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

               and is not stored in the database.  The translation always
               spans the entire transcript (no UTRs; all CDS) and does not
               have an associated dbID, stable_id or adaptor.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub translation {
  my $self = shift;

  #calculate translation on the fly
  my $strand = $self->strand();

  my $start_exon;
  my $end_exon;

  my @exons = @{$self->get_all_Exons()};

  return undef if(!@exons);

  $start_exon = $exons[0];
  $end_exon = $exons[-1];

  my $pta;

  if($self->adaptor()) {
    $pta = $self->adaptor()->db()->get_TranslationAdaptor();
  } else {
    #warning("PredictionTranscript has no adaptor, may not be able to obtain " .
           # "translation");
  }

  my $Xseq = $self->spliced_seq();
  my $start_phase = $start_exon->phase;
  if( $start_phase > 0 ) {
    $Xseq = "N"x$start_phase . $Xseq;
  }

  my $tmpSeq = new Bio::Seq( -id       => $self->display_id,
                             -seq      => $Xseq,
                             -moltype  => 'dna',
                             -alphabet => 'dna' );

  return Bio::EnsEMBL::Translation->new
    (-ADAPTOR    => $pta,
     -START_EXON => $start_exon,
     -END_EXON   => $end_exon,
     -SEQ_START  => 1,
     -SEQ_END    => $end_exon->length(),
     -SEQ        => $tmpSeq->translate()->seq());
}



=head2 translate

  Arg [1]   : Boolean, emulate the behavior of old bioperl versions where
              an incomplete final codon of 2 characters is padded and guessed
  Function  : Give a peptide translation of all exons currently in
              the PT. Gives empty string when none is in.
  Returntype: a Bio::Seq as in transcript->translate()
  Exceptions: none
  Caller    : general
  Status     : Stable

=cut


sub translate {
  my ($self, $complete_codon) = @_;

  my $dna = $self->translateable_seq();

  my $codon_table_id;
  if ( defined( $self->slice() ) ) {
      my $attrib;
      
      ($attrib) = @{ $self->slice()->get_all_Attributes('codon_table') };
      if ( defined($attrib) ) {
	  $codon_table_id = $attrib->value();
      }
  }
  $codon_table_id ||= 1; #default will be vertebrates

  # Remove the final stop codon from the mrna
  # sequence produced if it is present, this is so any peptide produced
  # won't have a terminal stop codon
  # if you want to have a terminal stop codon either comment this line out
  # or call translatable seq directly and produce a translation from it
  if( CORE::length( $dna ) % 3 == 0 ) {
   # $dna =~ s/TAG$|TGA$|TAA$//i;
      my $codon_table =  Bio::Tools::CodonTable->new( -id => $codon_table_id );
      
      if ( $codon_table->is_ter_codon( substr( $dna, -3, 3 ) ) ) {
	  substr( $dna, -3, 3, '' );
      }
  } elsif ( CORE::length($dna) % 3 == 2 ) {
      # If we have a partial codon of 2 bp we need to decide if we
      # trim it or not to fix some bad behaviour in older bioperl
      # versions
      if ( $complete_codon ) {
	  # If we want to do the bad behavior of bioperl 1.6.1 and older
	  # where we guess the last codon if inomplete, pad an N
	  # to the mrna sequence
	  $dna .= 'N';
      } else {
	  # Otherwise trim those last two bp off so the behavior is
	  # consistent across bioperl versions
	  substr( $dna, -2, 2, '' );
      }
  }

  my $bioseq = new Bio::Seq( -id       => $self->display_id,
                             -seq      => $dna,
                             -moltype  => 'dna',
                             -alphabet => 'dna' );

  my $translation = $bioseq->translate(undef,undef,undef,$codon_table_id);

  return $translation;
}


=head2 cdna_coding_start

  Arg [1]    : none
  Example    : $relative_coding_start = $transcript->cdna_coding_start();
  Description: Retrieves the position of the coding start of this transcript
               in cdna coordinates (relative to the start of the 5prime end of
               the transcript, excluding introns, including utrs). This is
               always 1 for prediction transcripts because they have no UTRs.
  Returntype : int
  Exceptions : none
  Caller     : five_prime_utr, get_all_snps, general
  Status     : Stable

=cut

sub cdna_coding_start { return 1 }



=head2 cdna_coding_end

  Arg [1]    : none
  Example    : $relative_coding_start = $transcript->cdna_coding_end();
  Description: Retrieves the position of the coding end of this transcript
               in cdna coordinates (relative to the start of the 5prime end of
               the transcript, excluding introns, including utrs). This is
               always te length of the cdna for prediction transcripts because
               they have no UTRs.
  Returntype : int
  Exceptions : none
  Caller     : five_prime_utr, get_all_snps, general
  Status     : Stable

=cut

sub cdna_coding_end {
  my ($self) = @_;
  return length( $self->spliced_seq() );
}