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

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::TinyGene - lightweight gene object

SYNOPSIS

# fetch a gene from the db and create a lightweight gene object from it
 my $gene = $gene_adaptor->fetch_by_stable_id('ENSG000345437');
 my $lightweight_gene = Bio::EnsEMBL::IdMapping::TinyGene->new_fast( [
     $gene->dbID,                   $gene->stable_id,
     $gene->version,                $gene->created_date,
     $gene->modified_date,          $gene->start,
     $gene->end,                    $gene->strand,
     $gene->slice->seq_region_name, $gene->biotype,
     $gene->analysis->logic_name,
 ] );

DESCRIPTION

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

METHODS

start
end
strand
seq_region_name
biotype
logic_name
add_Transcript
get_all_Transcripts
length

start

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

end

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

strand

Arg[1]      : (optional) Int - the gene's strand
Description : Getter/setter for the gene's strand.
Return type : Int
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

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

logic_name

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

add_Transcript

Arg[1]      : Bio::EnsEMBL::IdMapping::TinyTranscript $tr - the transcript to
              add
Example     : $tiny_gene->add_Transcript($tiny_transcript);
Description : Adds a transcript to a gene.
Return type : none
Exceptions  : thrown on wrong or missing argument
Caller      : general
Status      : At Risk
            : under development

get_all_Transcripts

Example     : foreach my $tr (@{ $tiny_gene->get_all_Transcripts }) {
                # do something with transcript
              }
Description : Returns all transcripts attached to that gene.
Return type : Arrayref of Bio::EnsEMBL::IdMapping::TinyTranscript objects
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

length

Description : Returns the gene length (distance between start and end).
Return type : Int
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development