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
  <http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::UTR - A UTR feature with a location and a type (five prime/3 prime)

SYNOPSIS

  use Bio::EnsEMBL::UTR;

  $feature = Bio::EnsEMBL::UTR->new(
    -start         => 100,
    -end           => 220,
    -strand        => -1,
    -slice         => $slice,
    -type          => 'five_prime_UTR',
    -transcript    => $transcript
  );

DESCRIPTION

This is a UTR feature within the Ensembl system. A UTR repsents the non-coding (untranslated) regions of a transcript. It can be 5' or 3'

METHODS

new

  Arg [...]  : Named arguments passed to superclass
  Example    : $feature = Bio::EnsEMBL::UTR->new
                        (-start   => 1,
                         -end     => 100,
                         -strand  => 1,
                         -slice   => $slice,
                         -dbID    => 10,
                         -transcript  => $transcript,
                         -type    => 'five_prime_UTR');
  Description: Constructs a new Bio::EnsEMBL::UTR.
  Returntype : Bio::EnsEMBL::UTR
  Exceptions : Thrown on invalid -SLICE, -STRAND arguments
  Caller     : general, subclass constructors
  Status     : Stable

transcript

  Arg [1]    : (optional) Bio::EnsEMBL::Transcript
  Example    : $transcript = $utr->transcript();
  Description: Getter/Setter for the transcript associated with this
               UTR.
  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

seq_region_start

  Arg [1]    : (optional) string $seq_region_start
  Example    : $seq_region_start = $cds->seq_region_start();
  Description: Getter/Setter for the seq_region_start for this UTR.
               Overwrite default method from Feature as UTR does not have
               a table
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

seq_region_end

  Arg [1]    : (optional) string $seq_region_end
  Example    : $seq_region_end = $cds->seq_region_end();
  Description: Getter/Setter for the seq_region_end for this UTR.
               Overwrite default method from Feature as UTR does not have
               a table
  Returntype : String
  Exceptions : none
  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

type

  Arg [1]    : (optional) string $type
  Example    : print $utr->type();
  Description: This method returns a string that describes
               the type of UTR feature (5 prime or 3 prime)
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

feature_so_acc

  Example    : print $utr->feature_so_acc;
  Description: This method returns a string containing the SO accession number of the UTR, based on type.
               Overrides Bio::EnsEMBL::Feature::feature_so_acc
  Returntype : string (Sequence Ontology accession number)

feature_so_term

  Example    : print $utr->feature_so_term;
  Description: This method returns a string containing the SO accession term of the UTR, based on type.
               Overrides Bio::EnsEMBL::Feature::feature_so_term
  Returntype : string (Sequence Ontology term)

summary_as_hash

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

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL