=head1 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
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.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
Questions may also be sent to the Ensembl help desk at
=cut
=head1 NAME
Bio::EnsEMBL::CircularSlice - Arbitary Slice of a genome
=head1 SYNOPSIS
$sa = $db->get_SliceAdaptor;
$slice =
$sa->fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 );
# get some attributes of the slice
my $seqname = $slice->seq_region_name();
my $start = $slice->start();
my $end = $slice->end();
# get the sequence from the slice
my $seq = $slice->seq();
# get some features from the slice
foreach $gene ( @{ $slice->get_all_Genes } ) {
# do something with a gene
}
foreach my $feature ( @{ $slice->get_all_DnaAlignFeatures } ) {
# do something with dna-dna alignments
}
=head1 DESCRIPTION
A Slice object represents a region of a genome. It can be used to
retrieve sequence or features from an area of interest.
=head1 METHODS
=cut
$Bio::EnsEMBL::CircularSlice::VERSION = '113.0.0'; # TRIAL
use vars qw(@ISA);
use strict;
qw(throw warning);
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
#use Bio::EnsEMBL::IndividualSlice;
#use Bio::EnsEMBL::IndividualSliceFactory;
use Scalar::Util qw(weaken isweak);
my $reg = "Bio::EnsEMBL::Registry";
@ISA = qw(Bio::EnsEMBL::Slice);
=head2 new
Arg [...] : List of named arguments
Bio::EnsEMBL::CoordSystem COORD_SYSTEM
string SEQ_REGION_NAME,
int START,
int END,
int SEQ_REGION_LENGTH, (optional)
string SEQ (optional)
int STRAND, (optional, defaults to 1)
Bio::EnsEMBL::DBSQL::SliceAdaptor ADAPTOR (optional)
Example :
$slice =
Bio::EnsEMBL::CircularSlice->new( -coord_system => $cs,
-start => 1,
-end => 10000,
-strand => 1,
-seq_region_name => 'X',
-seq_region_length => 12e6,
-adaptor => $slice_adaptor );
Description: Creates a new slice object. A slice represents a
region of sequence in a particular coordinate system.
Slices can be used to retrieve sequence and features
from an area of interest in a genome.
Coordinates start at 1 and are inclusive. Negative
coordinates or coordinates exceeding the length of
the seq_region are permitted. Start must be less
than or equal. to end regardless of the strand.
Slice objects are immutable. Once instantiated their
attributes (with the exception of the adaptor) may
not be altered. To change the attributes a new slice
must be created.
Returntype : Bio::EnsEMBL::CircularSlice
Exceptions : throws if start, end, coordsystem or seq_region_name not
specified or not of the correct type
Caller : general, Bio::EnsEMBL::SliceAdaptor
Status : Stable
=cut
sub new {
my $caller = shift;
#new can be called as a class or object method
my $class = ref($caller) || $caller;
my ( $seq, $coord_system, $seq_region_name, $seq_region_length,
$start, $end, $strand, $adaptor, $empty )
= rearrange( [
qw(SEQ COORD_SYSTEM SEQ_REGION_NAME SEQ_REGION_LENGTH
START END STRAND ADAPTOR EMPTY) ],
@_ );
if ( !defined($seq_region_name) ) {
throw('SEQ_REGION_NAME argument is required');
}
if ( !defined($start) ) { throw('START argument is required') }
if ( !defined($end) ) { throw('END argument is required') }
if ( !defined($seq_region_length) ) { $seq_region_length = $end }
if ( $seq_region_length <= 0 ) {
throw('SEQ_REGION_LENGTH must be > 0');
}
if ( defined($coord_system) ) {
assert_ref( $coord_system, 'Bio::EnsEMBL::CoordSystem' );
if ( $coord_system->is_top_level() ) {
throw('Cannot create circular slice on toplevel CoordSystem.');
}
} else {
warning("CircularSlice without coordinate system");
}
$strand ||= 1;
if ( $strand != 1 && $strand != -1 ) {
throw('STRAND argument must be -1 or 1');
}
if ( defined($adaptor) ) {
assert_ref( $adaptor, 'Bio::EnsEMBL::DBSQL::SliceAdaptor' );
}
my $seq1 = { 'coord_system' => $coord_system,
'seq' => $seq,
'seq_region_name' => $seq_region_name,
'seq_region_length' => $seq_region_length,
'start' => int($start),
'end' => int($end),
'strand' => $strand };
bless $seq1, $class;
$seq1->adaptor($adaptor);
return $seq1;
} ## end sub new
=head2 centrepoint
Arg [1] : none
Example : $cp = $slice->centrepoint();
Description: Returns the mid position of this slice relative to the
start of the sequence region that it was created on.
Coordinates are inclusive and start at 1.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub centrepoint {
my $self = shift;
my ( $s, $e, $length ) =
( $self->{'start'}, $self->{'end'}, $self->{'seq_region_length'} );
if ( $s < $e ) {
return ( $s + $e )/2;
}
my $r1 = $length - $s;
my $r2 = $e;
my $r = ( $r1 + $r2 )/2;
my $m = $s + $r;
if ( $m > $length ) {
$m = $m - $length;
}
return $m;
}
=head2 length
Arg [1] : none
Example : $length = $slice->length();
Description: Returns the length of this slice in basepairs
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub length {
my ($self) = @_;
if ( $self->{'start'} < $self->{'end'} ) {
return $self->{'end'} - $self->{'start'} + 1;
}
my $r1 = $self->{'seq_region_length'} - $self->{'start'};
my $r2 = $self->{'end'};
my $ln = $r1 + $r2 + 1;
return $ln;
}
sub _split {
my $self = shift;
my $sl1 =
Bio::EnsEMBL::CircularSlice->new(
-COORD_SYSTEM => $self->{'coord_system'},
-SEQ_REGION_NAME => $self->{'seq_region_name'},
-SEQ_REGION_LENGTH => $self->{'seq_region_length'},
-START => $self->{'start'},
-END => $self->{'seq_region_length'},
-STRAND => $self->{'strand'},
-ADAPTOR => $self->adaptor() );
my $sl2 =
Bio::EnsEMBL::CircularSlice->new(
-COORD_SYSTEM => $self->{'coord_system'},
-SEQ_REGION_NAME => $self->{'seq_region_name'},
-SEQ_REGION_LENGTH => $self->{'seq_region_length'},
-START => 1,
-END => $self->{'end'},
-STRAND => $self->{'strand'},
-ADAPTOR => $self->adaptor() );
return ($sl1, $sl2);
}
=head2 seq
Arg [1] : none
Example : print "SEQUENCE = ", $slice->seq();
Description: Returns the sequence of the region represented by this
slice formatted as a string.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub seq {
my $self = shift;
# special case for in-between (insert) coordinates
return '' if ( $self->start() == $self->end() + 1 );
return $self->{'seq'} if ( $self->{'seq'} );
if ( $self->adaptor() ) {
my $seqAdaptor = $self->adaptor()->db()->get_SequenceAdaptor();
if ( $self->{'start'} > $self->{'end'} ) {
my $length = $self->{'seq_region_length'};
my ($sl1, $sl2) = $self->_split;
my $seq1 = ${
$seqAdaptor->fetch_by_Slice_start_end_strand( $sl1, 1, $sl1->end - $sl1->start + 1, $sl1->strand) };
my $seq2 = ${
$seqAdaptor->fetch_by_Slice_start_end_strand( $sl2, 1, $sl2->end - $sl2->start + 1, $sl2->strand) };
return $seq1 . $seq2;
} else {
my $seq1 = ${
$seqAdaptor->fetch_by_Slice_start_end_strand( $self, 1, undef,
1 ) };
return $seq1;
}
} ## end if ( $self->adaptor() )
# no attached sequence, and no db, so just return Ns
return 'N' x $self->length();
} ## end sub seq
=head2 subseq
Arg [1] : int $startBasePair
relative to start of slice, which is 1.
Arg [2] : int $endBasePair
relative to start of slice.
Arg [3] : (optional) int $strand
The strand of the slice to obtain sequence from. Default
value is 1.
Description: returns string of dna sequence
Returntype : txt
Exceptions : end should be at least as big as start
strand must be set
Caller : general
Status : Stable
=cut
sub subseq {
my ( $self, $start, $end, $strand ) = @_;
# handle 'between' case for insertions
return '' if ( $start == $end + 1 );
$strand = 1 unless ( defined $strand );
if ( $strand != -1 && $strand != 1 ) {
throw("Invalid strand [$strand] in call to Slice::subseq.");
}
my $subseq;
my $length = $self->{'seq_region_length'};
if ( $self->adaptor ) {
my $seqAdaptor = $self->adaptor->db->get_SequenceAdaptor();
if ( $end < $start ) {
my $subseq1 = ${
$seqAdaptor->fetch_by_Slice_start_end_strand( $self, $start,
$length, $strand )
};
my $subseq2 = ${
$seqAdaptor->fetch_by_Slice_start_end_strand( $self, 1, $end,
$strand ) };
$subseq = $subseq1 . $subseq2;
} else {
$subseq = ${
$seqAdaptor->fetch_by_Slice_start_end_strand( $self, $start,
$end, $strand ) };
}
} else {
## check for gap at the beginning and pad it with Ns
if ( $start < 1 ) {
$subseq = "N" x ( 1 - $start );
$start = 1;
}
$subseq .= substr( $self->seq(), $start - 1, $end - $start + 1 );
## check for gap at the end and pad it with Ns
if ( $end > $self->length() ) {
$subseq .= "N" x ( $end - $self->length() );
}
reverse_comp( \$subseq ) if ( $strand == -1 );
}
return $subseq;
} ## end sub subseq
=head2 expand
Arg [1] : (optional) int $five_prime_expand
The number of basepairs to shift this slices five_prime
coordinate by. Positive values make the slice larger,
negative make the slice smaller.
coordinate left.
Default = 0.
Arg [2] : (optional) int $three_prime_expand
The number of basepairs to shift this slices three_prime
coordinate by. Positive values make the slice larger,
negative make the slice smaller.
Default = 0.
Arg [3] : (optional) bool $force_expand
if set to 1, then the slice will be contracted even in the case
when shifts $five_prime_expand and $three_prime_expand overlap.
In that case $five_prime_expand and $three_prime_expand will be set
to a maximum possible number and that will result in the slice
which would have only 2pbs.
Default = 0.
Arg [4] : (optional) int* $fpref
The reference to a number of basepairs to shift this slices five_prime
coordinate by. Normally it would be set to $five_prime_expand.
But in case when $five_prime_expand shift can not be applied and
$force_expand is set to 1, then $$fpref will contain the maximum possible
shift
Arg [5] : (optional) int* $tpref
The reference to a number of basepairs to shift this slices three_prime
coordinate by. Normally it would be set to $three_prime_expand.
But in case when $five_prime_expand shift can not be applied and
$force_expand is set to 1, then $$tpref will contain the maximum possible
shift
Example : my $expanded_slice = $slice->expand( 1000, 1000);
my $contracted_slice = $slice->expand(-1000,-1000);
my $shifted_right_slice = $slice->expand(-1000, 1000);
my $shifted_left_slice = $slice->expand( 1000,-1000);
my $forced_contracted_slice = $slice->expand(-1000,-1000, 1, \$five_prime_shift, \$three_prime_shift);
Description: Returns a slice which is a resized copy of this slice. The
start and end are moved outwards from the center of the slice
if positive values are provided and moved inwards if negative
values are provided. This slice remains unchanged. A slice
may not be contracted below 1bp but may grow to be arbitrarily
large.
Returntype : Bio::EnsEMBL::Slice
Exceptions : warning if an attempt is made to contract the slice below 1bp
Caller : general
Status : Stable
=cut
sub expand {
my $self = shift;
my $five_prime_shift = shift || 0;
my $three_prime_shift = shift || 0;
my $force_expand = shift || 0;
my $fpref = shift;
my $tpref = shift;
if ( $self->{'seq'} ) {
warning(
"Cannot expand a slice which has a manually attached sequence ");
return undef;
}
my $new_start;
my $new_end;
my $sshift = $five_prime_shift;
my $eshift = $three_prime_shift;
if ( $self->{'strand'} != 1 ) {
$eshift = $five_prime_shift;
$sshift = $three_prime_shift;
}
$new_start = $self->{'start'} - $sshift;
$new_end = $self->{'end'} + $eshift;
# if($new_start > $new_end) {
# if ($force_expand) { # Apply max possible shift, if force_expand is set
# if ($sshift < 0) { # if we are contracting the slice from the start - move the start just before the end
# $new_start = $new_end - 1;
# $sshift = $self->{start} - $new_start;
# }
# if($new_start > $new_end) { # if the slice still has a negative length - try to move the end
# if ($eshift < 0) {
# $new_end = $new_start + 1;
# $eshift = $new_end - $self->{end};
# }
# }
# return the values by which the primes were actually shifted
# $$tpref = $self->{strand} == 1 ? $eshift : $sshift;
# $$fpref = $self->{strand} == 1 ? $sshift : $eshift;
# }
# if($new_start > $new_end) {
# throw('Slice start cannot be greater than slice end');
# }
# }
#fastest way to copy a slice is to do a shallow hash copy
my %new_slice = %$self;
$new_slice{'start'} = int($new_start);
$new_slice{'end'} = int($new_end);
return bless \%new_slice, ref($self);
} ## end sub expand
=head2 get_all_VariationFeatures
Args : $filter [optional]
Description:returns all variation features on this slice. This function will only work
correctly if the variation database has been attached to the core database.
If $filter is "genotyped" return genotyped Snps only... (nice likkle hack);
ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
Exceptions : none
Caller : contigview, snpview
Status : At Risk
: Variation database is under development.
=cut
sub get_all_VariationFeatures {
my $self = shift;
my $filter = shift;
$filter ||= '';
if ( !$self->adaptor() ) {
warning('Cannot get variation features without attached adaptor');
return [];
}
my $vf_adaptor =
Bio::EnsEMBL::DBSQL::MergedAdaptor->new(
-species => $self->adaptor()->db()->species,
-type => "VariationFeature" );
if ($vf_adaptor) {
if ( $filter eq 'genotyped' ) {
return $vf_adaptor->fetch_all_genotyped_by_Slice($self);
} else {
return $vf_adaptor->fetch_all_by_Slice($self);
}
} else {
warning( "Variation database must be attached to core database to "
. "retrieve variation information" );
return [];
}
}
=head2 get_all_genotyped_VariationFeatures
Args : none
Description: returns all variation features on this slice that have been genotyped.
This function will only work correctly if the variation database has
been attached to the core database.
ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
Exceptions : none
Caller : contigview, snpview, ldview
Status : At Risk
: Variation database is under development.
=cut
sub get_all_genotyped_VariationFeatures {
my $self = shift;
my $vfa;
if ( !$self->adaptor() ) {
warning('Cannot get variation features without attached adaptor');
return [];
}
my $vf_adaptor =
Bio::EnsEMBL::DBSQL::MergedAdaptor->new(
-species => $self->adaptor()->db()->species,
-type => "VariationFeature" );
if ($vf_adaptor) {
return $vf_adaptor->fetch_all_genotyped_by_Slice($self);
} else {
warning( "Variation database must be attached to core database to "
. "retrieve variation information" );
return [];
}
}
=head2 get_all_DASFeatures
Arg [1] : none
Example : $features = $slice->get_all_DASFeatures;
Description: Retrieves a hash reference to a hash of DAS feature
sets, keyed by the DNS, NOTE the values of this hash
are an anonymous array containing:
(1) a pointer to an array of features;
(2) a pointer to the DAS stylesheet
Returntype : hashref of Bio::SeqFeatures
Exceptions : ?
Caller : webcode
Status : Stable
=cut
sub get_all_DASFeatures {
my ( $self, $source_type ) = @_;
if ( !$self->adaptor() ) {
warning("Cannot retrieve features without attached adaptor");
return [];
}
my %genomic_features = map {
( $_->adaptor->dsn =>
[ $_->fetch_all_Features( $self, $source_type ) ] )
} $self->adaptor()->db()->_each_DASFeatureFactory;
return \%genomic_features;
}
=head2 project_to_slice
Arg [1] : Slice to project to.
Example : my $chr_projection = $clone_slice->project_to_slice($chrom_slice);
foreach my $segment ( @$chr_projection ){
$chr_slice = $segment->to_Slice();
print $clone_slice->seq_region_name(). ':'. $segment->from_start(). '-'.
$segment->from_end(). ' -> '.$chr_slice->seq_region_name(). ':'. $chr_slice->start().
'-'.$chr_slice->end().
$chr_slice->strand(). " length: ".($chr_slice->end()-$chr_slice->start()+1). "\n";
}
Description: Projection of slice to another specific slice. Needed for where we have multiple mappings
and we want to state which one to project to.
Returntype : list reference of Bio::EnsEMBL::ProjectionSegment objects which
can also be used as [$start,$end,$slice] triplets.
Exceptions : none
Caller : none
Status : At Risk
=cut
sub project_to_slice {
my $self = shift;
my $to_slice = shift;
throw('Slice argument is required') if ( !$to_slice );
my $slice_adaptor = $self->adaptor();
if ( !$slice_adaptor ) {
warning("Cannot project without attached adaptor.");
return [];
}
my $mapper_aptr = $slice_adaptor->db->get_AssemblyMapperAdaptor();
my $cs = $to_slice->coord_system();
my $slice_cs = $self->coord_system();
my @projection;
my $current_start = 1;
# decompose this slice into its symlinked components.
# this allows us to handle haplotypes and PARs
my $normal_slice_proj =
$slice_adaptor->fetch_normalized_slice_projection($self);
foreach my $segment (@$normal_slice_proj) {
my $normal_slice = $segment->[2];
$slice_cs = $normal_slice->coord_system();
my $asma = $self->adaptor->db->get_AssemblyMapperAdaptor();
my $asm_mapper = $asma->fetch_by_CoordSystems( $slice_cs, $cs );
# perform the mapping between this slice and the requested system
my @coords;
if ( defined $asm_mapper ) {
@coords = $asm_mapper->map( $normal_slice->seq_region_name(),
$normal_slice->start(),
$normal_slice->end(),
$normal_slice->strand(),
$slice_cs,
undef,
$to_slice );
} else {
$coords[0] =
Bio::EnsEMBL::Mapper::Gap->new( $normal_slice->start(),
$normal_slice->end() );
}
#construct a projection from the mapping results and return it
foreach my $coord (@coords) {
my $coord_start = $coord->start();
my $coord_end = $coord->end();
my $length = $coord_end - $coord_start + 1;
#skip gaps
if ( $coord->isa('Bio::EnsEMBL::Mapper::Coordinate') ) {
my $coord_cs = $coord->coord_system();
# If the normalised projection just ended up mapping to the
# same coordinate system we were already in then we should just
# return the original region. This can happen for example, if we
# were on a PAR region on Y which refered to X and a projection to
# 'toplevel' was requested.
# if($coord_cs->equals($slice_cs)) {
# # trim off regions which are not defined
# return $self->_constrain_to_region();
# }
#create slices for the mapped-to coord system
my $slice =
$slice_adaptor->fetch_by_seq_region_id( $coord->id(),
$coord_start, $coord_end, $coord->strand() );
my $current_end = $current_start + $length - 1;
push @projection,
bless( [ $current_start, $current_end, $slice ],
"Bio::EnsEMBL::ProjectionSegment" );
}
$current_start += $length;
} ## end foreach my $coord (@coords)
} ## end foreach my $segment (@$normal_slice_proj)
# delete the cache as we may want to map to different set next time and old
# results will be cached.
$mapper_aptr->delete_cache;
return \@projection;
} ## end sub project_to_slice
#
# Bioperl Bio::PrimarySeqI methods:
#
=head2 id
Description: Included for Bio::PrimarySeqI interface compliance (0.7)
=cut
sub id { name(@_); }
=head2 display_id
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
=cut
sub display_id { name(@_); }
=head2 primary_id
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
=cut
sub primary_id { name(@_); }
=head2 desc
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
=cut
sub desc {
return $_[0]->coord_system->name() . ' ' . $_[0]->seq_region_name();
}
=head2 moltype
Description: Included for Bio::PrimarySeqI interface compliance (0.7)
=cut
sub moltype { return 'dna'; }
=head2 alphabet
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
=cut
sub alphabet { return 'dna'; }
=head2 accession_number
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
=cut
sub accession_number { name(@_); }
=head2 is_circular
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
=cut
sub is_circular {
my ($self) = @_;
if ( !defined( $self->{'circular'} ) ) {
my @attrs =
grep { $_ } @{ $self->get_all_Attributes('circular_seq') };
$self->{'circular'} = @attrs ? 1 : 0;
}
return $self->{'circular'};
}
1;