.sql|ox_key_update
174 \N patch patch_95_96_a.sql|schema_version
175 \N patch patch_96_97_a.sql|schema_version
176 \N patch patch_96_97_b.sql|biotype_so_term
177 \N patch patch_96_97_c.sql|rnaproduct_tables
178 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
179 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
180 \N patch patch_97_98_a.sql|schema_version
188 \N patch patch_98_99_a.sql|schema_version
189 \N patch patch_99_100_a.sql|schema_version
modules/t/test-genome-DBs/homo_sapiens/core/object_xref.txt
View file @ a9f245b6
......@@ -203,3 +203,5 @@
253682 21727 Translation 168444 119 0
253683 21727 Translation 168445 119 0
253684 21727 Translation 168446 119 0
999998 1 RNAProduct 123456 \N 0
999999 2 RNAProduct 123457 \N 0
modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt
View file @ a9f245b6
27374 21716 76 99 45 75 0 41 0.00 0 0 \N \N
217249 21716 47 151 49 79 PF000001 41 87.10 8.2e-25 0 \N \N
242732 21716 80 160 71 101 0 41 0.00 0.000000000032 0 \N \N
217179 21717 1 94 49 79 PF000019 41 99.10 3.3e-28 0 \N \N
242734 21717 3 91 71 101 0 41 0.00 0.0000000000000017 0 \N \N
217309 21718 76 201 49 79 PF000019 41 118.90 8.9e-34 0 \N \N
242735 21718 1 185 71 101 0 41 0.00 0.00000000000003 0 \N \N
27378 21719 90 117 45 75 0 41 0.00 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 0.00 0.0017 0 \N \N
24545 21720 79 101 46 76 0 41 0.00 0 0 \N \N
24546 21720 106 123 46 76 0 41 0.00 0 0 \N \N
24547 21720 138 155 46 76 0 41 0.00 0 0 \N \N
24548 21720 192 214 46 76 0 41 0.00 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 0.00 0 0 \N \N
83051 21721 24 37 44 74 0 41 2.30 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 0.00 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 2.20 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 0.00 0 0 \N \N
116150 21723 268 290 42 72 0 41 1.00 0 0 \N \N
116151 21723 377 389 42 72 0 41 1.00 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 19.62 0 0 \N \N
161506 21723 144 158 40 70 0 41 394.00 0.00000981 0 \N \N
161508 21723 165 175 40 70 0 41 321.00 0.0000259 0 \N \N
161510 21723 177 188 40 70 0 41 288.00 0.00000103 0 \N \N
161512 21723 194 204 40 70 0 41 295.00 0.0000486 0 \N \N
161514 21723 215 229 40 70 0 41 349.00 0.0000007 0 \N \N
161516 21723 81 91 40 70 0 41 266.00 0.0000318 0 \N \N
161518 21723 95 110 40 70 0 41 334.00 0.000000138 0 \N \N
161520 21723 111 120 40 70 0 41 225.00 0.0222 0 \N \N
161522 21723 124 136 40 70 0 41 341.00 0.00000182 0 \N \N
161524 21723 83 103 40 70 0 41 565.00 0.00000000711 0 \N \N
161526 21723 103 119 40 70 0 41 188.00 0.099 0 \N \N
217502 21723 83 138 49 79 58 41 98.90 6.4e-27 0 \N \N
217503 21723 146 228 49 79 79 41 150.90 1.5e-42 0 \N \N
217504 21723 264 513 49 79 294 41 260.80 1.2e-75 0 \N \N
242780 21723 244 526 71 101 0 41 0.00 2.3e-79 0 \N \N
242781 21723 138 282 71 101 0 41 0.00 1.3e-33 0 \N \N
242782 21723 81 162 71 101 0 41 0.00 2.5e-22 0 \N \N
24549 21724 263 285 46 76 0 41 0.00 0 0 \N \N
24550 21724 329 351 46 76 0 41 0.00 0 0 \N \N
24551 21724 361 383 46 76 0 41 0.00 0 0 \N \N
24552 21724 396 418 46 76 0 41 0.00 0 0 \N \N
24553 21724 433 455 46 76 0 41 0.00 0 0 \N \N
24554 21724 483 505 46 76 0 41 0.00 0 0 \N \N
24555 21724 515 537 46 76 0 41 0.00 0 0 \N \N
24556 21724 550 572 46 76 0 41 0.00 0 0 \N \N
24557 21724 587 609 46 76 0 41 0.00 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 1244.70 0 0 \N \N
242783 21724 3 576 71 101 0 41 0.00 0.0058 0 \N \N
27431 21725 113 133 45 75 0 41 0.00 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 84.50 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 2.30 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 1.00 0 0 \N \N
116153 21726 100 120 42 72 0 41 1.00 0 0 \N \N
116154 21726 129 149 42 72 0 41 1.00 0 0 \N \N
116155 21726 158 178 42 72 0 41 1.00 0 0 \N \N
116156 21726 193 213 42 72 0 41 0.00 0 0 \N \N
116157 21726 221 242 42 72 0 41 1.00 0 0 \N \N
130099 21726 68 97 41 71 0 41 14.81 0 0 \N \N
130101 21726 98 125 41 71 0 41 11.68 0 0 \N \N
130103 21726 127 154 41 71 0 41 9.56 0 0 \N \N
130105 21726 156 183 41 71 0 41 9.54 0 0 \N \N
130107 21726 191 218 41 71 0 41 12.09 0 0 \N \N
130109 21726 219 247 41 71 0 41 11.28 0 0 \N \N
217476 21726 68 94 49 79 24 41 12.80 0.29 0 \N \N
217477 21726 100 122 49 79 24 41 25.30 0.000092 0 \N \N
217478 21726 129 151 49 79 24 41 19.70 0.0045 0 \N \N
217479 21726 158 180 49 79 24 41 19.20 0.0063 0 \N \N
217480 21726 193 215 49 79 24 41 22.90 0.00049 0 \N \N
217481 21726 221 244 49 79 24 41 24.00 0.00023 0 \N \N
242784 21726 80 124 71 101 0 41 0.00 0.0000000015 0 \N \N
242785 21726 205 245 71 101 0 41 0.00 0.0000000075 0 \N \N
242786 21726 58 85 71 101 0 41 0.00 0.0011 0 \N \N
34517 21727 1 26 43 73 0 41 0.00 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 0.00 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 0.00 0 0 \N \N
27437 21729 436 473 45 75 0 41 0.00 0 0 \N \N
27440 21729 482 519 45 75 0 41 0.00 0 0 \N \N
27443 21729 541 579 45 75 0 41 0.00 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 2.50 0 0 \N \N
83069 21729 537 548 44 74 0 41 1.90 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 0.00 0 0 \N \N
116159 21729 239 250 42 72 0 41 1.00 0 0 \N \N
130111 21729 6 256 41 71 0 41 55.45 0 0 \N \N
161528 21729 87 108 40 70 0 41 911.00 4.44e-16 0 \N \N
161530 21729 206 223 40 70 0 41 585.00 0.000000000263 0 \N \N
161532 21729 240 258 40 70 0 41 576.00 0.00000000000836 0 \N \N
161534 21729 290 311 40 70 0 41 833.00 4.44e-16 0 \N \N
217672 21729 55 341 49 79 373 41 576.30 1.3e-170 0 \N \N
242791 21729 4 365 71 101 0 41 0.00 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 2.20 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 0.00 0 0 \N \N
130113 21732 235 252 41 71 0 41 3.00 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 0.00 0 0 \N \N
116162 21737 643 655 42 72 0 41 0.00 0 0 \N \N
217810 21737 223 296 49 79 87 41 121.00 1.5e-33 0 \N \N
217811 21737 576 849 49 79 418 41 -74.00 0.0000085 0 \N \N
242841 21737 573 848 71 101 0 41 0.00 3e-50 0 \N \N
242842 21737 216 351 71 101 0 41 0.00 1.2e-41 0 \N \N
27455 21738 193 213 45 75 0 41 0.00 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 8.92 0 0 \N \N
217326 21738 15 117 49 79 106 41 28.00 0.000015 0 \N \N
217327 21738 210 257 49 79 56 41 106.00 4.7e-29 0 \N \N
242845 21738 13 115 71 101 0 41 0.00 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 9.70 0 0 \N \N
217297 21739 141 168 49 79 29 41 4.40 1.7 0 \N \N
217298 21739 176 204 49 79 29 41 12.70 0.15 0 \N \N
242846 21739 117 207 71 101 0 41 0.00 0.0000000004 0 \N \N
27374 21716 76 99 45 75 0 41 0 0 0 \N \N \N \N
217249 21716 47 151 49 79 PF000001 41 87.1 8.2e-25 0 \N \N \N \N
242732 21716 80 160 71 101 0 41 0 0.000000000032 0 \N \N \N \N
217179 21717 1 94 49 79 PF000019 41 99.1 3.3e-28 0 \N \N \N \N
242734 21717 3 91 71 101 0 41 0 0.0000000000000017 0 \N \N \N \N
217309 21718 76 201 49 79 PF000019 41 118.9 8.9e-34 0 \N \N \N \N
242735 21718 1 185 71 101 0 41 0 0.00000000000003 0 \N \N \N \N
27378 21719 90 117 45 75 0 41 0 0 0 \N \N \N \N
83043 21719 21 41 44 74 0 41 2.37 0 0 \N \N \N \N
242736 21719 76 124 71 101 0 41 0 0.0017 0 \N \N \N \N
24545 21720 79 101 46 76 0 41 0 0 0 \N \N \N \N
24546 21720 106 123 46 76 0 41 0 0 0 \N \N \N \N
24547 21720 138 155 46 76 0 41 0 0 0 \N \N \N \N
24548 21720 192 214 46 76 0 41 0 0 0 \N \N \N \N
83044 21720 37 59 44 74 0 41 2.67 0 0 \N \N \N \N
116148 21720 93 100 42 72 0 41 0 0 0 \N \N \N \N
83051 21721 24 37 44 74 0 41 2.3 0 0 \N \N \N \N
83052 21721 170 184 44 74 0 41 1.97 0 0 \N \N \N \N
83053 21721 212 235 44 74 0 41 2.47 0 0 \N \N \N \N
242779 21721 47 146 71 101 0 41 0 0.002 0 \N \N \N \N
83045 21722 135 149 44 74 0 41 1.97 0 0 \N \N \N \N
83046 21722 171 187 44 74 PF000001 41 1.66 0 0 \N \N \N \N
83047 21722 217 230 44 74 0 41 1.09 0 0 \N \N \N \N
83048 21722 361 376 44 74 0 41 2.44 0 0 \N \N \N \N
83049 21722 470 482 44 74 0 41 2.2 0 0 \N \N \N \N
83050 21722 512 520 44 74 0 41 0.76 0 0 \N \N \N \N
116149 21722 347 358 42 72 0 41 0 0 0 \N \N \N \N
116150 21723 268 290 42 72 0 41 1 0 0 \N \N \N \N
116151 21723 377 389 42 72 0 41 1 0 0 \N \N \N \N
130095 21723 144 241 41 71 0 41 26.88 0 0 \N \N \N \N
130097 21723 78 138 41 71 0 41 19.62 0 0 \N \N \N \N
161506 21723 144 158 40 70 0 41 394 0.00000981 0 \N \N \N \N
161508 21723 165 175 40 70 0 41 321 0.0000259 0 \N \N \N \N
161510 21723 177 188 40 70 0 41 288 0.00000103 0 \N \N \N \N
161512 21723 194 204 40 70 0 41 295 0.0000486 0 \N \N \N \N
161514 21723 215 229 40 70 0 41 349 0.0000007 0 \N \N \N \N
161516 21723 81 91 40 70 0 41 266 0.0000318 0 \N \N \N \N
161518 21723 95 110 40 70 0 41 334 0.000000138 0 \N \N \N \N
161520 21723 111 120 40 70 0 41 225 0.0222 0 \N \N \N \N
161522 21723 124 136 40 70 0 41 341 0.00000182 0 \N \N \N \N
161524 21723 83 103 40 70 0 41 565 0.00000000711 0 \N \N \N \N
161526 21723 103 119 40 70 0 41 188 0.099 0 \N \N \N \N
217502 21723 83 138 49 79 58 41 98.9 6.4e-27 0 \N \N \N \N
217503 21723 146 228 49 79 79 41 150.9 1.5e-42 0 \N \N \N \N
217504 21723 264 513 49 79 294 41 260.8 1.2e-75 0 \N \N \N \N
242780 21723 244 526 71 101 0 41 0 2.3e-79 0 \N \N \N \N
242781 21723 138 282 71 101 0 41 0 1.3e-33 0 \N \N \N \N
242782 21723 81 162 71 101 0 41 0 2.5e-22 0 \N \N \N \N
24549 21724 263 285 46 76 0 41 0 0 0 \N \N \N \N
24550 21724 329 351 46 76 0 41 0 0 0 \N \N \N \N
24551 21724 361 383 46 76 0 41 0 0 0 \N \N \N \N
24552 21724 396 418 46 76 0 41 0 0 0 \N \N \N \N
24553 21724 433 455 46 76 0 41 0 0 0 \N \N \N \N
24554 21724 483 505 46 76 0 41 0 0 0 \N \N \N \N
24555 21724 515 537 46 76 0 41 0 0 0 \N \N \N \N
24556 21724 550 572 46 76 0 41 0 0 0 \N \N \N \N
24557 21724 587 609 46 76 0 41 0 0 0 \N \N \N \N
83054 21724 270 275 44 74 0 41 0.92 0 0 \N \N \N \N
83055 21724 326 335 44 74 0 41 1.97 0 0 \N \N \N \N
83056 21724 367 378 44 74 0 41 2.05 0 0 \N \N \N \N
83057 21724 513 529 44 74 0 41 2.42 0 0 \N \N \N \N
217569 21724 37 583 49 79 600 41 1244.7 0 0 \N \N \N \N
242783 21724 3 576 71 101 0 41 0 0.0058 0 \N \N \N \N
27431 21725 113 133 45 75 0 41 0 0 0 \N \N \N \N
83058 21725 30 40 44 74 0 41 1.87 0 0 \N \N \N \N
83059 21725 109 135 44 74 0 41 2.49 0 0 \N \N \N \N
217397 21725 146 331 49 79 324 41 84.5 1.4e-22 0 \N \N \N \N
83060 21726 369 397 44 74 0 41 2.53 0 0 \N \N \N \N
83061 21726 417 432 44 74 0 41 2.3 0 0 \N \N \N \N
83062 21726 443 458 44 74 0 41 2.43 0 0 \N \N \N \N
116152 21726 70 92 42 72 0 41 1 0 0 \N \N \N \N
116153 21726 100 120 42 72 0 41 1 0 0 \N \N \N \N
116154 21726 129 149 42 72 0 41 1 0 0 \N \N \N \N
116155 21726 158 178 42 72 0 41 1 0 0 \N \N \N \N
116156 21726 193 213 42 72 0 41 0 0 0 \N \N \N \N
116157 21726 221 242 42 72 0 41 1 0 0 \N \N \N \N
130099 21726 68 97 41 71 0 41 14.81 0 0 \N \N \N \N
130101 21726 98 125 41 71 0 41 11.68 0 0 \N \N \N \N
130103 21726 127 154 41 71 0 41 9.56 0 0 \N \N \N \N
130105 21726 156 183 41 71 0 41 9.54 0 0 \N \N \N \N
130107 21726 191 218 41 71 0 41 12.09 0 0 \N \N \N \N
130109 21726 219 247 41 71 0 41 11.28 0 0 \N \N \N \N
217476 21726 68 94 49 79 24 41 12.8 0.29 0 \N \N \N \N
217477 21726 100 122 49 79 24 41 25.3 0.000092 0 \N \N \N \N
217478 21726 129 151 49 79 24 41 19.7 0.0045 0 \N \N \N \N
217479 21726 158 180 49 79 24 41 19.2 0.0063 0 \N \N \N \N
217480 21726 193 215 49 79 24 41 22.9 0.00049 0 \N \N \N \N
217481 21726 221 244 49 79 24 41 24 0.00023 0 \N \N \N \N
242784 21726 80 124 71 101 0 41 0 0.0000000015 0 \N \N \N \N
242785 21726 205 245 71 101 0 41 0 0.0000000075 0 \N \N \N \N
242786 21726 58 85 71 101 0 41 0 0.0011 0 \N \N \N \N
34517 21727 1 26 43 73 0 41 0 0 0 \N \N \N \N
83063 21727 15 22 44 74 0 41 0.81 0 0 \N \N \N \N
34518 21728 1 26 43 73 0 41 0 0 0 \N \N \N \N
83064 21728 15 22 44 74 0 41 0.81 0 0 \N \N \N \N
27435 21729 355 375 45 75 0 41 0 0 0 \N \N \N \N
27437 21729 436 473 45 75 0 41 0 0 0 \N \N \N \N
27440 21729 482 519 45 75 0 41 0 0 0 \N \N \N \N
27443 21729 541 579 45 75 0 41 0 0 0 \N \N \N \N
83065 21729 6 17 44 74 0 41 2.13 0 0 \N \N \N \N
83066 21729 370 407 44 74 0 41 2.15 0 0 \N \N \N \N
83067 21729 437 458 44 74 0 41 2.44 0 0 \N \N \N \N
83068 21729 493 514 44 74 0 41 2.5 0 0 \N \N \N \N
83069 21729 537 548 44 74 0 41 1.9 0 0 \N \N \N \N
83070 21729 685 697 44 74 0 41 2.26 0 0 \N \N \N \N
83071 21729 711 735 44 74 0 41 2.42 0 0 \N \N \N \N
116158 21729 96 103 42 72 0 41 0 0 0 \N \N \N \N
116159 21729 239 250 42 72 0 41 1 0 0 \N \N \N \N
130111 21729 6 256 41 71 0 41 55.45 0 0 \N \N \N \N
161528 21729 87 108 40 70 0 41 911 4.44e-16 0 \N \N \N \N
161530 21729 206 223 40 70 0 41 585 0.000000000263 0 \N \N \N \N
161532 21729 240 258 40 70 0 41 576 0.00000000000836 0 \N \N \N \N
161534 21729 290 311 40 70 0 41 833 4.44e-16 0 \N \N \N \N
217672 21729 55 341 49 79 373 41 576.3 1.3e-170 0 \N \N \N \N
242791 21729 4 365 71 101 0 41 0 8.4e-131 0 \N \N \N \N
83072 21730 3 16 44 74 0 41 1.78 0 0 \N \N \N \N
83073 21730 140 153 44 74 0 41 2.15 0 0 \N \N \N \N
83074 21730 442 469 44 74 0 41 1.89 0 0 \N \N \N \N
83075 21730 644 654 44 74 0 41 1.87 0 0 \N \N \N \N
83076 21730 1221 1235 44 74 0 41 2.15 0 0 \N \N \N \N
83077 21730 1250 1264 44 74 0 41 2.2 0 0 \N \N \N \N
83078 21731 194 211 44 74 0 41 1.95 0 0 \N \N \N \N
83079 21731 335 348 44 74 0 41 2.15 0 0 \N \N \N \N
83080 21731 637 664 44 74 0 41 1.89 0 0 \N \N \N \N
83081 21731 839 849 44 74 0 41 1.87 0 0 \N \N \N \N
83082 21732 33 61 44 74 0 41 2.68 0 0 \N \N \N \N
83083 21732 161 178 44 74 0 41 1.83 0 0 \N \N \N \N
83084 21732 375 396 44 74 0 41 1.93 0 0 \N \N \N \N
116160 21732 92 102 42 72 0 41 0 0 0 \N \N \N \N
130113 21732 235 252 41 71 0 41 3 0 0 \N \N \N \N
83085 21735 76 95 44 74 0 41 2.54 0 0 \N \N \N \N
83086 21735 104 122 44 74 0 41 2.65 0 0 \N \N \N \N
83087 21736 5 20 44 74 0 41 1.92 0 0 \N \N \N \N
83088 21737 47 65 44 74 0 41 2.35 0 0 \N \N \N \N
83089 21737 72 83 44 74 0 41 1.65 0 0 \N \N \N \N
83090 21737 110 125 44 74 0 41 2.42 0 0 \N \N \N \N
83091 21737 142 154 44 74 0 41 2.16 0 0 \N \N \N \N
83092 21737 166 177 44 74 0 41 2.08 0 0 \N \N \N \N
83093 21737 565 576 44 74 0 41 1.96 0 0 \N \N \N \N
116161 21737 309 316 42 72 0 41 0 0 0 \N \N \N \N
116162 21737 643 655 42 72 0 41 0 0 0 \N \N \N \N
217810 21737 223 296 49 79 87 41 121 1.5e-33 0 \N \N \N \N
217811 21737 576 849 49 79 418 41 -74 0.0000085 0 \N \N \N \N
242841 21737 573 848 71 101 0 41 0 3e-50 0 \N \N \N \N
242842 21737 216 351 71 101 0 41 0 1.2e-41 0 \N \N \N \N
27455 21738 193 213 45 75 0 41 0 0 0 \N \N \N \N
83094 21738 256 267 44 74 0 41 2.12 0 0 \N \N \N \N
130115 21738 14 116 41 71 0 41 8.92 0 0 \N \N \N \N
217326 21738 15 117 49 79 106 41 28 0.000015 0 \N \N \N \N
217327 21738 210 257 49 79 56 41 106 4.7e-29 0 \N \N \N \N
242845 21738 13 115 71 101 0 41 0 3e-17 0 \N \N \N \N
83095 21739 44 56 44 74 0 41 2.19 0 0 \N \N \N \N
130117 21739 144 201 41 71 0 41 9.7 0 0 \N \N \N \N
217297 21739 141 168 49 79 29 41 4.4 1.7 0 \N \N \N \N
217298 21739 176 204 49 79 29 41 12.7 0.15 0 \N \N \N \N
242846 21739 117 207 71 101 0 41 0 0.0000000004 0 \N \N \N \N
242847 21739 118 208 71 101 Q86UU9 8409 0 0.0000000004 0 \N \N MD:Z:35^VIVALE31^GRPLIQPRRKKAYQLEHTFQGLLGKRSLFTE10 mdtag
\ No newline at end of file
modules/t/test-genome-DBs/homo_sapiens/core/rnaproduct.txt 0 → 100644
View file @ a9f245b6
1 2 21717 46 162035 67 162035 ENSS00000000001 1 2018-05-14 12:00:00 2018-05-14 12:00:00
2 2 21717 7 \N 28 \N ENSS00000000002 1 2018-05-21 17:00:00 2018-05-21 17:00:00
modules/t/test-genome-DBs/homo_sapiens/core/rnaproduct_attrib.txt 0 → 100644
View file @ a9f245b6
1 10 Placeholder
1 22 3
2 10 Placeholder
2 22 5
modules/t/test-genome-DBs/homo_sapiens/core/rnaproduct_type.txt 0 → 100644
View file @ a9f245b6
1 generic generic Generic mature RNA
2 miRNA microRNA Mature microRNA strand
3 circRNA Circular RNA \N
modules/t/test-genome-DBs/homo_sapiens/core/seq_region.txt
View file @ a9f245b6
131538 20 4 64444167
368744 AL359765.6.1.13780 4 13780
317101 AL031658.11.1.162976 4 162976
339816 AL353092.6.1.25010 4 25010
......
modules/t/test-genome-DBs/homo_sapiens/core/seq_region_synonym.txt
View file @ a9f245b6
1 469283 alt_20 \N
2 469283 anoth_20 4200
3 469293 chrx 11000
4 469272 chr10 11000
5 469271 chr1 11000
modules/t/test-genome-DBs/homo_sapiens/core/xref.txt
View file @ a9f245b6
......@@ -181,5 +181,7 @@
103296 2 U24166 U24166 1 description D
103297 3 AAC09471 AAC09471 1 description D
103298 3 CAB53072 CAB53072 1 description D
123456 3300 MIMAT0000416 hsa-miR-1-3p 1 description D
123457 3300 MIMAT0031892 hsa-miR-1-5p 1 description D
999998 11 IPR000001 IPR000001 1 Test interpro desc1 D
999999 11 IPR000010 IPR000010 1 Test interpro desc2 D
modules/t/test-genome-DBs/multi/compara/genome_db.txt
View file @ a9f245b6
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 @ a9f245b6
36 \N schema_version 90
65 \N schema_version 99
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
......@@ -35,3 +35,22 @@
40 \N patch patch_89_90_d.sql|genomic_align_tree_left_node_id_null
41 \N patch patch_89_90_e.sql|seq_member_projection
42 \N patch patch_89_90_f.sql|gene_member_missing_biotype_groups
43 \N patch patch_90_91_b.sql|gene_member_qc.seq_member_id.unsigned
45 \N patch patch_90_91_a.sql|schema_version
46 \N patch patch_90_91_c.sql|gene_member.biotype_group-index
48 \N patch patch_91_92_a.sql|schema_version
49 \N patch patch_91_92_b.sql|mapping_session_new_type_hmm
50 \N patch patch_91_92_c.sql|gene_tree_root_tag_255
52 \N patch patch_92_93_a.sql|schema_version
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
62 \N patch patch_95_96_a.sql|schema_version
64 \N patch patch_96_97_a.sql|schema_version
66 \N patch patch_97_98_a.sql|schema_version
67 \N patch patch_97_98_b.sql|division_name
68 \N patch patch_98_99_a.sql|schema_version
modules/t/test-genome-DBs/multi/compara/method_link.txt
View file @ a9f245b6
401 PROTEIN_TREES ProteinTree.protein_tree_node
201 ENSEMBL_ORTHOLOGUES Homology.homology
202 ENSEMBL_PARALOGUES Homology.homology
402 NC_TREES NCTree.nc_tree_node
101 SYNTENY SyntenyRegion.synteny
16 LASTZ_NET GenomicAlignBlock.pairwise_alignment
401 PROTEIN_TREES ProteinTree.protein_tree_node Protein-trees
201 ENSEMBL_ORTHOLOGUES Homology.homology Orthologues
202 ENSEMBL_PARALOGUES Homology.homology Paralogues
402 NC_TREES NCTree.nc_tree_node ncRNA-trees
101 SYNTENY SyntenyRegion.synteny Synteny
16 LASTZ_NET GenomicAlignBlock.pairwise_alignment LastZ
modules/t/test-genome-DBs/multi/compara/table.sql
View file @ a9f245b6
......@@ -24,8 +24,8 @@ CREATE TABLE `conservation_score` (
`genomic_align_block_id` bigint(20) unsigned NOT NULL,
`window_size` smallint(5) unsigned NOT NULL,
`position` int(10) unsigned NOT NULL,
`expected_score` blob,
`diff_score` blob,
`expected_score` blob DEFAULT NULL,
`diff_score` blob DEFAULT NULL,
KEY `genomic_align_block_id` (`genomic_align_block_id`,`window_size`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=15000000 AVG_ROW_LENGTH=841;
......@@ -36,34 +36,32 @@ CREATE TABLE `constrained_element` (
`dnafrag_end` int(12) unsigned NOT NULL,
`dnafrag_strand` int(2) NOT NULL,
`method_link_species_set_id` int(10) unsigned NOT NULL,
`p_value` double NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
`p_value` double NOT NULL DEFAULT 0,
`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` (
`dnafrag_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`length` int(11) NOT NULL DEFAULT '0',
`length` int(11) NOT NULL DEFAULT 0,
`name` varchar(255) NOT NULL DEFAULT '',
`genome_db_id` int(10) unsigned NOT NULL,
`coord_system_name` varchar(40) NOT NULL DEFAULT '',
`cellular_component` enum('NUC','MT','PT') NOT NULL DEFAULT 'NUC',
`is_reference` tinyint(1) NOT NULL DEFAULT '1',
`codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT '1',
`is_reference` tinyint(1) NOT NULL DEFAULT 1,
`codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT 1,
PRIMARY KEY (`dnafrag_id`),
UNIQUE KEY `name` (`genome_db_id`,`name`)
) ENGINE=MyISAM AUTO_INCREMENT=14026981 DEFAULT CHARSET=latin1;
CREATE TABLE `dnafrag_region` (
`synteny_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT '0',
`dnafrag_start` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_end` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_strand` tinyint(4) NOT NULL DEFAULT '0',
`synteny_region_id` int(10) unsigned NOT NULL DEFAULT 0,
`dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT 0,
`dnafrag_start` int(10) unsigned NOT NULL DEFAULT 0,
`dnafrag_end` int(10) unsigned NOT NULL DEFAULT 0,
`dnafrag_strand` tinyint(4) NOT NULL DEFAULT 0,
KEY `synteny` (`synteny_region_id`,`dnafrag_id`),
KEY `synteny_reversed` (`dnafrag_id`,`synteny_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
......@@ -74,7 +72,7 @@ CREATE TABLE `exon_boundaries` (
`dnafrag_start` int(11) NOT NULL,
`dnafrag_end` int(11) NOT NULL,