Raw content of Bio::EnsEMBL::ChainedAssemblyMapper
<![CDATA[=head1 LICENSE
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
=head1 CONTACT
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>.
=cut
=head1 NAME
Bio::EnsEMBL::ChainedAssemblyMapper -
Handles mapping between two coordinate systems using the information
stored in the assembly table
=head1 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 );
=head1 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.
=head1 METHODS
=cut
my $FIRST = 'first';
my $MIDDLE = 'middle';
my $LAST = 'last';
package Bio::EnsEMBL::ChainedAssemblyMapper;
use strict;
use warnings;
use integer; #use proper arithmetic bitshifts
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::Mapper::RangeRegistry;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
#2^20 = approx 10^6
my $CHUNKFACTOR = 20;
# max size of the pair cache in the mappers
my $DEFAULT_MAX_PAIR_COUNT = 6000;
=head2 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 $dst_cs
Example : Should use AssemblyMapperAdaptor->fetch_by_CoordSystems
Description: Creates a new AssemblyMapper
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : thrown if wrong number of coord_systems are provided
Caller : AssemblyMapperAdaptor
Status : Stable
=cut
sub new {
my ($caller,$adaptor,@coord_systems) = @_;
my $class = ref($caller) || $caller;
my $self = {};
bless $self, $class;
$self->adaptor($adaptor);
if(@coord_systems != 3) {
throw('ChainedMapper can only map between 3 coordinate systems. ' .
scalar(@coord_systems) . ' were provided');
}
$adaptor->cache_seq_ids_with_mult_assemblys();
# Set the component, intermediate and assembled coordinate systems
$self->{'first_cs'} = $coord_systems[0];
$self->{'mid_cs'} = $coord_systems[1];
$self->{'last_cs'} = $coord_systems[2];
#maps between first and intermediate coord systems
$self->{'first_mid_mapper'} = Bio::EnsEMBL::Mapper->new($FIRST, $MIDDLE);
#maps between last and intermediate
$self->{'last_mid_mapper'} = Bio::EnsEMBL::Mapper->new($LAST, $MIDDLE);
#mapper that is actually used and is loaded by the mappings generated
#by the other two mappers
$self->{'first_last_mapper'} = Bio::EnsEMBL::Mapper->new($FIRST, $LAST,
$coord_systems[0],
$coord_systems[2]);
#need registries to keep track of what regions are registered in source
#and destination coordinate systems
$self->{'first_registry'} = Bio::EnsEMBL::Mapper::RangeRegistry->new();
$self->{'last_registry'} = Bio::EnsEMBL::Mapper::RangeRegistry->new();
$self->{'max_pair_count'} = $DEFAULT_MAX_PAIR_COUNT;
return $self;
}
=head2 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
=cut
sub max_pair_count {
my $self = shift;
$self->{'max_pair_count'} = shift if(@_);
return $self->{'max_pair_count'};
}
=head2 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
=cut
sub register_all {
my $self = shift;
$self->adaptor->register_all_chained($self);
return;
}
sub flush {
my $self = shift;
$self->{'first_registry'}->flush();
$self->{'last_registry'}->flush();
$self->{'first_mid_mapper'}->flush();
$self->{'last_mid_mapper'}->flush();
$self->{'first_last_mapper'}->flush();
}
=head2 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
=cut
sub size {
my $self = shift;
return ( $self->{'first_last_mapper'}->{'pair_count'} +
$self->{'last_mid_mapper'}->{'pair_count'} +
$self->{'first_mid_mapper'}->{'pair_count'} );
}
=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] : (optional) fastmap
Arg [7] : (optional) Bio::Ensembl::Slice
The slice to transform TO
Example : @coords = $asm_mapper->map('X', 1_000_000, 2_000_000,
1, $chr_cs);
Description: Transforms coordinates from one coordinate system
to another.
Returntype : List of Bio::EnsEMBL::Mapper::Coordinate and/or
Bio::EnsEMBL::Mapper:Gap objects
Exceptions : thrown if the specified TO coordinat system is not one
of the coordinate systems associated with this assembly mapper
Caller : general
Status : Stable
=cut
sub map {
throw('Incorrect number of arguments.') if(@_ < 6);
my ($self, $frm_seq_region_name, $frm_start,
$frm_end, $frm_strand, $frm_cs, $fastmap, $to_slice) = @_;
my $mapper = $self->{'first_last_mapper'};
my $first_cs = $self->{'first_cs'};
my $last_cs = $self->{'last_cs'};
my $is_insert = ($frm_end + 1 == $frm_start);
my $frm;
my $registry;
my @tmp;
push @tmp, $frm_seq_region_name;
my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs, \@tmp)}[0];
#speed critical section:
#try to do simple pointer equality comparisons of the coord system objects
#first since this is likely to work most of the time and is much faster
#than a function call
if($frm_cs == $first_cs ||
($frm_cs != $last_cs && $frm_cs->equals($first_cs))) {
$frm = $FIRST;
$registry = $self->{'first_registry'};
} elsif($frm_cs == $last_cs || $frm_cs->equals($last_cs)) {
$frm = $LAST;
$registry = $self->{'last_registry'};
} else {
throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
" is neither the first nor the last coordinate system " .
" of this ChainedAssemblyMapper");
}
#the minimum area we want to register if registration is necessary is
#about 1MB. Break requested ranges into chunks of 1MB and then register
#this larger region if we have a registry miss.
#use bitwise shift for fast and easy integer multiplication and division
my ($min_start, $min_end);
if($is_insert) {
$min_start = (($frm_end >> $CHUNKFACTOR) << $CHUNKFACTOR);
$min_end = ((($frm_start >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1 ;
} else {
$min_start = (($frm_start >> $CHUNKFACTOR) << $CHUNKFACTOR);
$min_end = ((($frm_end >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1 ;
}
#get a list of ranges in the requested region that have not been registered,
#and register them at the same
my $ranges;
if($is_insert) {
$ranges = $registry->check_and_register($seq_region_id, $frm_end,
$frm_start, $min_start, $min_end);
} else {
$ranges = $registry->check_and_register($seq_region_id, $frm_start,
$frm_end, $min_start, $min_end);
}
if(defined($ranges)) {
if( $self->size() > $self->{'max_pair_count'} ) {
$self->flush();
if($is_insert) {
$ranges = $registry->check_and_register
($seq_region_id, $frm_end, $frm_start, $min_start, $min_end);
} else {
$ranges = $registry->check_and_register
($seq_region_id, $frm_start, $frm_end, $min_start, $min_end);
}
}
$self->adaptor->register_chained($self,$frm,$seq_region_id,$ranges,$to_slice);
}
if($fastmap) {
return $mapper->fastmap($seq_region_id, $frm_start, $frm_end,
$frm_strand, $frm);
}
return $mapper->map_coordinates($seq_region_id, $frm_start, $frm_end,
$frm_strand, $frm);
}
sub fastmap {
my $self = shift;
return $self->map(@_,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,$chr_cs)) {...}
Description: Retrieves a list of overlapping seq_region internal identifiers
of another coordinate system. This is the same as the
list_seq_regions method but uses internal identfiers rather
than seq_region strings
Returntype : List of ints
Exceptions : none
Caller : general
Status : Stable
=cut
sub list_ids {
throw('Incorrect number of arguments.') if(@_ != 5);
my($self, $frm_seq_region_name, $frm_start, $frm_end, $frm_cs) = @_;
my $is_insert = ($frm_start == $frm_end + 1);
#the minimum area we want to register if registration is necessary is
#about 1MB. Break requested ranges into chunks of 1MB and then register
#this larger region if we have a registry miss.
#use bitwise shift for fast and easy integer multiplication and division
my ($min_start, $min_end);
if($is_insert) {
$min_start = (($frm_end >> $CHUNKFACTOR) << $CHUNKFACTOR);
$min_end = ((($frm_start >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1;
} else {
$min_start = (($frm_start >> $CHUNKFACTOR) << $CHUNKFACTOR);
$min_end = ((($frm_end >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1;
}
my @tmp;
push @tmp, $frm_seq_region_name;
my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs, \@tmp)}[0];
if($frm_cs->equals($self->{'first_cs'})) {
my $registry = $self->{'first_registry'};
my $ranges;
if($is_insert) {
$ranges = $registry->check_and_register
($seq_region_id, $frm_end, $frm_start, $min_start, $min_end);
} else {
$ranges = $registry->check_and_register
($seq_region_id, $frm_start, $frm_end, $min_start, $min_end);
}
if(defined($ranges)) {
$self->adaptor->register_chained($self,$FIRST,$seq_region_id,$ranges);
}
return map {$_->to()->id()}
$self->first_last_mapper()->list_pairs($seq_region_id, $frm_start,
$frm_end, $FIRST);
} elsif($frm_cs->equals($self->{'last_cs'})) {
my $registry = $self->{'last_registry'};
my $ranges;
if($is_insert) {
$ranges = $registry->check_and_register
($seq_region_id, $frm_end, $frm_start, $min_start, $min_end);
} else {
$ranges = $registry->check_and_register
($seq_region_id, $frm_start, $frm_end, $min_start, $min_end);
}
if(defined($ranges)) {
$self->adaptor->register_chained($self,$LAST,$seq_region_id,$ranges);
}
return map {$_->from()->id()}
$self->first_last_mapper()->list_pairs($seq_region_id, $frm_start,
$frm_end, $LAST);
} else {
throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
" is neither the first nor the last coordinate system " .
" of this ChainedAssemblyMapper");
}
}
=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,$ctg_cs)) {...}
Description: Retrieves a list of overlapping seq_region internal identifiers
of another coordinate system. This is the same as the
list_ids method but uses seq_region names rather internal ids
Returntype : List of strings
Exceptions : none
Caller : general
Status : Stable
=cut
sub list_seq_regions {
throw('Incorrect number of arguments.') if(@_ != 5);
my($self, $frm_seq_region, $frm_start, $frm_end, $frm_cs) = @_;
#retrieve the seq_region names
my @seq_regs =
$self->list_ids($frm_seq_region,$frm_start,$frm_end,$frm_cs);
#The seq_regions are from the 'to' coordinate system not the
#from coordinate system we used to obtain them
my $to_cs;
if($frm_cs->equals($self->first_CoordSystem())) {
$to_cs = $self->last_CoordSystem();
} else {
$to_cs = $self->first_CoordSystem();
}
#convert them to names
return @{$self->adaptor()->seq_ids_to_regions(\@seq_regs)};
}
=head2 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
=cut
sub first_last_mapper {
my $self = shift;
return $self->{'first_last_mapper'};
}
=head2 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
=cut
sub first_middle_mapper {
my $self = shift;
return $self->{'first_mid_mapper'};
}
=head2 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
=cut
sub last_middle_mapper {
my $self = shift;
return $self->{'last_mid_mapper'};
}
=head2 first_CoordSystem
Args : none
Example : $coordsys = $cam->first_CoordSystem();
Description: return the CoordSystem.
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : internal
Status : Stable
=cut
sub first_CoordSystem {
my $self = shift;
return $self->{'first_cs'};
}
=head2 middle_CoordSystem
Args : none
Example : $coordsys = $cam->middle_CoordSystem();
Description: return the CoordSystem.
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : internal
Status : Stable
=cut
sub middle_CoordSystem {
my $self = shift;
return $self->{'mid_cs'};
}
=head2 last_CoordSystem
Args : none
Example : $coordsys = $cam->last_CoordSystem();
Description: return the CoordSystem.
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : internal
Status : Stable
=cut
sub last_CoordSystem {
my $self = shift;
return $self->{'last_cs'};
}
=head2 first_registry
Args : none
Example : $coordsys = $cam->first_registry();
Description: return the Registry.
Returntype : Bio::EnsEMBL::Mapper::RangeRegistry
Exceptions : none
Caller : internal
Status : Stable
=cut
sub first_registry {
my $self = shift;
return $self->{'first_registry'};
}
=head2 lsst_registry
Args : none
Example : $coordsys = $cam->lsst_registry();
Description: return the Registry.
Returntype : Bio::EnsEMBL::Mapper::RangeRegistry
Exceptions : none
Caller : internal
Status : Stable
=cut
sub last_registry {
my $self = shift;
return $self->{'last_registry'};
}
#
# Methods supplied to maintain polymorphism with AssemblyMapper
# there is no real assembled or component in the chained mapper, since the
# ordering is arbitrary and both ends might actually be assembled, but these
# methods provide convenient synonyms
#
=head2 mapper
Args : none
Example : $mapper = $cam->mapper();
Description: return the first_last_mapper.
Returntype : Bio::EnsEMBL::Mapper
Exceptions : none
Caller : internal
Status : Stable
=cut
sub mapper {
my $self = shift;
return $self->first_last_mapper();
}
=head2 assembled_CoordSystem
Args : none
Example : $coordsys = $cam->assembled_CoordSystem();
Description: return the first CoordSystem.
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : internal
Status : Stable
=cut
sub assembled_CoordSystem {
my $self = shift;
return $self->{'first_cs'};
}
=head2 component_CoordSystem
Args : none
Example : $coordsys = $cam->component_CoordSystem();
Description: return the last CoordSystem.
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : internal
Status : Stable
=cut
sub component_CoordSystem {
my $self = shift;
return $self->{'last_cs'};
}
=head2 adaptor
Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor $adaptor
Example : none
Description: get/set for this objects database adaptor
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : none
Caller : general
Status : Stable
=cut
sub adaptor {
my $self = shift;
$self->{'adaptor'} = shift if(@_);
return $self->{'adaptor'};
}
=head2 in_assembly
Description: Deprecated. Use map() or list_ids() instead
=cut
sub in_assembly {
my ($self, $object) = @_;
deprecate('Use map() or list_ids() instead.');
my $csa = $self->db->get_CoordSystemAdaptor();
my $top_level = $csa->fetch_top_level();
my $asma = $self->adaptor->fetch_by_CoordSystems($object->coord_system(),
$top_level);
my @list = $asma->list_ids($object->seq_region(), $object->start(),
$object->end(), $object->coord_system());
return (@list > 0);
}
=head2 map_coordinates_to_assembly
Description: DEPRECATED use map() instead
=cut
sub map_coordinates_to_assembly {
my ($self, $contig_id, $start, $end, $strand) = @_;
deprecate('Use map() instead.');
#not sure if contig_id is seq_region_id or name...
return $self->map($contig_id, $start, $end, $strand,
$self->contig_CoordSystem());
}
=head2 fast_to_assembly
Description: DEPRECATED use map() instead
=cut
sub fast_to_assembly {
my ($self, $contig_id, $start, $end, $strand) = @_;
deprecate('Use map() instead.');
#not sure if contig_id is seq_region_id or name...
return $self->map($contig_id, $start, $end, $strand,
$self->contig_CoordSystem());
}
=head2 map_coordinates_to_rawcontig
Description: DEPRECATED use map() instead
=cut
sub map_coordinates_to_rawcontig {
my ($self, $chr_name, $start, $end, $strand) = @_;
deprecate('Use map() instead.');
return $self->map($chr_name, $start, $end, $strand,
$self->assembled_CoordSystem());
}
=head2 list_contig_ids
Description: DEPRECATED Use list_ids instead
=cut
sub list_contig_ids {
my ($self, $chr_name, $start, $end) = @_;
deprecate('Use list_ids() instead.');
return $self->list_ids($chr_name, $start, $end,
$self->assembled_CoordSystem());
}
1;
]]>