Raw content of Bio::EnsEMBL::Gene
<![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::Gene - Object representing a genes
=head1 SYNOPSIS
my $gene = Bio::EnsEMBL::Gene->new(
-START => 123,
-END => 1045,
-STRAND => 1,
-SLICE => $slice
);
# print gene information
print("gene start:end:strand is "
. join( ":", map { $gene->$_ } qw(start end strand) )
. "\n" );
# set some additional attributes
$gene->stable_id('ENSG000001');
$gene->description('This is the gene description');
=head1 DESCRIPTION
A representation of a Gene within the Ensembl system. A gene is a set of one or
more alternative transcripts.
=head1 METHODS
=cut
package Bio::EnsEMBL::Gene;
use strict;
use POSIX;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Feature);
=head2 new
Arg [-START] :
int - start postion of the gene
Arg [-END] :
int - end position of the gene
Arg [-STRAND] :
int - 1,-1 tehe strand the gene is on
Arg [-SLICE] :
Bio::EnsEMBL::Slice - the slice the gene is on
Arg [-STABLE_ID] :
string - the stable identifier of this gene
Arg [-VERSION] :
int - the version of the stable identifier of this gene
Arg [-EXTERNAL_NAME] :
string - the external database name associated with this gene
Arg [-EXTERNAL_DB] :
string - the name of the database the external name is from
Arg [-EXTERNAL_STATUS]:
string - the status of the external identifier
Arg [-DISPLAY_XREF]:
Bio::EnsEMBL::DBEntry - The external database entry that is used
to label this gene when it is displayed.
Arg [-TRANSCRIPTS]:
Listref of Bio::EnsEMBL::Transcripts - this gene's transcripts
Arg [-CREATED_DATE]:
string - the date the gene was created
Arg [-MODIFIED_DATE]:
string - the date the gene was last modified
Arg [-DESCRIPTION]:
string - the genes description
Arg [-BIOTYPE]:
string - the biotype e.g. "protein_coding"
Arg [-STATUS]:
string - the gene status i.e. "KNOWN","NOVEL"
Arg [-SOURCE]:
string - the genes source, e.g. "ensembl"
Arg [-IS_CURRENT]:
Boolean - specifies if this is the current version of the gene
Example : $gene = Bio::EnsEMBL::Gene->new(...);
Description: Creates a new gene object
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
Status : Stable
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ( $stable_id, $version, $external_name, $type, $external_db,
$external_status, $display_xref, $description, $transcripts,
$created_date, $modified_date, $confidence, $biotype, $source,
$status, $is_current, $canonical_transcript, $canonical_annotation ) =
rearrange( [ 'STABLE_ID', 'VERSION', 'EXTERNAL_NAME', 'TYPE',
'EXTERNAL_DB', 'EXTERNAL_STATUS', 'DISPLAY_XREF',
'DESCRIPTION',
'TRANSCRIPTS', 'CREATED_DATE', 'MODIFIED_DATE',
'CONFIDENCE', 'BIOTYPE', 'SOURCE', 'STATUS', 'IS_CURRENT',
'CANONICAL_TRANSCRIPT', 'CANONICAL_ANNOTATION'
],
@_ );
if ($transcripts) {
$self->{'_transcript_array'} = $transcripts;
$self->recalculate_coordinates();
}
$self->stable_id( $stable_id );
$self->version( $version );
$self->{'created_date'} = $created_date;
$self->{'modified_date'} = $modified_date;
$self->external_name( $external_name ) if( defined $external_name );
$self->external_db( $external_db ) if( defined $external_db );
$self->external_status( $external_status ) if( defined $external_status );
$self->display_xref( $display_xref ) if( defined $display_xref );
$self->biotype( $type ) if( defined $type );
$self->biotype( $biotype ) if( defined $biotype );
$self->description($description);
$self->status( $confidence ); # incase old naming is used.
# kept to ensure routine is backwards compatible.
$self->status( $status); # add new naming
$self->source( $source );
# default to is_current
$is_current = 1 unless (defined($is_current));
$self->{'is_current'} = $is_current;
$self->canonical_transcript($canonical_transcript) if(defined $canonical_transcript);
$self->canonical_annotation($canonical_annotation) if (defined $canonical_annotation);
return $self;
}
=head2 is_known
Example : print "Gene ".$gene->stable_id." is KNOWN\n" if $gene->is_known;
Description: Returns TRUE if this gene has a status of 'KNOWN'
Returntype : TRUE if known, FALSE otherwise
Exceptions : none
Caller : general
Status : Stable
=cut
sub is_known{
my $self = shift;
return ( $self->{'status'} eq "KNOWN" );
}
=head2 external_name
Arg [1] : (optional) String - the external name to set
Example : $gene->external_name('BRCA2');
Description: Getter/setter for attribute external_name.
Returntype : String or undef
Exceptions : none
Caller : general
Status : Stable
=cut
sub external_name {
my $self = shift;
$self->{'external_name'} = shift if (@_);
if (defined $self->{'external_name'}) {
return $self->{'external_name'};
}
my $display_xref = $self->display_xref();
if (defined $display_xref) {
return $display_xref->display_id();
} else {
return undef;
}
}
=head2 status
Arg [1] : (optional) String - status to set
Example : $gene->status('KNOWN');
Description: Getter/setter for attribute status
Returntype : String
Exceptions : none
Caller : general
Status : Medium Risk
=cut
sub status {
my $self = shift;
$self->{'status'} = shift if( @_ );
return $self->{'status'};
}
=head2 source
Arg [1] : (optional) String - the source to set
Example : $gene->source('ensembl');
Description: Getter/setter for attribute source
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub source {
my $self = shift;
$self->{'source'} = shift if( @_ );
return ( $self->{'source'} || "ensembl" );
}
=head2 external_db
Arg [1] : (optional) String - name of external db to set
Example : $gene->external_db('HGNC');
Description: Getter/setter for attribute external_db. The db is the one that
belongs to the external_name.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub external_db {
my $self = shift;
$self->{'external_db'} = shift if( @_ );
if( exists $self->{'external_db'} ) {
return $self->{'external_db'};
}
my $display_xref = $self->display_xref();
if( defined $display_xref ) {
return $display_xref->dbname()
} else {
return undef;
}
}
=head2 external_status
Arg [1] : (optional) String - status of the external db
Example : $gene->external_status('KNOWNXREF');
Description: Getter/setter for attribute external_status. The status of
the external db of the one that belongs to the external_name.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub external_status {
my $self = shift;
$self->{'_ext_status'} = shift if ( @_ );
return $self->{'_ext_status'} if exists $self->{'_ext_status'};
my $display_xref = $self->display_xref();
if( defined $display_xref ) {
return $display_xref->status()
} else {
return undef;
}
}
=head2 description
Arg [1] : (optional) String - the description to set
Example : $gene->description('This is the gene\'s description');
Description: Getter/setter for gene description
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub description {
my $self = shift;
$self->{'description'} = shift if( @_ );
return $self->{'description'};
}
=head2 canonical_transcript
Arg [1] : (optional) Bio::EnsEMBL::Transcipt - canonical_transcript object
Example : $gene->canonical_transcript($canonical_transcript);
Description: Getter/setter for the canonical_transcript
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
Status : Stable
=cut
sub canonical_transcript {
my $self = shift;
if (@_){
my $tr = shift;
if(defined($tr) && (!ref($tr) || !$tr->isa('Bio::EnsEMBL::Transcript'))) {
throw('analysis argument must be a Bio::EnsEMBL::Transcript');
}
$self->{'canonical_transcript'} = $tr;
}
return $self->{'canonical_transcript'};
}
=head2 canonical_annotation
Arg [1] : (optional) String - canonical_annotation
Example : $gene->canonical_transcript('This is the canonical_annotation');
Description: Getter/setter for the canonical_annotation
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub canonical_annotation {
my $self = shift;
$self->{'canonical_annotation'} = shift if( @_ );
return $self->{'canonical_annotation'};
}
=head2 get_all_Attributes
Arg [1] : (optional) String $attrib_code
The code of the attribute type to retrieve values for
Example : my ($author) = @{ $gene->get_all_Attributes('author') };
my @gene_attributes = @{ $gene->get_all_Attributes };
Description: Gets a list of Attributes of this gene.
Optionally just get Attributes for given code.
Returntype : Listref of Bio::EnsEMBL::Attribute
Exceptions : warning if gene does not have attached adaptor and attempts lazy
load.
Caller : general
Status : Stable
=cut
sub get_all_Attributes {
my $self = shift;
my $attrib_code = shift;
if ( ! exists $self->{'attributes' } ) {
if (!$self->adaptor() ) {
return [];
}
my $attribute_adaptor = $self->adaptor->db->get_AttributeAdaptor();
$self->{'attributes'} = $attribute_adaptor->fetch_all_by_Gene($self);
}
if ( defined $attrib_code ) {
my @results = grep { uc($_->code()) eq uc($attrib_code) }
@{$self->{'attributes'}};
return \@results;
} else {
return $self->{'attributes'};
}
}
=head2 add_Attributes
Arg [1-N] : list of Bio::EnsEMBL::Attribute's @attribs
Attribute(s) to add
Example : my $attrib = Bio::EnsEMBL::Attribute->new(...);
$gene->add_Attributes($attrib);
Description: Adds an Attribute to the Gene. If you add an attribute before
you retrieve any from database, lazy loading will be disabled.
Returntype : none
Exceptions : throw on incorrect arguments
Caller : general
Status : Stable
=cut
sub add_Attributes {
my $self = shift;
my @attribs = @_;
if( ! exists $self->{'attributes'} ) {
$self->{'attributes'} = [];
}
for my $attrib ( @attribs ) {
if( ! $attrib->isa( "Bio::EnsEMBL::Attribute" )) {
throw( "Argument to add_Attribute has to be an Bio::EnsEMBL::Attribute" );
}
push( @{$self->{'attributes'}}, $attrib );
}
return;
}
=head2 add_DBEntry
Arg [1] : Bio::EnsEMBL::DBEntry $dbe
The dbEntry to be added
Example : my $dbe = Bio::EnsEMBL::DBEntery->new(...);
$gene->add_DBEntry($dbe);
Description: Associates a DBEntry with this gene. Note that adding DBEntries
will prevent future lazy-loading of DBEntries for this gene
(see get_all_DBEntries).
Returntype : none
Exceptions : thrown on incorrect argument type
Caller : general
Status : Stable
=cut
sub add_DBEntry {
my $self = shift;
my $dbe = shift;
unless($dbe && ref($dbe) && $dbe->isa('Bio::EnsEMBL::DBEntry')) {
throw('Expected DBEntry argument');
}
$self->{'dbentries'} ||= [];
push @{$self->{'dbentries'}}, $dbe;
}
=head2 get_all_DBEntries
Example : @dbentries = @{ $gene->get_all_DBEntries };
Description: Retrieves DBEntries (xrefs) for this gene. This does _not_
include DBEntries that are associated with the transcripts and
corresponding translations of this gene (see get_all_DBLinks).
This method will attempt to lazy-load DBEntries from a
database if an adaptor is available and no DBEntries are present
on the gene (i.e. they have not already been added or loaded).
Returntype : Listref of Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : get_all_DBLinks, GeneAdaptor::store
Status : Stable
=cut
sub get_all_DBEntries {
my ($self, $db_name_exp, $ex_db_type) = @_;
my $cache_name = "dbentries";
if(defined($db_name_exp)){
$cache_name .= $db_name_exp;
}
if(defined($ex_db_type)){
$cache_name .= $ex_db_type;
}
# if not cached, retrieve all of the xrefs for this gene
if(!defined $self->{$cache_name} && $self->adaptor()) {
$self->{$cache_name} =
$self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Gene($self,$db_name_exp, $ex_db_type);
}
$self->{$cache_name} ||= [];
return $self->{$cache_name};
}
=head2 get_all_DBLinks
Example : @dblinks = @{ $gene->get_all_DBLinks };
: @dblinks = @{ $gene->get_all_DBLinks("Uniprot%") };
Arg [1] : <optional> database name. SQL wildcard characters (_ and %) can be used to
specify patterns.
Description: Retrieves _all_ related DBEntries for this gene. This includes
all DBEntries that are associated with the transcripts and
corresponding translations of this gene.
If you only want to retrieve the DBEntries associated with the
gene (and not the transcript and translations) then you should
use the get_all_DBEntries call instead.
Note: Each entry may be listed more than once. No uniqueness checks are done.
Also if you put in an incorrect external database name no checks are done
to see if this exists, you will just get an empty list.
Returntype : Listref of Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_DBLinks {
my $self = shift;
my $db_name_exp = shift;
my $ex_db_type = shift;
my @links = @{$self->get_all_DBEntries($db_name_exp, $ex_db_type)};
# add all of the transcript and translation xrefs to the return list
foreach my $transc (@{$self->get_all_Transcripts}) {
push @links, @{$transc->get_all_DBEntries($db_name_exp, $ex_db_type)};
my $transl = $transc->translation();
push @links, @{$transl->get_all_DBEntries($db_name_exp, $ex_db_type)} if($transl);
}
return \@links;
}
=head2 get_all_Exons
Example : my @exons = @{ $gene->get_all_Exons };
Description: Returns a set of all the exons associated with this gene.
Returntype : Listref of Bio::EnsEMBL::Exon objects
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_Exons {
my $self = shift;
my %h;
my @out = ();
foreach my $trans ( @{$self->get_all_Transcripts} ) {
foreach my $e ( @{$trans->get_all_Exons} ) {
$h{$e->start()."-".$e->end()."-".$e->strand()."-".$e->phase()."-".$e->end_phase()} = $e;
}
}
push @out, values %h;
return \@out;
}
=head2 get_all_homologous_Genes
Description: Queries the Ensembl Compara database and retrieves all
Genes from other species that are orthologous.
REQUIRES properly setup Registry conf file. Meaning that
one of the aliases for each core db has to be "Genus species"
e.g. "Homo sapiens" (as in the name column in genome_db table
in the compara database).
Returntype : listref [
Bio::EnsEMBL::Gene,
Bio::EnsEMBL::Compara::Homology,
string $species # needed as cannot get spp from Gene
]
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_homologous_Genes {
my $self = shift;
if( exists( $self->{'homologues'} ) ){
return $self->{'homologues'};
}
$self->{'homologues'} = [];
# TODO: Find a robust way of retrieving compara dba directly.
# For now look through all DBAs
my $compara_dba;
foreach my $dba( @{Bio::EnsEMBL::Registry->get_all_DBAdaptors} ){
if( $dba->isa('Bio::EnsEMBL::Compara::DBSQL::DBAdaptor') ){
$compara_dba = $dba;
last;
}
}
unless( $compara_dba ){
warning("No compara in Bio::EnsEMBL::Registry");
return $self->{'homologues'};
}
# Get the compara 'member' corresponding to self
my $member_adaptor = $compara_dba->get_adaptor('Member');
my $query_member = $member_adaptor->fetch_by_source_stable_id
("ENSEMBLGENE",$self->stable_id);
unless( $query_member ){ return $self->{'homologues'} };
# Get the compara 'homologies' corresponding to 'member'
my $homology_adaptor = $compara_dba->get_adaptor('Homology');
my @homolos = @{$homology_adaptor->fetch_all_by_Member($query_member)};
unless( scalar(@homolos) ){ return $self->{'homologues'} };
# Get the ensembl 'genes' corresponding to 'homologies'
foreach my $homolo( @homolos ){
foreach my $member_attrib( @{$homolo->get_all_Member_Attribute} ){
my ($member, $attrib) = @{$member_attrib};
my $hstable_id = $member->stable_id;
next if ($hstable_id eq $query_member->stable_id); # Ignore self
my $hgene = undef;
eval { $hgene = $member->get_Gene;} ;
unless( $hgene ){
# Something up with DB. Create a new gene is best we can do
$hgene = Bio::EnsEMBL::Gene->new
( -stable_id=>$hstable_id,
-description=>$member->description, );
}
my $hspecies = $member->genome_db->name;
push @{$self->{'homologues'}}, [$hgene,$homolo,$hspecies];
}
}
return $self->{'homologues'};
}
=head2 biotype
Arg [1] : (optional) String - the biotype to set
Example : $gene->biotype("protein_coding");
Description: Getter/setter for the attribute biotype
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub biotype {
my $self = shift;
$self->{'biotype'} = shift if( @_ );
return ( $self->{'biotype'} || "protein_coding" );
}
=head2 add_Transcript
Arg [1] : Bio::EnsEMBL::Transcript $trans
The transcript to add to the gene
Example : my $transcript = Bio::EnsEMBL::Transcript->new(...);
$gene->add_Transcript($transcript);
Description: Adds another Transcript to the set of alternatively
spliced Transcripts of this gene. If it shares exons
with another Transcript, these should be object-identical.
Returntype : none
Exceptions : none
Caller : general
Status : Stable
=cut
sub add_Transcript {
my ($self, $trans) = @_;
if( !ref $trans || ! $trans->isa("Bio::EnsEMBL::Transcript") ) {
throw("$trans is not a Bio::EnsEMBL::Transcript!");
}
$self->{'_transcript_array'} ||= [];
push(@{$self->{'_transcript_array'}},$trans);
$self->recalculate_coordinates();
}
=head2 get_all_Transcripts
Example : my @transcripts = @{ $gene->get_all_Transcripts };
Description: Returns the Transcripts in this gene.
Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_Transcripts {
my $self = shift;
if( ! exists $self->{'_transcript_array'} ) {
if( defined $self->adaptor() ) {
my $ta = $self->adaptor()->db()->get_TranscriptAdaptor();
my $transcripts = $ta->fetch_all_by_Gene( $self );
$self->{'_transcript_array'} = $transcripts;
}
}
return $self->{'_transcript_array'};
}
=head2 get_all_alt_alleles
Example : my @alt_genes = @{ $gene->get_all_alt_alleles };
foreach my $alt_gene (@alt_genes) {
print "Alternate allele: " . $alt_gene->stable_id() . "\n";
}
Description: Returns a listref of Gene objects that represent this Gene on
an alternative haplotype. Empty list if there is no such
Gene (eg there is no overlapping haplotype).
Returntype : listref of Bio::EnsEMBL::Gene objects
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_alt_alleles {
my $self = shift;
my $result = $self->adaptor()->fetch_all_alt_alleles( $self );
return $result;
}
=head2 version
Arg [1] : (optional) Int
A version number for the stable_id
Example : $gene->version(2);
Description: Getter/setter for version number
Returntype : Int
Exceptions : none
Caller : general
Status : Stable
=cut
sub version {
my $self = shift;
$self->{'version'} = shift if(@_);
return $self->{'version'};
}
=head2 stable_id
Arg [1] : (optional) String - the stable ID to set
Example : $gene->stable_id("ENSG0000000001");
Description: Getter/setter for stable id for this gene.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub stable_id {
my $self = shift;
$self->{'stable_id'} = shift if(@_);
return $self->{'stable_id'};
}
=head2 is_current
Arg [1] : Boolean $is_current
Example : $gene->is_current(1)
Description: Getter/setter for is_current state of this gene.
Returntype : Int
Exceptions : none
Caller : general
Status : Stable
=cut
sub is_current {
my $self = shift;
$self->{'is_current'} = shift if (@_);
return $self->{'is_current'};
}
=head2 created_date
Arg [1] : (optional) String - created date to set (as a UNIX time int)
Example : $gene->created_date('1141948800');
Description: Getter/setter for attribute created_date
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub created_date {
my $self = shift;
$self->{'created_date'} = shift if ( @_ );
return $self->{'created_date'};
}
=head2 modified_date
Arg [1] : (optional) String - modified date to set (as a UNIX time int)
Example : $gene->modified_date('1141948800');
Description: Getter/setter for attribute modified_date
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub modified_date {
my $self = shift;
$self->{'modified_date'} = shift if ( @_ );
return $self->{'modified_date'};
}
=head2 transform
Arg [1] : String - coordinate system name to transform to
Arg [2] : String - coordinate system version
Example : my $new_gene = $gene->transform('supercontig');
Description: Moves this gene to the given coordinate system. If this gene has
Transcripts attached, they move as well.
Returntype : Bio::EnsEMBL::Gene
Exceptions : throw on wrong parameters
Caller : general
Status : Stable
=cut
sub transform {
my $self = shift;
# catch for old style transform calls
if( !@_ || ( ref $_[0] && $_[0]->isa( "Bio::EnsEMBL::Slice" ))) {
deprecate('Calling transform without a coord system name is deprecated.');
return $self->_deprecated_transform(@_);
}
my $new_gene = $self->SUPER::transform( @_ );
if( ! defined $new_gene ) {
# check if this gene projects at all to requested coord system,
# if not we are done.
my @segments = $self->project( @_ );
if( ! @segments ) {
return undef;
}
$self->get_all_Transcripts();
}
if( exists $self->{'_transcript_array'} ) {
my @new_transcripts;
my ( $strand, $slice );
my $low_start = POSIX::INT_MAX;
my $hi_end = POSIX::INT_MIN;
for my $old_transcript ( @{$self->{'_transcript_array'}} ) {
my $new_transcript = $old_transcript->transform( @_ );
# this can fail if gene transform failed
return undef unless $new_transcript;
if( ! defined $new_gene ) {
if( $new_transcript->start() < $low_start ) {
$low_start = $new_transcript->start();
}
if( $new_transcript->end() > $hi_end ) {
$hi_end = $new_transcript->end();
}
$slice = $new_transcript->slice();
$strand = $new_transcript->strand();
}
push( @new_transcripts, $new_transcript );
}
if( ! defined $new_gene ) {
%$new_gene = %$self;
bless $new_gene, ref( $self );
$new_gene->start( $low_start );
$new_gene->end( $hi_end );
$new_gene->strand( $strand );
$new_gene->slice( $slice );
}
$new_gene->{'_transcript_array'} = \@new_transcripts;
}
return $new_gene;
}
=head2 transfer
Arg [1] : Bio::EnsEMBL::Slice $destination_slice
Example : my $new_gene = $gene->transfer($slice);
Description: Moves this Gene to given target slice coordinates. If Transcripts
are attached they are moved as well. Returns a new gene.
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
Status : Stable
=cut
sub transfer {
my $self = shift;
my $new_gene = $self->SUPER::transfer( @_ );
return undef unless $new_gene;
if( exists $self->{'_transcript_array'} ) {
my @new_transcripts;
for my $old_transcript ( @{$self->{'_transcript_array'}} ) {
my $new_transcript = $old_transcript->transfer( @_ );
push( @new_transcripts, $new_transcript );
}
$new_gene->{'_transcript_array'} = \@new_transcripts;
}
return $new_gene;
}
=head2 display_xref
Arg [1] : (optional) Bio::EnsEMBL::DBEntry - the display xref to set
Example : $gene->display_xref($db_entry);
Description: Getter/setter display_xref for this gene.
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : general
Status : Stable
=cut
sub display_xref {
my $self = shift;
$self->{'display_xref'} = shift if(@_);
return $self->{'display_xref'};
}
=head2 display_id
Example : print $gene->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For genes this is (depending on
availability and in this order) the stable Id, the dbID or an
empty string.
Returntype : String
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub display_id {
my $self = shift;
return $self->{'stable_id'} || $self->dbID || '';
}
=head2 recalculate_coordinates
Example : $gene->recalculate_coordinates;
Description: Called when transcript added to the gene, tries to adapt the
coords for the gene.
Returntype : none
Exceptions : none
Caller : internal
Status : Stable
=cut
sub recalculate_coordinates {
my $self = shift;
my $transcripts = $self->get_all_Transcripts();
return if(!$transcripts || !@$transcripts);
my ( $slice, $start, $end, $strand );
$slice = $transcripts->[0]->slice();
$strand = $transcripts->[0]->strand();
$start = $transcripts->[0]->start();
$end = $transcripts->[0]->end();
my $transsplicing = 0;
for my $t ( @$transcripts ) {
if( $t->start() < $start ) {
$start = $t->start();
}
if( $t->end() > $end ) {
$end = $t->end();
}
if( $t->slice()->name() ne $slice->name() ) {
throw( "Transcripts with different slices not allowed on one Gene" );
}
if( $t->strand() != $strand ) {
$transsplicing = 1;
}
}
if( $transsplicing ) {
warning( "Gene contained trans splicing event" );
}
$self->start( $start );
$self->end( $end );
$self->strand( $strand );
$self->slice( $slice );
}
=head2 get_all_DASFactories
Example : $dasref = $prot->get_all_DASFactories
Description: Retrieves a listref of registered DAS objects
TODO: Abstract to a DBLinkContainer obj
Returntype : [ DAS_objects ]
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_DASFactories {
my $self = shift;
return [ $self->adaptor()->db()->_each_DASFeatureFactory ];
}
=head2 get_all_DAS_Features
Example : $features = $prot->get_all_DAS_Features;
Description: Retreives a hash reference to a hash of DAS feature
sets, keyed by the DNS, NOTE the values of this hash
are an anonymous array containing:
(1) a pointer to an array of features
(2) a pointer to the DAS stylesheet
Returntype : hashref of Bio::SeqFeatures
Exceptions : none
Caller : webcode
Status : Stable
=cut
sub get_all_DAS_Features{
my ($self, @args) = @_;
my $slice = $self->feature_Slice;
return $self->SUPER::get_all_DAS_Features($slice);
}
=head2 add_unconventional_transcript_association
Arg [1] : Bio::EnsEMBL::Transcript $trans
The transcript to associate with the gene, in an unconventional manner.
Arg [2] : String $type
The type of association between this gene and this transcript, e.g.
"antisense","sense_intronic","sense_overlaping_exonic","chimeric_sense_exonic"
Example : my $transcript = Bio::EnsEMBL::Transcript->new(...);
$gene->add_unconventional_transcript_association($transcript, "antisense");
Description: Associate a transcript with this gene in a way that is
non-conventional.
Returntype : none
Exceptions : none
Caller : general
Status : At Risk.
=cut
sub add_unconventional_transcript_association {
my ($self, $transcript, $type) = @_;
if( !ref $transcript || ! $transcript->isa("Bio::EnsEMBL::Transcript") ) {
throw("$transcript is not a Bio::EnsEMBL::Transcript!");
}
my $uta = Bio::EnsEMBL::UnconventionalTranscriptAssociation->new($transcript, $self, $type);
$self->{'_unconventional_transcript_array'} ||= [];
push(@{$self->{'_unconventional_transcript_array'}}, $uta);
}
=head2 get_all_unconventional_transcript_associations
Arg [1] : (optional) String - Only get transcripts where the association
between this gene and the transcripts is of a certain type.
Example : my @transcripts = @{ $gene->get_all_unconventional_transcript_associations, "antisense" };
Description: Returns the unconventional transcripts associated with this gene.
Returntype : Listref of Bio::EnsEMBL::UnconventionalTranscriptAssociation objects
Exceptions : none
Caller : general
Status : At risk.
=cut
sub get_all_unconventional_transcript_associations {
my ($self, $type) = @_;
if( ! exists $self->{'_unconventional_transcript_array'} ) {
$self->{'_unconventional_transcript_array'} = [];
if( defined $self->adaptor() ) {
my $utaa = $self->adaptor()->db()->get_UnconventionalTranscriptAssociationAdaptor();
my $utas = $utaa->fetch_all_by_gene( $self, $type );
$self->{'_unconventional_transcript_array'} = $utas;
}
}
return $self->{'_unconventional_transcript_array'};
}
=head2 remove_unconventional_transcript_associations
Args : None
Example : $gene->remove__unconventional_transcript_associations();
Description: Returns the unconventional transcripts associated with this gene.
Returntype : Listref of Bio::EnsEMBL::UnconventionalTranscriptAssociation objects
Exceptions : none
Caller : general
Status : At risk.
=cut
sub remove_unconventional_transcript_associations {
my $self = shift;
$self->{'_unconventional_transcript_array'} = [];
}
###########################
# DEPRECATED METHODS FOLLOW
###########################
=head2 DEPRECATED add_DBLink
Description: DEPRECATED This method has been deprecated in favor of the
add_DBEntry method. Objects are responible for holding only
xrefs directly associated with themselves now.
=cut
sub add_DBLink{
my ($self,$value) = @_;
throw("add_DBLink is deprecated. You probably want add_DBEntry.");
# unless(defined $value && ref $value
# && $value->isa('Bio::Annotation::DBLink') ) {
# throw("This [$value] is not a DBLink");
# }
# if( !defined $self->{'_db_link'} ) {
# $self->{'_db_link'} = [];
# }
# push(@{$self->{'_db_link'}},$value);
}
=head2 temporary_id
Function: DEPRECATED: Use dbID or stable_id or something else instead
=cut
sub temporary_id {
my ($obj,$value) = @_;
deprecate( "I cant see what a temporary_id is good for, please use " .
"dbID or stableID or\n try without an id." );
if( defined $value) {
$obj->{'temporary_id'} = $value;
}
return $obj->{'temporary_id'};
}
=head2 chr_name
Description: DEPRECATED. Use project, tranform, or transfer to obtain this
gene in another coord system. Use $gene->slice->seq_region_name
to get the name of the underlying coord system. Or
$gene->slice->name().
=cut
sub chr_name {
my $self = shift;
deprecate( "Use project() to obtain other coordinate systems" );
my $gene_slice = $self->slice();
if( $gene_slice->coord_system()->name eq "chromosome" ) {
return $gene_slice->seq_region_name();
}
my $coords = $self->project( "toplevel" );
if( @$coords ) {
return $coords->[0]->[2]->seq_region_name();
}
}
=head2 fetch_coded_for_regulatory_factors
Arg [1] : none
Example : $gene->fetch_coded_for_regualtory_factors()
Description: DEPRECATED: Fetches any regulatory_factors that are coded for by
this gene.
Returntype : Listref of Bio::Ensembl::RegulatoryFactor
Exceptions :
Caller : ?
Status : At Risk
: under development
=cut
sub fetch_coded_for_regulatory_factors {
my ($self) = @_;
my $rfa = $self->adaptor->db->get_RegulatoryFactorAdaptor();
return $rfa->fetch_factors_coded_for_by_gene($self);
}
=head2 type
Description: DEPRECATED. Use biotype() instead.
=cut
sub type {
deprecate("Use biotype() instead");
biotype(@_);
}
=head2 confidence
Description: DEPRECATED. Use status() instead.
=cut
sub confidence {
deprecate("Use status() instead");
status(@_);
}
1;
]]>