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

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NAME

Bio::EnsEMBL::Biotype

SYNOPSIS

my $biotype = new Bio::EnsEMBL::Biotype(
  -name          => 'new_biotype,
  -object_type   => 'gene',
  -biotype_group => 'a_biotype_group',
  -so_acc        => 'SO::1234567',
  -description   => 'New biotype'
);

my $name = $biotype->name();
my $biotype_group = $biotype->biotype_group();
my $so_acc = $biotype->so_acc();

DESCRIPTION

This is the Biotype object class.
Gene and Transcript objects used to have a biotype() method that returned the biotype name
(the biotype field in the gene and transcript tables).
From e93 a new biotype table was added. However because of legacy code using direct sql
queries on the biotype column of gene and transcript tables, that column that contains the
biotype name was not replaced by biotype_id containing a foreign key to the new biotype table.
Gene and Transcripts can still link to a Biotype through the key (name, object_type).

METHODS

new

Arg [-BIOTYPE_ID]  :
    int - dbID of the biotype
Arg [-NAME]    :
    string - the name of the biotype (for ensembl)
Arg [-OBJECT_TYPE] :
    string - the object type this biotype applies to (gene or transcript)
Arg [-BIOTYPE_GROUP]  :
    string - the name of the biotype group (for ensembl)
Arg [-SO_ACC] :
    string - the Sequence Ontology accession of this biotype
Arg [-SO_TERM] :
    string - the Sequence Ontology term for the SO accession of this biotype
Arg [-DESCRIPTION] :
    string - the biotype description
Arg [-DB_TYPE] :
    string - the database type for this biotype
Arg [-ATTRIB_TYPE_ID] :
    int - attrib_type_id

Example    : $biotype = Bio::EnsEMBL::Biotype->new(...);
Description: Creates a new biotype object
Returntype : Bio::EnsEMBL::Biotype
Exceptions : none

new_fast

Arg [1]    : hashref to be blessed
Description: Construct a new Bio::EnsEMBL::Biotype using the hashref.
Exceptions : none
Returntype : Bio::EnsEMBL::Biotype

name

Arg [1]    : (optional) string $name
             The name of this biotype according to ensembl.
Example    : $name = $biotype->name()
Description: Getter/Setter for the name of this biotype.
Returntype : string
Exceptions : none

biotype_group

Arg [1]    : (optional) string $biotype_group
Example    : $biotype_group = $biotype->biotype_group();
Description: Getter/Setter for the biotype_group of this biotype.
             Biotype groups are used internally at ensembl pipelines
             and consist on few defined categories.
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

so_acc

Arg [1]    : (optional) string $so_acc
Example    : $feat->so_acc();
Description: Getter/Setter for the Sequence Ontology accession of this biotype.
             It must be a SO like accession.
Returntype : string
Exceptions : thrown if an invalid so_acc argument is passed

so_term

Arg [1]    : (optional) string $so_term
Example    : $feat->so_term();
Description: Getter/Setter for the Sequence Ontology term of this biotype.
Returntype : string
Exceptions : none

object_type

Arg [1]    : (optional) string $object_type
Example    : $object_type = $biotype->object_type();
Description: Getter/Setter for the object_type of this biotype.
             Biotypes can be assigned to either genes or transcripts,
             object_type refers to which of them.
Returntype : string
Exceptions : thrown if an invalid object_type argument is passed (not gene or transcript)