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Bio-EnsEMBL-112.0_53
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/ Bio::EnsEMBL::PredictionTranscript

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

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CONTACT

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NAME

PredictionTranscript

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

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

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

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

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

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

summary_as_hash

Example    : my $hash = $misc_feature->summary_as_hash();
Description: Retrieves a textual summary of this prediction.
             Not inherited from Features.
Returntype : Hashref of arrays of descriptive strings
Exceptions : none
Caller     : general
Status     : Stable

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

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

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

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

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

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

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

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

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

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