Raw content of Bio::EnsEMBL::DBSQL::GeneAdaptor
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::DBSQL::GeneAdaptor - Database adaptor for the retrieval and
storage of Gene objects
=head1 SYNOPSIS
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous',
);
$gene_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "gene" );
$gene = $gene_adaptor->fetch_by_dbID(1234);
$gene = $gene_adaptor->fetch_by_stable_id('ENSG00000184129');
@genes = @{ $gene_adaptor->fetch_all_by_external_name('BRCA2') };
$slice_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "slice" );
$slice =
$slice_adaptor->fetch_by_region( 'chromosome', '1', 1, 1000000 );
@genes = @{ $gene_adaptor->fetch_all_by_Slice($slice) };
=head1 DESCRIPTION
This is a database aware adaptor for the retrieval and storage of gene
objects.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::GeneAdaptor;
use strict;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::DBSQL::SliceAdaptor;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Gene;
use vars '@ISA';
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
# _tables
# Arg [1] : none
# Description: PROTECTED implementation of superclass abstract method.
# Returns the names, aliases of the tables to use for queries.
# Returntype : list of listrefs of strings
# Exceptions : none
# Caller : internal
# Status : Stable
sub _tables {
my $self = shift;
return ([ 'gene', 'g' ],
[ 'gene_stable_id', 'gsi' ],
[ 'xref', 'x' ],
[ 'external_db' , 'exdb' ]);
}
# _columns
# Arg [1] : none
# Example : none
# Description: PROTECTED implementation of superclass abstract method.
# Returns a list of columns to use for queries.
# Returntype : list of strings
# Exceptions : none
# Caller : internal
# Status : Stable
sub _columns {
my $self = shift;
my $created_date = $self->db->dbc->from_date_to_seconds("gsi.created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("gsi.modified_date");
return ( 'g.gene_id', 'g.seq_region_id', 'g.seq_region_start',
'g.seq_region_end', 'g.seq_region_strand',
'g.analysis_id' ,'g.biotype', 'g.display_xref_id',
'g.description', 'g.status', 'g.source', 'g.is_current',
'g.canonical_transcript_id', 'g.canonical_annotation',
'gsi.stable_id', 'gsi.version', $created_date, $modified_date,
'x.display_label' ,'x.dbprimary_acc', 'x.description', 'x.version',
'exdb.db_name', 'exdb.status', 'exdb.db_release',
'exdb.db_display_name', 'x.info_type', 'x.info_text');
}
sub _left_join {
return ( [ 'gene_stable_id', "gsi.gene_id = g.gene_id" ],
[ 'xref', "x.xref_id = g.display_xref_id" ],
[ 'external_db', "exdb.external_db_id = x.external_db_id" ] );
}
=head2 list_dbIDs
Example : @gene_ids = @{$gene_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all genes in the current db
Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : Listref of Ints
Exceptions : none
Caller : general
Status : Stable
=cut
sub list_dbIDs {
my ($self,$ordered) = @_;
return $self->_list_dbIDs("gene",undef, $ordered);
}
=head2 list_stable_ids
Example : @stable_gene_ids = @{$gene_adaptor->list_stable_ids()};
Description: Gets an listref of stable ids for all genes in the current db
Returntype : reference to a list of strings
Exceptions : none
Caller : general
Status : Stable
=cut
sub list_stable_ids {
my ($self) = @_;
return $self->_list_dbIDs("gene_stable_id", "stable_id");
}
sub list_seq_region_ids {
my $self = shift;
return $self->_list_seq_region_ids('gene');
}
=head2 fetch_by_display_label
Arg [1] : String $label - display label of gene to fetch
Example : my $gene = $geneAdaptor->fetch_by_display_label("BRCA2");
Description: Returns the gene which has the given display label or undef if
there is none. If there are more than 1, only the first is
reported.
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_by_display_label {
my $self = shift;
my $label = shift;
my $constraint = "x.display_label = ? AND g.is_current = 1";
$self->bind_param_generic_fetch($label,SQL_VARCHAR);
my ($gene) = @{ $self->generic_fetch($constraint) };
return $gene;
}
=head2 fetch_by_stable_id
Arg [1] : String $id
The stable ID of the gene to retrieve
Example : $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000148944');
Description: Retrieves a gene object from the database via its stable id.
The gene will be retrieved in its native coordinate system (i.e.
in the coordinate system it is stored in the database). It may
be converted to a different coordinate system through a call to
transform() or transfer(). If the gene or exon is not found
undef is returned instead.
Returntype : Bio::EnsEMBL::Gene or undef
Exceptions : if we cant get the gene in given coord system
Caller : general
Status : Stable
=cut
sub fetch_by_stable_id {
my ($self, $stable_id) = @_;
my $constraint = "gsi.stable_id = ? AND g.is_current = 1";
$self->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
my ($gene) = @{ $self->generic_fetch($constraint) };
return $gene;
}
=head2 fetch_all_by_biotype
Arg [1] : String $biotype
listref of $biotypes
The biotype of the gene to retrieve. You can have as an argument a reference
to a list of biotypes
Example : $gene = $gene_adaptor->fetch_all_by_biotype('protein_coding');
$gene = $gene_adaptor->fetch_all_by_biotypes(['protein_coding', 'sRNA', 'miRNA']);
Description: Retrieves an array reference of gene objects from the database via its biotype or biotypes.
The genes will be retrieved in its native coordinate system (i.e.
in the coordinate system it is stored in the database). It may
be converted to a different coordinate system through a call to
transform() or transfer(). If the gene or exon is not found
undef is returned instead.
Returntype : listref of Bio::EnsEMBL::Gene
Exceptions : if we cant get the gene in given coord system
Caller : general
Status : Stable
=cut
sub fetch_all_by_biotype {
my ($self, $biotype) = @_;
if (!defined $biotype){
throw("Biotype or listref of biotypes expected");
}
my $constraint;
if (ref($biotype) eq 'ARRAY'){
$constraint = "g.biotype IN (";
foreach my $b (@{$biotype}){
$constraint .= "?,";
$self->bind_param_generic_fetch($b,SQL_VARCHAR);
}
chop($constraint); #remove last , from expression
$constraint .= ") and g.is_current = 1";
}
else{
$constraint = "g.biotype = ? and g.is_current = 1";
$self->bind_param_generic_fetch($biotype,SQL_VARCHAR);
}
my @genes = @{ $self->generic_fetch($constraint) };
return \@genes ;
}
=head2 fetch_all_versions_by_stable_id
Arg [1] : String $stable_id
The stable ID of the gene to retrieve
Example : $gene = $gene_adaptor->fetch_all_versions_by_stable_id
('ENSG00000148944');
Description : Similar to fetch_by_stable_id, but retrieves all versions of a
gene stored in the database.
Returntype : listref of Bio::EnsEMBL::Gene
Exceptions : if we cant get the gene in given coord system
Caller : general
Status : At Risk
=cut
sub fetch_all_versions_by_stable_id {
my ($self, $stable_id) = @_;
my $constraint = "gsi.stable_id = ?";
$self->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
return $self->generic_fetch($constraint);
}
=head2 fetch_by_exon_stable_id
Arg [1] : String $id
The stable id of an exon of the gene to retrieve
Example : $gene = $gene_adptr->fetch_by_exon_stable_id('ENSE00000148944');
Description: Retrieves a gene object from the database via an exon stable id.
The gene will be retrieved in its native coordinate system (i.e.
in the coordinate system it is stored in the database). It may
be converted to a different coordinate system through a call to
transform() or transfer(). If the gene or exon is not found
undef is returned instead.
Returntype : Bio::EnsEMBL::Gene or undef
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_by_exon_stable_id {
my ($self, $stable_id, $version) = @_;
my $sql = qq(
SELECT t.gene_id
FROM transcript as t,
exon_transcript as et,
exon as e,
exon_stable_id as esi
WHERE t.transcript_id = et.transcript_id
AND et.exon_id = esi.exon_id
AND et.exon_id = e.exon_id
AND esi.stable_id = ?
AND e.is_current = 1
);
my $sth = $self->prepare($sql);
$sth->bind_param(1, $stable_id, SQL_VARCHAR);
$sth->execute();
my ($dbID) = $sth->fetchrow_array();
return undef if(!defined($dbID));
my $gene = $self->fetch_by_dbID($dbID);
return $gene;
}
=head2 fetch_all_by_domain
Arg [1] : String $domain
The domain to fetch genes from
Example : my @genes = $gene_adaptor->fetch_all_by_domain($domain);
Description: Retrieves a listref of genes whose translation contain interpro
domain $domain. The genes are returned in their native coord
system (i.e. the coord_system they are stored in). If the coord
system needs to be changed, then tranform or transfer should be
called on the individual objects returned.
Returntype : list of Bio::EnsEMBL::Genes
Exceptions : none
Caller : domainview
Status : Stable
=cut
sub fetch_all_by_domain {
my ($self, $domain) = @_;
throw("domain argument is required") unless ($domain);
my $sth = $self->prepare(qq(
SELECT tr.gene_id
FROM interpro i,
protein_feature pf,
transcript tr,
translation tl,
seq_region sr,
coord_system cs
WHERE cs.species_id = ?
AND cs.coord_system_id = sr.coord_system_id
AND sr.seq_region_id = tr.seq_region_id
AND tr.is_current = 1
AND tr.transcript_id = tl.transcript_id
AND tl.translation_id = pf.translation_id
AND pf.hit_name = i.id
AND i.interpro_ac = ?
GROUP BY tr.gene_id));
$sth->bind_param( 1, $self->species_id(), SQL_VARCHAR );
$sth->bind_param( 2, $domain, SQL_VARCHAR );
$sth->execute();
my @array = @{$sth->fetchall_arrayref()};
$sth->finish();
my @gene_ids = map {$_->[0]} @array;
return $self->fetch_all_by_dbID_list(\@gene_ids);
}
=head2 fetch_all_by_Slice_and_external_dbname_link
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice to fetch genes on.
Arg [2] : (optional) string $logic_name
the logic name of the type of features to obtain
Arg [3] : (optional) boolean $load_transcripts
if true, transcripts will be loaded immediately
rather than lazy loaded later.
Arg [4] : Name of the external database
Example : @genes = @{
$ga->fetch_all_by_Slice_and_external_dbname_link(
$slice, undef, undef, "HUGO" ) };
Description: Overrides superclass method to optionally load
transcripts immediately rather than lazy-loading them
later. This is more efficient when there are a lot
of genes whose transcripts are going to be used. The
genes are then filtered to return only those with
external database links of the type specified
Returntype : reference to list of genes
Exceptions : thrown if exon cannot be placed on transcript slice
Caller :
Status : Stable
=cut
sub fetch_all_by_Slice_and_external_dbname_link {
my $self = shift;
my $slice = shift;
my $logic_name = shift;
my $load_transcripts = shift;
my $db_name = shift;
my @genes_passed;
my $external_db_id;
#get the external_db_id from the name
my $sth = $self->prepare(
"SELECT external_db_id from external_db where db_name = ?");
$sth->bind_param(1,$db_name,SQL_VARCHAR);
$sth->execute();
$sth->bind_columns(\$external_db_id);
$sth->fetch;
if(!defined($external_db_id) || $external_db_id == 0){
warn "Could not find external database $db_name in the external_db table\navailable are:-\n";
$sth = $self->prepare(
"SELECT db_name from external_db");
$sth->execute();
$sth->bind_columns(\$external_db_id);
while($sth->fetch){
warn "\t$external_db_id\n";
}
return @genes_passed;
}
# get the gene_ids for those with links
my $dbe_adaptor = $self->db()->get_DBEntryAdaptor();
my %linked_genes= $dbe_adaptor->list_gene_ids_by_external_db_id($external_db_id);
# get all the genes on the slice
my $genes = $self->SUPER::fetch_all_by_Slice_constraint($slice,
'g.is_current = 1', $logic_name);
# create a list of those that are in the gene_ids list
foreach my $gene (@$genes){
if($linked_genes{$gene->dbID}){
push @genes_passed, $gene;
}
}
#return the list of those that passed
return \@genes_passed;
}
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice to fetch genes on.
Arg [2] : (optional) string $logic_name
the logic name of the type of features to obtain
Arg [3] : (optional) boolean $load_transcripts
if true, transcripts will be loaded immediately rather than
lazy loaded later.
Arg [4] : (optional) string $source
the source name of the features to obtain.
Arg [5] : (optional) string biotype
the biotype of the features to obtain.
Example : @genes = @{$gene_adaptor->fetch_all_by_Slice()};
Description: Overrides superclass method to optionally load transcripts
immediately rather than lazy-loading them later. This
is more efficient when there are a lot of genes whose
transcripts are going to be used.
Returntype : reference to list of transcripts
Exceptions : thrown if exon cannot be placed on transcript slice
Caller : Slice::get_all_Transcripts
Status : Stable
=cut
sub fetch_all_by_Slice {
my $self = shift;
my $slice = shift;
my $logic_name = shift;
my $load_transcripts = shift;
my $source = shift;
my $biotype = shift;
my $constraint = 'g.is_current = 1';
if(defined($source)){
$constraint .= " and g.source = '$source'";
}
if(defined($biotype)){
$constraint .= " and g.biotype = '$biotype'" ;
}
my $genes = $self->SUPER::fetch_all_by_Slice_constraint($slice,
$constraint , $logic_name);
# if there are 0 or 1 genes still do lazy-loading
if(!$load_transcripts || @$genes < 2) {
return $genes;
}
# preload all of the transcripts now, instead of lazy loading later
# faster than 1 query per transcript
# first check if transcripts are already preloaded
# coorectly we should check all of them ..
return $genes if( exists $genes->[0]->{'_transcript_array'} );
# get extent of region spanned by transcripts
my ($min_start, $max_end);
foreach my $g (@$genes) {
if(!defined($min_start) || $g->seq_region_start() < $min_start) {
$min_start = $g->seq_region_start();
}
if(!defined($max_end) || $g->seq_region_end() > $max_end) {
$max_end = $g->seq_region_end();
}
}
my $ext_slice;
if($min_start >= $slice->start() && $max_end <= $slice->end()) {
$ext_slice = $slice;
} else {
my $sa = $self->db()->get_SliceAdaptor();
$ext_slice = $sa->fetch_by_region
($slice->coord_system->name(), $slice->seq_region_name(),
$min_start,$max_end, $slice->strand(), $slice->coord_system->version());
}
# associate transcript identifiers with genes
my %g_hash = map {$_->dbID => $_} @$genes;
my $g_id_str = '(' . join(',', keys %g_hash) . ')';
my $sth = $self->prepare("SELECT gene_id, transcript_id " .
"FROM transcript " .
"WHERE gene_id IN $g_id_str");
$sth->execute();
my ($g_id, $tr_id);
$sth->bind_columns(\$g_id, \$tr_id);
my %tr_g_hash;
while($sth->fetch()) {
$tr_g_hash{$tr_id} = $g_hash{$g_id};
}
$sth->finish();
my $ta = $self->db()->get_TranscriptAdaptor();
my $transcripts = $ta->fetch_all_by_Slice($ext_slice, 1);
# move transcripts onto gene slice, and add them to genes
foreach my $tr (@$transcripts) {
if( !exists $tr_g_hash{$tr->dbID()} ) {
next;
}
my $new_tr;
if($slice != $ext_slice) {
$new_tr = $tr->transfer($slice) if($slice != $ext_slice);
if(!$new_tr) {
throw("Unexpected. Transcript could not be transfered onto Gene slice.");
}
} else {
$new_tr = $tr;
}
$tr_g_hash{$tr->dbID()}->add_Transcript($new_tr);
}
return $genes;
}
=head2 fetch_by_transcript_id
Arg [1] : Int $trans_id
Unique database identifier for the transcript whose gene should
be retrieved. The gene is returned in its native coord
system (i.e. the coord_system it is stored in). If the coord
system needs to be changed, then tranform or transfer should
be called on the returned object. undef is returned if the
gene or transcript is not found in the database.
Example : $gene = $gene_adaptor->fetch_by_transcript_id(1241);
Description: Retrieves a gene from the database via the database identifier
of one of its transcripts.
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_by_transcript_id {
my ($self, $trans_id) = @_;
# this is a cheap SQL call
my $sth = $self->prepare(qq(
SELECT tr.gene_id
FROM transcript tr
WHERE tr.transcript_id = ?
));
$sth->bind_param(1, $trans_id, SQL_INTEGER);
$sth->execute();
my ($geneid) = $sth->fetchrow_array();
$sth->finish();
return undef if( !defined $geneid );
my $gene = $self->fetch_by_dbID($geneid);
return $gene;
}
=head2 fetch_by_transcript_stable_id
Arg [1] : string $trans_stable_id
transcript stable ID whose gene should be retrieved
Example : my $gene = $gene_adaptor->fetch_by_transcript_stable_id
('ENST0000234');
Description: Retrieves a gene from the database via the stable ID of one of
its transcripts
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_by_transcript_stable_id {
my ($self, $trans_stable_id) = @_;
my $sth = $self->prepare(qq(
SELECT tr.gene_id
FROM transcript tr, transcript_stable_id tcl
WHERE tcl.stable_id = ?
AND tr.transcript_id = tcl.transcript_id
AND tr.is_current = 1
));
$sth->bind_param(1, $trans_stable_id, SQL_VARCHAR);
$sth->execute();
my ($geneid) = $sth->fetchrow_array();
$sth->finish;
return undef if (!defined $geneid);
my $gene = $self->fetch_by_dbID($geneid);
return $gene;
}
=head2 fetch_by_translation_stable_id
Arg [1] : String $translation_stable_id
The stable id of a translation of the gene to be obtained
Example : my $gene = $gene_adaptor->fetch_by_translation_stable_id
('ENSP00000278194');
Description: Retrieves a gene via the stable id of one of its translations.
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_by_translation_stable_id {
my ($self, $translation_stable_id) = @_;
my $sth = $self->prepare(qq(
SELECT tr.gene_id
FROM transcript tr,
translation tl,
translation_stable_id as trs
WHERE trs.stable_id = ?
AND trs.translation_id = tl.translation_id
AND tr.transcript_id = tl.transcript_id
AND tr.is_current = 1
));
$sth->bind_param(1, $translation_stable_id, SQL_VARCHAR);
$sth->execute();
my ($geneid) = $sth->fetchrow_array();
$sth->finish;
if( !defined $geneid ) {
return undef;
}
return $self->fetch_by_dbID($geneid);
}
=head2 fetch_all_by_external_name
Arg [1] : String $external_name
The external identifier for the gene to be obtained
Arg [2] : (optional) String $external_db_name
The name of the external database from which the
identifier originates.
Example : @genes = @{$gene_adaptor->fetch_all_by_external_name('BRCA2')}
Description: Retrieves a list of genes with an external database
identifier $external_name. The genes returned are in
their native coordinate system, i.e. in the coordinate
system they are stored in the database in. If another
coordinate system is required then the Gene::transfer or
Gene::transform method can be used.
Returntype : listref of Bio::EnsEMBL::Gene
Exceptions : none
Caller : goview, general
Status : Stable
=cut
sub fetch_all_by_external_name {
my ( $self, $external_name, $external_db_name ) = @_;
my $entryAdaptor = $self->db->get_DBEntryAdaptor();
my @ids =
$entryAdaptor->list_gene_ids_by_extids( $external_name,
$external_db_name );
my %genes_by_dbIDs =
map { $_->dbID(), $_ } @{ $self->fetch_all_by_dbID_list( \@ids ) };
my @result = map { $genes_by_dbIDs{$_} } @ids;
return \@result;
}
=head2 fetch_all_by_GOTerm
Arg [1] : Bio::EnsEMBL::OntologyTerm
The GO term for which genes should be fetched.
Example: @genes = @{
$gene_adaptor->fetch_all_by_GOTerm(
$go_adaptor->fetch_by_accession('GO:0030326') ) };
Description : Retrieves a list of genes that are associated with
the given GO term, or with any of its descendent
GO terms. The genes returned are in their native
coordinate system, i.e. in the coordinate system
in which they are stored in the database. If
another coordinate system is required then the
Gene::transfer or Gene::transform method can be
used.
Return type : listref of Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_all_by_GOTerm {
my ( $self, $term ) = @_;
my $entryAdaptor = $self->db->get_DBEntryAdaptor();
my %unique_dbIDs;
foreach my $accession ( map { $_->accession() }
( $term, @{ $term->descendants() } ) )
{
my @ids =
$entryAdaptor->list_gene_ids_by_extids( $accession, 'GO' );
foreach my $dbID (@ids) { $unique_dbIDs{$dbID} = 1 }
}
my @result = @{
$self->fetch_all_by_dbID_list(
[ sort { $a <=> $b } keys(%unique_dbIDs) ] ) };
return \@result;
}
=head2 fetch_all_alt_alleles
Arg [1] : Bio::EnsEMBL::Gene $gene
The gene to fetch alternative alleles for
Example : my @alt_genes = @{ $gene_adaptor->fetch_all_alt_alleles($gene) };
foreach my $alt_gene (@alt_genes) {
print "Alternate allele: " . $alt_gene->stable_id() . "\n";
}
Description: Retrieves genes which are alternate alleles to a provided gene.
Alternate alleles in Ensembl are genes which are similar and are
on an alternative haplotype of the same region. There are not
currently very many of these. This method will return a
reference to an empty list if no alternative alleles are found.
Returntype : listref of Bio::EnsEMBL::Genes
Exceptions : throw if incorrect arg provided
warning if gene arg does not have dbID
Caller : Gene::get_all_alt_alleles
Status : Stable
=cut
sub fetch_all_alt_alleles {
my $self = shift;
my $gene = shift;
if(!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
throw('Bio::EnsEMBL::Gene argument is required');
}
my $gene_id = $gene->dbID();
if(!$gene_id) {
warning('Cannot retrieve alternate alleles for gene without dbID');
return [];
}
my $sth = $self->prepare("SELECT aa1.gene_id " .
"FROM alt_allele aa1, alt_allele aa2 " .
"WHERE aa1.alt_allele_id = aa2.alt_allele_id " .
"AND aa2.gene_id = ? " .
"AND aa1.gene_id <> ?");
$sth->bind_param(1, $gene_id, SQL_INTEGER);
$sth->bind_param(2, $gene_id, SQL_INTEGER);
$sth->execute();
my @alt_ids;
my $row;
while($row = $sth->fetchrow_arrayref()) {
push @alt_ids, $row->[0];
}
$sth->finish();
if (@alt_ids) {
return $self->fetch_all_by_dbID_list(\@alt_ids);
}
return [];
}
=head2 store_alt_alleles
Arg [1] : reference to list of Bio::EnsEMBL::Genes $genes
Example : $gene_adaptor->store_alt_alleles([$gene1, $gene2, $gene3]);
Description: This method creates a group of alternative alleles (i.e. locus)
from a set of genes. The genes should be genes from alternate
haplotypes which are similar. The genes must already be stored
in this database. At least 2 genes must be in the list reference
provided.
Returntype : none
Exceptions : throw on incorrect arguments
throw on sql error (e.g. duplicate unique id)
Caller : general
Status : Stable
=cut
sub store_alt_alleles {
my $self = shift;
my $genes = shift;
if(!ref($genes) eq 'ARRAY') {
throw('List reference of Bio::EnsEMBL::Gene argument expected.');
}
my $num_genes = scalar(@$genes);
if($num_genes < 2) {
throw("At least 2 genes must be provided to construct alternate alleles.");
}
return if(!@$genes);
#
#insert the first gene seperately in order to get a unique identifier for
#the set of alleles
#
my $gene = $genes->[0];
if(!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
throw('List reference of Bio::EnsEMBL::Gene argument expected.');
}
my $gene_id = $gene->dbID();
if (!$gene_id) {
throw("Genes must have dbIDs in order to construct alternate alleles.");
}
my $sth = $self->prepare("INSERT INTO alt_allele (gene_id) VALUES (?)");
$sth->bind_param(1, $gene->dbID, SQL_INTEGER);
$sth->execute();
my $alt_allele_id = $sth->{'mysql_insertid'};
$sth->finish();
#
# Insert all subsequent alt alleles using the alt_allele identifier
# from the first insert
#
$sth = $self->prepare("INSERT INTO alt_allele (alt_allele_id, gene_id) " .
"VALUES (?,?)");
for (my $i = 1; $i < $num_genes; $i++) {
my $gene = $genes->[$i];
if (!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
throw("List reference of Bio::EnsEMBL::Gene argument expected");
}
$gene_id = $gene->dbID();
if (!$gene_id) {
# This is an error but we have already inserted into the database
# delete the already inserted entries to restore the state of the
# database
$sth->finish();
$sth->prepare("DELETE FROM alt_allele WHERE alt_allele_id = ?");
$sth->bind_param(1, $alt_allele_id, SQL_INTEGER);
$sth->execute();
$sth->finish();
throw('Genes must have dbIDs in order to construct alternate alleles.');
}
$sth->bind_param(1, $alt_allele_id, SQL_INTEGER);
$sth->bind_param(2, $gene_id, SQL_INTEGER);
eval {
$sth->execute();
};
if ($@) {
# an error occured, revert the db to the previous state
$sth = $self->prepare("DELETE FROM alt_allele WHERE alt_allele_id = ?");
$sth->bind_param(1, $alt_allele_id, SQL_INTEGER);
$sth->execute();
$sth->finish();
throw("An SQL error occured inserting alternate alleles:\n$@");
}
}
$sth->finish();
return;
}
=head2 store
Arg [1] : Bio::EnsEMBL::Gene $gene
The gene to store in the database
Arg [2] : ignore_release in xrefs [default 1] set to 0 to use release info
in external database references
Example : $gene_adaptor->store($gene);
Description: Stores a gene in the database.
Returntype : the database identifier (dbID) of the newly stored gene
Exceptions : thrown if the $gene is not a Bio::EnsEMBL::Gene or if
$gene does not have an analysis object
Caller : general
Status : Stable
=cut
sub store {
my ($self, $gene, $ignore_release) = @_;
if (!ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
throw("Must store a gene object, not a $gene");
}
if(!defined($ignore_release)){
$ignore_release = 1;
}
my $db = $self->db();
if ($gene->is_stored($db)) {
return $gene->dbID();
}
# ensure coords are correct before storing
$gene->recalculate_coordinates();
my $analysis = $gene->analysis();
throw("Genes must have an analysis object.") if(!defined($analysis));
my $analysis_id;
if ($analysis->is_stored($db)) {
$analysis_id = $analysis->dbID();
} else {
$analysis_id = $db->get_AnalysisAdaptor->store($analysis);
}
my $type = $gene->biotype || "";
# default to is_current = 1 if this attribute is not set
my $is_current = $gene->is_current;
$is_current = 1 unless (defined($is_current));
my $original = $gene;
my $original_transcripts = $gene->get_all_Transcripts();
my $seq_region_id;
($gene, $seq_region_id) = $self->_pre_store($gene);
my $store_gene_sql = qq(
INSERT INTO gene
SET biotype = ?,
analysis_id = ?,
seq_region_id = ?,
seq_region_start = ?,
seq_region_end = ?,
seq_region_strand = ?,
description = ?,
source = ?,
status = ?,
is_current = ?
);
# column status is used from schema version 34 onwards (before it was
# confidence)
my $sth = $self->prepare($store_gene_sql);
$sth->bind_param( 1, $type, SQL_VARCHAR );
$sth->bind_param( 2, $analysis_id, SQL_INTEGER );
$sth->bind_param( 3, $seq_region_id, SQL_INTEGER );
$sth->bind_param( 4, $gene->start, SQL_INTEGER );
$sth->bind_param( 5, $gene->end, SQL_INTEGER );
$sth->bind_param( 6, $gene->strand, SQL_TINYINT );
$sth->bind_param( 7, $gene->description, SQL_LONGVARCHAR );
$sth->bind_param( 8, $gene->source, SQL_VARCHAR );
$sth->bind_param( 9, $gene->status, SQL_VARCHAR );
$sth->bind_param( 10, $is_current, SQL_TINYINT );
$sth->execute();
$sth->finish();
my $gene_dbID = $sth->{'mysql_insertid'};
# store stable ids if they are available
if (defined($gene->stable_id)) {
my $statement = "INSERT INTO gene_stable_id
SET gene_id = ?,
stable_id = ?,
version = ?, ";
$statement .= "created_date = " .
$self->db->dbc->from_seconds_to_date($gene->created_date()) . ",";
$statement .= "modified_date = " .
$self->db->dbc->from_seconds_to_date($gene->modified_date());
$sth = $self->prepare($statement);
$sth->bind_param(1, $gene_dbID, SQL_INTEGER);
$sth->bind_param(2, $gene->stable_id, SQL_VARCHAR);
$sth->bind_param(3, $gene->version, SQL_INTEGER);
$sth->execute();
$sth->finish();
}
# store the dbentries associated with this gene
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
foreach my $dbe ( @{$gene->get_all_DBEntries} ) {
$dbEntryAdaptor->store($dbe, $gene_dbID, "Gene", $ignore_release);
}
# we allow transcripts not to share equal exons and instead have copies
# For the database we still want sharing though, to have easier time with
# stable ids. So we need to have a step to merge exons together before store
my %exons;
foreach my $trans ( @{$gene->get_all_Transcripts} ) {
foreach my $e ( @{$trans->get_all_Exons} ) {
my $key = $e->hashkey();
if( exists $exons{ $key } ) {
$trans->swap_exons( $e, $exons{$key} );
} else {
$exons{$key} = $e;
}
}
}
my $transcript_adaptor = $db->get_TranscriptAdaptor();
my $transcripts = $gene->get_all_Transcripts();
for(my $i = 0; $i < @$transcripts; $i++) {
my $new = $transcripts->[$i];
my $old = $original_transcripts->[$i];
$transcript_adaptor->store($new, $gene_dbID, $analysis_id);
# update the original transcripts since we may have made copies of
# them by transforming the gene
$old->dbID($new->dbID());
$old->adaptor($new->adaptor());
if($new->translation) {
$old->translation->dbID($new->translation()->dbID);
$old->translation->adaptor($new->translation()->adaptor);
}
}
# update gene to point to display xref if it is set
if(my $display_xref = $gene->display_xref) {
my $dxref_id;
if($display_xref->is_stored($db)) {
$dxref_id = $display_xref->dbID();
} else {
$dxref_id = $dbEntryAdaptor->exists($display_xref);
}
if(defined($dxref_id)) {
$sth = $self->prepare
("UPDATE gene SET display_xref_id = ? WHERE gene_id = ?");
$sth->bind_param(1, $dxref_id, SQL_INTEGER);
$sth->bind_param(2, $gene_dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
$display_xref->dbID($dxref_id);
$display_xref->adaptor($dbEntryAdaptor);
$display_xref->dbID($dxref_id);
$display_xref->adaptor($dbEntryAdaptor);
} else {
warning("Display_xref ".$display_xref->dbname().":".
$display_xref->display_id() . " is not stored in database.\n".
"Not storing relationship to this gene.");
$display_xref->dbID(undef);
$display_xref->adaptor(undef);
}
}
# store gene attributes if there are any
my $attr_adaptor = $db->get_AttributeAdaptor();
$attr_adaptor->store_on_Gene($gene_dbID, $gene->get_all_Attributes);
# store unconventional transcript associations if there are any
my $utaa = $db->get_UnconventionalTranscriptAssociationAdaptor();
foreach my $uta (@{$gene->get_all_unconventional_transcript_associations()}) {
$utaa->store($uta);
}
# set the adaptor and dbID on the original passed in gene not the
# transfered copy
$original->adaptor($self);
$original->dbID($gene_dbID);
return $gene_dbID;
}
=head2 remove
Arg [1] : Bio::EnsEMBL::Gene $gene
the gene to remove from the database
Example : $gene_adaptor->remove($gene);
Description: Removes a gene completely from the database. All associated
transcripts, exons, stable_identifiers, descriptions, etc.
are removed as well. Use with caution!
Returntype : none
Exceptions : throw on incorrect arguments
warning if gene is not stored in this database
Caller : general
Status : Stable
=cut
sub remove {
my $self = shift;
my $gene = shift;
if (!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
throw("Bio::EnsEMBL::Gene argument expected.");
}
if ( !$gene->is_stored($self->db()) ) {
warning("Cannot remove gene " . $gene->dbID() . ". Is not stored in " .
"this database.");
return;
}
# remove all object xrefs associated with this gene
my $dbe_adaptor = $self->db()->get_DBEntryAdaptor();
foreach my $dbe (@{$gene->get_all_DBEntries()}) {
$dbe_adaptor->remove_from_object($dbe, $gene, 'Gene');
}
# remove all alternative allele entries associated with this gene
my $sth = $self->prepare("DELETE FROM alt_allele WHERE gene_id = ?");
$sth->bind_param( 1, $gene->dbID, SQL_INTEGER );
$sth->execute();
$sth->finish();
# remove the attributes associated with this transcript
my $attrib_adaptor = $self->db->get_AttributeAdaptor;
$attrib_adaptor->remove_from_Gene($gene);
# remove all of the transcripts associated with this gene
my $transcriptAdaptor = $self->db->get_TranscriptAdaptor();
foreach my $trans ( @{$gene->get_all_Transcripts()} ) {
$transcriptAdaptor->remove($trans);
}
# remove the gene stable identifier
$sth =
$self->prepare("DELETE FROM gene_stable_id WHERE gene_id = ? ");
$sth->bind_param( 1, $gene->dbID, SQL_INTEGER );
$sth->execute();
$sth->finish();
# remove any unconventional transcript associations involving this gene
$sth =
$self->prepare( "DELETE FROM unconventional_transcript_association "
. "WHERE gene_id = ? " );
$sth->bind_param( 1, $gene->dbID, SQL_INTEGER );
$sth->execute();
$sth->finish();
# remove this gene from the database
$sth = $self->prepare("DELETE FROM gene WHERE gene_id = ? ");
$sth->bind_param( 1, $gene->dbID, SQL_INTEGER );
$sth->execute();
$sth->finish();
# unset the gene identifier and adaptor thereby flagging it as unstored
$gene->dbID(undef);
$gene->adaptor(undef);
return;
}
=head2 get_Interpro_by_geneid
Arg [1] : String $gene_stable_id
The stable ID of the gene to obtain
Example : @i = $gene_adaptor->get_Interpro_by_geneid($gene->stable_id());
Description: Gets interpro accession numbers by gene stable id. A hack really
- we should have a much more structured system than this.
Returntype : listref of strings (Interpro_acc:description)
Exceptions : none
Caller : domainview
Status : Stable
=cut
sub get_Interpro_by_geneid {
my ($self, $gene_stable_id) = @_;
my $sql = qq(
SELECT i.interpro_ac,
x.description
FROM transcript t,
translation tl,
protein_feature pf,
interpro i,
xref x,
gene_stable_id gsi
WHERE gsi.stable_id = ?
AND t.gene_id = gsi.gene_id
AND t.is_current = 1
AND tl.transcript_id = t.transcript_id
AND tl.translation_id = pf.translation_id
AND i.id = pf.hit_name
AND i.interpro_ac = x.dbprimary_acc);
my $sth = $self->prepare($sql);
$sth->bind_param( 1, $gene_stable_id, SQL_VARCHAR );
$sth->execute;
my @out;
my %h;
while( (my $arr = $sth->fetchrow_arrayref()) ) {
if( $h{$arr->[0]} ) { next; }
$h{$arr->[0]}=1;
my $string = $arr->[0] .":".$arr->[1];
push(@out,$string);
}
return \@out;
}
=head2 update
Arg [1] : Bio::EnsEMBL::Gene $gene
The gene to update
Example : $gene_adaptor->update($gene);
Description: Updates the type, analysis, display_xref, status, is_current and
description of a gene in the database.
Returntype : None
Exceptions : thrown if the $gene is not a Bio::EnsEMBL::Gene
Caller : general
Status : Stable
=cut
sub update {
my ($self, $gene) = @_;
my $update = 0;
if ( !defined $gene || !ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
throw("Must update a gene object, not a $gene");
}
my $update_gene_sql = qq(
UPDATE gene
SET biotype = ?,
analysis_id = ?,
display_xref_id = ?,
status = ?,
description = ?,
is_current = ?
WHERE gene_id = ?
);
my $display_xref = $gene->display_xref();
my $display_xref_id;
if ( $display_xref && $display_xref->dbID() ) {
$display_xref_id = $display_xref->dbID();
} else {
$display_xref_id = undef;
}
my $sth = $self->prepare( $update_gene_sql );
$sth->bind_param(1, $gene->biotype, SQL_VARCHAR);
$sth->bind_param(2, $gene->analysis->dbID, SQL_INTEGER);
$sth->bind_param(3, $display_xref_id, SQL_INTEGER);
$sth->bind_param(4, $gene->status, SQL_VARCHAR);
$sth->bind_param(5, $gene->description, SQL_VARCHAR);
$sth->bind_param(6, $gene->is_current, SQL_TINYINT);
$sth->bind_param(7, $gene->dbID, SQL_INTEGER);
$sth->execute();
# maybe should update stable id ???
}
# _objs_from_sth
# Arg [1] : StatementHandle $sth
# Arg [2] : Bio::EnsEMBL::AssemblyMapper $mapper
# Arg [3] : Bio::EnsEMBL::Slice $dest_slice
# Description: PROTECTED implementation of abstract superclass method.
# responsible for the creation of Genes
# Returntype : listref of Bio::EnsEMBL::Genes in target coordinate system
# Exceptions : none
# Caller : internal
# Status : Stable
sub _objs_from_sth {
my ($self, $sth, $mapper, $dest_slice) = @_;
#
# This code is ugly because an attempt has been made to remove as many
# function calls as possible for speed purposes. Thus many caches and
# a fair bit of gymnastics is used.
#
my $sa = $self->db()->get_SliceAdaptor();
my $aa = $self->db->get_AnalysisAdaptor();
my $ta = $self->db->get_TranscriptAdaptor();
my $dbEntryAdaptor = $self->db()->get_DBEntryAdaptor();
my @genes;
my %analysis_hash;
my %slice_hash;
my %sr_name_hash;
my %sr_cs_hash;
my ( $gene_id, $seq_region_id, $seq_region_start, $seq_region_end,
$seq_region_strand, $analysis_id, $biotype, $display_xref_id,
$gene_description, $stable_id, $version, $created_date,
$modified_date, $xref_display_id, $status, $source, $is_current,
$canonical_transcript_id, $canonical_annotation,
$xref_primary_acc, $xref_desc, $xref_version, $external_name,
$external_db, $external_status, $external_release, $external_db_name,
$info_type, $info_text);
$sth->bind_columns( \$gene_id, \$seq_region_id, \$seq_region_start,
\$seq_region_end, \$seq_region_strand, \$analysis_id,
\$biotype, \$display_xref_id, \$gene_description,
\$status, \$source, \$is_current,
\$canonical_transcript_id, \$canonical_annotation,
\$stable_id, \$version,
\$created_date, \$modified_date,
\$xref_display_id, \$xref_primary_acc, \$xref_desc,
\$xref_version,
\$external_db, \$external_status,
\$external_release, \$external_db_name,
\$info_type, \$info_text);
my $asm_cs;
my $cmp_cs;
my $asm_cs_vers;
my $asm_cs_name;
my $cmp_cs_vers;
my $cmp_cs_name;
if($mapper) {
$asm_cs = $mapper->assembled_CoordSystem();
$cmp_cs = $mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name();
$cmp_cs_vers = $cmp_cs->version();
}
my $dest_slice_start;
my $dest_slice_end;
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_sr_name;
my $dest_slice_sr_id;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
$dest_slice_end = $dest_slice->end();
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
$dest_slice_sr_name = $dest_slice->seq_region_name();
$dest_slice_sr_id = $dest_slice->get_seq_region_id();
}
FEATURE: while($sth->fetch()) {
#get the analysis object
my $analysis = $analysis_hash{$analysis_id} ||=
$aa->fetch_by_dbID($analysis_id);
#get the canonical_transcript object
my $canonical_transcript = $ta->fetch_by_dbID($canonical_transcript_id);
#need to get the internal_seq_region, if present
$seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
my $slice = $slice_hash{"ID:".$seq_region_id};
if(!$slice) {
$slice = $sa->fetch_by_seq_region_id($seq_region_id);
$slice_hash{"ID:".$seq_region_id} = $slice;
$sr_name_hash{$seq_region_id} = $slice->seq_region_name();
$sr_cs_hash{$seq_region_id} = $slice->coord_system();
}
my $sr_name = $sr_name_hash{$seq_region_id};
my $sr_cs = $sr_cs_hash{$seq_region_id};
#
# remap the feature coordinates to another coord system
# if a mapper was provided
#
if($mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($seq_region_id));
#get a slice in the coord system we just mapped to
# if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
# } else {
# $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
# $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
# $asm_cs_vers);
# }
}
#
# If a destination slice was provided convert the coords
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($dest_slice) {
if($dest_slice_start != 1 || $dest_slice_strand != 1) {
if($dest_slice_strand == 1) {
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
$seq_region_strand *= -1;
}
}
#throw away features off the end of the requested slice or on different seq_region
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_id ne $seq_region_id )) {
next FEATURE;
}
$slice = $dest_slice;
}
my $display_xref;
if( $display_xref_id ) {
$display_xref = Bio::EnsEMBL::DBEntry->new_fast
({ 'dbID' => $display_xref_id,
'adaptor' => $dbEntryAdaptor,
'display_id' => $xref_display_id,
'primary_id' => $xref_primary_acc,
'version' => $xref_version,
'description' => $xref_desc,
'release' => $external_release,
'dbname' => $external_db,
'db_display_name' => $external_db_name,
'info_type' => $info_type,
'info_text' => $info_text
});
$display_xref->status( $external_status );
}
# Finally, create the new Gene.
push( @genes,
$self->_create_feature_fast(
'Bio::EnsEMBL::Gene', {
'analysis' => $analysis,
'biotype' => $biotype,
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'adaptor' => $self,
'slice' => $slice,
'dbID' => $gene_id,
'stable_id' => $stable_id,
'version' => $version,
'created_date' => $created_date || undef,
'modified_date' => $modified_date
|| undef,
'description' => $gene_description,
'external_name' => $external_name || undef,
'external_db' => $external_db,
'external_status' => $external_status,
'display_xref' => $display_xref,
'status' => $status,
'source' => $source,
'is_current' => $is_current,
'canonical_transcript' => $canonical_transcript,
'canonical_annotation' => $canonical_annotation
} ) );
}
return \@genes;
}
=head2 cache_gene_seq_mappings
Example : $gene_adaptor->cache_gene_seq_mappings();
Description: caches all the assembly mappings needed for genes
Returntype : None
Exceptions : None
Caller : general
Status : At Risk
: New experimental code
=cut
sub cache_gene_seq_mappings {
my ($self) = @_;
# get the sequence level to map too
my $sql =
'SELECT name '
. 'FROM coord_system '
. 'WHERE attrib like "%%sequence_level%%"'
. 'AND species_id = ?';
my $sth = $self->prepare($sql);
$sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
$sth->execute();
my $sequence_level = $sth->fetchrow_array();
$sth->finish();
my $csa = $self->db->get_CoordSystemAdaptor();
my $ama = $self->db->get_AssemblyMapperAdaptor();
my $cs1 = $csa->fetch_by_name($sequence_level);
# get level to map to two
my $mcc = $self->db->get_MetaCoordContainerAdaptor();
my $csnew = $mcc->fetch_all_CoordSystems_by_feature_type('gene');
foreach my $cs2 (@$csnew) {
my $am = $ama->fetch_by_CoordSystems( $cs1, $cs2 );
$am->register_all();
}
} ## end sub cache_gene_seq_mappings
=head2 fetch_all_by_exon_supporting_evidence
Arg [1] : String $hit_name
Name of supporting feature
Arg [2] : String $feature_type
one of "dna_align_feature" or "protein_align_feature"
Arg [3] : (optional) Bio::Ensembl::Analysis
Example : $genes = $gene_adaptor->fetch_all_by_exon_supporting_evidence(
'XYZ', 'dna_align_feature');
Description: Gets all the genes with transcripts with exons which have a
specified hit on a particular type of feature. Optionally filter
by analysis.
Returntype : Listref of Bio::EnsEMBL::Gene
Exceptions : If feature_type is not of correct type.
Caller : general
Status : Stable
=cut
sub fetch_all_by_exon_supporting_evidence {
my ($self, $hit_name, $feature_type, $analysis) = @_;
if ($feature_type !~ /(dna)|(protein)_align_feature/) {
throw("feature type must be dna_align_feature or protein_align_feature");
}
my $anal_from = ", analysis a " if ($analysis);
my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
my $sql = qq(
SELECT DISTINCT(g.gene_id)
FROM gene g,
transcript t,
exon_transcript et,
supporting_feature sf,
$feature_type f
$anal_from
WHERE g.gene_id = t.gene_id
AND g.is_current = 1
AND t.transcript_id = et.transcript_id
AND et.exon_id = sf.exon_id
AND sf.feature_id = f.${feature_type}_id
AND sf.feature_type = ?
AND f.hit_name=?
$anal_where
);
my $sth = $self->prepare($sql);
$sth->bind_param(1, $feature_type, SQL_VARCHAR);
$sth->bind_param(2, $hit_name, SQL_VARCHAR);
$sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);
$sth->execute();
my @genes;
while ( my $id = $sth->fetchrow_array ) {
my $gene = $self->fetch_by_dbID($id);
push(@genes, $gene) if $gene;
}
return \@genes;
}
=head2 fetch_all_by_transcript_supporting_evidence
Arg [1] : String $hit_name
Name of supporting feature
Arg [2] : String $feature_type
one of "dna_align_feature" or "protein_align_feature"
Arg [3] : (optional) Bio::Ensembl::Analysis
Example : $genes = $gene_adaptor->fetch_all_by_transcript_supporting_evidence('XYZ', 'dna_align_feature');
Description: Gets all the genes with transcripts with evidence for a
specified hit on a particular type of feature. Optionally filter
by analysis.
Returntype : Listref of Bio::EnsEMBL::Gene
Exceptions : If feature_type is not of correct type.
Caller : general
Status : Stable
=cut
sub fetch_all_by_transcript_supporting_evidence {
my ($self, $hit_name, $feature_type, $analysis) = @_;
if($feature_type !~ /(dna)|(protein)_align_feature/) {
throw("feature type must be dna_align_feature or protein_align_feature");
}
my $anal_from = ", analysis a " if ($analysis);
my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
my $sql = qq(
SELECT DISTINCT(g.gene_id)
FROM gene g,
transcript t,
transcript_supporting_feature sf,
$feature_type f
$anal_from
WHERE g.gene_id = t.gene_id
AND g.is_current = 1
AND t.transcript_id = sf.transcript_id
AND sf.feature_id = f.${feature_type}_id
AND sf.feature_type = ?
AND f.hit_name=?
$anal_where
);
my $sth = $self->prepare($sql);
$sth->bind_param(1, $feature_type, SQL_VARCHAR);
$sth->bind_param(2, $hit_name, SQL_VARCHAR);
$sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);
$sth->execute();
my @genes;
while( my $id = $sth->fetchrow_array ) {
my $gene = $self->fetch_by_dbID($id);
push(@genes, $gene) if $gene;
}
return \@genes;
}
##########################
# #
# DEPRECATED METHODS #
# #
##########################
=head2 fetch_by_maximum_DBLink
Description: DEPRECATED - use fetch_all_by_external_name instead
=cut
sub fetch_by_maximum_DBLink {
my ($self, $external_id) = @_;
deprecate( "use fetch_all_by_external_name instead" );
my $genes=$self->fetch_all_by_external_name($external_id);
my $biggest;
my $max = 0;
my $size = scalar(@$genes);
if ($size > 0) {
foreach my $gene (@$genes) {
my $size = scalar(@{$gene->get_all_Exons});
if ($size > $max) {
$biggest = $gene;
$max = $size;
}
}
return $biggest;
}
return;
}
=head2 get_display_xref
Description: DEPRECATED use $gene->display_xref
=cut
sub get_display_xref {
my ($self, $gene) = @_;
deprecate( "display xref should retrieved from Gene object directly" );
if ( !defined $gene ) {
throw("Must call with a Gene object");
}
my $sth = $self->prepare(qq(
SELECT e.db_name,
x.display_label,
x.xref_id
FROM gene g,
xref x,
external_db e
WHERE g.gene_id = ?
AND g.display_xref_id = x.xref_id
AND x.external_db_id = e.external_db_id
));
$sth->bind_param(1, $gene->dbID, SQL_INTEGER);
$sth->execute();
my ($db_name, $display_label, $xref_id) = $sth->fetchrow_array();
if ( !defined $xref_id ) {
return undef;
}
my $db_entry = Bio::EnsEMBL::DBEntry->new(
-dbid => $xref_id,
-adaptor => $self->db->get_DBEntryAdaptor(),
-dbname => $db_name,
-display_id => $display_label
);
return $db_entry;
}
=head2 get_description
Description: DEPRECATED, use gene->get_description
=cut
sub get_description {
my ($self, $dbID) = @_;
deprecate( "Gene description should be loaded on gene retrieval. Use gene->get_description()" );
if ( !defined $dbID ) {
throw("must call with dbID");
}
my $sth = $self->prepare("SELECT description
FROM gene_description
WHERE gene_id = ?");
$sth->bind_param(1, $dbID, SQL_INTEGER);
$sth->execute();
my @array = $sth->fetchrow_array();
return $array[0];
}
=head2 fetch_by_Peptide_id
Description: DEPRECATED, use fetch_by_translation_stable_id()
=cut
sub fetch_by_Peptide_id {
my ( $self, $translation_stable_id) = @_;
deprecate( "Please use better named fetch_by_translation_stable_id \n".
caller(2) );
$self->fetch_by_translation_stable_id($translation_stable_id);
}
=head2 get_stable_entry_info
Description: DEPRECATED use $gene->stable_id instead
=cut
sub get_stable_entry_info {
my ($self,$gene) = @_;
deprecated("stable id info is loaded on default, no lazy loading necessary");
if ( !defined $gene || !ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
throw("Needs a gene object, not a $gene");
}
my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("modified_date");
my $sth = $self->prepare("SELECT stable_id, " . $created_date . "," .
$modified_date . ", version
FROM gene_stable_id
WHERE gene_id = ?");
$sth->bind_param(1, $gene->dbID, SQL_INTEGER);
$sth->execute();
my @array = $sth->fetchrow_array();
$gene->{'stable_id'} = $array[0];
$gene->{'created'} = $array[1];
$gene->{'modified'} = $array[2];
$gene->{'version'} = $array[3];
return 1;
}
=head2 fetch_all_by_DBEntry
Description: DEPRECATED - Use fetch_all_by_external_name instead
=cut
sub fetch_all_by_DBEntry {
my $self = shift;
deprecate('Use fetch_all_by_external_name instead.');
return $self->fetch_all_by_external_name(@_);
}
1;
]]>