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Bio-EnsEMBL-112.0_53
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

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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