Raw content of Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor
<![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::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::AlignStrainSlice
Bio::EnsEMBL::StrainSlice
=cut
package Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor;
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::MappedSlice;
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
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;
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