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Bio-EnsEMBL-112.0_54
River stage zero No dependents
/ Bio::EnsEMBL::ExonTranscript

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.

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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