Bio::EnsEMBL::Intron Class Reference

Inheritance diagram for Bio::EnsEMBL::Intron:

Public Member Functions
public Bio::EnsEMBL::Intron	new ()
public Int	length ()
public Bio::EnsEMBL::Exon	prev_Exon ()
public Bio::EnsEMBL::Exon	next_Exon ()
public Int	rank ()
public Boolean	is_splice_canonical ()
public ArrayRef	splice_seq ()
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

$intron = Bio::EnsEMBL::Intron->new( exon1, exon2, $analysis );

Definition at line 10 of file Intron.pm.

Member Function Documentation

is_splice_canonical()

public Boolean Bio::EnsEMBL::Intron::is_splice_canonical

(

)

  Example     :

my $canonical = $intron->is_splice_canonical(); 

  Description : Indicates if the splice site is considered normal. This means
                splice site variants equal to (D == donor, A == acceptor)
                  GT (D) => AG (A) 
                  AT (D) => AC (A)
                  GC (D) => AG (A)
  Returntype  : Boolean indicating if the splice was as expected
  Exceptions  : See splice_seq

Code:

length()

public Int Bio::EnsEMBL::Intron::length

(

)

  Args       : none
  Example    :

$length = $intron->length();

  Description: Returns the length of this intron
  Returntype : Integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::Intron Bio::EnsEMBL::Intron::new

(

)

  Arg [1]    : Bio::EnsEMBL::Exon The 5' exon for the intron; required
  Arg [2]    : Bio::EnsEMBL::Exon The 3' exon for the intron; required
  Arg [3]    : Bio::EnsEMBL::Analysis Analysis to link to this Intron
  Example    :

$intron = new Bio::EnsEMBL::Intron($exon1, $exon2)

  Description: Create an Intron object from two exons and an optional analysis
  Returntype : Bio::EnsEMBL::Intron
  Exceptions : exons not on the same strand or slice.
  Caller     : general
  Status     : Stable

Code:

next_Exon()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::Intron::next_Exon

(

)

  Args       : none
  Example    :

$exon = $intron->next_Exon

  Description: Returns the exon after this Intron
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

prev_Exon()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::Intron::prev_Exon

(

)

  Args       : none
  Example    :

$exon = $intron->prev_Exon

  Description: Returns the exon before this Intron
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

rank()

public Int Bio::EnsEMBL::Intron::rank

(

)

  Args       : none
  Example    :

$rank = $intron->rank

  Description: Returns the rank of this Intron
  Returntype : Integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

splice_seq()

public ArrayRef Bio::EnsEMBL::Intron::splice_seq

(

)

  Example     :

my ($donor, $acceptor) = @{$intron->splice_seq}; 

  Description : Get the donor and acceptor splice sites for this intron
  Returntype  : ArrayRef[String] The donor and acceptor sequences as Strings
  Exceptions  : Thrown if a feature Slice cannot be found

Code:

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

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