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
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  Questions may also be sent to the Ensembl help desk at
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NAME

Bio::EnsEMBL::IdMapping::TinyTranscript - lightweight transcript object

SYNOPSIS

  # fetch a transcript from the db and create a lightweight
  # transcript object from it
  my $tr = $transcript_adaptor->fetch_by_stable_id('ENST000345437');
  my $lightweight_tr =
    Bio::EnsEMBL::IdMapping::TinyTranscript->new_fast( [
      $tr->dbID,          $tr->stable_id,
      $tr->version,       $tr->created_date,
      $tr->modified_date, $tr->start,
      $tr->end,           $tr->strand,
      $tr->length,        md5_hex( $tr->spliced_seq ),
    ] );

DESCRIPTION

This is a lightweight transcript object for the stable Id mapping. See the documentation in TinyFeature for general considerations about its design.

METHODS

  start
  end
  strand
  length
  seq_md5_sum
  add_Translation
  translation
  add_Exon
  get_all_Exons

start

  Arg[1]      : (optional) Int - the transcript's start coordinate
  Description : Getter/setter for the transcript's start coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

end

  Arg[1]      : (optional) Int - the transcript's end coordinate
  Description : Getter/setter for the transcript's end coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

strand

  Arg[1]      : (optional) Int - the transcript's strand
  Description : Getter/setter for the transcript's strand.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

length

  Arg[1]      : (optional) Int - the transcript's length
  Description : Getter/setter for the transcript's length. Note that this is
                *not* the distance between start and end, but rather the sum of
                the lengths of all exons.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

seq_md5_sum

  Arg[1]      : (optional) String - the md5 digest of the transcript's sequence
  Description : Getter/setter for the md5 digest of the transcript's sequence.
                Note that when used as a setter, you are expected to pass a
                digest, not the raw sequence (i.e. the digest is not created for
                you).
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

add_Translation

  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyTranslation $tl - the translation
                to add
  Example     : $tiny_transcript->add_Translation($tiny_translation);
  Description : Adds a translation to this transcript.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

translation

  Description : Getter for the transcript's translation.
  Return type : Bio::EnsEMBL::IdMapping::TinyTranslation
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

add_Exon

  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyExon $exon - the exon to add
  Example     : $tiny_transcript->add_Exon($tiny_exon);
  Description : Adds an exon to this transcript.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

get_all_Exons

  Example     : foreach my $exon (@{ $tiny_transcript->get_all_Exons }) {
                  # do something with exon
                }
  Description : Returns all exons attached to that transcript.
  Return type : Arrayref of Bio::EnsEMBL::IdMapping::TinyExon objects
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

biotype

  Arg[1]      : (optional) String - the gene's biotype
  Description : Getter/setter for the gene's biotype.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

seq_region_name

  Arg[1]      : (optional) String - seq_region name
  Description : Getter/setter for the seq_region name of the slice the gene is
                on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL