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Commit 16824a3e authored by Monika Komorowska's avatar Monika Komorowska
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Stable_id table merged with main object table

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modules/t/test-genome-DBs/homo_sapiens/core/exon.txt
+ 160
− 160
View file @ 16824a3e
This diff is collapsed.
modules/t/test-genome-DBs/homo_sapiens/core/gene.sql
+ 26
− 18
View file @ 16824a3e
CREATE TABLE `gene` (
`gene_id` int(10) unsigned NOT NULL auto_increment,
`biotype` varchar(40) collate latin1_bin NOT NULL default '',
`analysis_id` int(11) default NULL,
`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(2) NOT NULL default '0',
`display_xref_id` int(10) unsigned default NULL,
`source` varchar(20) collate latin1_bin NOT NULL default '',
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION') collate latin1_bin default NULL,
`description` text collate latin1_bin,
`is_current` BOOLEAN DEFAULT 1,
CREATE TABLE gene (
gene_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
biotype VARCHAR(40) NOT NULL,
analysis_id SMALLINT 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,
display_xref_id INT(10) UNSIGNED,
source VARCHAR(20) NOT NULL,
status ENUM('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN'),
description TEXT,
is_current BOOLEAN NOT NULL DEFAULT 1,
canonical_transcript_id INT(10) UNSIGNED NOT NULL,
canonical_annotation VARCHAR(255) DEFAULT NULL,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY (gene_id),
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)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
PRIMARY KEY (`gene_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
modules/t/test-genome-DBs/homo_sapiens/core/gene.txt
+ 20
− 20
View file @ 16824a3e
18256 protein_coding 1282 469283 30274334 30300924 1 152202 ensembl KNOWN DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474, ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL;Acc:Q9BR18] 1 21716 longest transcript in gene
18257 protein_coding 1282 469283 30301733 30318881 1 0 ensembl NOVEL \N 1 21718 \N
18258 protein_coding 1282 469283 30320853 30327869 -1 40090 vega KNOWN \N 1 21719 \N
18259 protein_coding 1282 469283 30371004 30372906 1 102413 ensembl KNOWN DJ310O13.4 (NOVEL PROTEIN SIMILAR TO PREDICTED C. ELEGANS AND C. INTESTINALIS PROTEINS) (FRAGMENT). [Source:SPTREMBL;Acc:Q9NUG5] 1 21720 \N
18260 protein_coding 1282 469283 30386305 30408041 1 34986 vega KNOWN \N 1 21721 \N
18261 protein_coding 1282 469283 30428114 30477716 1 158525 ensembl KNOWN TYROSINE-PROTEIN KINASE HCK (EC 2.7.1.112) (P59-HCK AND P60-HCK) (HEMOPOIETIC CELL KINASE). [Source:SWISSPROT;Acc:P08631] 1 21723 \N
18262 protein_coding 1282 469283 30485596 30543114 1 120576 ensembl KNOWN TRANSMEMBRANE 9 SUPERFAMILY PROTEIN MEMBER 4. [Source:SWISSPROT;Acc:Q92544] 1 21724 \N
18263 protein_coding 1282 469283 30565065 30566129 -1 128607 ensembl KNOWN BA392M18.1 (NOVEL PROTEIN SIMILAR TO TESTIS SPECIFIC PROTEIN TSPY). [Source:SPTREMBL;Acc:Q9H489] 1 21725 \N
18264 protein_coding 1282 469283 30568364 30583588 -1 17034 ensembl KNOWN ZINC FINGER PROTEIN PLAGL2 (PLEIOMORPHIC ADENOMA-LIKE PROTEIN 2). [Source:SWISSPROT;Acc:Q9UPG8] 1 21726 \N
18265 protein_coding 1282 469283 30583753 30614524 1 128597 ensembl KNOWN GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1 PRECURSOR (EC 2.4.1.-) (O- FUCOSYLTRANSFERASE) (O-FUCT-1). [Source:SPTREMBL;Acc:Q9H488] 1 21728 \N
18266 protein_coding 1282 469283 30653524 30709209 1 28819 ensembl KNOWN KINESIN-LIKE PROTEIN KIF3B (MICROTUBULE PLUS END-DIRECTED KINESIN MOTOR 3B) (HH0048). [Source:SWISSPROT;Acc:O15066] 1 21729 1
18267 protein_coding 1282 469283 30735607 30815178 1 128324 ensembl KNOWN BA358N2.1 (KIAA0978) (FRAGMENT). [Source:SPTREMBL;Acc:Q9H466] 1 21731 \N
18268 protein_coding 1282 469283 30822726 30859269 -1 34892 ensembl KNOWN \N 1 21732 \N
18269 protein_coding 1282 469283 30885729 30911383 -1 89323 ensembl KNOWN DJ1184F4.4 (NOVEL PROTEIN SIMILAR TO NUCLEOLAR PROTEIN 4 (NOL4) (NOLP)). [Source:SPTREMBL;Acc:Q9NQF5] 1 21734 \N
18270 protein_coding 1282 469283 31070930 31071301 -1 332 ensembl KNOWN \N 1 21735 \N
18271 protein_coding 1282 469283 31074431 31089984 -1 168324 ensembl KNOWN \N 1 21736 \N
18272 protein_coding 1282 469283 31108924 31155894 1 15966 ensembl KNOWN DNA (CYTOSINE-5)-METHYLTRANSFERASE 3B (EC 2.1.1.37) (DNMT3B) (DNA METHYLTRANSFERASE HSAIIIB) (DNA MTASE HSAIIIB) (M.HSAIIIB). [Source:SWISSPROT;Acc:Q9UBC3] 1 21737 \N
18273 protein_coding 1282 469283 31166507 31196939 1 97759 ensembl KNOWN MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [Source:SWISSPROT;Acc:Q15691] 1 21738 \N
18274 protein_coding 1282 469283 31210077 31225346 1 0 ensembl NOVEL \N 1 21739 \N
18275 protein_coding 1282 965899 10060 10405 1 0 ensembl NOVEL \N 1 21740 \N
18256 protein_coding 1282 469283 30274334 30300924 1 152202 ensembl KNOWN DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474, ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL;Acc:Q9BR18] 1 21716 longest transcript in gene ENSG00000131044 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18257 protein_coding 1282 469283 30301733 30318881 1 0 ensembl NOVEL \N 1 21718 \N ENSG00000174873 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18258 protein_coding 1282 469283 30320853 30327869 -1 40090 vega KNOWN \N 1 21719 \N ENSG00000088356 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18259 protein_coding 1282 469283 30371004 30372906 1 102413 ensembl KNOWN DJ310O13.4 (NOVEL PROTEIN SIMILAR TO PREDICTED C. ELEGANS AND C. INTESTINALIS PROTEINS) (FRAGMENT). [Source:SPTREMBL;Acc:Q9NUG5] 1 21720 \N ENSG00000101321 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18260 protein_coding 1282 469283 30386305 30408041 1 34986 vega KNOWN \N 1 21721 \N ENSG00000101331 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18261 protein_coding 1282 469283 30428114 30477716 1 158525 ensembl KNOWN TYROSINE-PROTEIN KINASE HCK (EC 2.7.1.112) (P59-HCK AND P60-HCK) (HEMOPOIETIC CELL KINASE). [Source:SWISSPROT;Acc:P08631] 1 21723 \N ENSG00000101336 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18262 protein_coding 1282 469283 30485596 30543114 1 120576 ensembl KNOWN TRANSMEMBRANE 9 SUPERFAMILY PROTEIN MEMBER 4. [Source:SWISSPROT;Acc:Q92544] 1 21724 \N ENSG00000101337 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18263 protein_coding 1282 469283 30565065 30566129 -1 128607 ensembl KNOWN BA392M18.1 (NOVEL PROTEIN SIMILAR TO TESTIS SPECIFIC PROTEIN TSPY). [Source:SPTREMBL;Acc:Q9H489] 1 21725 \N ENSG00000125979 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18264 protein_coding 1282 469283 30568364 30583588 -1 17034 ensembl KNOWN ZINC FINGER PROTEIN PLAGL2 (PLEIOMORPHIC ADENOMA-LIKE PROTEIN 2). [Source:SWISSPROT;Acc:Q9UPG8] 1 21726 \N ENSG00000126003 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18265 protein_coding 1282 469283 30583753 30614524 1 128597 ensembl KNOWN GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1 PRECURSOR (EC 2.4.1.-) (O- FUCOSYLTRANSFERASE) (O-FUCT-1). [Source:SPTREMBL;Acc:Q9H488] 1 21728 \N ENSG00000101346 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18266 protein_coding 1282 469283 30653524 30709209 1 28819 ensembl KNOWN KINESIN-LIKE PROTEIN KIF3B (MICROTUBULE PLUS END-DIRECTED KINESIN MOTOR 3B) (HH0048). [Source:SWISSPROT;Acc:O15066] 1 21729 1 ENSG00000101350 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18267 protein_coding 1282 469283 30735607 30815178 1 128324 ensembl KNOWN BA358N2.1 (KIAA0978) (FRAGMENT). [Source:SPTREMBL;Acc:Q9H466] 1 21731 \N ENSG00000171456 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18268 protein_coding 1282 469283 30822726 30859269 -1 34892 ensembl KNOWN \N 1 21732 \N ENSG00000125964 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18269 protein_coding 1282 469283 30885729 30911383 -1 89323 ensembl KNOWN DJ1184F4.4 (NOVEL PROTEIN SIMILAR TO NUCLEOLAR PROTEIN 4 (NOL4) (NOLP)). [Source:SPTREMBL;Acc:Q9NQF5] 1 21734 \N ENSG00000088303 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18270 protein_coding 1282 469283 31070930 31071301 -1 332 ensembl KNOWN \N 1 21735 \N ENSG00000174852 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18271 protein_coding 1282 469283 31074431 31089984 -1 168324 ensembl KNOWN \N 1 21736 \N ENSG00000149600 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18272 protein_coding 1282 469283 31108924 31155894 1 15966 ensembl KNOWN DNA (CYTOSINE-5)-METHYLTRANSFERASE 3B (EC 2.1.1.37) (DNMT3B) (DNA METHYLTRANSFERASE HSAIIIB) (DNA MTASE HSAIIIB) (M.HSAIIIB). [Source:SWISSPROT;Acc:Q9UBC3] 1 21737 \N ENSG00000088305 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18273 protein_coding 1282 469283 31166507 31196939 1 97759 ensembl KNOWN MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [Source:SWISSPROT;Acc:Q15691] 1 21738 \N ENSG00000101367 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18274 protein_coding 1282 469283 31210077 31225346 1 0 ensembl NOVEL \N 1 21739 \N ENSG00000167097 1 2004-12-06 12:00:00 2004-12-06 12:00:00
18275 protein_coding 1282 965899 10060 10405 1 0 ensembl NOVEL \N 1 21740 \N ENSG00000355555 1 2004-12-06 12:00:00 2004-12-06 12:00:00
modules/t/test-genome-DBs/homo_sapiens/core/operon.sql
+ 17
− 44
View file @ 16824a3e
-- MySQL dump 10.13 Distrib 5.5.13, for Linux (x86_64)
--
-- Host: localhost Database: dstaines_test_db_homo_sapiens_core_20110630_160153
-- ------------------------------------------------------
-- Server version 5.5.13
CREATE TABLE operon (
operon_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
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,
display_label VARCHAR(255) DEFAULT NULL,
analysis_id SMALLINT UNSIGNED NOT NULL,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
/*!40101 SET NAMES utf8 */;
/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
/*!40103 SET TIME_ZONE='+00:00' */;
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='' */;
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
--
-- Table structure for table `operon`
--
DROP TABLE IF EXISTS `operon`;
/*!40101 SET @saved_cs_client = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `operon` (
`operon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`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,
`display_label` varchar(255) DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
PRIMARY KEY (`operon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `name_idx` (`display_label`)
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
-- Dump completed on 2011-06-30 16:03:42
PRIMARY KEY (operon_id),
KEY seq_region_idx (seq_region_id, seq_region_start),
KEY name_idx (display_label),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
modules/t/test-genome-DBs/homo_sapiens/core/operon.txt
+ 1
− 1
View file @ 16824a3e
1 469283 30371004 30477716 1 16152-16153-4840 1
1 469283 30371004 30477716 1 16152-16153-4840 1 16152-16153-4840 1 2011-06-30 16:03:09 2011-06-30 16:03:09
modules/t/test-genome-DBs/homo_sapiens/core/operon_transcript.sql
+ 18
− 45
View file @ 16824a3e
-- MySQL dump 10.13 Distrib 5.5.13, for Linux (x86_64)
--
-- Host: localhost Database: dstaines_test_db_homo_sapiens_core_20110630_160153
-- ------------------------------------------------------
-- Server version 5.5.13
CREATE TABLE operon_transcript (
operon_transcript_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
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,
operon_id INT(10) UNSIGNED NOT NULL,
display_label VARCHAR(255) DEFAULT NULL,
analysis_id SMALLINT UNSIGNED NOT NULL,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
/*!40101 SET NAMES utf8 */;
/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
/*!40103 SET TIME_ZONE='+00:00' */;
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='' */;
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
--
-- Table structure for table `operon_transcript`
--
DROP TABLE IF EXISTS `operon_transcript`;
/*!40101 SET @saved_cs_client = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`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,
`operon_id` int(10) unsigned NOT NULL,
`display_label` varchar(255) DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
PRIMARY KEY (`operon_transcript_id`),
KEY `operon_idx` (`operon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
-- Dump completed on 2011-06-30 16:03:42
PRIMARY KEY (operon_transcript_id),
KEY operon_idx (operon_id),
KEY seq_region_idx (seq_region_id, seq_region_start),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
modules/t/test-genome-DBs/homo_sapiens/core/operon_transcript.txt
+ 2
− 2
View file @ 16824a3e
1 469283 30371004 30477716 1 1 T16152-16153-4840 1
2 469283 30371004 30408041 1 1 T16152-16153 1
1 469283 30371004 30477716 1 1 T16152-16153-4840 1 T16152-16153-4840 1 2011-06-30 16:03:09 2011-06-30 16:03:09
2 469283 30371004 30408041 1 1 T16152-16153 1 T16152-16153 1 2011-06-30 16:03:09 2011-06-30 16:03:09
modules/t/test-genome-DBs/homo_sapiens/core/operon_transcript_stable_id.txt deleted 100644 → 0
+ 0
− 2
View file @ 3b9aea50
1 T16152-16153-4840 1 2011-06-30 16:03:09 2011-06-30 16:03:09
2 T16152-16153 1 2011-06-30 16:03:09 2011-06-30 16:03:09
modules/t/test-genome-DBs/homo_sapiens/core/transcript.sql
+ 28
− 19
View file @ 16824a3e
CREATE TABLE `transcript` (
`transcript_id` int(10) unsigned NOT NULL auto_increment,
`gene_id` int(10) unsigned NOT NULL default '0',
`analysis_id` INT(10) UNSIGNED NOT NULL,
`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(2) NOT NULL default '0',
`display_xref_id` int(10) unsigned default NULL,
`biotype` varchar(40) NOT NULL default '',
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION') collate latin1_bin default NULL,
`description` text collate latin1_bin,
`is_current` BOOLEAN DEFAULT 1,
`canonical_translation_id` int(10) unsigned,
PRIMARY KEY (`transcript_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `gene_index` (`gene_id`),
KEY `xref_id_index` (`display_xref_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE transcript (
transcript_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
gene_id INT(10) UNSIGNED,
analysis_id SMALLINT 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,
display_xref_id INT(10) UNSIGNED,
biotype VARCHAR(40) NOT NULL,
status ENUM('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN'),
description TEXT,
is_current BOOLEAN NOT NULL DEFAULT 1,
canonical_translation_id INT(10) UNSIGNED,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY (transcript_id),
KEY seq_region_idx (seq_region_id, seq_region_start),
KEY gene_index (gene_id),
KEY xref_id_index (display_xref_id),
KEY analysis_idx (analysis_id),
UNIQUE INDEX canonical_translation_idx (canonical_translation_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
modules/t/test-genome-DBs/homo_sapiens/core/transcript.txt
+ 25
− 25
View file @ 16824a3e
21716 18256 1282 469283 30274334 30298904 1 152202 protein_coding KNOWN \N 1 21716
21717 18256 1282 469283 30285705 30300924 1 152191 protein_coding KNOWN \N 1 21717
21718 18257 1282 469283 30301733 30318881 1 0 protein_coding NOVEL \N 1 21718
21719 18258 1282 469283 30320853 30327869 -1 40090 protein_coding KNOWN \N 1 21719
21720 18259 1282 469283 30371004 30372906 1 102413 protein_coding KNOWN \N 1 21720
21721 18260 1282 469283 30386305 30408041 1 34986 protein_coding KNOWN \N 1 21721
21722 18260 1282 469283 30386305 30408041 1 34986 protein_coding KNOWN \N 1 21722
21723 18261 1282 469283 30428114 30477716 1 158525 protein_coding KNOWN \N 1 21723
21724 18262 1282 469283 30485596 30543114 1 120576 protein_coding KNOWN \N 1 21724
21725 18263 1282 469283 30565065 30566129 -1 128607 protein_coding KNOWN \N 1 21725
21726 18264 1282 469283 30568364 30583588 -1 17034 protein_coding KNOWN \N 1 21726
21727 18265 1282 469283 30583753 30593764 1 168444 protein_coding KNOWN \N 1 21727
21728 18265 1282 469283 30583753 30614524 1 128597 protein_coding KNOWN \N 1 21728
21729 18266 1282 469283 30653524 30709209 1 28819 protein_coding KNOWN \N 1 21729
21730 18267 1282 469283 30805794 30813218 1 29946 protein_coding KNOWN \N 1 21730
21731 18267 1282 469283 30735607 30815178 1 128324 protein_coding KNOWN \N 1 21731
21732 18268 1282 469283 30822726 30850611 -1 34892 protein_coding KNOWN \N 1 21732
21733 18268 1282 469283 30840814 30859269 -1 89326 protein_coding KNOWN \N 1 21733
21734 18269 1282 469283 30885729 30911383 -1 89323 protein_coding KNOWN \N 1 21734
21735 18270 1282 469283 31070930 31071301 -1 332 protein_coding KNOWN \N 1 21735
21736 18271 1282 469283 31074431 31089984 -1 168324 protein_coding KNOWN \N 1 21736
21737 18272 1282 469283 31108924 31155894 1 15966 protein_coding KNOWN \N 1 21737
21738 18273 1282 469283 31166507 31196939 1 97759 protein_coding KNOWN \N 1 21738
21739 18274 1282 469283 31210077 31225346 1 0 protein_coding NOVEL \N 1 21739
21740 18275 1282 965899 10060 10405 1 0 protein_coding NOVEL \N 1 21740
21716 18256 1282 469283 30274334 30298904 1 152202 protein_coding KNOWN \N 1 21716 ENST00000310998 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21717 18256 1282 469283 30285705 30300924 1 152191 protein_coding KNOWN \N 1 21717 ENST00000278995 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21718 18257 1282 469283 30301733 30318881 1 0 protein_coding NOVEL \N 1 21718 ENST00000252021 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21719 18258 1282 469283 30320853 30327869 -1 40090 protein_coding KNOWN \N 1 21719 ENST00000202017 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21720 18259 1282 469283 30371004 30372906 1 102413 protein_coding KNOWN \N 1 21720 ENST00000217299 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21721 18260 1282 469283 30386305 30408041 1 34986 protein_coding KNOWN \N 1 21721 ENST00000300415 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21722 18260 1282 469283 30386305 30408041 1 34986 protein_coding KNOWN \N 1 21722 ENST00000262659 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21723 18261 1282 469283 30428114 30477716 1 158525 protein_coding KNOWN \N 1 21723 ENST00000262651 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21724 18262 1282 469283 30485596 30543114 1 120576 protein_coding KNOWN \N 1 21724 ENST00000217315 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21725 18263 1282 469283 30565065 30566129 -1 128607 protein_coding KNOWN \N 1 21725 ENST00000246203 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21726 18264 1282 469283 30568364 30583588 -1 17034 protein_coding KNOWN \N 1 21726 ENST00000246229 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21727 18265 1282 469283 30583753 30593764 1 168444 protein_coding KNOWN \N 1 21727 ENST00000278989 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21728 18265 1282 469283 30583753 30614524 1 128597 protein_coding KNOWN \N 1 21728 ENST00000217326 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21729 18266 1282 469283 30653524 30709209 1 28819 protein_coding KNOWN \N 1 21729 ENST00000262652 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21730 18267 1282 469283 30805794 30813218 1 29946 protein_coding KNOWN \N 1 21730 ENST00000306058 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21731 18267 1282 469283 30735607 30815178 1 128324 protein_coding KNOWN \N 1 21731 ENST00000306067 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21732 18268 1282 469283 30822726 30850611 -1 34892 protein_coding KNOWN \N 1 21732 ENST00000201962 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21733 18268 1282 469283 30840814 30859269 -1 89326 protein_coding KNOWN \N 1 21733 ENST00000216932 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21734 18269 1282 469283 30885729 30911383 -1 89323 protein_coding KNOWN \N 1 21734 ENST00000201961 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21735 18270 1282 469283 31070930 31071301 -1 332 protein_coding KNOWN \N 1 21735 ENST00000310461 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21736 18271 1282 469283 31074431 31089984 -1 168324 protein_coding KNOWN \N 1 21736 ENST00000278980 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21737 18272 1282 469283 31108924 31155894 1 15966 protein_coding KNOWN \N 1 21737 ENST00000201963 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21738 18273 1282 469283 31166507 31196939 1 97759 protein_coding KNOWN \N 1 21738 ENST00000217347 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21739 18274 1282 469283 31210077 31225346 1 0 protein_coding NOVEL \N 1 21739 ENST00000300425 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21740 18275 1282 965899 10060 10405 1 0 protein_coding NOVEL \N 1 21740 ENST00000355555 1 2004-12-06 12:00:00 2004-12-06 12:00:00
modules/t/test-genome-DBs/homo_sapiens/core/transcript_stable_id.sql deleted 100644 → 0
+ 0
− 10
View file @ 3b9aea50
CREATE TABLE `transcript_stable_id` (
`transcript_id` int(10) unsigned NOT NULL default '0',
`stable_id` varchar(128) collate latin1_bin NOT NULL default '',
`version` int(10) default NULL,
`created_date` datetime NOT NULL default '0000-00-00 00:00:00',
`modified_date` datetime NOT NULL default '0000-00-00 00:00:00',
PRIMARY KEY (`transcript_id`),
KEY `stable_id` (`stable_id`,`version`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
modules/t/test-genome-DBs/homo_sapiens/core/transcript_stable_id.txt deleted 100644 → 0
+ 0
− 25
View file @ 3b9aea50
21716 ENST00000310998 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21717 ENST00000278995 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21718 ENST00000252021 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21719 ENST00000202017 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21720 ENST00000217299 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21721 ENST00000300415 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21722 ENST00000262659 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21723 ENST00000262651 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21724 ENST00000217315 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21725 ENST00000246203 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21726 ENST00000246229 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21727 ENST00000278989 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21728 ENST00000217326 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21729 ENST00000262652 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21730 ENST00000306058 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21731 ENST00000306067 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21732 ENST00000201962 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21733 ENST00000216932 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21734 ENST00000201961 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21735 ENST00000310461 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21736 ENST00000278980 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21737 ENST00000201963 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21738 ENST00000217347 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21739 ENST00000300425 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21740 ENST00000355555 1 2004-12-06 12:00:00 2004-12-06 12:00:00
modules/t/test-genome-DBs/homo_sapiens/core/translation.sql
+ 17
− 10
View file @ 16824a3e
CREATE TABLE `translation` (
`translation_id` int(10) unsigned NOT NULL auto_increment,
`transcript_id` int(10) unsigned NOT NULL default '0',
`seq_start` int(10) NOT NULL default '0',
`start_exon_id` int(10) unsigned NOT NULL default '0',
`seq_end` int(10) NOT NULL default '0',
`end_exon_id` int(10) unsigned NOT NULL default '0',
PRIMARY KEY (`translation_id`),
KEY `transcript_id` (`transcript_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE translation (
translation_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
transcript_id INT(10) UNSIGNED NOT NULL,
seq_start INT(10) NOT NULL, # relative to exon start
start_exon_id INT(10) UNSIGNED NOT NULL,
seq_end INT(10) NOT NULL, # relative to exon start
end_exon_id INT(10) UNSIGNED NOT NULL,
stable_id VARCHAR(128) DEFAULT NULL,
version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY (translation_id),
KEY transcript_idx (transcript_id),
KEY stable_id_idx (stable_id, version)
) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
modules/t/test-genome-DBs/homo_sapiens/core/translation.txt
+ 25
− 25
View file @ 16824a3e
21716 21716 1 161881 82 161877
21717 21717 1 161875 56 161874
21718 21718 1 161885 77 161884
21719 21719 1 161890 80 161891
21720 21720 1 161894 542 161895
21721 21721 11 161912 86 161896
21722 21722 76 161907 311 161900
21723 21723 172 161926 200 161924
21724 21724 37 161935 147 161931
21725 21725 1 161945 1065 161945
21726 21726 115 161947 1228 161946
21727 21727 50 161955 40 161950
21728 21728 50 161955 186 161956
21729 21729 66 161957 94 161963
21730 21730 3 161973 2904 161974
21731 21731 1 161966 894 161967
21732 21732 43 161988 218 161986
21733 21733 1 161984 164 161980
21734 21734 1 161991 72 161994
21735 21735 1 161995 372 161995
21736 21736 1 161998 105 161996
21737 21737 7 162000 139 162009
21738 21738 4 162027 54 162028
21739 21739 1 162030 104 162031
21740 21740 1 162033 346 162033
21716 21716 1 161881 82 161877 ENSP00000308980 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21717 21717 1 161875 56 161874 ENSP00000278995 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21718 21718 1 161885 77 161884 ENSP00000252021 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21719 21719 1 161890 80 161891 ENSP00000202017 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21720 21720 1 161894 542 161895 ENSP00000217299 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21721 21721 11 161912 86 161896 ENSP00000300415 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21722 21722 76 161907 311 161900 ENSP00000262659 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21723 21723 172 161926 200 161924 ENSP00000262651 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21724 21724 37 161935 147 161931 ENSP00000217315 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21725 21725 1 161945 1065 161945 ENSP00000246203 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21726 21726 115 161947 1228 161946 ENSP00000246229 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21727 21727 50 161955 40 161950 ENSP00000278989 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21728 21728 50 161955 186 161956 ENSP00000217326 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21729 21729 66 161957 94 161963 ENSP00000262652 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21730 21730 3 161973 2904 161974 ENSP00000305119 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21731 21731 1 161966 894 161967 ENSP00000302298 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21732 21732 43 161988 218 161986 ENSP00000201962 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21733 21733 1 161984 164 161980 ENSP00000216932 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21734 21734 1 161991 72 161994 ENSP00000201961 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21735 21735 1 161995 372 161995 ENSP00000310454 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21736 21736 1 161998 105 161996 ENSP00000278980 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21737 21737 7 162000 139 162009 ENSP00000201963 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21738 21738 4 162027 54 162028 ENSP00000217347 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21739 21739 1 162030 104 162031 ENSP00000300425 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21740 21740 1 162033 346 162033 ENSP00000355555 1 2004-12-06 12:00:00 2004-12-06 12:00:00
modules/t/test-genome-DBs/homo_sapiens/core/translation_stable_id.sql deleted 100644 → 0
+ 0
− 10
View file @ 3b9aea50
CREATE TABLE `translation_stable_id` (
`translation_id` int(10) unsigned NOT NULL default '0',
`stable_id` varchar(128) collate latin1_bin NOT NULL default '',
`version` int(10) default NULL,
`created_date` datetime NOT NULL default '0000-00-00 00:00:00',
`modified_date` datetime NOT NULL default '0000-00-00 00:00:00',
PRIMARY KEY (`translation_id`),
UNIQUE KEY `stable_id` (`stable_id`,`version`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
modules/t/test-genome-DBs/homo_sapiens/core/translation_stable_id.txt deleted 100644 → 0
+ 0
− 25
View file @ 3b9aea50
21716 ENSP00000308980 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21717 ENSP00000278995 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21718 ENSP00000252021 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21719 ENSP00000202017 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21720 ENSP00000217299 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21721 ENSP00000300415 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21722 ENSP00000262659 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21723 ENSP00000262651 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21724 ENSP00000217315 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21725 ENSP00000246203 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21726 ENSP00000246229 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21727 ENSP00000278989 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21728 ENSP00000217326 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21729 ENSP00000262652 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21730 ENSP00000305119 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21731 ENSP00000302298 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21732 ENSP00000201962 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21733 ENSP00000216932 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21734 ENSP00000201961 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21735 ENSP00000310454 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21736 ENSP00000278980 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21737 ENSP00000201963 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21738 ENSP00000217347 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21739 ENSP00000300425 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21740 ENSP00000355555 1 2004-12-06 12:00:00 2004-12-06 12:00:00
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