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

  Please email comments or questions to the public Ensembl
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NAME

Bio::EnsEMBL::MANE - Object representing a MANE transcript

SYNOPSIS

  use Bio::EnsEMBL::MANE;

  $mane_transcript = Bio::EnsEMBL::MANE->new(
    -transcript    => $transcript
  );

DESCRIPTION

This is a MANE transcript It represents an Ensembl transcript that has a matching RefSeq equivalent

METHODS

new

  Arg [...]  : Named arguments passed to superclass
  Example    : $feature = Bio::EnsEMBL::MANE->new
                        (-transcript => $transcript);
  Description: Constructs a new Bio::EnsEMBL::MANE.
  Returntype : Bio::EnsEMBL::MANE
  Exceptions : 
  Caller     : general, subclass constructors
  Status     : Stable

transcript Arg [1] : Fetch the original transcript object Example : $transcript = $mane->transcript(); Description: Getter/Setter for the transcript object Returntype : Bio::EnsEMBL::Transcript Exceptions : none Caller : general Status : Stable

stable_id Arg [1] : (optional) string $stable_id Example : $stable_id = $mane->stable_id(); Description: Getter/Setter for the stable_id for the transcript associated with this MANE transcript Returntype : String Exceptions : none Caller : general Status : Stable

refseq

  Arg [1]    : Fetch the RefSeq accession associated with
               this transcript
  Example    : $refseq = $mane->refseq();
  Description: Getter/Setter for the RefSeq associated with this
               MANE transcript.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

type

  Arg [1]    : (optional) string mane class
  Example    : $mane = $mane->type();
  Description: Getter/Setter for the class of MANE
               associated with this transcript.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

summary_as_hash

  Example    : my $hash = $mane->summary_as_hash();
  Description: Generates a HashRef compatible with GFFSerializer. Adds
               Gene, RefSeq accession and MANE class to the basic feature hash
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable