Bio::EnsEMBL PredictionTranscript
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Summary
PredictionTranscript
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Feature
Bio::EnsEMBL::Transcript
Bio::EnsEMBL::Translation
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( deprecate throw warning )
Inherit
Bio::EnsEMBL::Transcript
Synopsis
Description
Container for single transcript ab initio gene prediction such as
GenScan or SNAP. Is directly storable/retrievable in Ensembl using
PredictionTranscriptAdaptor.
Creation:
  my $tran = new Bio::EnsEMBL::PredictionTranscript();
  $tran->add_Exon($pred_exon);

  my $tran =
    new Bio::EnsEMBL::PredictionTranscript( -EXONS => @pred_exons );
Manipulation:
  # Returns an array of PredictionExon objects
  my @pred_exons = @{ $tran->get_all_Exons };

  # Returns the peptide translation as string
  my $pep = $tran->translate()->seq();

  # Get the exon cdna sequence.
  my $cdna = $trans->spliced_seq();
Methods
add_DBEntry
No description
Code
cdna_coding_endDescriptionCode
cdna_coding_startDescriptionCode
coding_region_endDescriptionCode
coding_region_startDescriptionCode
display_idDescriptionCode
display_labelDescriptionCode
external_db
No description
Code
external_name
No description
Code
external_status
No description
Code
get_all_AttributesDescriptionCode
get_all_DBEntries
No description
Code
get_all_DBLinks
No description
Code
get_all_ExonsDescriptionCode
get_all_translateable_ExonsDescriptionCode
get_cdnaDescriptionCode
get_exon_countDescriptionCode
is_known
No description
Code
newDescriptionCode
set_exon_countDescriptionCode
stable_idDescriptionCode
transferDescriptionCode
transformDescriptionCode
translateDescriptionCode
translationDescriptionCode
Methods description
cdna_coding_endcode    nextTop
  Arg [1]    : none
  Example    : $relative_coding_start = $transcript->cdna_coding_start;
  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
cdna_coding_startcodeprevnextTop
  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
coding_region_endcodeprevnextTop
  Arg [1]    : none
  Example    : $coding_region_end = $transcript->coding_region_end
  Description: Retrieves the start of the coding region of this prediction
               transcript. For prediction transcripts this is always the same
               as the end since no UTRs are stored.
               By convention, the coding_region_end is always higher than the
               value returned by the coding_region_start method.
               The value returned by this function is NOT the biological
               coding start since on the reverse strand the biological coding
               end would be the lower genomic value.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
coding_region_startcodeprevnextTop
  Arg [1]    : none
  Example    : $coding_region_start = $pt->coding_region_start
  Description: Retrieves the start of the coding region of this transcript in
               slice coordinates.  For prediction transcripts this
               is always the start of the transcript (i.e. there is no UTR).
               By convention, the coding_region_start is always lower than
               the value returned by the coding_end method.
               The value returned by this function is NOT the biological
               coding start since on the reverse strand the biological coding
               start would be the higher genomic value.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
display_idcodeprevnextTop
  Arg [1]    : none
  Example    : print $rf->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier. For prediction transcripts this is
               (depending on availability and in this order) the stable Id, the
               dbID or an empty string.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable
display_labelcodeprevnextTop
  Arg [1]    : string $newval (optional)
               The new value to set the display_label attribute to
  Example    : $display_label = $pt->display_label()
  Description: Getter/Setter for a displayable identifier for this
               prediction transcript.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
get_all_AttributescodeprevnextTop
  Arg [1]    : none
  Example    :
  Description: DOES NOTHING, Returns empty listref. Provided here to prevent
               Transcript attributes being returned for PredictionTranscripts.
  Returntype : EMPTY listref Bio::EnsEMBL::Attribute
  Exceptions : none
  Caller     : general
  Status     : At risk
get_all_ExonscodeprevnextTop
  Arg [1]    : none
  Example    : my @exons = @{$transcript->get_all_Exons()};
  Description: Returns an listref of the exons in this transcipr in order.
               i.e. the first exon in the listref is the 5prime most exon in 
               the transcript.
  Returntype : a list reference to Bio::EnsEMBL::Exon objects
  Exceptions : none
  Caller     : general
  Status     : Stable
get_all_translateable_ExonscodeprevnextTop
  Arg [1]    : none
  Example    : $exons = $self->get_all_translateable_Exons
  Description: Retrieves the translateable portion of all exons in this
               transcript.  For prediction transcripts this means all exons
               since no UTRs are stored for them.
  Returntype : listref of Bio::EnsEMBL::PredictionExons
  Exceptions : none
  Caller     : general
  Status     : Stable
get_cdnacodeprevnextTop
  Description : DEPRECATED - use spliced_seq() or translateable_seq instead
get_exon_countcodeprevnextTop
  Description: DEPRECATED - use get_all_Exons instead
newcodeprevnextTop
  Arg [-DISPLAY_LABEL]
    string - a displayable identifier for this prediction
  Arg [...]  : See Bio::EnsEMBL::Transcript superclass constructor
  Example    : $pt = Bio::EnsEMBL::PredictionTranscript->new
                  ( '-start'         =>  $seq_region_start,
                    '-end'           =>  $seq_region_end,
                    '-strand'        =>  $seq_region_strand,
                    '-adaptor'       =>  $self,
                    '-slice'         =>  $slice,
                    '-analysis'      =>  $analysis,
                    '-dbID'          =>  $prediction_transcript_id,
                    '-display_label' =>  $display_label);
  Description: Constructor. Creates a new Bio::EnsEMBL::PredictionTranscript
               object
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable
set_exon_countcodeprevnextTop
  Description: DEPRECATED - this method does nothing now
stable_idcodeprevnextTop
  Arg [1]    : none
  Example    : print $pt->stable_id();
  Description: Gets a 'stable' identifier for this prediction transcript.  Note
               that prediction transcripts do not have true *stable*
               identifiers (i.e. identifiers maintained between releases).
               This method chains to the display_label method and is intended
               to provide polymorphism with the Transcript class.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
transfercodeprevnextTop
  Arg  1     : Bio::EnsEMBL::Slice $destination_slice
  Example    : $ptrans = $ptrans->transfer($slice);
  Description: Moves this PredictionTranscript to the given slice.
               If this Transcripts has Exons attached, they move as well.
               If this transcript cannot be moved then undef is returned
               instead.
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable
transformcodeprevnextTop
  Arg  1     : String $coordinate_system_name
  Arg [2]    : String $coordinate_system_version
  Example    : $ptrans = $ptrans->transform('chromosome', 'NCBI33');
               $ptrans = $ptrans->transform('clone');
  Description: Moves this PredictionTranscript to the given coordinate system.
               If this Transcript has Exons attached, they move as well.
               A new Transcript is returned or undefined if this PT is not
               defined in the new coordinate system.
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : wrong parameters
  Caller     : general
  Status     : Stable
translatecodeprevnextTop
  Args      : none
  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
translationcodeprevnextTop
  Arg [1]    : none
  Example    : $translation = $pt->translation();
  Description: Retrieves a Bio::EnsEMBL::Translation object for this prediction
               transcript.  Note that this translation is generated on the fly
               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
Methods code
add_DBEntrydescriptionprevnextTop
sub add_DBEntry {}
cdna_coding_enddescriptionprevnextTop
sub cdna_coding_end {
  my $self = shift;
  return length($self->spliced_seq);
}
cdna_coding_startdescriptionprevnextTop
sub cdna_coding_start {
 return 1;
}
coding_region_enddescriptionprevnextTop
sub coding_region_end {
  my $self = shift;
  return $self->end();
}
coding_region_startdescriptionprevnextTop
sub coding_region_start {
  my $self = shift;
  return $self->start();
}
display_iddescriptionprevnextTop
sub display_id {
  my $self = shift;
  return $self->stable_id || $self->dbID || '';
}
display_labeldescriptionprevnextTop
sub display_label {
  my $self = shift;
  return $self->{'display_label'} = shift if(@_);
  return $self->{'display_label'};
}
external_dbdescriptionprevnextTop
sub external_db {
 return undef;
}
external_namedescriptionprevnextTop
sub external_name {
 return undef;
}
external_statusdescriptionprevnextTop
sub external_status {
 return undef;
}
get_all_AttributesdescriptionprevnextTop
sub get_all_Attributes {
  my $self = shift;

  return [];
}
get_all_DBEntriesdescriptionprevnextTop
sub get_all_DBEntries {
 return [];
}
get_all_DBLinksdescriptionprevnextTop
sub get_all_DBLinks {
 return [];
}
get_all_ExonsdescriptionprevnextTop
sub get_all_Exons {
   my ($self) = @_;
   if( ! defined $self->{'_trans_exon_array'} && defined $self->adaptor() ) {
     $self->{'_trans_exon_array'} = $self->adaptor()->db()->
       get_PredictionExonAdaptor()->fetch_all_by_PredictionTranscript( $self );
   }
   return $self->{'_trans_exon_array'};
}
get_all_translateable_ExonsdescriptionprevnextTop
sub get_all_translateable_Exons {
  my $self = shift;
  return $self->get_all_Exons();
}
get_cdnadescriptionprevnextTop
sub get_cdna {
  my $self = shift;
  deprecate('use spliced_seq instead');
  return $self->spliced_seq();
}

1;
}
get_exon_countdescriptionprevnextTop
sub get_exon_count {
   my $self = shift;
   deprecate('Use scalar(@{$transcript->get_all_Exon()s}) instead');
   return scalar( @{$self->get_all_Exons} );
}
is_knowndescriptionprevnextTop
sub is_known {
 return 0;
}
newdescriptionprevnextTop
sub new {
  my $class = shift;

  my $self = $class->SUPER::new(@_);

  my ($display_label) = rearrange(['DISPLAY_LABEL'], @_);

  $self->{'display_label'} = $display_label;

  return $self;
}
set_exon_countdescriptionprevnextTop
sub set_exon_count {
  deprecate('This method no longer does anything.');
}
stable_iddescriptionprevnextTop
sub stable_id {
 return display_label(@_);
}
transferdescriptionprevnextTop
sub transfer {
  my $self = shift;

  my $new_transcript = $self->SUPER::transfer( @_ );
  return undef unless $new_transcript;

  if( exists $self->{'_trans_exon_array'} ) {
    my @new_exons;
    for my $old_exon ( @{$self->{'_trans_exon_array'}} ) {
      my $new_exon = $old_exon->transfer( @_ );
      push( @new_exons, $new_exon );
    }

    $new_transcript->{'_trans_exon_array'} =\@ new_exons;
  }

  return $new_transcript;
}
transformdescriptionprevnextTop
sub transform {
  my $self = shift;

  # catch for old style transform calls
  if( ref $_[0] && $_[0]->isa( "Bio::EnsEMBL::Slice" )) {
    throw("transform needs coordinate systems details now," .
          "please use transfer");
  }

  my $new_transcript = Bio::EnsEMBL::Feature::transform($self, @_ );
  return undef unless $new_transcript;

  #go through the _trans_exon_array so as not to prompt lazy-loading
  if(exists($self->{'_trans_exon_array'})) {
    my @new_exons;
    foreach my $old_exon ( @{$self->{'_trans_exon_array'}} ) {
      my $new_exon = $old_exon->transform(@_);
      push(@new_exons, $new_exon);
    }
    $new_transcript->{'_trans_exon_array'} =\@ new_exons;
  }

  return $new_transcript;
}
translatedescriptionprevnextTop
sub translate {
  my ($self) = @_;

  my $dna = $self->translateable_seq();
  if( CORE::length( $dna ) % 3 == 0 ) {
    $dna =~ s/TAG$|TGA$|TAA$//i;
  }
  # the above line will 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

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

  return $bioseq->translate();
}
translationdescriptionprevnextTop
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 => "dummy",
			     -seq => $Xseq,
			     -moltype => "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());
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.