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::ExonTranscript - An Exon feature in relation to a transcript

SYNOPSIS

  use Bio::EnsEMBL::ExonTranscript;

  $feature = Bio::EnsEMBL::ExonTranscript->new(-exon => $exon, -transcript => $transcript);

DESCRIPTION

This is a feature which extends the Exon class to add the relation to a specific transcript.

METHODS

new

  Arg [Exon]: The Exon object
  Arg [Transcript]: The Transcript object the exon belongs to
  Example    : $feature = Bio::EnsEMBL::ExonTranscript->new(-exon => $exon, -transcript => $transcript);
  Description: Constructs a new Bio::EnsEMBL::ExonTranscript.
  Returntype : Bio::EnsEMBL::ExonTranscript
  Exceptions : Thrown on invalid -SLICE, -STRAND arguments
  Caller     : general, subclass constructors
  Status     : Stable

exon

  Arg [1]    : (optional) Bio::EnsEMBL::Exon
  Example    : $exon = $exon_transcript->exon();
  Description: Getter/Setter for the exon forming this
               ExonTranscript.
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : none
  Caller     : general
  Status     : Stable

transcript

  Arg [1]    : (optional) Bio::EnsEMBL::Transcript
  Example    : print $utr->type();
  Description: Getter/Setter for the parent transcript
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

translation

    Description: Fetch the translation associated with
                 this transcript, if it exists. Return undef
                 if there is no translation, ie. a pseudogene
    Returntype : Bio::EnsEMBL::Translation or undef
    Caller     : general
    Status     : Stable

get_Gene

  Description: Get the gene associated with the ExonTranscript,
               if a transcript has been set
  Returntype : Bio::EnsEMBL::Gene or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

rank

  Example    : print $et->rank();
  Description: Getter/Setter for the exon rank
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

summary_as_hash

  Example    : my $hash = $utr->summary_as_hash();
  Description: Generates a HashRef compatible with GFFSerializer. Adds
               rank and transcript attributes to the basic Feature
               hash
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable