Raw content of Bio::EnsEMBL::MappedSlice
<![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::MappedSlice - an object representing a mapped slice
=head1 SYNOPSIS
# get a reference slice
my $slice =
$slice_adaptor->fetch_by_region( 'chromosome', 14, 900000, 950000 );
# create MappedSliceContainer based on the reference slice
my $msc = Bio::EnsEMBL::MappedSliceContainer->new( -SLICE => $slice );
# set the adaptor for fetching AssemblySlices
my $asa = $slice->adaptor->db->get_AssemblySliceAdaptor;
$msc->set_AssemblySliceAdaptor($asa);
# add an AssemblySlice to your MappedSliceContainer
$msc->attach_AssemblySlice('NCBIM36');
foreach my $mapped_slice ( @{ $msc->get_all_MappedSlices } ) {
print $mapped_slice->name, "\n";
foreach my $sf ( @{ $mapped_slice->get_all_SimpleFeatures } ) {
print " ", &to_string($sf), "\n";
}
}
=head1 DESCRIPTION
NOTE: this code is under development and not fully functional nor tested
yet. Use only for development.
This object represents a mapped slice, i.e. a slice that's attached
to a reference slice and a mapper to convert coordinates to/from the
reference. The attachment is done via a MappedSliceContainer which
has the reference slice and the "container slice" defining the common
coordinate system for all MappedSlices.
A MappedSlice is supposed to behave as close to a Bio::EnsEMBL::Slice
as possible. Most Slice methods are implemented in MappedSlice and will
return an equivalent value to what Slice does. There are some exceptions
of unimplemented methods, either because there is no useful equivalent
for a MappedSlice to do, or they are too complicated.
Not supported Bio::EnsEMBL::Slice methods:
All deprecated methods
All Bio::PrimarySeqI compliance methods
expand
get_generic_features
get_seq_region_id
seq_region_Slice
Not currently supported but maybe should/could:
calculate_pi
calculate_theta
get_base_count
get_by_Individual
get_by_strain
invert
Internally, a MappedSlice is a collection of Bio::EnsEMBL::Slices and
associated Bio::EnsEMBL::Mappers which map the slices to the common
container coordinate system.
MappedSlices are usually created and attached to a MappedSliceContainer
by an adaptor/factory.
=head1 METHODS
new
add_Slice_Mapper_pair
get_all_Slice_Mapper_pairs
adaptor
container
name
seq_region_name
start
end
strand
length
seq_region_length
centrepoint
coord_system
coord_system_name
is_toplevel
seq (not implemented yet)
subseq (not implemented yet)
get_repeatmasked_seq (not implemented yet)
sub_MappedSlice (not implemented yet)
project (not implemented yet)
=head1 RELATED MODULES
Bio::EnsEMBL::MappedSlice
Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor
Bio::EnsEMBL::Compara::AlignSlice
Bio::EnsEMBL::Compara::AlignSlice::Slice
Bio::EnsEMBL::AlignStrainSlice
Bio::EnsEMBL::StrainSlice
=cut
package Bio::EnsEMBL::MappedSlice;
use strict;
use warnings;
no warnings 'uninitialized';
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Mapper;
use Scalar::Util qw(weaken);
use vars qw($AUTOLOAD);
=head2 new
Arg [ADAPTOR] : Adaptor $adaptor - an adaptor of the appropriate type
Arg [CONTAINER] : Bio::EnsEMBL::MappedSliceContainer $container - the
container this MappedSlice is attached to
Arg [NAME] : String $name - name
Example : my $mapped_slice = Bio::EnsEMBL::MappedSlice->new(
-ADAPTOR => $adaptor,
-CONTAINER => $container,
-NAME => $name,
);
Description : Constructor. Usually you won't call this method manually, but
the MappedSlice will be constructed by an adaptor/factory.
Return type : Bio::EnsEMBL::MappedSlice
Exceptions : thrown on wrong or missing arguments
Caller : general, MappedSlice adaptors
Status : At Risk
: under development
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my ($adaptor, $container, $name) =
rearrange([qw(ADAPTOR CONTAINER NAME)], @_);
# arguement check
unless ($container and ref($container) and
$container->isa('Bio::EnsEMBL::MappedSliceContainer')) {
throw("Need a MappedSliceContainer.");
}
my $self = {};
bless ($self, $class);
#
# initialise object
#
# need to weaken reference to prevent circular reference
weaken($self->{'container'} = $container);
$self->{'adaptor'} = $adaptor if (defined($adaptor));
$self->{'name'} = $name if (defined($name));
$self->{'slice_mapper_pairs'} = [];
return $self;
}
=head2 add_Slice_Mapper_pair
Arg[1] : Bio::EnsEMBL::Slice $slice - slice to add
Arg[2] : Bio::EnsEMBL::Mapper $mapper - the mapper for this slice
Example : $mapped_slice->add_Slice_Mapper_pair($slice, $mapper);
Description : Adds a native slice and a corresponding mapper to map to/from
the artificial container coord system.
Return type : listref of Bio::EnsEMBL::MappedSlice
Exceptions : thrown on wrong or missing arguments
Caller : general, MappedSlice adaptors
Status : At Risk
: under development
=cut
sub add_Slice_Mapper_pair {
my $self = shift;
my $slice = shift;
my $mapper = shift;
# argument check
unless ($slice and ref($slice) and $slice->isa('Bio::EnsEMBL::Slice')) {
throw("You must provide a slice.");
}
unless ($mapper and ref($mapper) and $mapper->isa('Bio::EnsEMBL::Mapper')) {
throw("You must provide a mapper.");
}
push @{ $self->{'slice_mapper_pairs'} }, [ $slice, $mapper ];
return $self->{'slice_mapper_pairs'};
}
=head2 get_all_Slice_Mapper_pairs
Example : foreach my $pair (@{ $self->get_all_Slice_Mapper_pairs }) {
my ($slice, $mapper) = @$pair;
# get container coordinates
my @coords = $mapper->map_coordinates(
$slice->seq_region_name,
$slice->start,
$slice->end,
$slice->strand,
'mapped_slice'
);
# ....
}
Description : Gets all Slice/Mapper pairs this MappedSlice is composed of.
Each slice (and features on it) can be mapped onto the
artificial container coord system using the mapper.
Return type : listref of listref of a Bio::EnsEMBL::Slice and
Bio::EnsEMBL::Mapper pair
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_all_Slice_Mapper_pairs {
my $self = shift;
return $self->{'slice_mapper_pairs'};
}
=head2 adaptor
Arg[1] : (optional) Adaptor $adaptor - the adaptor/factory for this
object
Example : $mapped_slice->adaptor($assembly_slice_adaptor);
Description : Getter/setter for the adaptor/factory for this object.
Return type : Adaptor of appropriate type
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub adaptor {
my $self = shift;
$self->{'adaptor'} = shift if (@_);
return $self->{'adaptor'};
}
=head2 container
Arg[1] : (optional) Bio::EnsEMBL::MappedSliceContainer - the container
this object is attached to
Example : my $container = $mapped_slice->container;
print $container->ref_slice->name, "\n";
Description : Getter/setter for the container this object is attached to. The
container will give you access to the reference slice, a common
artificial container slice, and a mapper to map to it from the
container coord system.
The implementation uses a weak reference to attach the container
since the container holds a list of MappedSlices itself.
Return type : Bio::EnsEMBL::MappedSliceContainer
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub container {
my $self = shift;
weaken($self->{'container'} = shift) if (@_);
return $self->{'container'};
}
=head2 name
Arg[1] : String - the name of this object
Example : my $name = $mapped_slice->container->ref_slice->name .
":mapped_" . $ident_string;
$mapped_slice->name($name);
Description : Getter/setter for this object's name
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub name {
my $self = shift;
$self->{'name'} = shift if (@_);
return $self->{'name'};
}
=head2 seq_region_name
Example : my $sr_name = $mapped_slice->seq_region_name;
Description : Returns the seq_region name of the reference slice.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub seq_region_name {
my $self = shift;
return $self->container->ref_slice->seq_region_name;
}
=head2 start
Example : my $start = $mapped_slice->start;
Description : Returns the start of the container slice.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub start {
my $self = shift;
return $self->container->container_slice->start;
}
=head2 end
Example : my $end = $mapped_slice->end;
Description : Returns the end of the container slice.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub end {
my $self = shift;
return $self->container->container_slice->end;
}
=head2 strand
Example : my $strand = $mapped_slice->strand;
Description : Returns the strand of the container slice.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub strand {
my $self = shift;
return $self->container->container_slice->strand;
}
=head2 length
Example : my $length = $mapped_slice->length;
Description : Returns the length of the container slice
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub length {
my $self = shift;
return $self->container->container_slice->length;
}
=head2 seq_region_length
Example : my $sr_length = $mapped_slice->seq_region_length;
Description : Returns the seq_region length of the reference slice.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub seq_region_length {
my $self = shift;
return $self->container->ref_slice->seq_region_length;
}
=head2 centrepoint
Example : my $centrepoint = $mapped_slice->centrepoint;
Description : Returns the centrepoint of the container slice.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub centrepoint {
my $self = shift;
return $self->container->container_slice->centrepoint;
}
=head2 coord_system
Example : my $cs = $mapped_slice->coord_system;
Description : Returns the coord system of the container slice.
Return type : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub coord_system {
my $self = shift;
return $self->container->container_slice->coord_system;
}
=head2 coord_system_name
Example : my $cs_name = $mapped_slice->coord_system_name;
Description : Returns the coord system name of the container slice.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub coord_system_name {
my $self = shift;
return $self->container->container_slice->coord_system_name;
}
=head2 is_toplevel
Example : my $toplevel_flag = $mapped_slice->is_toplevel;
Description : Returns weather the container slice is toplevel.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub is_toplevel {
my $self = shift;
return $self->container->container_slice->is_toplevel;
}
sub seq {
}
sub subseq {
}
sub get_repeatmasked_seq {
}
sub sub_MappedSlice {
}
sub project {
}
=head2 AUTOLOAD
Arg[1..N] : Arguments passed on to the calls on the underlying slices.
Example : my @simple_features = @{ $mapped_slice->get_all_SimpleFeatures };
Description : Aggregate data gathered from composing Slices.
This will call Slice->get_all_* and combine the results.
Coordinates will be transformed to be on the container slice
coordinate system.
Calls involving DAS features are skipped since the DAS adaptor
handles coordinate conversions natively.
Return type : listref of features (same type as corresponding Slice method)
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub AUTOLOAD {
my $self = shift;
my $method = $AUTOLOAD;
$method =~ s/.*:://;
# AUTOLOAD should only deal with get_all_* methods
return unless ($method =~ /^get_all_/);
# skip DAS methods
return if ($method =~ /DAS/);
my @mapped_features = ();
foreach my $pair (@{ $self->get_all_Slice_Mapper_pairs }) {
my ($slice, $mapper) = @$pair;
#warn $slice->name;
# call $method on each native slice composing the MappedSlice
my @features = @{ $slice->$method(@_) };
# map features onto the artificial container coordinate system
foreach my $f (@features) {
my @coords = $mapper->map_coordinates(
$f->slice->seq_region_name,
$f->start,
$f->end,
$f->strand,
'mapped_slice'
);
# sanity check
if (scalar(@coords) > 1) {
warning("Got more than one Coordinate returned, expected only one!\n");
}
$f->start($coords[0]->start);
$f->end($coords[0]->end);
$f->strand($coords[0]->strand);
$f->slice($self->container->container_slice);
push @mapped_features, $f;
}
}
return \@mapped_features;
}
1;
]]>