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Bio-EnsEMBL-112.0_52
River stage zero No dependents
/ Bio::EnsEMBL::ChainedAssemblyMapper

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
  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>.

NAME

Bio::EnsEMBL::ChainedAssemblyMapper - Handles mapping between two coordinate systems using the information stored in the assembly table

SYNOPSIS

    $db   = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
    $asma = $db->get_AssemblyMapperAdaptor();
    $csa  = $db->get_CoordSystemAdaptor();

    my $chr_cs = $cs_adaptor->fetch_by_name( 'chromosome', 'NCBI33' );
    my $cln_cs = $cs_adaptor->fetch_by_name('clone');

    $asm_mapper = $map_adaptor->fetch_by_CoordSystems( $cs1, $cs2 );

    # Map to contig coordinate system from chromosomal
    @cln_coords =
      $asm_mapper->map( 'X', 1_000_000, 2_000_000, 1, $chr_cs );

    # Map to chromosome coordinate system from contig
    @chr_coords =
      $asm_mapper->map( 'AL30421.1', 100, 10000, -1, $cln_cs );

    # List contig names for a region of chromsome
    @cln_ids = $asm_mapper->list_ids( '13', 1_000_000, 1, $chr_cs );

    # List chromosome names for a contig region
    @chr_ids =
      $asm_mapper->list_ids( 'AL30421.1', 1, 1000, -1, $cln_cs );

DESCRIPTION

The ChainedAssemblyMapper is an extension of the regular AssemblyMapper that allows for mappings between coordinate systems that require multi-step mapping. For example if explicit mappings are defined between the following coordinate systems,

  chromosome <-> contig
  contig     <-> clone

the ChainedAssemblyMapper would be able to perform implicit mapping between the chromosome and clone coordinate systems. This should be transparent to the user of this module, and users should not even realise that they are using a chained assembly mapper as opposed to a normal assembly mapper.

METHODS

new

  Arg [1]    : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
  Arg [2]    : Bio::EnsEMBL::CoordSystem $src_cs
  Arg [3]    : Bio::EnsEMBL::CoordSystem $int_cs
  Arg [4]    : Bio::EnsEMBL::CoordSystem $dst_cs
  Example    : Should use AssemblyMapperAdaptor->fetch_by_CoordSystems
  Description: Creates a new AssemblyMapper
  Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
  Exceptions : thrown if wrong number of coord_systems are provided
  Caller     : AssemblyMapperAdaptor
  Status     : Stable

max_pair_count

  Arg [1]    : (optional) int $max_pair_count
  Example    : $mapper->max_pair_count(100000)
  Description: Getter/Setter for the number of mapping pairs allowed in the
               internal cache. This can be used to override the default value
               (6000) to tune the performance and memory usage for certain
               scenarios. Higher value = bigger cache, more memory used
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

register_all

  Arg [1]    : none
  Example    : $mapper->max_pair_count(10e6);
               $mapper->register_all();
  Description: Pre-registers all assembly information in this mapper.  The
               cache size should be set to a sufficiently large value
               so that all of the information can be stored.  This method
               is useful when *a lot* of mapping will be done in regions
               which are distributed around the genome.   After registration
               the mapper will consume a lot of memory but will not have to
               perform any SQL and will be faster.
  Returntype : none
  Exceptions : none
  Caller     : specialised programs doing a lot of mapping
  Status     : Stable

size

  Args       : none
  Example    : $num_of_pairs = $mapper->size();
  Description: return the number of pairs currently stored.
  Returntype : int
  Exceptions : none
  Caller     : general
  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]    : (optional) fastmap
  Arg [7]    : (optional) Bio::Ensembl::Slice
               The slice to transform TO
  Arg [8]    : (optional) boolean
               Whether to include the original coordinates or not
  Example    : @coords = $asm_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 the specified TO coordinat system is not one
               of the coordinate systems associated with this assembly mapper
  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 : none
  Caller     : general
  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 internal identifiers
               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

first_last_mapper

  Args       : none
  Example    : $mapper = $cam->first_last_mapper();
  Description: return the mapper.
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : internal
  Status     : Stable

first_middle_mapper

  Args       : none
  Example    : $mapper = $cam->first_middle_mapper();
  Description: return the mapper.
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : internal
  Status     : Stable

last_middle_mapper

  Args       : none
  Example    : $mapper = $cam->last_middle_mapper();
  Description: return the mapper.
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : internal
  Status     : Stable

first_CoordSystem

  Args       : none
  Example    : $coordsys = $cam->first_CoordSystem();
  Description: return the CoordSystem.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal
  Status     : Stable

middle_CoordSystem

  Args       : none
  Example    : $coordsys = $cam->middle_CoordSystem();
  Description: return the CoordSystem.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal
  Status     : Stable

last_CoordSystem

  Args       : none
  Example    : $coordsys = $cam->last_CoordSystem();
  Description: return the CoordSystem.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal
  Status     : Stable

first_registry

  Args       : none
  Example    : $rr = $cam->first_registry();
  Description: return the Registry.
  Returntype : Bio::EnsEMBL::Mapper::RangeRegistry
  Exceptions : none
  Caller     : internal
  Status     : Stable

last_registry

  Args       : none
  Example    : $rr = $cam->last_registry();
  Description: return the Registry.
  Returntype : Bio::EnsEMBL::Mapper::RangeRegistry
  Exceptions : none
  Caller     : internal
  Status     : Stable

mapper

  Args       : none
  Example    : $mapper = $cam->mapper();
  Description: return the first_last_mapper.
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : internal
  Status     : Stable

assembled_CoordSystem

  Args       : none
  Example    : $coordsys = $cam->assembled_CoordSystem();
  Description: return the first CoordSystem.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal
  Status     : Stable

component_CoordSystem

  Args       : none
  Example    : $coordsys = $cam->component_CoordSystem();
  Description: return the last CoordSystem.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : internal
  Status     : Stable

adaptor

  Arg [1]    : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor $adaptor
  Description: get/set for this objects database adaptor
  Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
  Exceptions : none
  Caller     : general
  Status     : Stable