Raw content of Bio::EnsEMBL::PredictionTranscript
<![CDATA[=head1 LICENSE
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
=head1 CONTACT
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>.
=cut
=head1 NAME
PredictionTranscript
=head1 SYNOPSIS
=head1 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();
=head1 METHODS
=cut
package Bio::EnsEMBL::PredictionTranscript;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Translation;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw(Bio::EnsEMBL::Transcript);
=head2 new
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
=cut
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
my ($display_label) = rearrange(['DISPLAY_LABEL'], @_);
$self->{'display_label'} = $display_label;
return $self;
}
=head2 coding_region_start
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
=cut
sub coding_region_start {
my $self = shift;
return $self->start();
}
=head2 coding_region_end
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
=cut
sub coding_region_end {
my $self = shift;
return $self->end();
}
=head2 get_all_translateable_Exons
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
=cut
sub get_all_translateable_Exons {
my $self = shift;
return $self->get_all_Exons();
}
=head2 display_label
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
=cut
sub display_label{
my $self = shift;
return $self->{'display_label'} = shift if(@_);
return $self->{'display_label'};
}
=head2 stable_id
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
=cut
sub stable_id { return display_label(@_); }
sub get_all_DBEntries { return []; }
sub get_all_DBLinks { return []; }
sub add_DBEntry {}
sub external_db { return undef; }
sub external_status { return undef; }
sub external_name { return undef; }
sub is_known { return 0;}
=head2 translation
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
=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 => "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 => $tmpSeq->translate()->seq());
}
=head2 translate
Args : none
Function : Give a peptide translation of all exons currently in
the PT. Gives empty string when none is in.
Returntype: a Bio::Seq as in transcript->translate()
Exceptions: none
Caller : general
Status : Stable
=cut
sub translate {
my ($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();
}
=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_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
=cut
sub cdna_coding_end {
my $self = shift;
return length($self->spliced_seq);
}
=head2 transform
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
=cut
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;
}
=head2 transfer
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
=cut
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 $new_transcript;
}
=head2 get_all_Exons
Arg [1] : none
Example : my @exons = @{$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
=cut
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'};
}
=head2 display_id
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
=cut
sub display_id {
my $self = shift;
return $self->stable_id || $self->dbID || '';
}
=head2 get_all_Attributes
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
=cut
sub get_all_Attributes {
my $self = shift;
return [];
}
=head2 get_exon_count
Description: DEPRECATED - use get_all_Exons instead
=cut
sub get_exon_count {
my $self = shift;
deprecate('Use scalar(@{$transcript->get_all_Exon()s}) instead');
return scalar( @{$self->get_all_Exons} );
}
=head2 set_exon_count
Description: DEPRECATED - this method does nothing now
=cut
sub set_exon_count {
deprecate('This method no longer does anything.');
}
=head2 get_cdna
Description : DEPRECATED - use spliced_seq() or translateable_seq instead
=cut
sub get_cdna {
my $self = shift;
deprecate('use spliced_seq instead');
return $self->spliced_seq();
}
1;
]]>