From 705540d3804d63c986e64d44eab8b65ebcccae75 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Thu, 8 Aug 2013 15:05:15 +0000
Subject: [PATCH] [ENSCORESW-566]. Synchronised the core test database with the
e73 schema.
The test schema was out of sync for ages due to it never being patched
using the patch sets. This is no longer the case. We needed a one
shot resynchronisation between the live schema and this test schema. All
test cases have been run and still pass. Assuming the processes
has not destroyed data. Any data changes seem to be related to different
levels of precision being emitted in the files.
Meta coord was updated.
---
.../homo_sapiens/core/analysis.txt | 1 -
.../homo_sapiens/core/density_feature.txt | 24 +-
.../homo_sapiens/core/meta_coord.txt | 15 +-
.../homo_sapiens/core/protein_feature.txt | 216 ++---
.../homo_sapiens/core/splicing_event.txt | 0
.../core/splicing_event_feature.txt | 0
.../core/splicing_transcript_pair.txt | 0
.../homo_sapiens/core/table.sql | 740 ++++++++++--------
8 files changed, 521 insertions(+), 475 deletions(-)
create mode 100644 modules/t/test-genome-DBs/homo_sapiens/core/splicing_event.txt
create mode 100644 modules/t/test-genome-DBs/homo_sapiens/core/splicing_event_feature.txt
create mode 100644 modules/t/test-genome-DBs/homo_sapiens/core/splicing_transcript_pair.txt
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/analysis.txt b/modules/t/test-genome-DBs/homo_sapiens/core/analysis.txt
index 9f6766b895..129bb28914 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/analysis.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/analysis.txt
@@ -24,7 +24,6 @@
44 0000-00-00 00:00:00 Seg low_complexity NULL NULL /usr/local/ensembl/bin/seg NULL /usr/local/ensembl/bin/seg NULL Seg NULL Seg annot
42 0000-00-00 00:00:00 scanprosite prosite NULL /acari/analysis/iprscan/data/prosite.patterns /acari/analysis/iprscan/bin/scanregexpf.pl /acari/analysis/iprscan/data/confirm.pat /acari/analysis/iprscan/bin/scanregexpf.pl Prosite NULL PROSITE domain
71 0000-00-00 00:00:00 Superfamily Superfamily 1 /data/blastdb/Ensembl/sam/superfamily /acari/work1/mongin/superfamily/superfamily.pl 1 /acari/work1/mongin/superfamily/superfamily.pl Superfamily 1 Superfamily annot
-119 2006-03-14 15:48:36 XrefExonerateDNA \N \N \N \N \N \N \N \N \N \N \N
1292 0000-00-00 00:00:00 SNPDensity \N \N \N \N \N \N \N \N \N \N \N
1293 0000-00-00 00:00:00 RepeatCoverage \N \N \N \N \N \N \N \N \N \N \N
1500 0000-00-00 00:00:00 miRanda \N \N \N \N \N \N \N \N \N \N \N
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/density_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/core/density_feature.txt
index bd5a82cdf4..9d783b32e8 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/density_feature.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/density_feature.txt
@@ -1,12 +1,12 @@
-1 1 469283 1 100 50.3
-2 1 469283 101 200 68.8
-3 1 469283 201 300 32
-4 1 469283 301 400 90.9
-5 1 469283 401 500 88.8
-6 1 469283 501 600 12
-7 2 469283 1 100 50.3
-8 2 469283 101 200 68.8
-9 2 469283 201 300 32
-10 2 469283 301 400 90.9
-11 2 469283 401 500 88.8
-12 2 469283 501 600 12
+1 1 469283 1 100 50.30
+2 1 469283 101 200 68.80
+3 1 469283 201 300 32.00
+4 1 469283 301 400 90.90
+5 1 469283 401 500 88.80
+6 1 469283 501 600 12.00
+7 2 469283 1 100 50.30
+8 2 469283 101 200 68.80
+9 2 469283 201 300 32.00
+10 2 469283 301 400 90.90
+11 2 469283 401 500 88.80
+12 2 469283 501 600 12.00
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta_coord.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta_coord.txt
index c97f2679cc..f916a91a64 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta_coord.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta_coord.txt
@@ -1,24 +1,21 @@
assembly_exception 1 500001
-density_feature 1 6000000
-dna_align_feature 4 4366
+density_feature 1 100
exon 1 5179
gene 1 79572
karyotype 1 2400001
marker_feature 4 363
misc_feature 1 26257626
-prediction_exon 4 1984
-prediction_transcript 4 78040
-protein_align_feature 4 1983
qtl_feature 1 736330
repeat_feature 4 1851
simple_feature 4 2900
transcript 1 79572
-dna_align_feature 1 2082
-protein_align_feature 1 1914
-prediction_transcript 1 202
-prediction_exon 1 101
+dna_align_feature 4 4366
+protein_align_feature 4 1983
+prediction_transcript 4 78040
+prediction_exon 4 1984
affy_feature 1 25
regulatory_feature 1 121
regulatory_search_region 1 121
operon 1 106713
operon_transcript 1 106713
+ditag_feature 1 19
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt
index 1dfadacee4..c53b2ff91e 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt
@@ -1,124 +1,124 @@
-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 0.000000000032 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 0.0000000000000017 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 0.00000000000003 0 \N \N
-27378 21719 90 117 45 75 0 41 0 0 0 \N \N
+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 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
+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 0 0 \N \N
-83051 21721 24 37 44 74 0 41 2.3 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 0.002 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 2.2 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 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
+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 19.623 0 0 \N \N
-161506 21723 144 158 40 70 0 41 394 0.00000981 0 \N \N
-161508 21723 165 175 40 70 0 41 321 0.0000259 0 \N \N
-161510 21723 177 188 40 70 0 41 288 0.00000103 0 \N \N
-161512 21723 194 204 40 70 0 41 295 0.0000486 0 \N \N
-161514 21723 215 229 40 70 0 41 349 0.0000007 0 \N \N
-161516 21723 81 91 40 70 0 41 266 0.0000318 0 \N \N
-161518 21723 95 110 40 70 0 41 334 0.000000138 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 0.00000182 0 \N \N
-161524 21723 83 103 40 70 0 41 565 0.00000000711 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
+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 1244.7 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
+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 84.5 1.4e-22 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 2.3 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 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 0.000092 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 0.0000000015 0 \N \N
-242785 21726 205 245 71 101 0 41 0 0.0000000075 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
+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 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 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
+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 2.5 0 0 \N \N
-83069 21729 537 548 44 74 0 41 1.9 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 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 0.000000000263 0 \N \N
-161532 21729 240 258 40 70 0 41 576 0.00000000000836 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
+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 2.2 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
@@ -126,8 +126,8 @@
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
+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
@@ -137,20 +137,20 @@
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 0.0000085 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
+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 8.924 0 0 \N \N
-217326 21738 15 117 49 79 106 41 28 0.000015 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
+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 9.695 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 0.0000000004 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
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/splicing_event.txt b/modules/t/test-genome-DBs/homo_sapiens/core/splicing_event.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/splicing_event_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/core/splicing_event_feature.txt
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/splicing_transcript_pair.txt b/modules/t/test-genome-DBs/homo_sapiens/core/splicing_transcript_pair.txt
new file mode 100644
index 0000000000..e69de29bb2
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 6d61a5b6b5..1bc41b2077 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -4,75 +4,74 @@ CREATE TABLE `alt_allele` (
`gene_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`alt_allele_id`),
KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
-) ENGINE=InnoDB ;
+) ENGINE=MyISAM ;
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=InnoDB ;
+) ENGINE=MyISAM ;
CREATE TABLE `alt_allele_group` (
`alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
PRIMARY KEY (`alt_allele_group_id`)
-) ENGINE=InnoDB ;
+) ENGINE=MyISAM ;
CREATE TABLE `analysis` (
- `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
- `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
- `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
- `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `parameters` text COLLATE latin1_bin,
- `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
- `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+ `logic_name` varchar(128) NOT NULL,
+ `db` varchar(120) DEFAULT NULL,
+ `db_version` varchar(40) DEFAULT NULL,
+ `db_file` varchar(120) DEFAULT NULL,
+ `program` varchar(80) DEFAULT NULL,
+ `program_version` varchar(40) DEFAULT NULL,
+ `program_file` varchar(80) DEFAULT NULL,
+ `parameters` text ,
+ `module` varchar(80) DEFAULT NULL,
+ `module_version` varchar(40) DEFAULT NULL,
+ `gff_source` varchar(40) DEFAULT NULL,
+ `gff_feature` varchar(40) DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
- UNIQUE KEY `logic_name` (`logic_name`),
- KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM ;
+ UNIQUE KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM ;
CREATE TABLE `analysis_description` (
- `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
- `description` text COLLATE latin1_bin,
- `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `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 COLLATE latin1_bin,
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM ;
+ `web_data` text ,
+ UNIQUE KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM ;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `asm_start` int(10) NOT NULL DEFAULT '0',
- `asm_end` int(10) NOT NULL DEFAULT '0',
- `cmp_start` int(10) NOT NULL DEFAULT '0',
- `cmp_end` int(10) NOT NULL DEFAULT '0',
- `ori` tinyint(4) NOT NULL DEFAULT '0',
+ `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_id` (`cmp_seq_region_id`),
- KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
-) ENGINE=MyISAM ;
+ KEY `cmp_seq_region_idx` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_idx` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=MyISAM ;
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(11) NOT NULL DEFAULT '0',
- `seq_region_start` int(11) NOT NULL DEFAULT '0',
- `seq_region_end` int(11) NOT NULL DEFAULT '0',
- `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
- `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
- `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
- `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
- `ori` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `exc_type` enum('HAP','PAR','PATCH_FIX','PATCH_NOVEL') NOT NULL,
+ `exc_seq_region_id` int(10) unsigned NOT NULL,
+ `exc_seq_region_start` int(10) unsigned NOT NULL,
+ `exc_seq_region_end` int(10) unsigned NOT NULL,
+ `ori` int(11) NOT NULL,
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -98,12 +97,12 @@ CREATE TABLE `associated_xref` (
CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
- `code` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin,
+ `code` varchar(15) NOT NULL DEFAULT '',
+ `name` varchar(255) NOT NULL DEFAULT '',
+ `description` text ,
PRIMARY KEY (`attrib_type_id`),
- UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM ;
+ UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM ;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -134,26 +133,26 @@ CREATE TABLE `data_file` (
) ENGINE=MyISAM ;
CREATE TABLE `density_feature` (
- `density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `density_type_id` int(11) NOT NULL DEFAULT '0',
- `seq_region_id` int(11) NOT NULL DEFAULT '0',
- `seq_region_start` int(11) NOT NULL DEFAULT '0',
- `seq_region_end` int(11) NOT NULL DEFAULT '0',
- `density_value` float NOT NULL DEFAULT '0',
+ `density_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `density_type_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,
+ `density_value` float(8,2) NOT NULL,
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `density_type` (
- `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
- `analysis_id` int(11) NOT NULL DEFAULT '0',
- `block_size` int(11) NOT NULL DEFAULT '0',
- `region_features` int(11) NOT NULL DEFAULT '0',
- `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
+ `density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `block_size` int(11) NOT NULL,
+ `region_features` int(11) NOT NULL,
+ `value_type` enum('sum','ratio') NOT NULL,
PRIMARY KEY (`density_type_id`),
- UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM ;
+ UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM ;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -165,11 +164,11 @@ CREATE TABLE `dependent_xref` (
) ENGINE=MyISAM ;
CREATE TABLE `ditag` (
- `ditag_id` int(10) NOT NULL AUTO_INCREMENT,
- `name` varchar(30) DEFAULT NULL,
- `type` varchar(30) DEFAULT NULL,
- `tag_count` smallint(6) DEFAULT '1',
- `sequence` text,
+ `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=MyISAM ;
@@ -181,41 +180,42 @@ CREATE TABLE `ditag_feature` (
`seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
`seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`hit_start` int(10) unsigned NOT NULL DEFAULT '0',
`hit_end` int(10) unsigned NOT NULL DEFAULT '0',
`hit_strand` tinyint(1) NOT NULL DEFAULT '0',
- `cigar_line` text,
- `ditag_side` char(1) DEFAULT '',
+ `cigar_line` tinytext NOT NULL,
+ `ditag_side` enum('F','L','R') NOT NULL,
PRIMARY KEY (`ditag_feature_id`),
- KEY `ditag_id` (`ditag_id`),
- KEY `ditag_pair_id` (`ditag_pair_id`)
+ KEY `ditag_idx` (`ditag_id`),
+ KEY `ditag_pair_idx` (`ditag_pair_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
) ENGINE=MyISAM ;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `sequence` mediumtext COLLATE latin1_bin NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `sequence` longtext NOT NULL,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM 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 DEFAULT '0',
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `hit_start` int(11) NOT NULL DEFAULT '0',
- `hit_end` int(11) NOT NULL DEFAULT '0',
- `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
- `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `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(1) NOT NULL,
+ `hit_start` int(11) NOT NULL,
+ `hit_end` int(11) NOT NULL,
+ `hit_strand` tinyint(1) NOT NULL,
+ `hit_name` varchar(40) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin,
- `external_db_id` smallint(5) unsigned DEFAULT NULL,
+ `cigar_line` text ,
+ `external_db_id` int(10) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
- `external_data` text COLLATE latin1_bin,
+ `external_data` text ,
`pair_dna_align_feature_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -224,14 +224,14 @@ CREATE TABLE `dna_align_feature` (
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`),
KEY `pair_idx` (`pair_dna_align_feature_id`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `dnac` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL,
`sequence` mediumblob NOT NULL,
- `n_line` text COLLATE latin1_bin,
+ `n_line` text ,
PRIMARY KEY (`seq_region_id`)
-) ENGINE=MyISAM MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+) ENGINE=MyISAM MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -253,34 +253,35 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM ;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
- `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
- `rank` int(10) NOT NULL DEFAULT '0',
+ `exon_id` int(10) unsigned NOT NULL,
+ `transcript_id` int(10) unsigned NOT NULL,
+ `rank` int(10) NOT NULL,
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `external_db` (
- `external_db_id` int(11) NOT NULL DEFAULT '0',
- `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
- `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
- `priority` int(11) NOT NULL DEFAULT '0',
- `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
- `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin,
- PRIMARY KEY (`external_db_id`)
+ `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `db_name` varchar(100) NOT NULL,
+ `db_release` varchar(255) DEFAULT NULL,
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
+ `priority` int(11) NOT NULL,
+ `db_display_name` varchar(255) DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
+ `secondary_db_name` varchar(255) DEFAULT NULL,
+ `secondary_db_table` varchar(255) DEFAULT NULL,
+ `description` text ,
+ PRIMARY KEY (`external_db_id`),
+ UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM ;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
- `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `xref_id` int(10) unsigned NOT NULL,
+ `synonym` varchar(100) NOT NULL,
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -292,7 +293,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(20) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -305,51 +306,54 @@ CREATE TABLE `gene` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
- KEY `stable_id_idx` (`stable_id`,`version`)
+ KEY `stable_id_idx` (`stable_id`,`version`),
+ KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
) ENGINE=MyISAM ;
CREATE TABLE `gene_archive` (
- `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `gene_version` smallint(6) NOT NULL DEFAULT '0',
- `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `transcript_version` smallint(6) NOT NULL DEFAULT '0',
- `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `translation_version` smallint(6) NOT NULL DEFAULT '0',
- `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
- `mapping_session_id` int(11) NOT NULL DEFAULT '0',
+ `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`)
-) ENGINE=MyISAM ;
+ KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+ KEY `peptide_archive_id_idx` (`peptide_archive_id`)
+) ENGINE=MyISAM ;
CREATE TABLE `gene_attrib` (
`gene_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- KEY `type_val_idx` (`attrib_type_id`,`value`),
- KEY `gene_idx` (`gene_id`)
-) ENGINE=MyISAM ;
+ `value` text NOT NULL,
+ KEY `gene_idx` (`gene_id`),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40))
+) ENGINE=MyISAM ;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `object_xref_id` int(10) unsigned NOT NULL,
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin,
+ `cigar_line` text ,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `interpro` (
- `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
- KEY `id` (`id`)
-) ENGINE=MyISAM ;
+ `interpro_ac` varchar(40) NOT NULL,
+ `id` varchar(40) NOT NULL,
+ UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+ KEY `id_idx` (`id`)
+) ENGINE=MyISAM ;
CREATE TABLE `intron_supporting_evidence` (
`intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -369,32 +373,32 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_start` int(10) NOT NULL DEFAULT '0',
- `seq_region_end` int(10) NOT NULL DEFAULT '0',
- `band` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `stain` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `band` varchar(40) NOT NULL,
+ `stain` varchar(40) NOT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `map_name` varchar(30) NOT NULL,
PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `mapping_session` (
- `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
- `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
- `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
- `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
- `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
- `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
- `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `old_db_name` varchar(80) NOT NULL DEFAULT '',
+ `new_db_name` varchar(80) NOT NULL DEFAULT '',
+ `old_release` varchar(5) NOT NULL DEFAULT '',
+ `new_release` varchar(5) NOT NULL DEFAULT '',
+ `old_assembly` varchar(20) NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
@@ -407,74 +411,76 @@ CREATE TABLE `mapping_set` (
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) COLLATE latin1_bin NOT NULL DEFAULT '',
- `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
- `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `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') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('est','microsatellite') DEFAULT NULL,
PRIMARY KEY (`marker_id`),
- KEY `marker_idx` (`marker_id`,`priority`)
-) ENGINE=MyISAM ;
+ KEY `marker_idx` (`marker_id`,`priority`),
+ KEY `display_idx` (`display_marker_synonym_id`)
+) ENGINE=MyISAM ;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `marker_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,
+ `analysis_id` smallint(5) unsigned NOT NULL,
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
- `map_id` int(10) unsigned NOT NULL DEFAULT '0',
- `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
- `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `marker_id` int(10) unsigned NOT NULL,
+ `map_id` int(10) unsigned NOT NULL,
+ `chromosome_name` varchar(15) NOT NULL,
+ `marker_synonym_id` int(10) unsigned NOT NULL,
+ `position` varchar(15) NOT NULL,
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
- `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
- `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
+ `marker_id` int(10) unsigned NOT NULL,
+ `source` varchar(20) DEFAULT NULL,
+ `name` varchar(50) DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
- `meta_value` varchar(255) NOT NULL,
+ `meta_value` varchar(255) DEFAULT NULL,
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 ;
CREATE TABLE `meta_coord` (
- `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(11) NOT NULL DEFAULT '0',
+ `table_name` varchar(40) NOT NULL,
+ `coord_system_id` int(10) unsigned NOT NULL,
`max_length` int(11) DEFAULT NULL,
- UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
-) ENGINE=MyISAM ;
+ UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
+) ENGINE=MyISAM ;
CREATE TABLE `misc_attrib` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- KEY `type_val_idx` (`attrib_type_id`,`value`),
- KEY `misc_feature_idx` (`misc_feature_id`)
-) ENGINE=MyISAM ;
+ `value` text NOT NULL,
+ KEY `misc_feature_idx` (`misc_feature_id`),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40))
+) ENGINE=MyISAM ;
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -484,44 +490,45 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
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=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `misc_set` (
`misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
- `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
- `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin NOT NULL,
- `max_length` int(10) unsigned NOT NULL DEFAULT '0',
+ `code` varchar(25) NOT NULL DEFAULT '',
+ `name` varchar(255) NOT NULL DEFAULT '',
+ `description` text NOT NULL,
+ `max_length` int(10) unsigned NOT NULL,
PRIMARY KEY (`misc_set_id`),
- UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM ;
+ UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM ;
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','Operon','OperonTranscript','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+ `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','Marker') NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
- `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `analysis_id` smallint(5) unsigned NOT NULL,
- UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
- KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
- KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
-) ENGINE=MyISAM ;
+ `linkage_annotation` varchar(255) DEFAULT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ PRIMARY KEY (`object_xref_id`),
+ UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
+ KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM ;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
- UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
- KEY `object_xref_id` (`object_xref_id`),
- KEY `source_xref_id` (`source_xref_id`)
+ UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+ KEY `source_idx` (`source_xref_id`),
+ KEY `object_idx` (`object_xref_id`)
) ENGINE=MyISAM ;
CREATE TABLE `operon` (
@@ -568,57 +575,57 @@ CREATE TABLE `operon_transcript_gene` (
) ENGINE=MyISAM ;
CREATE TABLE `peptide_archive` (
- `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
- `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
- `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
+ `peptide_archive_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `md5_checksum` varchar(32) DEFAULT NULL,
+ `peptide_seq` mediumtext NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
- `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
- `start_phase` tinyint(4) NOT NULL DEFAULT '0',
+ `prediction_transcript_id` int(10) unsigned NOT NULL,
+ `exon_rank` smallint(5) 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(4) NOT NULL,
+ `start_phase` tinyint(4) NOT NULL,
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
- KEY `prediction_transcript_id` (`prediction_transcript_id`),
- KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM ;
+ KEY `transcript_idx` (`prediction_transcript_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM ;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
- `analysis_id` int(11) DEFAULT NULL,
- `display_label` varchar(255) COLLATE latin1_bin DEFAULT 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(4) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `display_label` varchar(255) DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
- KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM ;
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM ;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `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(1) NOT NULL DEFAULT '1',
- `hit_start` int(10) NOT NULL DEFAULT '0',
- `hit_end` int(10) NOT NULL DEFAULT '0',
- `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL,
+ `hit_end` int(10) NOT NULL,
+ `hit_name` varchar(40) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin,
- `external_db_id` smallint(5) unsigned DEFAULT NULL,
+ `cigar_line` text ,
+ `external_db_id` int(10) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
PRIMARY KEY (`protein_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
@@ -626,158 +633,198 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(11) NOT NULL DEFAULT '0',
- `seq_start` int(10) NOT NULL DEFAULT '0',
- `seq_end` int(10) NOT NULL DEFAULT '0',
- `hit_start` int(10) NOT NULL DEFAULT '0',
- `hit_end` int(10) NOT NULL DEFAULT '0',
- `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
- `score` double NOT NULL DEFAULT '0',
+ `translation_id` int(10) unsigned NOT NULL,
+ `seq_start` int(10) NOT NULL,
+ `seq_end` int(10) NOT NULL,
+ `hit_start` int(10) NOT NULL,
+ `hit_end` int(10) NOT NULL,
+ `hit_name` varchar(40) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `score` double(8,2) DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text COLLATE latin1_bin,
- `hit_description` text COLLATE latin1_bin,
+ `external_data` text ,
+ `hit_description` text ,
PRIMARY KEY (`protein_feature_id`),
- KEY `translation_id` (`translation_id`),
- KEY `hitname_index` (`hit_name`),
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM ;
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `translation_idx` (`translation_id`),
+ KEY `hitname_idx` (`hit_name`)
+) ENGINE=MyISAM ;
CREATE TABLE `qtl` (
`qtl_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `trait` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `trait` varchar(255) NOT NULL,
`lod_score` float DEFAULT NULL,
- `flank_marker_id_1` int(11) DEFAULT NULL,
- `flank_marker_id_2` int(11) DEFAULT NULL,
- `peak_marker_id` int(11) DEFAULT NULL,
+ `flank_marker_id_1` int(10) unsigned DEFAULT NULL,
+ `flank_marker_id_2` int(10) unsigned DEFAULT NULL,
+ `peak_marker_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`qtl_id`),
KEY `trait_idx` (`trait`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `qtl_feature` (
- `seq_region_id` int(11) NOT NULL DEFAULT '0',
- `seq_region_start` int(11) NOT NULL DEFAULT '0',
- `seq_region_end` int(11) NOT NULL DEFAULT '0',
- `qtl_id` int(11) NOT NULL DEFAULT '0',
- `analysis_id` int(11) NOT NULL DEFAULT '0',
- KEY `qtl_id` (`qtl_id`),
+ `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 `loc_idx` (`seq_region_id`,`seq_region_start`),
- KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM ;
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `qtl_idx` (`qtl_id`)
+) ENGINE=MyISAM ;
CREATE TABLE `qtl_synonym` (
`qtl_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `qtl_id` int(10) unsigned NOT NULL DEFAULT '0',
- `source_database` enum('rat genome database','ratmap') COLLATE latin1_bin NOT NULL DEFAULT 'rat genome database',
- `source_primary_id` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `qtl_id` int(10) unsigned NOT NULL,
+ `source_database` enum('rat genome database','ratmap') NOT NULL,
+ `source_primary_id` varchar(255) NOT NULL,
PRIMARY KEY (`qtl_synonym_id`),
KEY `qtl_idx` (`qtl_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_consensus` text COLLATE latin1_bin,
+ `repeat_name` varchar(255) NOT NULL,
+ `repeat_class` varchar(100) NOT NULL,
+ `repeat_type` varchar(40) NOT NULL,
+ `repeat_consensus` text ,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `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(1) NOT NULL DEFAULT '1',
- `repeat_start` int(10) NOT NULL DEFAULT '0',
- `repeat_end` int(10) NOT NULL DEFAULT '0',
- `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `repeat_start` int(10) NOT NULL,
+ `repeat_end` int(10) NOT NULL,
+ `repeat_consensus_id` int(10) unsigned NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(10) NOT NULL DEFAULT '0',
- `length` int(10) NOT NULL DEFAULT '0',
+ `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 `coord_system_id` (`coord_system_id`,`name`),
- KEY `name_idx` (`name`)
-) ENGINE=MyISAM ;
+ UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+ KEY `cs_idx` (`coord_system_id`)
+) ENGINE=MyISAM ;
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',
- `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- KEY `type_val_idx` (`attrib_type_id`,`value`),
- KEY `seq_region_idx` (`seq_region_id`)
-) ENGINE=MyISAM ;
+ `value` text NOT NULL,
+ KEY `seq_region_idx` (`seq_region_id`),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40))
+) ENGINE=MyISAM ;
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_id` (`mapping_set_id`)
+ KEY `mapping_set_idx` (`mapping_set_id`)
) ENGINE=MyISAM ;
CREATE TABLE `seq_region_synonym` (
`seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(10) unsigned NOT NULL,
`synonym` varchar(40) NOT NULL,
- `external_db_id` smallint(5) unsigned DEFAULT NULL,
+ `external_db_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`seq_region_synonym_id`),
- UNIQUE KEY `syn_idx` (`synonym`)
+ UNIQUE KEY `syn_idx` (`synonym`),
+ KEY `seq_region_idx` (`seq_region_id`)
) ENGINE=MyISAM ;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
- `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `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(1) NOT NULL,
+ `display_label` varchar(255) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+
+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=MyISAM ;
+
+CREATE TABLE `splicing_event_feature` (
+ `splicing_event_feature_id` int(10) unsigned NOT NULL,
+ `splicing_event_id` int(10) unsigned NOT NULL,
+ `exon_id` int(10) unsigned NOT NULL,
+ `transcript_id` int(10) unsigned NOT NULL,
+ `feature_order` int(10) unsigned NOT NULL,
+ `transcript_association` int(10) unsigned NOT NULL,
+ `type` enum('constitutive_exon','exon','flanking_exon') DEFAULT NULL,
+ `start` int(10) unsigned NOT NULL,
+ `end` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`splicing_event_feature_id`,`exon_id`,`transcript_id`),
+ KEY `se_idx` (`splicing_event_id`),
+ KEY `transcript_idx` (`transcript_id`)
+) ENGINE=MyISAM ;
+
+CREATE TABLE `splicing_transcript_pair` (
+ `splicing_transcript_pair_id` int(10) unsigned NOT NULL,
+ `splicing_event_id` int(10) unsigned NOT NULL,
+ `transcript_id_1` int(10) unsigned NOT NULL,
+ `transcript_id_2` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`splicing_transcript_pair_id`),
+ KEY `se_idx` (`splicing_event_id`)
+) ENGINE=MyISAM ;
CREATE TABLE `stable_id_event` (
- `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
+ `old_stable_id` varchar(128) DEFAULT NULL,
`old_version` smallint(6) DEFAULT NULL,
- `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
+ `new_stable_id` varchar(128) DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
+ `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `type` enum('gene','transcript','translation') NOT NULL,
`score` float NOT NULL DEFAULT '0',
- UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
+ UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `supporting_feature` (
- `exon_id` int(11) NOT NULL DEFAULT '0',
- `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT '0',
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+ `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -789,7 +836,7 @@ CREATE TABLE `transcript` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`biotype` varchar(40) NOT NULL,
- `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -809,10 +856,11 @@ CREATE TABLE `transcript` (
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- KEY `type_val_idx` (`attrib_type_id`,`value`),
- KEY `transcript_idx` (`transcript_id`)
-) ENGINE=MyISAM ;
+ `value` text NOT NULL,
+ KEY `transcript_idx` (`transcript_id`),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40))
+) ENGINE=MyISAM ;
CREATE TABLE `transcript_intron_supporting_evidence` (
`transcript_id` int(10) unsigned NOT NULL,
@@ -823,12 +871,12 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM ;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(11) NOT NULL DEFAULT '0',
- `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+ `feature_id` int(10) unsigned NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
-) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -849,56 +897,58 @@ CREATE TABLE `translation` (
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
- `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- KEY `type_val_idx` (`attrib_type_id`,`value`),
- KEY `translation_idx` (`translation_id`)
-) ENGINE=MyISAM ;
+ `value` text NOT NULL,
+ KEY `translation_idx` (`translation_id`),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40))
+) ENGINE=MyISAM ;
CREATE TABLE `unconventional_transcript_association` (
`transcript_id` int(10) unsigned NOT NULL,
`gene_id` int(10) unsigned NOT NULL,
`interaction_type` enum('antisense','sense_intronic','sense_overlaping_exonic','chimeric_sense_exonic') DEFAULT NULL,
- KEY `transcript_id` (`transcript_id`),
- KEY `gene_id` (`gene_id`)
+ KEY `transcript_idx` (`transcript_id`),
+ KEY `gene_idx` (`gene_id`)
) ENGINE=MyISAM ;
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
- `analysis_id` int(10) unsigned NOT NULL,
- `external_db_id` int(11) DEFAULT NULL,
- `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
+ `type` enum('xref','cDNA','Marker') NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `external_db_id` int(10) unsigned DEFAULT NULL,
+ `identifier` varchar(255) NOT NULL,
`unmapped_reason_id` smallint(5) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`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,
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
+ `parent` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
- KEY `id_idx` (`identifier`),
- KEY `anal_idx` (`analysis_id`),
- KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
-) ENGINE=MyISAM ;
+ UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),
+ KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`),
+ KEY `id_idx` (`identifier`(50)),
+ KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`)
+) ENGINE=MyISAM ;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
- `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `summary_description` varchar(255) DEFAULT NULL,
+ `full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `external_db_id` int(11) NOT NULL,
- `dbprimary_acc` varchar(40) COLLATE latin1_bin NOT NULL,
- `display_label` varchar(128) COLLATE latin1_bin NOT NULL,
- `version` varchar(10) COLLATE latin1_bin NOT NULL DEFAULT '0',
- `description` text COLLATE latin1_bin,
- `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
- `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `external_db_id` int(10) unsigned NOT NULL,
+ `dbprimary_acc` varchar(40) NOT NULL,
+ `display_label` varchar(128) NOT NULL,
+ `version` varchar(10) NOT NULL DEFAULT '0',
+ `description` text ,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') NOT NULL DEFAULT 'NONE',
+ `info_text` varchar(255) NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
-) ENGINE=MyISAM ;
+) ENGINE=MyISAM ;
--
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