Bio::SeqFeature::Gene::Intron - An intron feature

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  Title   : upstream_Exon 
  Usage   : $intron->upstream_Exon()
  Function: exon upstream of the intron 
  Returns : Bio::EnsEMBL::Exon
  Args    : 

  Title   : downstream_Exon 
  Usage   : $intron->downstream_Exon()
  Function: exon downstream of the intron 
  Returns : Bio::EnsEMBL::Exon
  Args    : 

  Title   : phase 
  Usage   : $intron->phase()
  Function: returns the phase of the intron(where it interrupts the codon)  
  Returns : int(0,1,2)
  Args    : 

  Title   : acceptor_splice_site 
  Usage   : $intron->acceptor_splice_site(21,3)
  Function: returns the sequence corresponding to the 
            consensus acceptor splice site. If start and
            end are provided, it will number of base pairs
            left and right of the canonical AG. Here 21 means
            21 bp into intron and 3 means 3 bp into the exon.
            --Intron--21----|AG|-3-----Exon
            Defaults to 21,3

  Returns : Bio::Seq
  Args    : start and end

  Title   : donor_splice_site 
  Usage   : $intron->donor_splice_site(3,6)
  Function: returns the sequence corresponding to the 
            consensus donor splice site. If start and
            end are provided, it will number of base pairs
            left and right of the canonical GT. Here 3 means
            3 bp into exon and 6 means 6 bp into the intron.
            --Exon-3--|GT|-6----Intron-
            Defaults to 3,6

  Returns : Bio::Seq
  Args    : start and end

#
# BioPerl module for Bio::SeqFeature::Gene::Intron
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by David Block <dblock@gene.pbi.nrc.ca>
#
# Copyright David Block
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

# Let the code begin...


package Bio::SeqFeature::Gene::Intron;
use strict;

use Bio::SeqFeature::Gene::Exon;

use base qw(Bio::SeqFeature::Gene::NC_Feature);

sub new {
    my($class,@args) = @_;

    # introns are non-coding by default
    if(! grep { lc($_) eq '-is_coding'; } @args) {
	push(@args, '-is_coding', 0);
    }
    my $self = $class->SUPER::new(@args);

    my ($primary, $prim) = 
	$self->_rearrange([qw(PRIMARY PRIMARY_TAG)],@args);
    $self->primary_tag('intron') unless $primary || $prim;

    return $self;
}

sub upstream_Exon {
    my( $self, $exon ) = @_;
    
    if ($exon) {
        $self->{'_intron_location'} = undef;
        $self->throw("'$exon' is not a Bio::SeqFeature::Gene::ExonI") 
	    unless $exon->isa('Bio::SeqFeature::Gene::ExonI');
        $self->{'_upstream_exon'} = $exon;
    }
    return $self->{'_upstream_exon'};
}

sub downstream_Exon {
    my( $self, $exon ) = @_;
    
    if ($exon) {
        $self->{'_intron_location'} = undef;
        $self->throw("'$exon' is not a Bio::SeqFeature::Gene::ExonI")
            unless $exon->isa('Bio::SeqFeature::Gene::ExonI');
        $self->{'_downstream_exon'} = $exon;
    }
    return $self->{'_downstream_exon'};
}

sub phase {
  my ($self) = @_;
  return $self->downstream_Exon->phase;
}

sub acceptor_splice_site {
  my ($self,$ss_start,$ss_end) = @_;
  $ss_start = 21 unless defined $ss_start;
  $ss_end   = 3 unless defined $ss_end;
  if($self->strand < 0){
    my $tmp= $ss_start;
    $ss_start = $ss_end;
    $ss_end = $tmp;
  }
  my $intron_end= $self->location->end;
  my $down_exon = $self->downstream_Exon;
  my $acceptor;  
  if($self->strand < 0){
      $ss_start= $ss_start >  $down_exon->length ? $down_exon->length: $ss_start;
      $ss_end= $ss_end > $self->length-2 ? $self->length-2 : $ss_end;
      $acceptor = Bio::SeqFeature::Generic->new(-start=>$self->start - ($ss_start) ,  
                                               -end=>$self->start + ($ss_end+1),
                                               -strand=>$self->strand,    
                                               -primary_tag=>"donor splice site");
  } 
  else {
    $ss_start = $ss_start > $self->length-2 ? $self->length-2 : $ss_start;
    $ss_end = $ss_end > $down_exon->length ? $down_exon->length : $ss_end;
 

    $acceptor = Bio::SeqFeature::Generic->new(-start=>$self->end - ($ss_start + 1),  
                                               -end=>$self->end + $ss_end,
                                               -strand=>$self->strand,    
                                               -primary_tag=>"donor splice site");
  }
  $acceptor->attach_seq($self->entire_seq);

  return $acceptor;

}

sub donor_splice_site {
  my ($self,$ss_start,$ss_end) = @_;
  $ss_start = 3 unless defined $ss_start;
  $ss_end   = 10 unless defined $ss_end;
  if($self->strand < 0){
    my $tmp= $ss_start;
    $ss_start = $ss_end;
    $ss_end = $tmp;
  }
  my $up_exon = $self->upstream_Exon;
  my $donor;
  if($self->strand < 0){
    $ss_end = $ss_end > $up_exon->length ? $up_exon->length : $ss_end;
    $ss_start   = $ss_start> $self->length -2 ? $self->length -2 : $ss_start;
    $donor = Bio::SeqFeature::Generic->new(-start=>$self->end -  ($ss_start+1),
                                            -end  => $self->end + ($ss_end),
                                            -strand=>$self->strand,
                                            -primary_tag=>"acceptor splice site");
  } 
  else {
    $ss_start = $ss_start > $up_exon->length ? $up_exon->length : $ss_start;
    $ss_end   = $ss_end > $self->length -2 ? $self->length -2 : $ss_end;
    $donor = Bio::SeqFeature::Generic->new(-start=>$self->start - $ss_start,
                                           -end  => $self->start +($ss_end+1),
                                            -strand=>$self->strand,
                                            -primary_tag=>"acceptor splice site");
  }
  $donor->attach_seq($self->entire_seq);
  return $donor;
} 

sub location {
    my( $self ) = @_;
    
    unless ($self->{'_intron_location'}) {
        my $loc = Bio::Location::Simple->new;
    
        my $up_exon = $self->upstream_Exon;
        my $down_exon = $self->downstream_Exon;
        
        # Get the PrimarySeqs attached to both and check it is the same sequence
        my $up_seq   = $up_exon  ->entire_seq;
        my $down_seq = $down_exon->entire_seq;
        unless (ref($up_seq) eq ref($down_seq) ) {
            $self->throw("upstream and downstream exons are attached to different sequences\n'$up_seq' and '$down_seq'");
        }
        
        # Check that the exons are on the same strand.  (Do I need to bother?)
        my $up_strand   = $up_exon  ->strand;
        my $down_strand = $down_exon->strand;
        unless ($up_strand == $down_strand) {
            $self->throw("upstream and downstream exons are on different strands "
                . "('$up_strand' and '$down_strand')");
        }
        $loc->strand($up_strand);
        
        #   $exon_end is the  end  of the exon which is 5' of the intron on the genomic sequence.
        # $exon_start is the start of the exon which is 3' of the intron on the genomic sequence.
        my( $exon_end, $exon_start );
        if ($up_strand == 1) {
            $exon_end   = $up_exon  ->end;
            $exon_start = $down_exon->start;
        } else {
            $exon_end   = $down_exon->end;
            $exon_start = $up_exon  ->start;
        }
        unless ($exon_end < $exon_start) {
            $self->throw("Intron gap begins after '$exon_end' and ends before '$exon_start'");
        }
        $loc->start($exon_end   + 1);
        $loc->end  ($exon_start - 1);
        
        # Attach the sequence and location objects to the intron
        $self->{'_intron_location'} = $loc;
        
    }
    return $self->{'_intron_location'};
}
1;