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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NAME

Bio::EnsEMBL::PredictionExon - A class representing an Exon from an ab initio prediction method

SYNOPSIS

  $exon = new Bio::EnsEMBL::PredictionExon(
    -START   => 100,
    -END     => 200,
    -STRAND  => 1,
    -SLICE   => $slice,
    -DBID    => $dbID,
    -P_VALUE => 23.5,
    -SCORE   => 99
  );

  # seq() returns a Bio::Seq
  my $seq = $exon->seq->seq();

  # peptide() only makes sense within transcript context
  my $pep = $exon->peptide($transcript)->seq();

  # Normal feature operations can be performed:
  $exon = $exon->transform('clone');
  $exon->move( $new_start, $new_end, $new_strand );
  print $exon->slice->seq_region_name();

DESCRIPTION

This is a class which represents an prediction exon which is part of a predcition transcript. See Bio::EnsEMBL:PredictionTranscript

METHODS

new

  Args       : see SUPERCLASS Bio::EnsEMBL::Exon
  Example    : none
  Description: create an Exon object
  Returntype : Bio::EnsEMBL::PredictionExon 
  Exceptions : none
  Caller     : general
  Status     : Stable

score

  Arg [1]    : string $newval (optional) 
               The new value to set the score attribute to
  Example    : $score = $obj->score()
  Description: Getter/Setter for the score attribute
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

p_value

  Arg [1]    : string $newval (optional) 
               The new value to set the p_value attribute to
  Example    : $p_value = $obj->p_value()
  Description: Getter/Setter for the p_value attribute
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

end_phase

  Arg [1]    : (optional) int $end_phase
  Example    : $end_phase = $feat->end_phase;
  Description: Gets/Sets the end phase of the exon.
               end_phase = number of bases from the last incomplete codon of 
               this exon.
               Usually, end_phase = (phase + exon_length)%3
               but end_phase could be -1 if the exon is half-coding and its 3 
               prime end is UTR.
  Returntype : int
  Exceptions : warning if end_phase is called without an argument and the
               value is not set.
  Caller     : general
  Status     : Stable

transform

  Arg  1     : String $coordinate_system_name
  Arg [2]    : String $coordinate_system_version
  Description: moves this exon to the given coordinate system. If this exon has
               attached supporting evidence, they move as well.
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : wrong parameters
  Caller     : general
  Status     : Stable

transfer

  Arg [1]    : Bio::EnsEMBL::Slice $destination_slice
  Example    : none
  Description: Moves this Exon to given target slice coordinates. If Features
               are attached they are moved as well. Returns a new exon.
  Returntype : Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : Stable

summary_as_hash

  Example       : $exon_summary = $exon->summary_as_hash();
  Description   : Extends Feature::summary_as_hash
                  Retrieves a summary of this prediction exon.
  Returns       : hashref of descriptive strings
  Status        : Intended for internal use

transcript Example : $prediction_transcript = $exon->transcript; Description : Locates the parent prediction transcript using an exon dbID Same as prediction_transcript, duplicated for compatibility with Exon feature Returns : Bio::EnsEMBL::PredictionTranscript

prediction_transcript

  Example     : $prediction_transcript = $exon->prediction_transcript;
  Description : Locates the parent prediction transcript using an exon dbID
  Returns     : Bio::EnsEMBL::PredictionTranscript

add_supporting_features

  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing.
  Returntype : none
  Status     : Stable

get_all_supporting_features

  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing and returns empty list
  Returntype : empty list.
  Status     : Stable

find_supporting_evidence

  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing.
  Returntype : empty list.
  Status     : Stable

cpanm Bio::EnsEMBL::CDS

perl -MCPAN -e shell
install Bio::EnsEMBL::CDS