Bio::EnsEMBL::MANE Class Reference

Inheritance diagram for Bio::EnsEMBL::MANE:

Public Member Functions
public Bio::EnsEMBL::MANE	new ()
public Bio::EnsEMBL::Transcript	transcript ()
public String	stable_id ()
public String	refseq ()
public String	type ()
public	display_id ()
public Hash	summary_as_hash ()
Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()
public Int	start ()
public Int	end ()
public Int	strand ()
public void	move ()
public Int	length ()
public Bio::EnsEMBL::Analysis	analysis ()
public Bio::EnsEMBL::Slice	slice ()
public Boolean Or Undef	equals ()
public Bio::EnsEMBL::Feature	transform ()
public Bio::EnsEMBL::Feature	transfer ()
public Listref	project_to_slice ()
public Listref	project ()
public String	seqname ()
public String	display_id ()
public String	version ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public String	seq_region_name ()
public Int	seq_region_length ()
public Boolean	seq_region_strand ()
public Int	seq_region_start ()
public Int	seq_region_end ()
public String	coord_system_name ()
public String	seq ()
public Listref	get_all_alt_locations ()
public Boolean	overlaps ()
public Boolean	overlaps_local ()
public List	get_overlapping_Genes ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public String	feature_so_acc ()
public String	feature_so_term ()
public Hashref	summary_as_hash ()
public String	species ()
public	sub_SeqFeature ()
public	add_sub_SeqFeature ()
public	flush_sub_SeqFeature ()
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

use Bio::EnsEMBL::MANE;
 
$mane_transcript = Bio::EnsEMBL::MANE->new(
  -transcript    => $transcript
);

Description

This is a MANE transcript
It represents an Ensembl transcript that has a matching RefSeq equivalent

Definition at line 23 of file MANE.pm.

Member Function Documentation

display_id()

public Bio::EnsEMBL::MANE::display_id

(

)

Undocumented method

Code:

new()

public Bio::EnsEMBL::MANE Bio::EnsEMBL::MANE::new

(

)

  Arg [...]  : Named arguments passed to superclass
  Example    :

$feature = Bio::EnsEMBL::MANE->new
                       (-transcript => $transcript);

  Description: Constructs a new Bio::EnsEMBL::MANE.
  Returntype : Bio::EnsEMBL::MANE
  Exceptions : 
  Caller     : general, subclass constructors
  Status     : Stable

Code:

refseq()

public String Bio::EnsEMBL::MANE::refseq

(

)

  Arg [1]    : Fetch the RefSeq accession associated with
               this transcript
  Example    :

$refseq = $mane->refseq();

  Description: Getter/Setter for the RefSeq associated with this
               MANE transcript.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

stable_id()

public String Bio::EnsEMBL::MANE::stable_id

(

)

  Arg [1]    : (optional) string $stable_id
  Example    :

$stable_id = $mane->stable_id();

  Description: Getter/Setter for the stable_id for
               the transcript associated with this MANE transcript
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

summary_as_hash()

public Hash Bio::EnsEMBL::MANE::summary_as_hash

(

)

  Example    :

my $hash = $mane->summary_as_hash();

  Description: Generates a HashRef compatible with GFFSerializer. Adds
               Gene, RefSeq accession and MANE class to the basic feature hash
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

transcript()

public Bio::EnsEMBL::Transcript Bio::EnsEMBL::MANE::transcript

(

)

  Arg [1]    : Fetch the original transcript object
  Example    :

$transcript = $mane->transcript();

  Description: Getter/Setter for the transcript object
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

type()

public String Bio::EnsEMBL::MANE::type

(

)

  Arg [1]    : (optional) string mane class
  Example    :

$mane = $mane->type();

  Description: Getter/Setter for the class of MANE
               associated with this transcript.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/MANE.pm