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

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL