Commit 910a09b7 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

updated test cases to check integrity of api once deprecated tables, columns...

updated test cases to check integrity of api once deprecated tables, columns and methods have been removed
test databases patched to schema 74
parent c57a1a9a
......@@ -23,10 +23,6 @@ $test_adaptor = $db->get_ArchiveStableIdAdaptor();
if (defined $test_adaptor) {
ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor"));
}
$test_adaptor = $db->get_QtlFeatureAdaptor();
ok($test_adaptor->isa("Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor"));
$test_adaptor = $db->get_QtlAdaptor();
ok($test_adaptor->isa("Bio::EnsEMBL::Map::DBSQL::QtlAdaptor"));
$test_adaptor = $db->get_ProteinFeatureAdaptor();
ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor"));
$test_adaptor = $db->get_PredictionTranscriptAdaptor();
......
......@@ -56,7 +56,6 @@ ok($feat);
print_features([$feat]);
ok($feat->db_name eq 'EMBL');
ok($feat->db_display_name eq 'EMBL');
ok($feat->pair_dna_align_feature_id == 1449321);
$feat = $feat->transform('supercontig');
......@@ -96,7 +95,6 @@ my $evalue = 23.2;
my $cigar_string = '100M';
my $hcoverage = 99.5;
my $external_db_id = 2200;
my $pair_dna_align_feature_id = 10;
$feat = Bio::EnsEMBL::DnaDnaAlignFeature->new
(-START => $start,
......@@ -113,8 +111,7 @@ $feat = Bio::EnsEMBL::DnaDnaAlignFeature->new
-P_VALUE => $evalue,
-ANALYSIS => $analysis,
-HCOVERAGE => $hcoverage,
-EXTERNAL_DB_ID => $external_db_id,
-PAIR_DNA_ALIGN_FEATURE_ID => $pair_dna_align_feature_id );
-EXTERNAL_DB_ID => $external_db_id);
ok(!$feat->is_stored($db));
......@@ -142,7 +139,6 @@ ok($feat->p_value == $evalue);
ok($feat->analysis->logic_name eq $analysis->logic_name);
ok($feat->external_db_id == $external_db_id);
ok($feat->hcoverage == $hcoverage);
ok($feat->pair_dna_align_feature_id == $pair_dna_align_feature_id);
$multi->restore('core', 'dna_align_feature');
......@@ -166,4 +162,4 @@ sub print_features {
}
}
done_testing();
\ No newline at end of file
done_testing();
......@@ -766,47 +766,6 @@ ok($gene->is_current == 1);
$multi->restore;
#
# Tests for unconventional transcript association functionality
#
# test a gene with existing associations
$gene = $ga->fetch_by_dbID(18256);
ok(@{$gene->get_all_unconventional_transcript_associations()} == 3);
# test removing them all
$gene->remove_unconventional_transcript_associations();
ok(@{$gene->get_all_unconventional_transcript_associations()} == 0);
# test adding to a new gene
my $new_gene = $ga->fetch_by_dbID(18260);
my $new_transcript = $db->get_TranscriptAdaptor()->fetch_by_dbID(21720);
ok(@{$new_gene->get_all_unconventional_transcript_associations()} == 0);
$new_gene->add_unconventional_transcript_association($new_transcript, 'sense_intronic');
ok(@{$new_gene->get_all_unconventional_transcript_associations()} == 1);
# test storing
$new_gene = $ga->fetch_by_dbID(18261);
ok(@{$new_gene->get_all_unconventional_transcript_associations()} == 0);
$new_gene->add_unconventional_transcript_association($new_transcript, 'sense_intronic');
$new_gene->add_unconventional_transcript_association($new_transcript, 'antisense');
$ga->store($new_gene);
# test removing
$new_gene->remove_unconventional_transcript_associations();
my $utaa = $db->get_UnconventionalTranscriptAssociationAdaptor();
ok(@{$utaa->fetch_all_by_gene($new_gene)} == 0);
#testing canonical_transcript information
$new_gene = $ga->fetch_by_dbID(18256);
ok($new_gene->canonical_transcript->dbID == 21716); #test 85
ok($new_gene->canonical_annotation eq 'longest transcript in gene'); #test 86
#test the get_species_and_object_type method from the Registry
my $registry = 'Bio::EnsEMBL::Registry';
my ($species, $object_type, $db_type) = $registry->get_species_and_object_type('ENSG00000355555');
......@@ -814,7 +773,7 @@ ok($species eq 'homo_sapiens' && $object_type eq 'Gene');
# Testing compara dba retrieval
{
dies_ok { $new_gene->get_all_homologous_Genes(); } 'No Compara DBAdaptor has been configured. No way to retrieve data';
dies_ok { $gene->get_all_homologous_Genes(); } 'No Compara DBAdaptor has been configured. No way to retrieve data';
}
done_testing();
......@@ -26,7 +26,6 @@ my $expected_keys = {
is_current biotype status source
description
canonical_transcript canonical_transcript_id _transcript_array
canonical_annotation
dbentries display_xref external_name external_db external_status
/],
'transcript' => [sort @generic_keys, @location_keys, qw/
......@@ -85,4 +84,4 @@ sub assert_keys {
sub get_keys {
return [sort keys %{$_[0]}];
}
\ No newline at end of file
}
use strict;
use warnings;
use Test::More;
use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Map::Marker;
use Bio::EnsEMBL::Map::MarkerSynonym;
use Bio::EnsEMBL::Map::DBSQL::QtlAdaptor;
use Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor;
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::Test::TestUtils;
our $verbose = 0; #set to 1 to turn on debug printouts
my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
my $sa = $db->get_SliceAdaptor();
my $slice = $sa->fetch_by_region( 'chromosome', "20" );
my $qtl_features = $slice->get_all_QtlFeatures();
debug( "found ".scalar( @$qtl_features ) );
debug( join( "\n", map { "$_" } %{$qtl_features->[0]})."\n" );
debug( join( "\n", map { "$_" } %{$qtl_features->[1]})."\n" );
ok( scalar( @$qtl_features ) == 2 );
my $qtladptor = $db->get_QtlAdaptor();
my $traits = $qtladptor->list_traits();
debug( join( "\n", map {"Trait: $_"} @$traits ));
ok( scalar( @$traits ) == 2 );
my $qtls = $qtladptor->fetch_all_by_trait( $traits->[0] );
my $qf = $qtls->[0]->get_QtlFeature();
debug( join( "\n", %$qf ));
ok( $qf->isa( "Bio::EnsEMBL::Map::QtlFeature" ));
my $qtl = $qtls->[0];
ok($qtl->flank_marker_1->isa('Bio::EnsEMBL::Map::Marker'));
ok($qtl->flank_marker_2->isa('Bio::EnsEMBL::Map::Marker'));
my $synonyms = $qtl->get_synonyms;
ok($synonyms->{'rat genome database'} eq 'rqtl2');
done_testing();
......@@ -3,8 +3,13 @@
58 \N patch patch_72_73_a.sql|schema_version
59 \N patch patch_72_73_b.sql|alt_allele_type
60 \N patch patch_72_73_c.sql|add_object_type_marker
62 \N patch patch_73_74_a.sql|schema_version
63 \N patch patch_73_74_c.sql|remove_unconventional_transcript_association
64 \N patch patch_73_74_d.sql|remove_qtl
65 \N patch patch_73_74_e.sql|remove_canonical_annotation
66 \N patch patch_73_74_f.sql|remove_pair_dna_align
1 \N schema_type core
2 \N schema_version 73
2 \N schema_version 74
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
......@@ -21,6 +26,7 @@
16 1 genebuild.method Generated from ENA annotation
13 1 genebuild.start_date 2012-08-EnsemblBacteria
12 1 genebuild.version 2012-08-EnsemblBacteria
61 1 patch patch_73_74_b.sql|remove_dnac
42 1 provider.name European Nucleotide Archive
43 1 provider.url http://www.ebi.ac.uk/ena/data/view/GCA_000292705
18 1 repeat.analysis Dust
......@@ -45,8 +51,8 @@
21 1 species.classification Bacillus thuringiensis
20 1 species.classification Bacillus thuringiensis HD-789
28 1 species.classification Bacteria
27 1 species.classification Firmicutes
29 1 species.classification cellular organisms
27 1 species.classification Firmicutes
34 1 species.common_name Bacillus thuringiensis HD-789
39 1 species.db_name bacillus_thuringiensis
33 1 species.display_name Bacillus thuringiensis HD-789
......
......@@ -102,7 +102,7 @@ CREATE TABLE `attrib_type` (
`description` text,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=InnoDB AUTO_INCREMENT=14078 DEFAULT CHARSET=latin1;
) ENGINE=InnoDB AUTO_INCREMENT=391 DEFAULT CHARSET=latin1;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -142,7 +142,7 @@ CREATE TABLE `density_feature` (
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=InnoDB AUTO_INCREMENT=1051 DEFAULT CHARSET=latin1;
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
CREATE TABLE `density_type` (
`density_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -152,7 +152,7 @@ CREATE TABLE `density_type` (
`value_type` enum('sum','ratio') NOT NULL,
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
) ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
......@@ -216,14 +216,12 @@ CREATE TABLE `dna_align_feature` (
`external_db_id` int(10) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`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`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`),
KEY `pair_idx` (`pair_dna_align_feature_id`)
KEY `external_db_idx` (`external_db_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
......@@ -290,7 +288,6 @@ CREATE TABLE `gene` (
`description` text,
`is_current` tinyint(1) 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(5) unsigned NOT NULL DEFAULT '1',
`created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
......@@ -454,11 +451,11 @@ 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) CHARACTER SET latin1 COLLATE latin1_bin DEFAULT 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=InnoDB AUTO_INCREMENT=61 DEFAULT CHARSET=latin1;
) ENGINE=InnoDB AUTO_INCREMENT=67 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -649,37 +646,6 @@ CREATE TABLE `protein_feature` (
KEY `analysis_idx` (`analysis_id`)
) ENGINE=InnoDB AUTO_INCREMENT=24117 DEFAULT CHARSET=latin1;
CREATE TABLE `qtl` (
`qtl_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`trait` varchar(255) NOT NULL,
`lod_score` float 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=InnoDB DEFAULT CHARSET=latin1;
CREATE TABLE `qtl_feature` (
`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 `qtl_idx` (`qtl_id`),
KEY `loc_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
CREATE TABLE `qtl_synonym` (
`qtl_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`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=InnoDB DEFAULT CHARSET=latin1;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`repeat_name` varchar(255) NOT NULL,
......@@ -718,7 +684,7 @@ CREATE TABLE `seq_region` (
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=InnoDB AUTO_INCREMENT=15 DEFAULT CHARSET=latin1;
) ENGINE=InnoDB AUTO_INCREMENT=14 DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -744,7 +710,7 @@ CREATE TABLE `seq_region_synonym` (
PRIMARY KEY (`seq_region_synonym_id`),
UNIQUE KEY `syn_idx` (`synonym`),
KEY `seq_region_idx` (`seq_region_id`)
) ENGINE=InnoDB AUTO_INCREMENT=15 DEFAULT CHARSET=latin1;
) ENGINE=InnoDB AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -897,14 +863,6 @@ CREATE TABLE `translation_attrib` (
KEY `translation_idx` (`translation_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
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_idx` (`transcript_id`),
KEY `gene_idx` (`gene_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
CREATE TABLE `unmapped_object` (
`unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('xref','cDNA','Marker') NOT NULL,
......
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
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ENSG00000355555 1 2004-12-06 12:00:00 2004-12-06 12:00:00
1 \N schema_version 73
1 \N schema_version 74
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
31 1 species.classification Mammalia
30 1 species.classification Eutheria
29 1 species.classification Primates
28 1 species.classification Catarrhini
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
27 1 species.classification Hominidae
28 1 species.classification Catarrhini
29 1 species.classification Primates
30 1 species.classification Eutheria
31 1 species.classification Mammalia
32 1 species.classification Vertebrata
33 1 species.classification Chordata
34 1 species.classification Metazoa
35 1 species.classification Eukaryota
26 1 species.classification Homo sapiens
36 1 species.common_name Human
70 1 species.scientific_name Homo sapiens
3 1 species.taxonomy_id 9606
55 1 assembly.mapping chromosome:NCBI33|contig
56 1 assembly.mapping clone|contig
57 1 assembly.mapping supercontig|contig
......@@ -23,6 +22,7 @@
65 1 assembly.mapping alt_chrom#chromosome:NCBI33
66 1 assembly.mapping alt_chrom|chromosome:NCBI33|contig
67 1 species.production_name homo_sapiens
70 1 species.scientific_name Homo sapiens
71 \N patch patch_68_69_a.sql|schema_version
72 \N patch patch_69_70_a.sql|schema_version
73 \N patch patch_69_70_b.sql|add_mapping_set_history
......@@ -37,3 +37,9 @@
82 \N patch patch_72_73_a.sql|schema_version
83 \N patch patch_72_73_b.sql|alt_allele_type
84 \N patch patch_72_73_c.sql|add_object_type_marker
85 \N patch patch_73_74_b.sql|remove_dnac
88 \N patch patch_73_74_a.sql|schema_version
89 \N patch patch_73_74_c.sql|remove_unconventional_transcript_association
90 \N patch patch_73_74_d.sql|remove_qtl
97 \N patch patch_73_74_e.sql|remove_canonical_annotation
98 \N patch patch_73_74_f.sql|remove_pair_dna_align
1 stupidity -0.2 20 92 94
2 long nose -0.1 20 65 66
469283 30100000 30400000 1 10
469283 30268968 31005297 2 10
1 1 rat genome database rqtl1
2 1 ratmap rmqtl1
3 2 rat genome database rqtl2
21716 18256 antisense
21717 18256 antisense
21719 18256 sense_intronic
21718 18257 sense_intronic
21718 18258 antisense
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