Bio::EnsEMBL::IdMapping::TinyGene Class Reference

Inheritance diagram for Bio::EnsEMBL::IdMapping::TinyGene:

Public Member Functions
public Int	start ()
public Int	end ()
public Int	strand ()
public String	seq_region_name ()
public String	biotype ()
public String	logic_name ()
public void	add_Transcript ()
public Arrayref	get_all_Transcripts ()
public Int	length ()
Public Member Functions inherited from Bio::EnsEMBL::IdMapping::TinyFeature
public Bio::EnsEMBL::IdMapping::TinyFeature	new_fast ()
public Int	id ()
public String	stable_id ()
public Int	version ()
public String	created_date ()
public String	modified_date ()
public String	to_string ()

Detailed Description

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.

Definition at line 28 of file TinyGene.pm.

Member Function Documentation

add_Transcript()

public void Bio::EnsEMBL::IdMapping::TinyGene::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

Code:

biotype()

public String Bio::EnsEMBL::IdMapping::TinyGene::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

Code:

end()

public Int Bio::EnsEMBL::IdMapping::TinyGene::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

Code:

get_all_Transcripts()

public Arrayref Bio::EnsEMBL::IdMapping::TinyGene::get_all_Transcripts

(

)

  Example     :

 foreach my $tr (@{ $tiny_gene->get_all_Transcripts }) {
@section autotoc_md16 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

Code:

length()

public Int Bio::EnsEMBL::IdMapping::TinyGene::length

(

)

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

Code:

logic_name()

public String Bio::EnsEMBL::IdMapping::TinyGene::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

Code:

seq_region_name()

public String Bio::EnsEMBL::IdMapping::TinyGene::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

Code:

start()

public Int Bio::EnsEMBL::IdMapping::TinyGene::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

Code:

strand()

public Int Bio::EnsEMBL::IdMapping::TinyGene::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

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/IdMapping/TinyGene.pm