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Bio-EnsEMBL-112.0_56
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/ Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor

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

http://www.apache.org/licenses/LICENSE-2.0

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.

CONTACT

Please email comments or questions to the public Ensembl
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Questions may also be sent to the Ensembl help desk at
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NAME

Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor - adaptor/factory for MappedSlices representing alternative assemblies

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' ) };

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.

METHODS

new
fetch_by_version

REALTED MODULES

Bio::EnsEMBL::MappedSlice
Bio::EnsEMBL::MappedSliceContainer
Bio::EnsEMBL::Compara::AlignSlice
Bio::EnsEMBL::Compara::AlignSlice::Slice
Bio::EnsEMBL::Variation::StrainSlice

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

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

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