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Commit b68a8e67 authored by Dan Staines's avatar Dan Staines
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revisions to CliHelper to support dbs where no production name is set, and to... 

revisions to CliHelper to support dbs where no production name is set, and to improve default behaviour where single_species mode not specified. Also expanded test coverage to support this, adding the nameless and test_collection test dbs for this purpose
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modules/Bio/EnsEMBL/Utils/CliHelper.pm
+ 111
− 101
View file @ b68a8e67
......@@ -45,8 +45,8 @@ $Revision$
# get the basic options for connecting to a database server
my $optsd = $cli->get_dba_opts();
# add the print option
push(@$optsd,"print|p");
# add another option
push(@$optsd,"print");
# process the command line with the supplied options plus a reference to a help subroutine
my $opts = $cli->process_args($optsd,\&usage);
......@@ -56,6 +56,9 @@ $Revision$
# use the args to create a DBA
my $dba = new Bio::EnsEMBL::DBSQL::DBAdaptor(%{$db_args});
...
if(defined $opts->{print}) {
...
}
}
For adding secondary databases, a prefix can be supplied. For instance, to add a second set of
......@@ -94,15 +97,15 @@ use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
my $dba_opts = [ { args => [ 'host', 'dbhost', 'h' ], type => '=s' },
{ args => [ 'port', 'dbport', 'P' ], type => ':i' },
{ args => [ 'user', 'dbuser', 'u' ], type => '=s' },
{ args => [ 'pass', 'dbpass', 'p' ], type => ':s' },
{ args => [ 'dbname', 'D' ], type => ':s' },
{ args => [ 'pattern', 'dbpattern' ], type => ':s' },
{ args => ['driver'], type => ':s' },
{ args => ['species_id'], type => ':i' },
{ args => ['species'], type => ':i' }, ];
my $dba_opts = [{args => ['host', 'dbhost', 'h'], type => '=s'},
{args => ['port', 'dbport', 'P'], type => ':i'},
{args => ['user', 'dbuser', 'u'], type => '=s'},
{args => ['pass', 'dbpass', 'p'], type => ':s'},
{args => ['dbname', 'D'], type => ':s'},
{args => ['pattern', 'dbpattern'], type => ':s'},
{args => ['driver'], type => ':s'},
{args => ['species_id'], type => ':i'},
{args => ['species'], type => ':i'},];
=head2 new()
......@@ -113,8 +116,8 @@ my $dba_opts = [ { args => [ 'host', 'dbhost', 'h' ], type => '=s' },
=cut
sub new {
my ( $class, @args ) = @_;
my $self = bless( {}, ref($class) || $class );
my ($class, @args) = @_;
my $self = bless({}, ref($class) || $class);
return $self;
}
......@@ -128,11 +131,11 @@ sub new {
=cut
sub get_dba_opts {
my ( $self, $prefix ) = @_;
my ($self, $prefix) = @_;
$prefix ||= '';
my @dba_opts = map {
my $opt = join '|', map { $prefix . $_ } @{ $_->{args} };
$opt . $_->{type};
my $opt = join '|', map { $prefix . $_ } @{$_->{args}};
$opt . $_->{type};
} @{$dba_opts};
return \@dba_opts;
}
......@@ -148,18 +151,18 @@ sub get_dba_opts {
=cut
sub process_args {
my ( $self, $opts_def, $usage_sub ) = @_;
my ($self, $opts_def, $usage_sub) = @_;
my $opts = {};
push @{$opts_def}, q/help|?/ => $usage_sub;
GetOptions( $opts, @{$opts_def} ) ||
croak 'Could not parse command line arguments';
GetOptions($opts, @{$opts_def}) ||
croak 'Could not parse command line arguments';
return $opts;
}
=head2 get_dba_args_for_opts()
Arg [1] : Hash of options (e.g. parsed from command line options by process_args())
Arg [2] : If set to 1, the databases are assumed to have a single species only. Default is 0.
Arg [2] : If set to 1, the databases are assumed to have a single species only. Default is 0 if database name matches collection, 1 otherwise.
Arg [3] : Optional prefix to use when parsing e.g. dna
Description : Uses the parsed command line options to generate an array of DBAdaptor arguments
: (e.g. expands dbpattern, finds all species_ids for multispecies databases)
......@@ -170,80 +173,88 @@ sub process_args {
=cut
sub get_dba_args_for_opts {
my ( $self, $opts, $single_species, $prefix ) = @_;
$prefix ||= '';
$single_species ||= 0;
my ( $host, $port, $user, $pass, $dbname,
$pattern, $driver, $species, $species_id )
= map { $prefix . $_ }
qw(host port user pass dbname dbpattern driver species species_id);
my ($self, $opts, $single_species_opt, $prefix) = @_;
$prefix ||= '';
my ($host, $port, $user, $pass, $dbname,
$pattern, $driver, $species, $species_id)
= map { $prefix . $_ }
qw(host port user pass dbname dbpattern driver species species_id);
my @db_args;
if ( defined $opts->{$host} ) {
my $dbc =
Bio::EnsEMBL::DBSQL::DBConnection->new(-USER => $opts->{$user},
-PASS => $opts->{$pass},
-HOST => $opts->{$host},
-PORT => $opts->{$port},
-DRIVER => $opts->{$driver}
);
my @dbnames;
if ( defined $opts->{$dbname} ) {
push @dbnames, $opts->{$dbname};
}
elsif ( defined $opts->{$pattern} ) {
if (defined $opts->{$host}) {
my $dbc =
Bio::EnsEMBL::DBSQL::DBConnection->new(-USER => $opts->{$user},
-PASS => $opts->{$pass},
-HOST => $opts->{$host},
-PORT => $opts->{$port},
-DRIVER => $opts->{$driver}
);
my @dbnames;
if (defined $opts->{$dbname}) {
push @dbnames, $opts->{$dbname};
}
elsif (defined $opts->{$pattern}) {
# get a basic DBConnection and use to find out which dbs are involved
@dbnames =
grep { m/$opts->{$pattern}/smx }
@{ $dbc->sql_helper()->execute_simple(q/SHOW DATABASES/) };
}
else {
croak 'dbname or dbpattern arguments required';
}
for my $dbname (@dbnames) {
@dbnames = grep { m/$opts->{$pattern}/smx }
@{$dbc->sql_helper()->execute_simple(q/SHOW DATABASES/)};
}
else {
croak 'dbname or dbpattern arguments required';
}
for my $dbname (@dbnames) {
#Decipher group of DBAdaptor by capturing the name_name(_name?)_core_ code. Otherwise we don't know
my ($group) = $dbname =~
/^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?_([a-z]+)(?:_\d+)?_\d+/;
# set multi where we have collections
my $multi = $dbname =~ m/_collection_/ ? 1 : 0;
my $species_ids;
if ( $single_species != 1 ) {
$species_ids =
$dbc->sql_helper()
->execute(
my ($group) = $dbname =~
/^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?_([a-z]+)(?:_\d+)?_\d+/;
# set multi where we have collections
my $multi = $dbname =~ m/_collection_/ ? 1 : 0;
my $species_ids;
my $single_species = $single_species_opt;
if (!defined $single_species) {
# if we're dealing with a collection, turn off single species mode by default
$single_species = $dbname =~ m/_collection_/ ? 0 : 1;
}
if ($single_species != 1) {
# for multispecies, get the list of species from meta
$species_ids =
$dbc->sql_helper()
->execute(
"SELECT species_id,meta_value FROM $dbname.meta WHERE meta_key='species.production_name'"
);
if ( !defined $opts->{$species_id} &&
scalar( @{$species_ids} ) == 0 )
{
croak "No species.production_name found in database";
}
}
if ( defined $species_id ) {
$species_ids = [ [ $opts->{$species_id}, $opts->{$species} ] ];
}
else {
$species_ids = [ [ 1, undef ] ];
}
for my $species_id ( @{$species_ids} ) {
my $args = { -HOST => $opts->{$host},
-USER => $opts->{$user},
-PORT => $opts->{$port},
-PASS => $opts->{$pass},
-DBNAME => $dbname,
-DRIVER => $opts->{$driver},
-SPECIES_ID => $species_id->[0],
-SPECIES => $species_id->[1],
-MULTISPECIES_DB => $multi };
$args->{-GROUP} = $group if $group;
push( @db_args, $args );
}
} ## end for my $dbname (@dbnames)
} ## end if ( defined $opts->{$host...})
);
if (!defined $opts->{$species_id} &&
scalar(@{$species_ids}) == 0)
{
croak "No species.production_name found in database";
}
}
# if we didn't get a list from meta, go ahead and use the supplied arguments if we have them
if (defined $opts->{$species_id}) {
$species_ids = [[$opts->{$species_id}, $opts->{$species}]];
}
# otherwise assume the default species
elsif(!defined $species_ids) {
$species_ids = [[1, undef]];
}
# deal with each species in turn
for my $species_id (@{$species_ids}) {
my $args = {-HOST => $opts->{$host},
-USER => $opts->{$user},
-PORT => $opts->{$port},
-PASS => $opts->{$pass},
-DBNAME => $dbname,
-DRIVER => $opts->{$driver},
-SPECIES_ID => $species_id->[0],
-SPECIES => $species_id->[1],
-MULTISPECIES_DB => $multi};
$args->{-GROUP} = $group if $group;
push(@db_args, $args);
}
} ## end for my $dbname (@dbnames)
} ## end if (defined $opts->{$host...})
else {
croak '(db)host arguments required';
croak '(db)host arguments required';
}
return \@db_args;
} ## end sub get_dba_args_for_opts
......@@ -261,15 +272,14 @@ sub get_dba_args_for_opts {
=cut
sub get_dbas_for_opts {
my ( $self, $opts, $single_species, $prefix ) = @_;
my ($self, $opts, $single_species, $prefix) = @_;
# get all the DBA details that we want to work with and create DBAs for each in turn
my $dbas;
for my $args (
@{ $self->get_dba_args_for_opts( $opts, $single_species, $prefix ) }
)
@{$self->get_dba_args_for_opts($opts, $single_species, $prefix)})
{
push @{$dbas}, Bio::EnsEMBL::DBSQL::DBAdaptor->new( %{$args} );
push @{$dbas}, Bio::EnsEMBL::DBSQL::DBAdaptor->new(%{$args});
}
return $dbas;
}
......@@ -288,17 +298,17 @@ sub get_dbas_for_opts {
=cut
sub load_registry_for_opts {
my ( $self, $opts, $prefix ) = @_;
my ($self, $opts, $prefix) = @_;
$prefix ||= q{};
if ( $opts->{registry} ) {
my $location = $opts->{registry};
return Bio::EnsEMBL::Registry->load_all($location);
if ($opts->{registry}) {
my $location = $opts->{registry};
return Bio::EnsEMBL::Registry->load_all($location);
}
my ( $host, $port, $user, $pass ) =
map { $prefix . $_ } qw(host port user pass);
my %args = ( -HOST => $opts->{$host},
-PORT => $opts->{$port},
-USER => $opts->{$user}, );
my ($host, $port, $user, $pass) =
map { $prefix . $_ } qw(host port user pass);
my %args = (-HOST => $opts->{$host},
-PORT => $opts->{$port},
-USER => $opts->{$user},);
$args{-PASS} = $opts->{$pass};
return Bio::EnsEMBL::Registry->load_registry_from_db(%args);
}
......
modules/t/cliHelper.t
+ 82
− 9
View file @ b68a8e67
......@@ -21,6 +21,7 @@ use Bio::EnsEMBL::Operon;
use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Utils::CliHelper;
debug("Startup test");
ok(1);
......@@ -28,9 +29,6 @@ my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $dba = $multi->get_DBAdaptor("core");
debug("Test database instatiated");
ok($dba);
my $cli_helper = Bio::EnsEMBL::Utils::CliHelper->new();
debug("Checking default options");
......@@ -49,8 +47,8 @@ is( $dba_args->[0]->{-PASS}, $opts->{pass} );
is( $dba_args->[0]->{-PORT}, $opts->{port} );
is( $dba_args->[0]->{-DBNAME}, $opts->{dbname} );
ok( !defined $dba_args->[0]->{-SPECIES} );
ok( !defined $dba_args->[0]->{-SPECIES_ID} );
is( $dba_args->[0]->{-MULTISPECIES_DB}, 0 );
is( $dba_args->[0]->{-SPECIES_ID},1 );
is( $dba_args->[0]->{-MULTISPECIES_DB}, 0);
$opts->{species_id} = 1;
$opts->{species} = "homo_sapiens";
......@@ -73,7 +71,7 @@ my $srcopts = { srchost => $dba->dbc()->host(),
srcport => $dba->dbc()->port(),
srcdbname => $dba->dbc()->dbname(), };
debug("Checking prefix options");
debug("Checking prefix options without single species specified");
my $src_dba_args =
$cli_helper->get_dba_args_for_opts( $srcopts, 0, "src" );
......@@ -83,10 +81,11 @@ is( $src_dba_args->[0]->{-USER}, $srcopts->{srcuser} );
is( $src_dba_args->[0]->{-PASS}, $srcopts->{srcpass} );
is( $src_dba_args->[0]->{-PORT}, $srcopts->{srcport} );
is( $src_dba_args->[0]->{-DBNAME}, $srcopts->{srcdbname} );
ok( !defined $src_dba_args->[0]->{-SPECIES} );
ok( !defined $src_dba_args->[0]->{-SPECIES_ID} );
ok( defined $src_dba_args->[0]->{-SPECIES} );
is( $src_dba_args->[0]->{-SPECIES_ID},1 );
is( $src_dba_args->[0]->{-MULTISPECIES_DB}, 0 );
debug("Checking prefix options with single species specified");
$src_dba_args =
$cli_helper->get_dba_args_for_opts( $srcopts, 1, "src" );
......@@ -96,10 +95,84 @@ is( $src_dba_args->[0]->{-USER}, $srcopts->{srcuser} );
is( $src_dba_args->[0]->{-PASS}, $srcopts->{srcpass} );
is( $src_dba_args->[0]->{-PORT}, $srcopts->{srcport} );
is( $src_dba_args->[0]->{-DBNAME}, $srcopts->{srcdbname} );
is( $src_dba_args->[0]->{-SPECIES_ID},1 );
ok( !defined $src_dba_args->[0]->{-SPECIES} );
is( $src_dba_args->[0]->{-MULTISPECIES_DB}, 0 );
debug("Checking prefix options with single species undefined");
$src_dba_args =
$cli_helper->get_dba_args_for_opts( $srcopts, undef, "src" );
is( scalar(@$src_dba_args), 1 );
is( $src_dba_args->[0]->{-HOST}, $srcopts->{srchost} );
is( $src_dba_args->[0]->{-USER}, $srcopts->{srcuser} );
is( $src_dba_args->[0]->{-PASS}, $srcopts->{srcpass} );
is( $src_dba_args->[0]->{-PORT}, $srcopts->{srcport} );
is( $src_dba_args->[0]->{-DBNAME}, $srcopts->{srcdbname} );
is( $src_dba_args->[0]->{-SPECIES_ID},1 );
ok( !defined $src_dba_args->[0]->{-SPECIES} );
ok( !defined $src_dba_args->[0]->{-SPECIES_ID} );
is( $src_dba_args->[0]->{-MULTISPECIES_DB}, 0 );
$multi->restore('core');
debug("Test database restored");
ok($dba);
my $nameless = Bio::EnsEMBL::Test::MultiTestDB->new("nameless");
$dba = $nameless->get_DBAdaptor("core");
debug("Nameless test database instantiated");
ok($dba);
debug("Checking default options");
$opts = { host => $dba->dbc()->host(),
user => $dba->dbc()->username(),
pass => $dba->dbc()->password(),
port => $dba->dbc()->port(),
dbname => $dba->dbc()->dbname(), };
$dba_args = $cli_helper->get_dba_args_for_opts($opts);
is( scalar(@$dba_args), 1 );
is( $dba_args->[0]->{-HOST}, $opts->{host} );
is( $dba_args->[0]->{-USER}, $opts->{user} );
is( $dba_args->[0]->{-PASS}, $opts->{pass} );
is( $dba_args->[0]->{-PORT}, $opts->{port} );
is( $dba_args->[0]->{-DBNAME}, $opts->{dbname} );
ok( !defined $dba_args->[0]->{-SPECIES} );
is( $dba_args->[0]->{-SPECIES_ID},1 );
is( $dba_args->[0]->{-MULTISPECIES_DB}, 0 );
my $collection = Bio::EnsEMBL::Test::MultiTestDB->new('test_collection');
$dba = $collection->get_DBAdaptor("core");
debug("Collection test database instantiated");
ok($dba);
debug("Checking default options");
$opts = { host => $dba->dbc()->host(),
user => $dba->dbc()->username(),
pass => $dba->dbc()->password(),
port => $dba->dbc()->port(),
dbname => $dba->dbc()->dbname(), };
$dba_args = $cli_helper->get_dba_args_for_opts($opts);
is(scalar(@$dba_args),2);
is( $dba_args->[0]->{-HOST}, $opts->{host} );
is( $dba_args->[0]->{-USER}, $opts->{user} );
is( $dba_args->[0]->{-PASS}, $opts->{pass} );
is( $dba_args->[0]->{-PORT}, $opts->{port} );
is( $dba_args->[0]->{-DBNAME}, $opts->{dbname} );
ok( defined $dba_args->[0]->{-SPECIES} );
is( $dba_args->[0]->{-SPECIES_ID},1 );
is( $dba_args->[0]->{-MULTISPECIES_DB}, 1 );
is( $dba_args->[1]->{-HOST}, $opts->{host} );
is( $dba_args->[1]->{-USER}, $opts->{user} );
is( $dba_args->[1]->{-PASS}, $opts->{pass} );
is( $dba_args->[1]->{-PORT}, $opts->{port} );
is( $dba_args->[1]->{-DBNAME}, $opts->{dbname} );
ok( defined $dba_args->[1]->{-SPECIES} );
is( $dba_args->[1]->{-SPECIES_ID},2 );
is( $dba_args->[1]->{-MULTISPECIES_DB}, 1 );
done_testing();
modules/t/test-genome-DBs/nameless/core/meta.txt 0 → 100644
+ 44
− 0
View file @ b68a8e67
1 \N schema_version 74
2 1 assembly.default NCBI34
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
36 1 species.common_name Human
55 1 assembly.mapping chromosome:NCBI33|contig
56 1 assembly.mapping clone|contig
57 1 assembly.mapping supercontig|contig
58 1 assembly.mapping chromosome:NCBI33|contig|clone
59 1 assembly.mapping chromosome:NCBI33|contig|supercontig
60 1 assembly.mapping supercontig|contig|clone
64 1 assembly.mapping chromosome:NCBI33#chunk
65 1 assembly.mapping alt_chrom#chromosome:NCBI33
66 1 assembly.mapping alt_chrom|chromosome:NCBI33|contig
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
74 \N patch patch_69_70_c.sql|column_datatype_consistency
75 \N patch patch_69_70_d.sql|data_file_id_auto_increment
76 \N patch patch_69_70_e.sql|protein_feature_hit_description
77 \N schema_type core
78 \N patch patch_70_71_a.sql|schema_version
79 \N patch patch_70_71_b.sql|mapping_set_index
80 \N patch patch_71_72_a.sql|schema_version
81 \N patch patch_71_72_b.sql|associated_xref
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
modules/t/test-genome-DBs/nameless/core/table.sql 0 → 100644
+ 905
− 0
View file @ b68a8e67
This diff is collapsed.
modules/t/test-genome-DBs/test_collection/core/meta.txt 0 → 100644
+ 120
− 0
View file @ b68a8e67
3 \N patch patch_71_72_a.sql|schema_version
4 \N patch patch_71_72_b.sql|associated_xref
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 74
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
11 1 assembly.description Bacillus thuringiensis HD-789 Genome sequencing
45 1 assembly.mapping chromosome:GCA_000292705.1#contig
44 1 assembly.mapping plasmid:GCA_000292705.1#contig
17 1 assembly.master_accession CP003763
9 1 assembly.name ASM29270v1
56 1 exonbuild.level toplevel
53 1 genebuild.hash 6538e11c93c6a472265adaf11a8ad2ce
14 1 genebuild.initial_release_date 2012-08-EnsemblBacteria
15 1 genebuild.last_geneset_update 2012-08
54 1 genebuild.level toplevel
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
19 1 repeat.analysis TRF
48 1 sample.gene_param BTF1_30792
49 1 sample.gene_text BTF1_30792
46 1 sample.location_param p02:80287-81642
47 1 sample.location_text p02:80287-81642
52 1 sample.search_text synthetase
50 1 sample.transcript_param AFQ30259
51 1 sample.transcript_text BTF1_30792-1
5 1 schema.load_started 2013-07-16 13:02:46
6 1 schema.load_started 2013-07-16 13:02:53
57 1 simple_featurebuild.level toplevel
37 1 species.alias Bacillus thuringiensis HD-789
38 1 species.alias bacillus_thuringiensis
24 1 species.classification Bacillaceae
25 1 species.classification Bacillales
26 1 species.classification Bacilli
23 1 species.classification Bacillus
22 1 species.classification Bacillus cereus group
21 1 species.classification Bacillus thuringiensis
20 1 species.classification Bacillus thuringiensis HD-789
28 1 species.classification Bacteria
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
41 1 species.division EnsemblBacteria
36 1 species.ensembl_alias_name Bacillus thuringiensis HD-789
30 1 species.production_name bacillus_thuringiensis
32 1 species.scientific_name Bacillus thuringiensis HD-789
35 1 species.short_name Bacillus thuringiensis HD-789
40 1 species.taxonomy_id 1217737
31 1 species.url Bacillus_thuringiensis
55 1 transcriptbuild.level toplevel
118 2 assembly.accession GCA_000292706.1
110 2 assembly.date 2012-08
107 2 assembly.default GCA_000292706.1
111 2 assembly.description Bacillus thuringiensis HD-790 Genome sequencing
145 2 assembly.mapping chromosome:GCA_000292706.1#contig
144 2 assembly.mapping plasmid:GCA_000292706.1#contig
117 2 assembly.master_accession CP003763
109 2 assembly.name ASM29270v2
156 2 exonbuild.level toplevel
153 2 genebuild.hash 6538e11c93c6a472265adaf11a8ad2ce
114 2 genebuild.initial_release_date 2012-08-EnsemblBacteria
115 2 genebuild.last_geneset_update 2012-08
154 2 genebuild.level toplevel
116 2 genebuild.method Generated from ENA annotation
113 2 genebuild.start_date 2012-08-EnsemblBacteria
112 2 genebuild.version 2012-08-EnsemblBacteria
161 2 patch patch_73_74_b.sql|remove_dnac
142 2 provider.name European Nucleotide Archive
143 2 provider.url http://www.ebi.ac.uk/ena/data/view/GCA_000292706
118 2 repeat.analysis Dust
119 2 repeat.analysis TRF
148 2 sample.gene_param BTF1_30792
149 2 sample.gene_text BTF1_30792
146 2 sample.location_param p02:80287-81642
147 2 sample.location_text p02:80287-81642
152 2 sample.search_text synthetase
150 2 sample.transcript_param AFQ30259
151 2 sample.transcript_text BTF1_30792-1
105 2 schema.load_started 2013-07-16 13:02:46
106 2 schema.load_started 2013-07-16 13:02:53
157 2 simple_featurebuild.level toplevel
137 2 species.alias Bacillus thuringiensis HD-790
138 2 species.alias bacillus_thuringiensis
124 2 species.classification Bacillaceae
125 2 species.classification Bacillales
126 2 species.classification Bacilli
123 2 species.classification Bacillus
122 2 species.classification Bacillus cereus group
121 2 species.classification Bacillus thuringiensis
120 2 species.classification Bacillus thuringiensis HD-790
128 2 species.classification Bacteria
129 2 species.classification cellular organisms
127 2 species.classification Firmicutes
134 2 species.common_name Bacillus thuringiensis HD-790
139 2 species.db_name bacillus_thuringiensis_hd_790
133 2 species.display_name Bacillus thuringiensis HD-790
141 2 species.division EnsemblBacteria
136 2 species.ensembl_alias_name Bacillus thuringiensis HD-790
130 2 species.production_name bacillus_thuringiensis_hd_790
132 2 species.scientific_name Bacillus thuringiensis HD-790
135 2 species.short_name Bacillus thuringiensis HD-790
140 2 species.taxonomy_id 1217737
131 2 species.url Bacillus_thuringiensis_hd_790
155 2 transcriptbuild.level toplevel
modules/t/test-genome-DBs/test_collection/core/table.sql 0 → 100644
+ 906
− 0
View file @ b68a8e67
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