Raw content of Bio::EnsEMBL::External::ExternalFeatureAdaptor
<![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::External::ExternalFeatureAdaptor
=head 1 SUMMARY
Allows features created externally from Ensembl in a single
coordinate system to be retrieved in several other (Ensembl-style)
coordinate systems. This is intended to be a replacement for the old
Bio::EnsEMBL::DB::ExternalFeatureFactoryI interface.
=head1 SYNOPSIS
$database_adaptor = new Bio::EnsEMBL::DBSQL::DBAdaptor(
-host => 'kaka.sanger.ac.uk',
-dbname => 'homo_sapiens_core_9_30',
-pass => 'anonymous'
);
$xf_adaptor = new ExternalFeatureAdaptorSubClass;
# Connect the Ensembl core database:
$xf_adaptor->db($database_adaptor);
# get some features in vontig coords
@feats =
@{ $xf_adaptor->fetch_all_by_contig_name('AC000087.2.1.42071') };
# get some features in assembly coords
@feats =
@{ $xf_adaptor->fetch_all_by_chr_start_end( 'X', 100000, 200000 ) };
# get some features in clone coords
@feats = @{ $xf_adaptor->fetch_all_by_clone_accession('AC000087') };
# Add the adaptor to the ensembl core dbadaptor (implicitly sets db
# attribute)
$database_adaptor->add_ExternalFeatureAdaptor($xf_adaptor);
# get some features in Slice coords
$slice_adaptor = $database_adaptor->get_SliceAdaptor;
$slice =
$slice_adaptor->fetch_all_by_chr_start_end( 1, 100000, 200000 );
@feats = @{ $xf_adaptor->fetch_all_by_Slice($slice) };
# now features can be retrieved directly from Slice
@feats = @{ $slice->get_all_ExternalFeatures };
=head1 DESCRIPTION
This class is intended to be used as a method of getting external
features into EnsEMBL. To work, this class must be extended and must
implement the the coordinate_systems method. As well, the subclass
is required to implement a single fetch method so that the external
features may be retrieved. By implementing a single fetch_method in a
single coordinate system all of the other ExternalFeatureAdaptor fetch
methods become available for retrieving the data in several different
coordinate systems.
The coordinate_systems method should return a list of strings indicating
which coordinate system(s) have been implemented. If a given string is
returned from the coordinate_systems method then the corresponding fetch
method must be implemented. The reverse is also true: if a fetch method
is implemented then coordinate_systems must return the appropriate
string in its list of return values. The following are the valid
coordinate system values and the corresponding fetch methods that must
be implemented:
COORD SYSTEM STRING FETCH_METHOD
------------------- ------------
'ASSEMBLY' fetch_all_by_chr_start_end
'CLONE' fetch_all_by_clone_accession
'CONTIG' fetch_all_by_contig_name
'SUPERCONTIG' fetch_all_by_supercontig_name
'SLICE' fetch_all_by_Slice
The objects returned by the fetch methods should be EnsEMBL or BioPerl
style Feature objects. These objects MUST have start, end and strand
methods.
Before the non-overridden ExternalFeatureAdaptor fetch methods may
be called an EnsEMBL core database adaptor must be attached to the
ExternalFeatureAdaptor . This database adaptor is required to perform
the remappings between various coordinate system. This may be done
implicitly by adding the ExternalFeatureAdaptor to the database adaptor
through a call to the DBAdaptor add_ExternalFeatureAdaptor method or
explicitly by calling the ExternalFeatureAdaptor ensembl_db method.
=head1 METHODS
=cut
package Bio::EnsEMBL::External::ExternalFeatureAdaptor;
use strict;
use Bio::EnsEMBL::Utils::Exception qw(warning throw);
=head2 new
Arg [1] : none
Example : $xfa = new Bio::EnsEMBL::External::ExternalFeatureAdaptor;
Description: Creates a new ExternalFeatureAdaptor object. You may wish to
extend this constructor and provide your own set of paremeters.
Returntype : Bio::EnsEMBL::External::ExternalFeatureAdaptor
Exceptions : none
Caller : general
=cut
sub new {
my $class = shift;
if(ref $class) {
return bless {}, ref $class;
}
return bless {}, $class;
}
=head2 ensembl_db
Arg [1] : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor
Example : $external_feature_adaptor->ensembl_db($new_val);
Description: none
Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
Exceptions : none
Caller : internal
=cut
sub ensembl_db {
my ($self, $value) = @_;
if($value) {
$self->{'ensembl_db'} = $value;
}
return $self->{'ensembl_db'};
}
=head2 coordinate_systems
Arg [1] : none
Example : @implemented_coord_systems = $ext_adaptor->coordinate_systems;
Description: ABSTRACT method. Must be implemented by all
ExternalFeatureAdaptor subclasses. This method returns a list
of coordinate systems which are implemented by the subclass.
A minimum of on valid coordinate system must be implemented.
Valid coordinate systems are: 'SLICE', 'ASSEMBLY', 'CONTIG',
and 'CLONE'.
Returntype : list of strings
Exceptions : none
Caller : internal
=cut
sub coordinate_systems {
my $self = shift;
throw("abstract method coordinate_systems not implemented\n");
return '';
}
=head2 track_name
Arg [1] : none
Example : $track_name = $xf_adaptor->track_name;
Description: Currently this is not really used. In the future it may be
possible to have ExternalFeatures automatically displayed by
the EnsEMBL web code. By default this method returns
'External features' but you are encouraged to override this
method and provide your own meaningful name for the features
your adaptor provides. This also allows you to distinguish the
type of features retrieved from Slices. See
the PODs for Bio::EnsEMBL::Slice::get_all_ExternalFeatures and
Bio::EnsEMBL::DBSQL::DBAdaptor::add_ExternalFeatureAdaptor
methods.
Returntype : string
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::DBAdaptor::add_ExternalFeatureAdaptor
=cut
sub track_name {
my $self = shift;
return 'External features';
}
=head2 feature_type
Arg [1] : none
Example : $feature_type = $xf_adaptor->track_name
Description: Currently this is not used. In the future it may be possible
to have ExternalFeatures automatically displayed by the EnsEMBL
web code. This method would then be used do determine the
type of glyphs used to draw the features which are returned
from this external adaptor.
Returntype : string
Exceptions : none
Caller : none
=cut
sub feature_type {
my $self = shift;
return qw(SIMPLE);
}
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice $slice
Example : @features = @{$ext_adaptor->fetch_all_by_Slice($slice)};
Description: Retrieves all features which lie in the region defined
by $slice in slice coordinates.
If this method is overridden then the coordinate_systems method
must return 'SLICE' as one of its values.
This method will work as is (i.e. without overriding it)
providing at least one of the other fetch methods is overridden.
Returntype : reference to a list of Bio::SeqFeature objects in the Slice
coordinate system
Exceptions : Thrown on incorrect input arguments
Caller : general, fetch_all_by_chr_start_end
=cut
sub fetch_all_by_Slice {
my ($self, $slice) = @_;
unless($slice && ref $slice && $slice->isa('Bio::EnsEMBL::Slice')) {
throw("[$slice] is not a Bio::EnsEMBL::Slice");
}
my $out = [];
my $csa = $self->ensembl_db->get_CoordSystemAdaptor();
my $slice_start = $slice->start;
my $slice_end = $slice->end;
my $slice_strand = $slice->strand;
my $slice_seq_region = $slice->seq_region_name;
my $slice_seq_region_id = $slice->get_seq_region_id;
my $coord_system = $slice->coord_system;
if($self->_supported('SLICE')) {
throw("ExternalFeatureAdaptor supports SLICE coordinate system" .
" but fetch_all_by_Slice not implemented");
}
my %features;
my $from_coord_system;
my $fetch_method;
#
# Get all of the features from whatever coord system they are computed in
#
if($self->_supported('CLONE')) {
$fetch_method = sub {
my $self = shift;
my $name = shift;
my ($acc, $ver) = split(/\./, $name);
$self->fetch_all_by_clone_accession($acc,$ver,@_);
};
$from_coord_system = $csa->fetch_by_name('clone');
} elsif($self->_supported('ASSEMBLY')) {
$from_coord_system = $csa->fetch_by_name('chromosome');
$fetch_method = $self->can('fetch_all_by_chr_start_end');
} elsif($self->_supported('CONTIG')) {
$from_coord_system = $csa->fetch_by_name('contig');
$fetch_method = $self->can('fetch_all_by_contig_name');
} elsif($self->_supported('SUPERCONTIG')) {
$from_coord_system = $csa->fetch_by_name('supercontig');
$fetch_method = $self->can('fetch_all_by_supercontig_name');
} else {
$self->_no_valid_coord_systems();
}
if($from_coord_system->equals($coord_system)) {
$features{$slice_seq_region} = &$fetch_method($self, $slice_seq_region,
$slice_start,$slice_end);
} else {
foreach my $segment (@{$slice->project($from_coord_system->name,
$from_coord_system->version)}) {
my ($start,$end,$pslice) = @$segment;
$features{$pslice->seq_region_name } ||= [];
push @{$features{$pslice->seq_region_name }},
@{&$fetch_method($self, $pslice->seq_region_name,
$pslice->start(),
$pslice->end())};
}
}
my @out;
if(!$coord_system->equals($from_coord_system)) {
my $asma = $self->ensembl_db->get_AssemblyMapperAdaptor();
my $mapper = $asma->fetch_by_CoordSystems($from_coord_system,
$coord_system);
my %slice_cache;
my $slice_adaptor = $self->ensembl_db->get_SliceAdaptor();
my $slice_setter;
#convert the coordinates of each of the features retrieved
foreach my $fseq_region (keys %features) {
my $feats = $features{$fseq_region};
next if(!$feats);
$slice_setter = _guess_slice_setter($feats) if(!$slice_setter);
foreach my $f (@$feats) {
my($sr_id, $start, $end, $strand) =
$mapper->fastmap($fseq_region,$f->start,$f->end,$f->strand,
$from_coord_system);
#maps to gap
next if(!defined($sr_id));
#maps to unexpected seq region, probably error in the externally
if($sr_id ne $slice_seq_region_id) {
warning("Externally created Feature mapped to [$sr_id] " .
"which is not on requested seq_region_id [$slice_seq_region_id]");
next;
}
#update the coordinates of the feature
&$slice_setter($f,$slice);
$f->start($start);
$f->end($end);
$f->strand($strand);
push @out, $f;
}
}
} else {
#we already know the seqregion the featues are on, we just have
#to put them on the slice
@out = @{$features{$slice_seq_region}};
my $slice_setter = _guess_slice_setter(\@out);
foreach my $f (@out) {
&$slice_setter($f,$slice);
}
}
#shift the feature coordinates again if
#the requested slice is not the full seqregion
if($slice->start != 1 || $slice->strand != 1) {
#convert from assembly coords to slice coords
my($f_start, $f_end, $f_strand);
foreach my $f (@out) {
if($slice_strand == 1) {
$f_start = $f->start - $slice_start + 1;
$f_end = $f->end - $slice_start + 1;
$f_strand = $f->strand;
} else {
$f_start = $slice_end - $f->end + 1;
$f_end = $slice_end - $f->start + 1;
$f_strand = $f->strand * -1;
}
$f->start($f_start);
$f->end($f_end);
$f->strand($f_strand);
}
}
return \@out;
}
sub _guess_slice_setter {
my $features = shift;
#we do not know what type of features these are. They might
#be bioperl features or old ensembl features, hopefully they are new
#style features. Try to come up with a setter method for the
#slice.
return undef if(!@$features);
my ($f) = @$features;
my $slice_setter;
foreach my $method (qw(slice contig attach_seq)) {
last if($slice_setter = $f->can($method));
}
if(!$slice_setter) {
if($f->can('seqname')) {
$slice_setter = sub { $_[0]->seqname($_[1]->seq_region_name()); };
} else {
$slice_setter = sub{} if(!$slice_setter);
}
}
return $slice_setter;
}
=head2 fetch_all_by_contig_name
Arg [1] : string $contig_name
Arg [2] : int $start (optional)
The start of the region on the contig to retrieve features on
if not specified the whole of the contig is used.
Arg [3] : int $end (optional)
The end of the region on the contig to retrieve features on
if not specified the whole of the contig is used.
Example : @fs = @{$self->fetch_all_by_contig_name('AB00879.1.1.39436')};
Description: Retrieves features on the contig defined by the name
$contig_name in contig coordinates.
If this method is overridden then the coordinate_systems
method must return 'CONTIG' as one of its values.
This method will work as is (i.e. without being overridden)
providing at least one other fetch method has
been overridden.
Returntype : reference to a list of Bio::SeqFeature objects in the contig
coordinate system.
Exceptions : thrown if the input argument is incorrect
thrown if the coordinate_systems method returns the value
'CONTIG' and this method has not been overridden.
Caller : general, fetch_all_by_Slice
=cut
sub fetch_all_by_contig_name {
my ($self, $contig_name, $start, $end) = @_;
unless($contig_name) {
throw("contig_name argument not defined");
}
if($self->_supported('CONTIG')) {
throw("ExternalFeatureAdaptor supports CONTIG coordinate system" .
" but fetch_all_by_contig_name is not implemented");
}
unless($self->ensembl_db) {
throw('DB attribute not set. This value must be set for the ' .
'ExternalFeatureAdaptor to function correctly');
}
my $slice_adaptor = $self->ensembl_db->get_SliceAdaptor();
my $slice = $slice_adaptor->fetch_by_region('contig', $contig_name,
$start, $end);
return $self->fetch_all_by_Slice($slice);
}
=head2 fetch_all_by_supercontig_name
Arg [1] : string $supercontig_name
Arg [2] : int $start (optional)
The start of the region on the contig to retrieve features on
if not specified the whole of the contig is used.
Arg [3] : int $end (optional)
The end of the region on the contig to retrieve features on
if not specified the whole of the contig is used.
Example : @fs = @{$self->fetch_all_by_contig_name('NT_004321')};
Description: Retrieves features on the contig defined by the name
$supercontigname in supercontig coordinates.
If this method is overridden then the coordinate_systems
method must return 'SUPERCONTIG' as one of its values.
This method will work as is (i.e. without being overridden)
providing at least one other fetch method has
been overridden.
Returntype : reference to a list of Bio::SeqFeature objects in the contig
coordinate system.
Exceptions : thrown if the input argument is incorrect
thrown if the coordinate_systems method returns the value
'SUPERCONTIG' and this method has not been overridden.
Caller : general, fetch_all_by_Slice
=cut
sub fetch_all_by_supercontig_name {
my ($self, $supercontig_name, $start, $end) = @_;
unless($supercontig_name) {
throw("supercontig_name argument not defined");
}
if($self->_supported('SUPERCONTIG')) {
throw("ExternalFeatureAdaptor supports SUPERCONTIG coordinate system" .
" but fetch_all_by_supercontig_name is not implemented");
}
unless($self->ensembl_db) {
throw('DB attribute not set. This value must be set for the ' .
'ExternalFeatureAdaptor to function correctly');
}
my $slice_adaptor = $self->ensembl_db->get_SliceAdaptor();
my $slice = $slice_adaptor->fetch_by_region('supercontig', $supercontig_name,
$start, $end);
return $self->fetch_all_by_Slice($slice);
}
=head2 fetch_all_by_clone_accession
Arg [1] : string $acc
The EMBL accession number of the clone to fetch features from.
Arg [2] : (optional) string $ver
Arg [3] : (optional) int $start
Arg [4] : (optional) int $end
Example : @fs = @{$self->fetch_all_by_clone_accession('AC000093')};
Description: Retrieves features on the clone defined by the $acc arg in
Clone coordinates.
If this method is overridden then the coordinate_systems method
must return 'CLONE' as one of its values. The arguments
start, end, version are passed if this method is overridden and
can optionally be used to reduce the scope of the query and
improve performance.
This method will work as is - providing at least one other
fetch method has been overridden.
Returntype : reference to a list of Bio::SeqFeature objects in the Clone
coordinate system
Exceptions : thrown if the input argument is incorrect
thrown if the coordinate system method returns the value 'CLONE'
and this method is not overridden.
thrown if the coordinate systems method does not return any
valid values.
Caller : general, fetch_all_by_clone_accession
=cut
sub fetch_all_by_clone_accession {
my ($self, $acc, $version, $start, $end) = @_;
unless($acc) {
throw("clone accession argument not defined");
}
if($self->_supported('CLONE')) {
throw('ExternalFeatureAdaptor supports CLONE coordinate system ' .
'but does not implement fetch_all_by_clone_accession');
}
unless($self->ensembl_db) {
throw('DB attribute not set. This value must be set for the ' .
'ExternalFeatureAdaptor to function correctly');
}
if(defined($version)) {
$acc = "$acc.$version";
} elsif(!$acc =~ /\./) {
$acc = "$acc.1";
}
my $slice_adaptor = $self->ensembl_db->get_SliceAdaptor;
my $slice = $slice_adaptor->fetch_by_region('clone', $acc, $start, $end);
return $self->fetch_all_by_Slice($slice);
}
=head2 fetch_all_by_chr_start_end
Arg [1] : string $chr_name
The name of the chromosome to retrieve features from
Arg [2] : int $start
The start coordinate of the chromosomal region to retrieve
features from.
Arg [3] : int $end
The end coordinate of the chromosomal region to retrieve
features from.
Example : @features
Description: Retrieves features on the region defined by the $chr_name,
$start, and $end args in assembly (chromosomal) coordinates.
If this method is overridden then the coordinate_systems method
must return 'ASSEMBLY' as one of its values.
This method will work as is (i.e. without overriding it)
providing at least one of the other fetch methods is overridden.
Returntype : reference to a list of Bio::SeqFeatures
Exceptions : Thrown if the coordinate_systems method returns ASSEMBLY as a
value and this method is not overridden.
Thrown if any of the input arguments are incorrect
Caller : general, fetch_all_by_Slice
=cut
sub fetch_all_by_chr_start_end {
my ($self, $chr_name, $start, $end) = @_;
unless($chr_name && defined $start && defined $end && $start < $end) {
throw("Incorrect start [$start] end [$end] or chr [$chr_name] arg");
}
unless($self->ensembl_db) {
throw('DB attribute not set. This value must be set for the ' .
'ExternalFeatureAdaptor to function correctly');
}
my $slice_adaptor = $self->ensembl_db->get_SliceAdaptor();
my $slice = $slice_adaptor->fetch_by_region('toplevel', $chr_name, $start,
$end);
return $self->fetch_all_by_Slice($slice);
}
=head2 _no_valid_coord_system
Arg [1] : none
Example : none
Description: PRIVATE method - throws an error with a descriptive message
Returntype : none
Exceptions : always thrown
Caller : internal
=cut
sub _no_valid_coord_system {
my $self = shift;
throw("This ExternalFeatureAdaptor does not support a known " .
"coordinate system.\n Valid coordinate systems are: " .
"[SLICE,ASSEMBLY,SUPERCONTIG,CONTIG,CLONE].\n This External Adaptor " .
"supports: [" . join(', ', $self->coordinate_systems) . "]");
}
=head2 _supported
Arg [1] : string $system
Example : print "CONTIG system supported" if($self->_supported('CONTIG'));
Description: PRIVATE method. Tests if the coordinate system defined by
the $system argument is implemented.
Returntype : boolean
Exceptions : none
Caller : internal
=cut
sub _supported {
my ($self, $system) = @_;
#construct the hash of supported features if it has not been already
unless(exists $self->{_supported}) {
$self->{_supported} = {};
foreach my $coord_system ($self->coordinate_systems) {
$self->{_supported}->{$coord_system} = 1;
}
}
return $self->{_supported}->{$system};
}
1;
]]>