=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
Questions may also be sent to the Ensembl help desk at
=cut
=head1 NAME
Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor - adaptor/factory for MappedSlices
representing alternative assemblies
=head1 SYNOPSIS
my $slice =
$slice_adaptor->fetch_by_region( 'chromosome', 14, 900000, 950000 );
my $msc = Bio::EnsEMBL::MappedSliceContainer->new( -SLICE => $slice );
my $asa = Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor->new;
my ($mapped_slice) = @{ $asa->fetch_by_version( $msc, 'NCBIM36' ) };
=head1 DESCRIPTION
NOTE: this code is under development and not fully functional nor tested
yet. Use only for development.
This adaptor is a factory for creating MappedSlices representing
alternative assemblies and attaching them to a MappedSliceContainer. A
mapper will be created to map between the reference slice and the common
container slice coordinate system.
=head1 METHODS
new
fetch_by_version
=head1 REALTED MODULES
Bio::EnsEMBL::MappedSlice
Bio::EnsEMBL::MappedSliceContainer
Bio::EnsEMBL::Compara::AlignSlice
Bio::EnsEMBL::Compara::AlignSlice::Slice
Bio::EnsEMBL::Variation::StrainSlice
=cut
$Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor::VERSION = '112.0.0_58'; # TRIAL
$Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor::VERSION = '112.0.058';
use strict;
no warnings 'uninitialized';
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 new
Example : my $assembly_slice_adaptor =
Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor->new;
Description : Constructor.
Return type : Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
return $self;
}
=head2 fetch_by_version
Arg[1] : Bio::EnsEMBL::MappedSliceContainer $container - the container
to attach MappedSlices to
Arg[2] : String $version - the assembly version to fetch
Example : my ($mapped_slice) = @{ $msc->fetch_by_version('NCBIM36') };
Description : Creates a MappedSlice representing an alternative assembly
version of the container's reference slice.
Return type : listref of Bio::EnsEMBL::MappedSlice
Exceptions : thrown on wrong or missing arguments
Caller : general, Bio::EnsEMBL::MappedSliceContainer
Status : At Risk
: under development
=cut
sub fetch_by_version {
my $self = shift;
my $container = shift;
my $version = shift;
# arguement check
unless ($container and ref($container) and
$container->isa('Bio::EnsEMBL::MappedSliceContainer')) {
throw("Need a MappedSliceContainer.");
}
unless ($version) {
throw("Need an assembly version.");
}
my $slice = $container->ref_slice;
# project slice onto other assembly and construct MappedSlice for result
my $mapped_slice = Bio::EnsEMBL::MappedSlice->new(
-ADAPTOR => $self,
-CONTAINER => $container,
-NAME => $slice->name."\#mapped_$version",
);
my $cs_name = $slice->coord_system_name;
foreach my $seg (@{ $slice->project($cs_name, $version) }) {
my $proj_slice = $seg->to_Slice;
# create a Mapper to map to/from the mapped_slice artificial coord system
my $mapper = Bio::EnsEMBL::Mapper->new('mapped_slice', 'native_slice');
# tell the mapper how to map this segment
$mapper->add_map_coordinates(
'mapped_slice',
$seg->from_start,
$seg->from_end,
($slice->strand * $proj_slice->strand),
$proj_slice->seq_region_name,
$proj_slice->start,
$proj_slice->end
);
# add the Slice/Mapper pair to the MappedSlice
$mapped_slice->add_Slice_Mapper_pair($proj_slice, $mapper);
}
return [$mapped_slice];
}
=head2 fetch_by_name
Arg[1] : Bio::EnsEMBL::MappedSliceContainer $container - the container
to attach MappedSlices to
Arg[2] : String $name - the assembly name to fetch
Arg[3] : (optional) String $version -- the version for the new assembly
Example : my ($mapped_slice) = @{ $msc->fetch_by_name('LRG1','1') };
Description : Creates a MappedSlice representing an alternative assembly
version of the container's reference slice.
Return type : listref of Bio::EnsEMBL::MappedSlice
Exceptions : thrown on wrong or missing arguments
Caller : general, Bio::EnsEMBL::MappedSliceContainer
Status : At Risk
: under development
=cut
sub fetch_by_name {
my $self = shift;
my $container = shift;
my $name = shift;
my $version = shift;
# arguement check
unless ($container and ref($container) and
$container->isa('Bio::EnsEMBL::MappedSliceContainer')) {
throw("Need a MappedSliceContainer.");
}
unless ($name) {
throw("Need an assembly name.");
}
$version ||= '';
my $slice = $container->ref_slice;
# project slice onto other assembly and construct MappedSlice for result
my $mapped_slice = Bio::EnsEMBL::MappedSlice->new(
-ADAPTOR => $self,
-CONTAINER => $container,
-NAME => $slice->name."\#mapped_$name:$version",
);
foreach my $seg (@{ $slice->project($name, $version) }) {
my $proj_slice = $seg->to_Slice;
# create a Mapper to map to/from the mapped_slice artificial coord system
my $mapper = Bio::EnsEMBL::Mapper->new('mapped_slice', 'native_slice');
# tell the mapper how to map this segment
$mapper->add_map_coordinates(
'mapped_slice',
$seg->from_start,
$seg->from_end,
($slice->strand * $proj_slice->strand),
$proj_slice->seq_region_name,
$proj_slice->start,
$proj_slice->end
);
# add the Slice/Mapper pair to the MappedSlice
$mapped_slice->add_Slice_Mapper_pair($proj_slice, $mapper);
}
return [$mapped_slice];
}
1;