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