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

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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