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Ace/Sequence/Gene.pm  view on Meta::CPAN

package Ace::Sequence::Gene;

use strict;
use Ace;
use Ace::Sequence::Feature;
use vars '$AUTOLOAD';
use overload 
  '""' => 'asString',
  ;


# autoload delegates everything to the Ace::Sequence::Feature object
# contained in base
sub AUTOLOAD {
  my($pack,$func_name) = $AUTOLOAD=~/(.+)::([^:]+)$/;
  my $self = shift;
  $self->{base}->$func_name(@_);
}

sub new {
  my $class = shift;
  my $args = shift;
  bless $args,$class;
  return $args;

# for documentation only
#  my %args = @_;
#  my $introns  = $args{intron};
#  my $exons    = $args{exon};
#  my $sequence = $args{base};  # this is the Ace::Sequence::Feature object
#  return bless {base => $sequence,
#		introns  => $introns,
#		exons    => $exons},$class;

}

sub asString {
  shift->{base}->info;
}

sub relative {
  my $self = shift;
  my $d = $self->{relative};
  $self->{relative} = shift if @_;
  $d;
}

sub introns {
  my $self = shift;
  return $self->{intron} ? @{$self->{intron}} : () unless $self->relative;
  # otherwise, we have to handle relative coordinates
  my $base   = $self->{base};
  my @e = map {Ace::Sequence->new(-refseq=>$base,-seq=>$_)} @{$self->{intron}};
  return $self->strand < 0 ? reverse @e : @e;
}

sub exons {
  my $self = shift;
  return $self->{exon} ? @{$self->{exon}} : () unless $self->relative;
  # otherwise, we have to handle relative coordinates
  my $base   = $self->{base};
  my @e = map {Ace::Sequence->new(-refseq=>$base,-seq=>$_)} @{$self->{exon}};
  return $self->strand < 0 ? reverse @e : @e;
}

1;

__END__

=head1 NAME

Ace::Sequence::Gene - Simple "Gene" Object

=head1 SYNOPSIS

    # open database connection and get an Ace::Object sequence
    use Ace::Sequence;

    # get a megabase from the middle of chromosome I
    $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
                              -db     => $db,
			      -offset => 3_000_000,
			      -length => 1_000_000);

    # get all the genes
    @genes = $seq->genes;

    # get the exons from the first one
    @exons = $genes[0]->exons;

    # get the introns