Raw content of Bio::EnsEMBL::AssemblyMapper
<![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::AssemblyMapper -
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 $ctg_cs = $cs_adaptor->fetch_by_name('contig');
$asm_mapper = $map_adaptor->fetch_by_CoordSystems( $cs1, $cs2 );
# Map to contig coordinate system from chromosomal.
@ctg_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( 'AL30421.1.200.92341', 100, 10000, -1,
$ctg_cs );
# List contig names for a region of chromsome.
@ctg_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( 'AL30421.1.200.92341', 1, 1000, -1,
$ctg_cs );
=head1 DESCRIPTION
The AssemblyMapper is a database aware mapper which faciliates
conversion of coordinates between any two coordinate systems with an
relationship explicitly defined in the assembly table. In the future
it may be possible to perform multiple step (implicit) mapping between
coordinate systems.
It is implemented using the Bio::EnsEMBL::Mapper object, which is a
generic mapper object between disjoint coordinate systems.
=head1 METHODS
=cut
package Bio::EnsEMBL::AssemblyMapper;
use strict;
use warnings;
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
my $ASSEMBLED = 'assembled';
my $COMPONENT = 'component';
my $DEFAULT_MAX_PAIR_COUNT = 1000;
=head2 new
Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Arg [2] : Bio::EnsEMBL::CoordSystem $asm_cs
Arg [3] : Bio::EnsEMBL::CoordSystem $cmp_cs
Example : Should use AssemblyMapperAdaptor->fetch_by_CoordSystems()
Description: Creates a new AssemblyMapper
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : Throws if multiple coord_systems are provided
Caller : AssemblyMapperAdaptor
Status : Stable
=cut
sub new {
my ( $proto, $adaptor, @coord_systems ) = @_;
my $class = ref($proto) || $proto;
my $self = bless( {}, $class );
$self->adaptor($adaptor);
$adaptor->cache_seq_ids_with_mult_assemblys();
if ( @coord_systems != 2 ) {
throw( 'Can only map between two coordinate systems. '
. scalar(@coord_systems)
. ' were provided' );
}
# Set the component and assembled coordinate systems
$self->{'asm_cs'} = $coord_systems[0];
$self->{'cmp_cs'} = $coord_systems[1];
# We load the mapper calling the 'ASSEMBLED' the 'from' coord system
# and the 'COMPONENT' the 'to' coord system.
$self->{'mapper'} = Bio::EnsEMBL::Mapper->new( $ASSEMBLED, $COMPONENT,
$coord_systems[0], $coord_systems[1] );
$self->{'max_pair_count'} = $DEFAULT_MAX_PAIR_COUNT;
return $self;
} ## end sub new
=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 (1000) to tune the performance and
memory usage for certain scenarios. Higher value
means bigger cache, more memory used.
Return type: int
Exceptions : None
Caller : General
Status : Stable
=cut
sub max_pair_count {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'max_pair_count'} = $value;
}
return $self->{'max_pair_count'};
}
=head2 register_all
Arg [1] : None
Example : $mapper->max_pair_count(10e6);
$mapper->register_all();
Description: Pre-registers all assembly information in this
mapper. The cache size should be set to a
sufficiently large value so that all of the
information can be stored. This method is useful
when *a lot* of mapping will be done in regions
which are distributed around the genome. After
registration the mapper will consume a lot of memory
but will not have to perform any SQL and will be
faster.
Return type: None
Exceptions : None
Caller : Specialised programs doing a lot of mapping.
Status : Stable
=cut
sub register_all {
my ($self) = @_;
$self->adaptor()->register_all($self);
}
=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
Example : @coords =
$asm_mapper->map( 'X', 1_000_000, 2_000_000, 1,
$chr_cs );
Description: Transforms coordinates from one coordinate system to
another.
Return type: List of Bio::EnsEMBL::Mapper::Coordinate and/or
Bio::EnsEMBL::Mapper:Gap objects.
Exceptions : Throws if 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 )
= @_;
my $mapper = $self->{'mapper'};
my $asm_cs = $self->{'asm_cs'};
my $cmp_cs = $self->{'cmp_cs'};
my $adaptor = $self->{'adaptor'};
my $frm;
my $seq_region_id =
$self->adaptor()
->seq_regions_to_ids( $frm_cs, [$frm_seq_region_name] )->[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 == $cmp_cs
|| ( $frm_cs != $asm_cs && $frm_cs->equals($cmp_cs) ) )
{
if ( !$self->{'cmp_register'}->{$seq_region_id} ) {
$adaptor->register_component( $self, $seq_region_id );
}
$frm = $COMPONENT;
} elsif ( $frm_cs == $asm_cs || $frm_cs->equals($asm_cs) ) {
# This can be probably be sped up some by only calling registered
# assembled if needed.
$adaptor->register_assembled( $self, $seq_region_id, $frm_start,
$frm_end );
$frm = $ASSEMBLED;
} else {
throw(
sprintf( "Coordinate system %s %s is neither the assembled "
. "nor the component coordinate system "
. "of this AssemblyMapper",
$frm_cs->name(), $frm_cs->version() ) );
}
return
$mapper->map_coordinates( $seq_region_id, $frm_start, $frm_end,
$frm_strand, $frm );
} ## end sub map
=head2 flush
Args : None
Example : None
Description: Remove all cached items from this AssemblyMapper.
Return type: None
Exceptions : None
Caller : AssemblyMapperAdaptor
Status : Stable
=cut
sub flush {
my ($self) = @_;
$self->{'mapper'}->flush();
$self->{'cmp_register'} = {};
$self->{'asm_register'} = {};
}
=head2 size
Args : None
Example : $num_of_pairs = $mapper->size();
Description: Returns the number of pairs currently stored.
Return type: int
Exceptions : None
Caller : General
Status : Stable
=cut
sub size {
my ($self) = @_;
return $self->{'mapper'}->{'pair_count'};
}
=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 =
$asm_mapper->map( 'X', 1_000_000, 2_000_000, 1,
$chr_cs );
Description: Transforms coordinates from one coordinate system to
another.
Return type: List of Bio::EnsEMBL::Mapper::Coordinate and/or
Bio::EnsEMBL::Mapper:Gap objects.
Exceptions : Throws if the specified TO coordinat system is not
one of the coordinate systems associated with this
assembly mapper.
Caller : General
Status : Stable
=cut
sub fastmap {
if ( @_ != 6 ) {
throw('Incorrect number of arguments.');
}
my ( $self, $frm_seq_region_name, $frm_start, $frm_end, $frm_strand,
$frm_cs )
= @_;
my $mapper = $self->{'mapper'};
my $asm_cs = $self->{'asm_cs'};
my $cmp_cs = $self->{'cmp_cs'};
my $adaptor = $self->{'adaptor'};
my $frm;
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 == $cmp_cs
|| ( $frm_cs != $asm_cs && $frm_cs->equals($cmp_cs) ) )
{
if ( !$self->{'cmp_register'}->{$seq_region_id} ) {
$adaptor->register_component( $self, $seq_region_id );
}
$frm = $COMPONENT;
} elsif ( $frm_cs == $asm_cs || $frm_cs->equals($asm_cs) ) {
# This can be probably be sped up some by only calling registered
# assembled if needed
$adaptor->register_assembled( $self, $seq_region_id, $frm_start,
$frm_end );
$frm = $ASSEMBLED;
} else {
throw(
sprintf( "Coordinate system %s %s is neither the assembled "
. "nor the component coordinate system "
. "of this AssemblyMapper",
$frm_cs->name(), $frm_cs->version() ) );
}
return
$mapper->fastmap( $seq_region_id, $frm_start, $frm_end, $frm_strand,
$frm );
} ## end sub fastmap
=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 my $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.
Return type: List of strings.
Exceptions : None
Caller : General
Status : Stable
=cut
sub list_ids {
if ( @_ != 5 ) {
throw('Incorrect number of arguments.');
}
my ( $self, $frm_seq_region_name, $frm_start, $frm_end, $frm_cs ) =
@_;
my @tmp = ($frm_seq_region_name);
my $seq_region_id =
$self->adaptor()->seq_regions_to_ids( $frm_cs, \@tmp )->[0];
if ( $frm_cs->equals( $self->component_CoordSystem() ) ) {
if ( !$self->have_registered_component($seq_region_id) ) {
$self->adaptor->register_component( $self, $seq_region_id );
}
# Pull out the 'from' identifiers of the mapper pairs. The we
# loaded the assembled side as the 'from' side in the constructor.
return
map ( { $_->from()->id() }
$self->mapper()->list_pairs(
$seq_region_id, $frm_start, $frm_end, $COMPONENT
) );
} elsif ( $frm_cs->equals( $self->assembled_CoordSystem() ) ) {
$self->adaptor->register_assembled( $self, $seq_region_id,
$frm_start, $frm_end );
# Pull out the 'to' identifiers of the mapper pairs we loaded the
# component side as the 'to' coord system in the constructor.
return
map ( { $_->to->id() }
$self->mapper()->list_pairs(
$seq_region_id, $frm_start, $frm_end, $ASSEMBLED
) );
} else {
throw(
sprintf( "Coordinate system %s %s is neither the assembled "
. "nor the component coordinate system "
. "of this AssemblyMapper",
$frm_cs->name(), $frm_cs->version() ) );
}
} ## end sub list_ids
#sub list_seq_regions {
# throw('Incorrect number of arguments.') if(@_ != 5);
# my($self, $frm_seq_region_name, $frm_start, $frm_end, $frm_cs) = @_;
# if($frm_cs->equals($self->component_CoordSystem())) {
# if(!$self->have_registered_component($seq_region_id)) {
# $self->adaptor->register_component($self,$seq_region_id);
# }
# #pull out the 'from' identifiers of the mapper pairs. The
# #we loaded the assembled side as the 'from' side in the constructor
# return
# map {$_->from()->id()}
# $self->mapper()->list_pairs($seq_region_id, $frm_start,
# $frm_end, $COMPONENT);
# } elsif($frm_cs->equals($self->assembled_CoordSystem())) {
# $self->adaptor->register_assembled($self,
# $frm_seq_region,$frm_start,$frm_end);
# #pull out the 'to' identifiers of the mapper pairs
# #we loaded the component side as the 'to' coord system in the constructor
# return
# map {$_->to->id()}
# $self->mapper()->list_pairs($frm_seq_region, $frm_start,
# $frm_end, $ASSEMBLED);
# } else {
# throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
# " is neither the assembled nor the component coordinate system " .
# " of this AssemblyMapper");
# }
#}
=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 my $id (
$asm_mapper->list_seq_regions(
'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.
Return type: List of ints.
Exceptions : None
Caller : General
Status : Stable
=cut
sub list_seq_regions {
if ( @_ != 5 ) {
throw('Incorrect number of arguments.');
}
my ( $self, $frm_seq_region, $frm_start, $frm_end, $frm_cs ) = @_;
# Retrieve the seq_region names.
my @seq_ids =
$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->assembled_CoordSystem() ) ) {
$to_cs = $self->component_CoordSystem();
} else {
$to_cs = $self->assembled_CoordSystem();
}
# Convert them to IDs.
return @{ $self->adaptor()->seq_ids_to_regions( \@seq_ids ) };
}
#sub list_ids {
# throw('Incorrect number of arguments.') if(@_ != 5);
# my($self, $frm_seq_region, $frm_start, $frm_end, $frm_cs) = @_;
# #retrieve the seq_region names
# my @seq_regs =
# $self->list_seq_regions($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->assembled_CoordSystem())) {
# $to_cs = $self->component_CoordSystem();
# } else {
# $to_cs = $self->assembled_CoordSystem();
# }
# #convert them to ids
# return @{$self->adaptor()->seq_regions_to_ids($to_cs, \@seq_regs)};
#}
=head2 have_registered_component
Arg [1] : string $cmp_seq_region
The name of the sequence region to check for
registration.
Example : if ( $asm_mapper->have_registered_component('AL240214.1') ) {}
Description: Returns true if a given component region has
been registered with this assembly mapper. This
should only be called by this class or the
AssemblyMapperAdaptor. In other words, do not use
this method unless you really know what you are
doing.
Return type: Boolean (0 or 1)
Exceptions : Throws on incorrect arguments.
Caller : Internal, AssemblyMapperAdaptor
Status : Stable
=cut
sub have_registered_component {
my ( $self, $cmp_seq_region ) = @_;
if ( !defined($cmp_seq_region) ) {
throw('cmp_seq_region argument is required');
}
if ( exists( $self->{'cmp_register'}->{$cmp_seq_region} ) ) {
return 1;
}
return 0;
}
=head2 have_registered_assembled
Arg [1] : string $asm_seq_region
The name of the sequence region to check for
registration.
Arg [2] : int $chunk_id
The chunk number of the provided seq_region to check
for registration.
Example : if ( $asm_mapper->have_registered_component( 'X', 9 ) ) { }
Description: Returns true if a given assembled region chunk
has been registered with this assembly mapper.
This should only be called by this class or the
AssemblyMapperAdaptor. In other words, do not use
this method unless you really know what you are
doing.
Return type: Boolean (0 or 1)
Exceptions : Throws on incorrect arguments
Caller : Internal, AssemblyMapperAdaptor
Status : Stable
=cut
sub have_registered_assembled {
my ( $self, $asm_seq_region, $chunk_id ) = @_;
if ( !defined($asm_seq_region) ) {
throw('asm_seq_region argument is required');
}
if ( !defined($chunk_id) ) {
throw('chunk_id is required');
}
if (
exists( $self->{'asm_register'}->{$asm_seq_region}->{$chunk_id} ) )
{
return 1;
}
return 0;
}
=head2 register_component
Arg [1] : string $cmp_seq_region
The name of the component sequence region to
register.
Example : $asm_mapper->register_component('AL312341.1');
Description: Flags a given component sequence region as registered
in this assembly mapper. This should only be called
by this class or the AssemblyMapperAdaptor.
Return type: None
Exceptions : Throws on incorrect arguments
Caller : Internal, AssemblyMapperAdaptor
Status : Stable
=cut
sub register_component {
my ( $self, $cmp_seq_region ) = @_;
if ( !defined($cmp_seq_region) ) {
throw('cmp_seq_region argument is required');
}
$self->{'cmp_register'}->{$cmp_seq_region} = 1;
}
=head2 register_assembled
Arg [1] : string $asm_seq_region
The name of the sequence region to register.
Arg [2] : int $chunk_id
The chunk number of the provided seq_region to register.
Example : $asm_mapper->register_assembled( 'X', 4 );
Description: Flags a given assembled region as registered in this
assembly mapper. This should only be called by this
class or the AssemblyMapperAdaptor. Do not call this
method unless you really know what you are doing.
Return type: None
Exceptions : Throws on incorrect arguments
Caller : Internal, AssemblyMapperAdaptor
Status : Stable
=cut
sub register_assembled {
my ( $self, $asm_seq_region, $chunk_id ) = @_;
if ( !defined($asm_seq_region) ) {
throw('asm_seq_region argument is required');
}
if ( !defined($chunk_id) ) {
throw('chunk_id srgument is required');
}
$self->{'asm_register'}->{$asm_seq_region}->{$chunk_id} = 1;
}
=head2 mapper
Arg [1] : None
Example : $mapper = $asm_mapper->mapper();
Description: Retrieves the internal mapper used by this Assembly
Mapper. This is unlikely to be useful unless you
_really_ know what you are doing.
Return type: Bio::EnsEMBL::Mapper
Exceptions : None
Caller : Internal, AssemblyMapperAdaptor
Status : Stable
=cut
sub mapper {
my ($self) = @_;
return $self->{'mapper'};
}
=head2 assembled_CoordSystem
Arg [1] : None
Example : $cs = $asm_mapper->assembled_CoordSystem();
Description: Retrieves the assembled CoordSystem from this
assembly mapper.
Return type: Bio::EnsEMBL::CoordSystem
Exceptions : None
Caller : Internal, AssemblyMapperAdaptor
Status : Stable
=cut
sub assembled_CoordSystem {
my ($self) = @_;
return $self->{'asm_cs'};
}
=head2 component_CoordSystem
Arg [1] : None
Example : $cs = $asm_mapper->component_CoordSystem();
Description: Retrieves the component CoordSystem from this
assembly mapper.
Return type: Bio::EnsEMBL::CoordSystem
Exceptions : None
Caller : Internal, AssemblyMapperAdaptor
Status : Stable
=cut
sub component_CoordSystem {
my ($self) = @_;
return $self->{'cmp_cs'};
}
=head2 adaptor
Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor $adaptor
Example : None
Description: Getter/set terfor this object's database adaptor.
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : None
Caller : General
Status : Stable
=cut
sub adaptor {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'adaptor'} = $value;
}
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;
]]>