TopLevelAssemblyMapper.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
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.
 
=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=cut
 
=head1 NAME
 
Bio::EnsEMBL::TopLevelAssemblyMapper -
Handles mapping between a given coordinate system and the toplevel
pseudo coordinate system.
 
=head1 SYNOPSIS
 
  $db   = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
  $asma = $db->get_AssemblyMapperAdaptor();
  $csa  = $db->get_CoordSystemAdaptor();
 
  my $toplevel = $cs_adaptor->fetch_by_name('toplevel');
  my $ctg_cs   = $cs_adaptor->fetch_by_name('contig');
 
  $asm_mapper = $map_adaptor->fetch_by_CoordSystems( $toplevel, $ctg_cs );
 
  # map to toplevel coord system for this region
  @chr_coords =
    $asm_mapper->map( 'AL30421.1.200.92341', 100, 10000, -1, $ctg_cs );
 
  # list toplevel seq_region_ids for this region
  @chr_ids =
    $asm_mapper->list_ids( 'AL30421.1.200.92341', 1, 1000, -1,
    $ctg_cs );
 
=head1 DESCRIPTION
 
The TopLevelAssemblyMapper performs mapping between a provided
coordinate system and the toplevel pseudo cooordinate system.  The
toplevel coordinate system is not a real coordinate system, but
represents the highest coordinate system that can be mapped to in a
given region.  It is only possible to perform unidirectional mapping
using this mapper, because it does not make sense to map from the
toplevel coordinate system to another coordinate system.
 
=head1 METHODS
 
=cut
 
 
use strict;
use warnings;
 
package Bio::EnsEMBL::TopLevelAssemblyMapper;
 
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::CoordSystem;
use Scalar::Util qw(weaken);
 
=head2 new
 
  Arg [1]    : Bio::EnsEMBL::DBAdaptor $dbadaptor the adaptor for
               the database this mapper is using.
  Arg [2]    : Toplevel CoordSystem
  Arg [3]    : Other CoordSystem
  Description: Creates a new TopLevelAssemblyMapper object
  Returntype : Bio::EnsEMBL::DBSQL::TopLevelAssemblyMapper
  Exceptions : throws if any of the 3 arguments are missing/ not 
             : of the correct type.
  Caller     : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
  Status     : Stable
 
=cut
 
 
sub new {
  my ($caller, $adaptor, $toplevel_cs, $other_cs) = @_;
 
  my $class = ref($caller) || $caller;
 
  if(!ref($toplevel_cs)) {
    throw('Toplevel CoordSystem argument expected.');
  }
  if(!ref($other_cs)) {
    throw('Other CoordSystem argument expected.');
  }
 
  if(!$toplevel_cs->is_top_level()) {
    throw($toplevel_cs->name() . " is not the toplevel CoordSystem.");
  }
  if($other_cs->is_top_level()) {
    throw("Other CoordSystem argument should not be toplevel CoordSystem.");
  }
 
  my $cs_adaptor    = $adaptor->db()->get_CoordSystemAdaptor();
  my $coord_systems = $cs_adaptor->fetch_all();
 
  my $self = bless {'coord_systems' => $coord_systems,
            'toplevel_cs'   => $toplevel_cs,
            'other_cs'      => $other_cs}, $class;
 
  $self->adaptor($adaptor);
  return $self;
}
 
sub adaptor {
  my $self = shift;
 
  weaken($self->{'adaptor'} = shift) if(@_);
 
  return $self->{'adaptor'};
}
 
=head2 map
 
  Arg [1]    : string $frm_seq_region
               The name of the sequence region to transform FROM
  Arg [2]    : int $frm_start
               The start of the region to transform FROM
  Arg [3]    : int $frm_end
               The end of the region to transform FROM
  Arg [4]    : int $strand
               The strand of the region to transform FROM
  Arg [5]    : Bio::EnsEMBL::CoordSystem
               The coordinate system to transform FROM
  Arg [6]    : if set will do a fastmap
  Arg [7]    : (optional) dummy placeholder to keep the interface
               consistent across different mappers
  Arg [8]    : (optional) boolean
               Whether or not to include the original coordinates
  Example    : @coords = $mapper->map('X', 1_000_000, 2_000_000,
                                            1, $chr_cs);
  Description: Transforms coordinates from one coordinate system
               to another.
  Returntype : List of Bio::EnsEMBL::Mapper::Coordinate and/or
               Bio::EnsEMBL::Mapper:Gap objects
  Exceptions : thrown if if the specified TO coordinate system is not one
               of the coordinate systems associated with this mapper
  Caller     : general
  Status     : Stable
 
=cut
 
 
sub map {
  throw('Incorrect number of arguments.') if @_ < 6;
 
  my($self, $frm_seq_region_name, $frm_start, $frm_end, $frm_strand, $frm_cs,
    $fastmap, $dummy, $include_org_coord) = @_;
 
  if($frm_cs->is_top_level()) {
    throw("The toplevel CoordSystem can only be mapped TO, not FROM.");
  }
 
  my @tmp;
  push @tmp, $frm_seq_region_name;
  my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs, \@tmp)}[0];
 
  my $mapper      = $self->{'mapper'};
  my $toplevel_cs = $self->{'toplevel_cs'};
  my $other_cs    = $self->{'other_cs'};
  my $adaptor     = $self->adaptor;
 
  if($frm_cs != $other_cs && !$frm_cs->equals($other_cs)) {
    throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
          " is neither the assembled nor the component coordinate system " .
          " of this AssemblyMapper");
  }
 
  my $coord_systems = $self->{'coord_systems'};
 
  my $csa = $self->adaptor()->db()->get_CoordSystemAdaptor();
 
  #
  # TBD try to make this more efficient
  #
  my $from_rank = $other_cs->rank();
  foreach my $cs (@$coord_systems) {
    last if($cs->rank >= $from_rank);
 
    #check if a mapping path even exists to this coordinate system
    my @mapping_path = @{ $csa->get_mapping_path( $cs, $other_cs ) };
 
    if(@mapping_path) {
 
      # Try to map to this coord system. If we get back any coordinates then
      # it is our 'toplevel' that we were looking for
      my $mapper = $adaptor->fetch_by_CoordSystems($other_cs, $cs);
 
      if($fastmap) {
        my @result = $mapper->fastmap($frm_seq_region_name, $frm_start, $frm_end,
                                      $frm_strand, $frm_cs);
        return @result if(@result);
      } else {
        my @coords = $mapper->map($frm_seq_region_name, $frm_start, $frm_end,
                                  $frm_strand, $frm_cs, undef, undef, $include_org_coord);
 
        if(@coords > 1) {
      return @coords;
    } elsif ($include_org_coord) {
      return @coords unless $coords[0]{mapped}->isa('Bio::EnsEMBL::Mapper::Gap');
    } else {
      return @coords unless $coords[0]->isa('Bio::EnsEMBL::Mapper::Gap');
    }
      }
    }
  }
 
  #
  # the toplevel coordinate system for the region requested *is* the requested region.
  #
  if ($fastmap) {
    return ($seq_region_id, $frm_start, $frm_end, $frm_strand, $other_cs);
  }
 
  my $coord = Bio::EnsEMBL::Mapper::Coordinate->new($seq_region_id, $frm_start,$frm_end, $frm_strand, $other_cs);
  if ($include_org_coord) {
    return { 'original' => $coord, 'mapped' => $coord };
  } else {
    return $coord;
  }
}
 
=head2 flush
 
  Args       : none
  Example    : none
  Description: polymorphism with AssemblyMapper, does nothing
  Returntype : none
  Exceptions : none
  Status     : Stable
 
=cut
 
sub flush {}
 
=head2 fastmap
 
  Arg [1]    : string $frm_seq_region
               The name of the sequence region to transform FROM
  Arg [2]    : int $frm_start
               The start of the region to transform FROM
  Arg [3]    : int $frm_end
               The end of the region to transform FROM
  Arg [4]    : int $strand
               The strand of the region to transform FROM
  Arg [5]    : Bio::EnsEMBL::CoordSystem
               The coordinate system to transform FROM
  Example    : @coords = $mapper->fastmap('X', 1_000_000, 2_000_000,
                                            1, $chr_cs);
  Description: Transforms coordinates from one coordinate system
               to another.
  Returntype : List of Bio::EnsEMBL::Mapper::Coordinate and/or
               Bio::EnsEMBL::Mapper:Gap objects
  Exceptions : thrown if if the specified TO coordinate system is not one
               of the coordinate systems associated with this mapper
  Caller     : general
  Status     : Stable
 
=cut
 
sub fastmap {
  my $self = shift;
  return $self->map(@_,1);
}
 
=head2 assembled_CoordSystem
 
  Arg [1]    : none
  Example    : $cs = $mapper->assembled_CoordSystem
  Description: Retrieves the assembled CoordSystem from this mapper
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal, AssemblyMapperAdaptor
  Status     : Stable
 
=cut
 
sub assembled_CoordSystem {
  my $self = shift;
  return $self->{'toplevel_cs'};
}
 
=head2 component_CoordSystem
 
  Arg [1]    : none
  Example    : $cs = $mapper->component_CoordSystem
  Description: Retrieves the component CoordSystem from this  mapper
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal, AssemblyMapperAdaptor
  Status     : Stable
 
=cut
 
sub component_CoordSystem {
  my $self = shift;
  return $self->{'other_cs'};
}
 
 
sub _list {
  my($self, $frm_seq_region_name, $frm_start, $frm_end, $frm_cs, $seq_regions) = @_;
 
  my $mapper      = $self->{'mapper'};
  my $toplevel_cs = $self->{'toplevel_cs'};
  my $other_cs    = $self->{'other_cs'};
  my $adaptor     = $self->adaptor;
 
  if($frm_cs->is_top_level()) {
    throw("The toplevel CoordSystem can only be mapped TO, not FROM.");
  }
  if($frm_cs != $other_cs && !$frm_cs->equals($other_cs)) {
    throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
          " is neither the assembled nor the component coordinate system " .
          " of this AssemblyMapper");
  }
 
  my $coord_systems = $self->{'coord_systems'};
  my $csa = $self->adaptor()->db()->get_CoordSystemAdaptor();
 
  #
  # TBD try to make this more efficient
  #
  my $from_rank = $other_cs->rank();
  foreach my $cs (@$coord_systems) {
    last if($cs->rank >= $from_rank);
 
    #check if a mapping path even exists to this coordinate system
    my @mapping_path = @{ $csa->get_mapping_path( $cs, $other_cs ) };
 
    if(@mapping_path) {
 
      # Try to map to this coord system. If we get back any coordinates then
      # it is our 'toplevel' that we were looking for
      my $mapper = $adaptor->fetch_by_CoordSystems($other_cs, $cs);
 
      my @result;
 
      my @tmp;
      push @tmp, $frm_seq_region_name;
      my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs, \@tmp)}[0];
 
      if($seq_regions) {
        @result = $mapper->list_seq_regions($frm_seq_region_name, $frm_start,
                                            $frm_end, $frm_cs);
      } else {
        @result = $mapper->list_ids($frm_seq_region_name, $frm_start,
                                    $frm_end, $frm_cs);
      }
 
      return @result if(@result);
    }
  }
 
  # the toplevel coordinate system for the region requested *is* the
  return ($frm_seq_region_name);
 
 
  # requested region.
  if($seq_regions) {
    return ($frm_seq_region_name);
  }
 
  #this seems a bit silly and inefficient, but it is probably never
  #called anyway.
  my $slice_adaptor = $adaptor->db()->get_SliceAdaptor();
  my $slice = $slice_adaptor->fetch_by_region($other_cs->name(),
                                              $frm_seq_region_name,
                                              undef,undef,undef,$other_cs);
  return ($slice_adaptor->get_seq_region_id($slice));
}
 
 
 
=head2 list_seq_regions
 
  Arg [1]    : string $frm_seq_region
               The name of the sequence region of interest
  Arg [2]    : int $frm_start
               The start of the region of interest
  Arg [3]    : int $frm_end
               The end of the region to transform of interest
  Arg [5]    : Bio::EnsEMBL::CoordSystem $frm_cs
               The coordinate system to obtain overlapping ids of
  Example    : foreach $id ($asm_mapper->list_ids('X',1,1000,$ctg_cs)) {...}
  Description: Retrieves a list of overlapping seq_region names
               of another coordinate system.  This is the same as the
               list_ids method but uses seq_region names rather internal ids
  Returntype : List of strings
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub list_seq_regions {
  throw('Incorrect number of arguments.') if(@_ != 5);
  return _list(@_,1);
}
 
 
=head2 list_ids
 
  Arg [1]    : string $frm_seq_region
               The name of the sequence region of interest.
  Arg [2]    : int $frm_start
               The start of the region of interest
  Arg [3]    : int $frm_end
               The end of the region to transform of interest
  Arg [5]    : Bio::EnsEMBL::CoordSystem $frm_cs
               The coordinate system to obtain overlapping ids of
  Example    : foreach $id ($asm_mapper->list_ids('X',1,1000,$chr_cs)) {...}
  Description: Retrieves a list of overlapping seq_region internal identifiers
               of another coordinate system.  This is the same as the
               list_seq_regions method but uses internal identfiers rather 
               than seq_region strings
  Returntype : List of ints
  Exceptions : thrown if the from CoordSystem is the toplevel coord system
               thrown if the from CoordSystem is not the one used in the mapper
  Caller     : general
  Status     : Stable
 
=cut
 
sub list_ids {
  throw('Incorrect number of arguments.') if(@_ != 5);
  return _list(@_,0);
}
 
 
 
 
 
1;