Raw content of Bio::EnsEMBL::Funcgen::DBSQL::SliceAdaptor
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#
# Ensembl module for Bio::EnsEMBL::Funcgen::DBSQL::SliceAdaptor
#
#
# Copyright (c) 2004 Ensembl
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Funcgen::DBSQL::SliceAdaptor - A database aware adaptor responsible for
the creation of Slices in the context of eFG objects.
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor;
$db = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(...);
$slice_adaptor = $db->get_SliceAdaptor();
# get a slice on the entire chromosome X
$gene_regulation_slice = $slice_adaptor->fetch_by_Gene_FeatureSets($gene, \@fsets);
=head1 DESCRIPTION
This module is simple wrapper class for the core SliceAdaptor, extending new
methods to generate Slices for eFG features associated with a given gene or transcript.
=head1 CONTACT
This module is part of the Ensembl project
For more information email <ensembl-dev@ebi.ac.uk>
=head1 METHODS
=cut
package Bio::EnsEMBL::Funcgen::DBSQL::SliceAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::SliceAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
@ISA = ('Bio::EnsEMBL::DBSQL::SliceAdaptor');
sub new {
my ($caller, $efgdb) = @_;
my $class = ref($caller) || $caller;
#Now have to reset the efg db to the dnadb
#Does work using just efg.seq_region_id
#But this is undesirable as we want to perform
#other non seq_region table style queries on core DB
my $self = $class->SUPER::new($efgdb->dnadb);
$self->efgdb($efgdb);
return $self;
}
sub efgdb{
my ($self, $efgdb) = @_;
if($efgdb){
if(! (ref($efgdb) && $efgdb->isa('Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor'))){
throw('Must provide a Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor');
}
$self->{'efgdb'} = $efgdb;
}
return $self->{'efgdb'};
}
=head2 fetch_by_Gene_FeatureSets
Arg [1] : Bio::EnsEMBL::Gene
Example : my $gene_reg_slice = $efg_slice_adaptor->fetch_by_gene($gene);
Description: Fetches a slice by finding the associated regulatory
elements associated with a given gene(and it's transcripts and
translations), and extending the gene feature slice to
encapsulate the associated regulatory elements.
Returntype : Bio::EnsEMBL::Slice or undef
Exceptions : throw if incorrent arg provided
Caller : General
Status : At risk
=cut
sub fetch_by_Gene_FeatureSets {
my ($self, $gene, $fsets) = @_;
if(! ( ref($gene) && $gene->isa('Bio::EnsEMBL::Gene'))){
throw("You must pass a valid Bio::EnsEMBL::Gene object");
}
#Now we want to get all the eFG feature associated with this gene and build the slice
#resitrict to RegFeats for now.
my $cs_name = $gene->slice->coord_system_name;
my $gene_chr = $gene->seq_region_name;
my $start = $gene->seq_region_start;
my $end = $gene->seq_region_end;
($start, $end) = $self->_set_bounds_by_xref_FeatureSets
($gene_chr, $start, $end, $gene, $fsets);
#Now need to do this for all transcripts and proteins too?
foreach my $trans(@{$gene->get_all_Transcripts}){
($start, $end) = $self->_set_bounds_by_xref_FeatureSets
($gene_chr, $start, $end, $trans, $fsets);
my $translation = $trans->translation;
($start, $end) = $self->_set_bounds_by_xref_FeatureSets
($gene_chr, $start, $end, $translation, $fsets) if $translation;
}
return $self->fetch_by_region($cs_name, $gene_chr, $start, $end, $gene->strand);
}
=head2 fetch_by_Transcript_FeatureSets
Arg [1] : Bio::EnsEMBL::Transcript
Example : my $trans_reg_slice = $efg_slice_adaptor->fetch_by_transcript($transcript);
Description: Fetches a slice by finding the associated regulatory
elements associated with a given transcript(and it's translation), and
extending the gene feature slice to encapsulate the associated regulatory
elements.
Returntype : Bio::EnsEMBL::Slice or undef
Exceptions : throw if incorrent arg provided
Caller : self
Status : at risk
=cut
sub fetch_by_Transcript_FeatureSets{
my ($self, $transcript, $fsets) = @_;
if(! ( ref($transcript) && $transcript->isa('Bio::EnsEMBL::Transcript'))){
throw("You must pass a valid Bio::EnsEMBL::Transcript object");
}
#Now we want to get all the eFG feature associated with this gene and build the slice
#resitrict to RegFeats for now.
my $cs_name = $transcript->slice->coord_system_name;
my $trans_chr = $transcript->seq_region_name;
my $start = $transcript->seq_region_start;
my $end = $transcript->seq_region_end;
($start, $end) = $self->_set_bounds_by_xref_FeatureSets
($trans_chr, $start, $end, $transcript, $fsets);
#Now need to do this for the protein too
my $translation = $transcript->translation;
($start, $end) = $self->_set_bounds_by_xref_FeatureSets
($trans_chr, $start, $end, $translation, $fsets) if $translation;
return $self->fetch_by_region($cs_name, $trans_chr, $start, $end, $transcript->strand);
}
#Do we need fetch_by_translation?
=head2 _set_bounds_by_xref_FeatureSets
Arg [1] : string - seq_region_name i.e. chromosome name.
Arg [2] : string - seq_region_start of current slice bound
Arg [3] : string - seq_region_end of current slice bound.
Arg [4] : Bio::EnsEMBL::Gene|Transcript|Translation
Arg [5] : arrayref - Bio::EnsEMBL::Funcgen::FeatureSet
Example : ($start, $end) = $self->_set_bounds_by_regulatory_feature_xref
($trans_chr, $start, $end, $transcript, $fsets);
Description: Internal method to set an xref Slice bounds given a list of
FeatureSets.
Returntype : List - ($start, $end);
Exceptions : throw if incorrent args provided
Caller : self
Status : at risk
=cut
sub _set_bounds_by_xref_FeatureSets{
my ($self, $chr, $start, $end, $obj, $fsets) = @_;
my ($extdb_name, $efg_feature);
my $dbe_adaptor = $self->efgdb->get_DBEntryAdaptor;
#do we need to test for start/end/chr here?
#Is implicit if we test for obj and fsets, but
#does not check if defined.
#Set ext_dbname and validate obj
#Do we need a central store for ensembl db names?
if($obj->isa('Bio::EnsEMBL::Gene')){
$extdb_name = 'ensembl_core_Gene';
}
elsif($obj->isa('Bio::EnsEMBL::Transcript')){
$extdb_name = 'ensembl_core_Transcript';
}
elsif($obj->isa('Bio::EnsEMBL::Translation')){
$extdb_name = 'ensembl_core_Translation';
}
else{
throw('Currently only handles Ensembl Gene, Transcript and Translation xrefs');
}
#warn "Setting bounds by $obj ".$obj->stable_id;
#Set which eFG features we want to look at.
if(ref($fsets) ne 'ARRAY' || scalar(@$fsets) == 0){
throw('Must define an array of Bio::EnsEMBL::FeatureSets to extend xref Slice bound. You passed: '.$fsets);
}
my %feature_set_types;
foreach my $fset(@$fsets){
$self->efgdb->is_stored_and_valid('Bio::EnsEMBL::Funcgen::FeatureSet', $fset);
$feature_set_types{$fset->type} ||= [];
push @{$feature_set_types{$fset->type}}, $fset;
}
#We can list the outer loop here and put in the BaseFeatureAdaptor, or possible storable as we do have FeatureType xrefs.
#This would be useful for fetching all the efg features for a given xref and FeatureSets
#Don't implement as a parent sub and call from here as this would mean looping through array twice.
#Altho we could pass a code ref to do the filtering?
#Just copy and paste for now to avoid obfuscation
#Get xrefs for each eFG feature set type
foreach my $fset_type(keys %feature_set_types){
my $xref_method = 'list_'.$fset_type.'_feature_ids_by_extid';
#e.g. list_regulatory_feature_ids_by_extid
my $adaptor_method = 'get_'.ucfirst($fset_type).'FeatureAdaptor';
my $adaptor = $self->efgdb->$adaptor_method;
my %feature_set_ids;
map $feature_set_ids{$_->dbID} = 1, @{$feature_set_types{$fset_type}};
#my $cnt = 0;
#This should use fetch_all_by_external_name method
foreach my $efg_feature(@{$adaptor->fetch_all_by_external_name($obj->stable_id, $extdb_name)}){
next if ! exists $feature_set_ids{$efg_feature->feature_set->dbID};
next if $efg_feature->seq_region_name ne $chr;
#warn "found xref ".$efg_feature->display_label.' with start '.$efg_feature->seq_region_start;
#$cnt ++;
$start = $efg_feature->seq_region_start if $efg_feature->seq_region_start < $start;
$end = $efg_feature->seq_region_end if $efg_feature->seq_region_end > $end;
}
#warn "Found $cnt $fset_type xrefs";
}
return ($start, $end);
}
1;
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