Commit ab9f2f08 authored by cvs2git's avatar cvs2git
Browse files

This commit was manufactured by cvs2svn to create tag 'tag-

ensemblgenomes-20-73'.

Sprout from master 2013-08-22 09:32:14 UTC Magali Ruffier <mr6@sanger.ac.uk> 'added fetch_stable_id_event and get_event methods for archivestableid, in adaptor and object modules respectively'
Cherrypick from master 2013-09-06 15:16:53 UTC Alessandro Vullo <avullo@ebi.ac.uk> 'Tests for subroutines in the Bio::EnsEMBL::Utils::IO module.':
    modules/t/io.t
    modules/t/test-genome-DBs/ontology/ontology/table.sql
    sql/patch_73_74_a.sql
    sql/patch_73_74_b.sql
    sql/patch_73_74_c.sql
    sql/patch_73_74_d.sql
    sql/patch_73_74_e.sql
    sql/patch_73_74_f.sql
Cherrypick from branch-ensembl-73 2013-08-30 09:06:03 UTC Magali Ruffier <mr6@sanger.ac.uk> 'revert changes for metacontainer support':
    misc-scripts/ontology/sql/patch_72_73_b.sql
    misc-scripts/ontology/sql/tables.sql
    modules/Bio/EnsEMBL/DBSQL/AssemblyAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
    modules/Bio/EnsEMBL/RepeatFeature.pm
    modules/Bio/EnsEMBL/Slice.pm
    modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
parent 9ab3baca
-- patch_72_73_a.sql
--
-- Title: Insert schema version.
--
-- Description:
-- Adding schema version to the meta table (set to 73)
-- so that script schema_patcher.pl would work
ALTER TABLE meta ADD COLUMN species_id INT(1) UNSIGNED DEFAULT NULL;
-- Patch identifier
INSERT INTO meta (meta_key, meta_value)
VALUES ('patch', 'patch_72_73_b.sql|meta_species');
...@@ -7,6 +7,7 @@ CREATE TABLE meta ( ...@@ -7,6 +7,7 @@ CREATE TABLE meta (
meta_id INT UNSIGNED NOT NULL AUTO_INCREMENT, meta_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
meta_key VARCHAR(64) NOT NULL, meta_key VARCHAR(64) NOT NULL,
meta_value VARCHAR(128), meta_value VARCHAR(128),
species_id INT UNSIGNED DEFAULT NULL,
PRIMARY KEY (meta_id), PRIMARY KEY (meta_id),
UNIQUE INDEX key_value_idx (meta_key, meta_value) UNIQUE INDEX key_value_idx (meta_key, meta_value)
...@@ -20,6 +21,8 @@ INSERT INTO meta (meta_key, meta_value) VALUES ...@@ -20,6 +21,8 @@ INSERT INTO meta (meta_key, meta_value) VALUES
# Patches included in this schema file # Patches included in this schema file
INSERT INTO meta (meta_key, meta_value) INSERT INTO meta (meta_key, meta_value)
VALUES ('patch', 'patch_72_73_a.sql|schema_version'); VALUES ('patch', 'patch_72_73_a.sql|schema_version');
INSERT INTO meta (meta_key, meta_value)
VALUES ('patch', 'patch_72_73_b.sql|meta_species');
CREATE TABLE ontology ( CREATE TABLE ontology (
ontology_id INT UNSIGNED NOT NULL AUTO_INCREMENT, ontology_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
......
...@@ -109,27 +109,26 @@ sub fetch_info { ...@@ -109,27 +109,26 @@ sub fetch_info {
$assembly_info{'schema_build'} = $schema_build; $assembly_info{'schema_build'} = $schema_build;
} }
#fetch available coordinate systems #fetch available coordinate systems
my $csa = $self->db()->get_adaptor('CoordSystem'); my $csa = $self->db()->get_adaptor('CoordSystem');
my %versions; my $coord_systems = $csa->fetch_all();
foreach my $cs (@{$csa->fetch_all()}) { my %versions = map { $_->version(), 1 } @{$coord_systems};
$versions{$cs->version()} = 1; $assembly_info{'coord_system_versions'} = [keys %versions];
} my ($default_assembly) = @{$coord_systems};
my @coord_system_versions = keys %versions; $assembly_info{default_coord_system_version} = $default_assembly->version();
$assembly_info{'coord_system_versions'} = \@coord_system_versions;
#fetch top level seq_region names #fetch top level seq_region names
my $sa = $self->db()->get_adaptor('Slice'); my $sa = $self->db()->get_adaptor('Slice');
my $slices = $sa->fetch_all('toplevel'); my $slices = $sa->fetch_all('toplevel');
my %unique = map { $_->seq_region_name(), 0 } @{$slices}; my %unique = map { $_->seq_region_name(), 0 } @{$slices};
my $names = [sort { $a cmp $b } keys %unique]; my $names = [sort { $a cmp $b } keys %unique];
$assembly_info{'top_level_seq_region_names'} = $names; $assembly_info{'top_level_seq_region_names'} = $names;
my $karyotype = $sa->fetch_all_karyotype();
$assembly_info{karyotype} = [ map { $_->seq_region_name() } @{$karyotype}];
return \%assembly_info; return \%assembly_info;
} }
......
...@@ -1147,18 +1147,18 @@ sub fetch_all_karyotype { ...@@ -1147,18 +1147,18 @@ sub fetch_all_karyotype {
my $sth = my $sth =
$self->prepare( 'SELECT sr.seq_region_id, sr.name, ' $self->prepare( 'SELECT sr.seq_region_id, sr.name, '
. 'sr.length, sr.coord_system_id ' . 'sr.length, sr.coord_system_id, sra.value '
. 'FROM seq_region sr, seq_region_attrib sra, ' . 'FROM seq_region sr, seq_region_attrib sra, '
. 'attrib_type at, coord_system cs ' . 'attrib_type at, coord_system cs '
. 'WHERE at.code = "karyotype_rank" ' . 'WHERE at.code = "karyotype_rank" '
. 'AND at.attrib_type_id = sra.attrib_type_id ' . 'AND at.attrib_type_id = sra.attrib_type_id '
. 'AND sra.seq_region_id = sr.seq_region_id ' . 'AND sra.seq_region_id = sr.seq_region_id '
. 'AND sr.coord_system_id = cs.coord_system_id ' . 'AND sr.coord_system_id = cs.coord_system_id '
. 'AND cs.species_id = ?' ); . 'AND cs.species_id = ?');
$sth->bind_param( 1, $self->species_id(), SQL_INTEGER ); $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
$sth->execute(); $sth->execute();
my ( $seq_region_id, $name, $length, $cs_id ); my ( $seq_region_id, $name, $length, $cs_id, $rank );
$sth->bind_columns( \( $seq_region_id, $name, $length, $cs_id ) ); $sth->bind_columns( \( $seq_region_id, $name, $length, $cs_id, $rank ) );
my @out; my @out;
while($sth->fetch()) { while($sth->fetch()) {
...@@ -1166,17 +1166,22 @@ sub fetch_all_karyotype { ...@@ -1166,17 +1166,22 @@ sub fetch_all_karyotype {
my $slice = Bio::EnsEMBL::Slice->new_fast({ my $slice = Bio::EnsEMBL::Slice->new_fast({
'start' => 1, 'start' => 1,
'end' => $length, 'end' => ($length+0),
'strand' => 1, 'strand' => 1,
'seq_region_name' => $name, 'seq_region_name' => $name,
'seq_region_length'=> $length, 'seq_region_length'=> ($length+0),
'coord_system' => $cs, 'coord_system' => $cs,
'adaptor' => $self}); 'adaptor' => $self,
'karyotype' => 1,
'karyotype_rank' => ($rank+0),
});
push @out, $slice; push @out, $slice;
} }
#Sort using Perl as value in MySQL is a text field and not portable
@out = sort { $a->{karyotype_rank} <=> $b->{karyotype_rank} } @out;
return \@out; return \@out;
} }
......
...@@ -258,6 +258,28 @@ sub display_id { ...@@ -258,6 +258,28 @@ sub display_id {
} }
=head2 summary_as_hash
Example : $repeat_feature_summary = $protein_feature->summary_as_hash();
Description : Retrieves a textual summary of this Repeat feature.
Not inherited from Feature.
Returns : hashref of arrays of descriptive strings
Status : Intended for internal use
=cut
sub summary_as_hash {
my $self = shift;
my %summary;
$summary{'start'} = $self->seq_region_start;
$summary{'end'} = $self->seq_region_end;
$summary{'strand'} = $self->strand;
$summary{'seq_region_name'} = $self->seq_region_name;
$summary{'description'} = $self->display_id;
return \%summary;
}
1; 1;
__END__ __END__
......
...@@ -551,6 +551,24 @@ sub has_karyotype { ...@@ -551,6 +551,24 @@ sub has_karyotype {
return $self->{'karyotype'}; return $self->{'karyotype'};
} }
=head2 karyotype_rank
Arg : none
Example : my $rank = $slice->karyotype_rank()
Description: Returns the numeric ranking in the karyotype. Otherwise 0 is returned
Returntype : int
Caller : general
Status : At Risk
=cut
sub karyotype_rank {
my ($self) = @_;
if(! defined( $self->{karyotype_rank})) {
my $rank = $self->adaptor()->get_karyotype_rank($self->get_seq_region_id());
$self->{karyotype_rank} = $rank if $rank;
}
return $self->{karyotype_rank} || 0;
}
=head2 is_circular =head2 is_circular
Arg : none Arg : none
......
...@@ -109,7 +109,7 @@ sub gen_load { ...@@ -109,7 +109,7 @@ sub gen_load {
} }
$pre_hook = \&Bio::EnsEMBL::Utils::ConfigRegistry::pre_funcgen_hook; $pre_hook = \&Bio::EnsEMBL::Utils::ConfigRegistry::pre_funcgen_hook;
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_funcgen; $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_funcgen;
} elsif ( $dba->isa('Bio::Ensembl::DBSQL::OntologyTermAdaptor') ) { } elsif ( $dba->isa('Bio::EnsEMBL::DBSQL::OntologyDBAdaptor') || $dba->isa('Bio::Ensembl::DBSQL::OntologyTermAdaptor') ) {
if ( !defined( $dba->group() ) ) { if ( !defined( $dba->group() ) ) {
$dba->group('ontology'); $dba->group('ontology');
} }
......
################################################
# #
# io.t #
# #
# A set of tests to verify various subroutines #
# in the Bio::EnsEMBL::Utils::IO module #
# #
################################################
use strict;
use warnings;
use Test::More;
use File::Temp;
use Bio::EnsEMBL::Utils::IO qw /:all/;
ok(1, 'module compiles');
#
# test filtering the content of a directory
#
my $tmpdir = File::Temp->newdir();
my $dirname = $tmpdir->dirname;
my $perl_tmp_file1 = File::Temp->new(DIR => $dirname,
SUFFIX => '.pl');
my $perl_tmp_file2 = File::Temp->new(DIR => $dirname,
SUFFIX => '.pl');
my $perl_tmp_file3 = File::Temp->new(DIR => $dirname,
SUFFIX => '.pl');
my $other_tmp_file1 = File::Temp->new(DIR => $dirname,
SUFFIX => '.dat');
my $other_tmp_file2 = File::Temp->new(DIR => $dirname,
SUFFIX => '.dat');
is(scalar @{Bio::EnsEMBL::Utils::IO::filter_dir($dirname, sub {
my $file = shift;
return $file if $file =~ /\.pl$/;
})}, 3, "filter_dir: number of entries in dir");
done_testing();
CREATE TABLE `alt_id` (
`alt_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`term_id` int(10) unsigned NOT NULL,
`accession` varchar(64) NOT NULL,
PRIMARY KEY (`alt_id`),
UNIQUE KEY `term_alt_idx` (`term_id`,`alt_id`),
KEY `accession_idx` (`accession`(50))
) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_Cross_product_review_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_goslim_aspergillus_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_goslim_candida_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_goslim_generic_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_goslim_metagenomics_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_goslim_pir_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_goslim_plant_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_goslim_pombe_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_goslim_yeast_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_gosubset_prok_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_high_level_annotation_qc_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_mf_needs_review_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_virus_checked_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_SO_DBVAR_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_SO_SOFA_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `aux_SO_biosapiens_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `closure` (
`closure_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`child_term_id` int(10) unsigned NOT NULL,
`parent_term_id` int(10) unsigned NOT NULL,
`subparent_term_id` int(10) unsigned DEFAULT NULL,
`distance` tinyint(3) unsigned NOT NULL,
`ontology_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`closure_id`),
UNIQUE KEY `child_parent_idx` (`child_term_id`,`parent_term_id`,`subparent_term_id`,`ontology_id`),
KEY `parent_subparent_idx` (`parent_term_id`,`subparent_term_id`)
) ENGINE=MyISAM AUTO_INCREMENT=1453438 DEFAULT CHARSET=latin1;
CREATE TABLE `meta` (
`meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`meta_key` varchar(64) NOT NULL,
`meta_value` varchar(128) DEFAULT NULL,
`species_id` int(1) unsigned DEFAULT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `key_value_idx` (`meta_key`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=13 DEFAULT CHARSET=latin1;
CREATE TABLE `ontology` (
`ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(64) NOT NULL,
`namespace` varchar(64) NOT NULL,
PRIMARY KEY (`ontology_id`),
UNIQUE KEY `name_namespace_idx` (`name`,`namespace`)
) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
CREATE TABLE `relation` (
`relation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`child_term_id` int(10) unsigned NOT NULL,
`parent_term_id` int(10) unsigned NOT NULL,
`relation_type_id` int(10) unsigned NOT NULL,
`intersection_of` tinyint(3) unsigned NOT NULL DEFAULT '0',
`ontology_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`relation_id`),
UNIQUE KEY `child_parent_idx` (`child_term_id`,`parent_term_id`,`relation_type_id`,`intersection_of`,`ontology_id`),
KEY `parent_idx` (`parent_term_id`)
) ENGINE=MyISAM AUTO_INCREMENT=68750 DEFAULT CHARSET=latin1;
CREATE TABLE `relation_type` (
`relation_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(64) NOT NULL,
PRIMARY KEY (`relation_type_id`),
UNIQUE KEY `name_idx` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=85 DEFAULT CHARSET=latin1;
CREATE TABLE `subset` (
`subset_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(64) NOT NULL,
`definition` varchar(128) NOT NULL,
PRIMARY KEY (`subset_id`),
UNIQUE KEY `name_idx` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=18 DEFAULT CHARSET=latin1;
CREATE TABLE `synonym` (
`synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`term_id` int(10) unsigned NOT NULL,
`name` text NOT NULL,
PRIMARY KEY (`synonym_id`),
UNIQUE KEY `term_synonym_idx` (`term_id`,`synonym_id`),
KEY `name_idx` (`name`(50))
) ENGINE=MyISAM AUTO_INCREMENT=104283 DEFAULT CHARSET=latin1;
CREATE TABLE `term` (
`term_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`ontology_id` int(10) unsigned NOT NULL,
`subsets` text,
`accession` varchar(64) NOT NULL,
`name` varchar(255) NOT NULL,
`definition` text,
`is_root` int(11) DEFAULT NULL,
`is_obsolete` int(11) DEFAULT NULL,
PRIMARY KEY (`term_id`),
UNIQUE KEY `accession_idx` (`accession`),
UNIQUE KEY `ontology_acc_idx` (`ontology_id`,`accession`),
KEY `name_idx` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=35406 DEFAULT CHARSET=latin1;
# patch_73_74_a.sql
#
# Title: Update schema version.
#
# Description:
# Update schema_version in meta table to 74.
UPDATE meta SET meta_value='74' WHERE meta_key='schema_version';
# Patch identifier
INSERT INTO meta (species_id, meta_key, meta_value)
VALUES (NULL, 'patch', 'patch_73_74_a.sql|schema_version');
# patch_73_74_b.sql
#
# title: dnac removal
#
# description:
# Removal dnac table which is not used any more
DROP TABLE dnac;
# patch identifier
INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_73_74_b.sql|remove_dnac');
# patch_73_74_c.sql
#
# title: Unconventional_transcript_association removal
#
# description:
# Removal unconventional_transcript_association table which is not used any more
DROP TABLE unconventional_transcript_association;
# patch identifier
INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_73_74_c.sql|remove_unconventional_transcript_association');
# patch_73_74_d.sql
#
# title: Qtl removal
#
# description:
# Removal of the qtl tables (qtl, qtl_feature, qtl_synonym) which are not used any more
DROP TABLE qtl;
DROP TABLE qtl_feature;
DROP TABLE qtl_synonym;
# patch identifier
INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_73_74_d.sql|remove_qtl');
# patch_73_74_f.sql
#
# title: Canonical_annotation removal
#
# description:
# Removal of the canonical_annotation column in the gene table, as it is not used any more
ALTER TABLE gene DROP COLUMN canonical_annotation ;
# patch identifier
INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_73_74_e.sql|remove_canonical_annotation');
# patch_73_74_f.sql
#
# title: Pair_dna_align_feature removal
#
# description:
# Removal of the pair_dna_align_feature_id column in the dna_align_feature table, as it is not used any more
ALTER TABLE dna_align_feature DROP INDEX pair_idx;
ALTER TABLE dna_align_feature DROP COLUMN pair_dna_align_feature_id ;
# patch identifier
INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_73_74_f.sql|remove_pair_dna_align');
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