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Bio-EnsEMBL-112.0.0
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/ Bio::EnsEMBL::IdMapping::TinyTranscript

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

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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