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Bio-EnsEMBL-112.0.0
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/ Bio::EnsEMBL::MANE

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

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
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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