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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CONTACT

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NAME

Bio::EnsEMBL::TopLevelAssemblyMapper - Handles mapping between a given coordinate system and the toplevel pseudo coordinate system.

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 );

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.

METHODS

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

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

flush

  Args       : none
  Example    : none
  Description: polymorphism with AssemblyMapper, does nothing
  Returntype : none
  Exceptions : none
  Status     : Stable

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

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

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

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

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