Raw content of Bio::EnsEMBL::RepeatMaskedSlice
<![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::RepeatMaskedSlice - Arbitary Slice of a genome
=head1 SYNOPSIS
$sa = $db->get_SliceAdaptor();
$slice =
$sa->fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 );
$repeat_masked_slice = $slice->get_repeatmasked_seq();
# get repeat masked sequence:
my $dna = $repeat_masked_slice->seq();
$dna = $repeat_masked_slice->subseq( 1, 1000 );
=head1 DESCRIPTION
This is a specialised Bio::EnsEMBL::Slice class that is used to retrieve
repeat masked genomic sequence rather than normal genomic sequence.
=head1 METHODS
=cut
package Bio::EnsEMBL::RepeatMaskedSlice;
use strict;
use warnings;
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Utils::Exception;
use vars qw(@ISA);
@ISA = ('Bio::EnsEMBL::Slice');
# The BLOCK_PWR is the lob_bin of the chunksize where you want your repeat features
# to be retreived. This will create repeat feature retrieval calls that are likely
# to be on the same slice and hopefully create cache hits and less database traffic
my $BLOCK_PWR = 18;
=head2 new
Arg [-REPEAT_MASK] : The logic name of the repeats to be used for masking.
If not provided, all repeats in the database are used.
Arg [...] : Named superclass arguments. See B<Bio::EnsEMBL::Slice>.
Example : my $slice = Bio::EnsEMBL::RepeatMaskedSlice->new
(-START => $start,
-END => $end,
-STRAND => $strand,
-SEQ_REGION_NAME => $seq_region,
-SEQ_REGION_LENGTH => $seq_region_length,
-COORD_SYSTEM => $cs,
-ADAPTOR => $adaptor,
-REPEAT_MASK => ['repeat_masker'],
-SOFT_MASK => 1,
-NOT_DEFAULT_MASKING_CASES => {"repeat_class_SINE/MIR" => 1,
"repeat_name_AluSp" => 0});
Description: Creates a Slice which behaves exactly as a normal slice but
that returns repeat masked sequence from the seq method.
Returntype : Bio::EnsEMBL::RepeatMaskedSlice
Exceptions : none
Caller : RawComputes (PredictionTranscript creation code).
Status : Stable
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my ($logic_names, $soft_mask, $not_default_masking_cases) = rearrange(['REPEAT_MASK',
'SOFT_MASK',
'NOT_DEFAULT_MASKING_CASES'], @_);
my $self = $class->SUPER::new(@_);
$logic_names ||= [''];
if(ref($logic_names) ne 'ARRAY') {
throw("Reference to list of logic names argument expected.");
}
$self->{'repeat_mask_logic_names'} = $logic_names;
$self->{'soft_mask'} = $soft_mask;
$self->{'not_default_masking_cases'} = $not_default_masking_cases;
$self->{'not_default_masking_cases'} ||= {};
return $self;
}
=head2 repeat_mask_logic_names
Arg [1] : reference to list of strings $logic_names (optional)
Example : $rm_slice->repeat_mask_logic_name(['repeat_masker']);
Description: Getter/Setter for the logic_names of the repeats that are used
to mask this slices sequence.
Returntype : reference to list of strings
Exceptions : none
Caller : seq() method
Status : Stable
=cut
sub repeat_mask_logic_names {
my $self = shift;
if(@_) {
my $array = shift;
if(ref($array) ne 'ARRAY') {
throw('Reference to list of logic names argument expected.');
}
}
return $self->{'repeat_mask_logic_names'};
}
=head2 soft_mask
Arg [1] : boolean $soft_mask (optional)
Example : $rm_slice->soft_mask(0);
Description: Getter/Setter which is used to turn on/off softmasking of the
sequence returned by seq.
Returntype : boolean
Exceptions : none
Caller : seq() method
Status : Stable
=cut
sub soft_mask {
my $self = shift;
$self->{'soft_mask'} = shift if(@_);
return $self->{'soft_mask'} || 0;
}
=head2 not_default_masking_cases
Arg [1] : hash reference $not_default_masking_cases (optional, default is {})
The values are 0 or 1 for hard and soft masking respectively
The keys of the hash should be of 2 forms
"repeat_class_" . $repeat_consensus->repeat_class,
e.g. "repeat_class_SINE/MIR"
"repeat_name_" . $repeat_consensus->name
e.g. "repeat_name_MIR"
depending on which base you want to apply the not default masking either
the repeat_class or repeat_name. Both can be specified in the same hash
at the same time, but in that case, repeat_name setting has priority over
repeat_class. For example, you may have hard masking as default, and
you may want soft masking of all repeat_class SINE/MIR,
but repeat_name AluSp (which are also from repeat_class SINE/MIR)
Example : $rm_slice->not_default_masking_cases({"repeat_class_SINE/MIR" => 1,
"repeat_name_AluSp" => 0});
Description: Getter/Setter which is used to escape some repeat class or name from the default
masking in place.
Returntype : hash reference
Exceptions : none
Caller : seq() and subseq() methods
Status : Stable
=cut
sub not_default_masking_cases {
my $self = shift;
$self->{'not_default_masking_cases'} = shift if (@_);
return $self->{'not_default_masking_cases'};
}
=head2 seq
Arg [1] : none
Example : print $rmslice->seq(), "\n";
Description: Retrieves the entire repeat masked sequence for this slice.
See also the B<Bio::EnsEMBL::Slice> implementation of this
method.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub seq {
my $self = shift;
#
# get all the features
#
my $logic_names = $self->repeat_mask_logic_names();
my $soft_mask = $self->soft_mask();
my $not_default_masking_cases = $self->not_default_masking_cases;
my $repeats = [];
foreach my $l (@$logic_names) {
push @{$repeats}, @{$self->get_all_RepeatFeatures($l)};
}
#
# get the dna
#
my $dna = $self->SUPER::seq(@_);
#
# mask the dna
#
$self->_mask_features(\$dna,$repeats,$soft_mask,$not_default_masking_cases);
return $dna;
}
=head2 subseq
Arg [1] : none
Example : print $rmslice->subseq(1, 1000);
Description: Retrieves a repeat masked sequence from a specified subregion
of this slice. See also the B<Bio::EnsEMBL::Slice>
implementation of this method.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub subseq {
my $self = shift;
my $start = shift;
my $end = shift;
my $strand = shift;
#
# get all the features
#
my $logic_names = $self->repeat_mask_logic_names();
my $soft_mask = $self->soft_mask();
my $not_default_masking_cases = $self->not_default_masking_cases;
# If frequent subseqs happen on repeatMasked sequence this results in
# a lot of feature retrieval from the database. To avoid this, features
# are only retrieved from subslices with fixed space boundaries.
# The access happens in block to make cache hits more likely
# The blocksize can be defined on the top of this module.
my $seq_region_slice = $self->seq_region_Slice();
my $block_min = ($self->start()-1) >> $BLOCK_PWR;
my $block_max = ($self->end()-1) >> $BLOCK_PWR;
my $repeats = [];
my $sub_start = ($block_min << $BLOCK_PWR)+1;
my $sub_end = ($block_max+1)<<$BLOCK_PWR;
if ($sub_end > $seq_region_slice->length) {
$sub_end = $seq_region_slice->length ;
}
my $subslice = $seq_region_slice->sub_Slice( $sub_start, $sub_end);
foreach my $l (@$logic_names) {
push @{$repeats}, @{$subslice->get_all_RepeatFeatures($l)};
}
#
# get the dna
#
my $subsequence_slice = $self->sub_Slice( $start, $end, $strand );
my $dna = $subsequence_slice->seq();
#
# mask the dna
#
$subsequence_slice->_mask_features(\$dna,$repeats,$soft_mask,$not_default_masking_cases);
return $dna;
}
1;
]]>