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lib/Bio/EnsEMBL/CircularSlice.pm  view on Meta::CPAN

=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

package Bio::EnsEMBL::CircularSlice;
$Bio::EnsEMBL::CircularSlice::VERSION = '114.0.0';
use vars qw(@ISA);
use strict;

use Bio::PrimarySeqI;

use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception
  qw(throw warning);
use Bio::EnsEMBL::RepeatMaskedSlice;
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
use Bio::EnsEMBL::ProjectionSegment;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::DBSQL::MergedAdaptor;

#use Bio::EnsEMBL::IndividualSlice;
#use Bio::EnsEMBL::IndividualSliceFactory;
use Bio::EnsEMBL::Mapper::RangeRegistry;
use Bio::EnsEMBL::Slice;
use Data::Dumper;
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