Bio::EnsEMBL::DBSQL AssemblySliceAdaptor
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Summary
Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor - adaptor/factory for MappedSlices
representing alternative assemblies
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::DBSQL::BaseAdaptor
Bio::EnsEMBL::MappedSlice
Bio::EnsEMBL::Mapper
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::DBSQL::BaseAdaptor
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
fetch_by_nameDescriptionCode
fetch_by_versionDescriptionCode
newDescriptionCode
Methods description
fetch_by_namecode    nextTop
  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
fetch_by_versioncodeprevnextTop
  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
newcodeprevnextTop
  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
Methods code
fetch_by_namedescriptionprevnextTop
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;
}
fetch_by_versiondescriptionprevnextTop
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];
}
newdescriptionprevnextTop
sub new {
  my $caller = shift;

  my $class = ref($caller) || $caller;
  my $self = $class->SUPER::new(@_);
  
  return $self;
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.
REALTED MODULESTop
  Bio::EnsEMBL::MappedSlice
  Bio::EnsEMBL::MappedSliceContainer
  Bio::EnsEMBL::Compara::AlignSlice
  Bio::EnsEMBL::Compara::AlignSlice::Slice
  Bio::EnsEMBL::AlignStrainSlice
  Bio::EnsEMBL::StrainSlice