Bio::EnsEMBL::Biotype Class Reference

Inheritance diagram for Bio::EnsEMBL::Biotype:

Public Member Functions
public Bio::EnsEMBL::Biotype	new ()
public Bio::EnsEMBL::Biotype	new_fast ()
public String	name ()
public String	biotype_group ()
public String	so_acc ()
public String	so_term ()
public String	object_type ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

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).

Definition at line 35 of file Biotype.pm.

Member Function Documentation

biotype_group()

public String Bio::EnsEMBL::Biotype::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

Code:

name()

public String 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

Code:

new()

public Bio::EnsEMBL::Biotype Bio::EnsEMBL::Biotype::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

Code:

new_fast()

public Bio::EnsEMBL::Biotype Bio::EnsEMBL::Biotype::new_fast

(

)

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

Code:

object_type()

public String Bio::EnsEMBL::Biotype::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)

Code:

so_acc()

public String Bio::EnsEMBL::Biotype::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

Code:

so_term()

public String Bio::EnsEMBL::Biotype::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

Code:

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The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/Biotype.pm