LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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     http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::MicroRNA - A class representing a microRNA product of a transcript

DESCRIPTION

A specialisation of Bio::EnsEMBL::RNAProduct describing MicroRNAs. Mostly takes care of wrapping miRNA-specific RNAProduct attributes in methods which make them look like ordinary class members.

SYNOPSIS

  my $miR = Bio::EnsEMBL::MicroRNA->new(
    -SEQ_START => 36,
    -SEQ_END   => 58
  );

  # Stable-ID setter
  $miR->stable_id('ENSS00090210');

  # Get start and end position in the precursor transcript
  my $start = $miR->start();
  my $end = $miR->end();

new

  Arg: [-ARM]         : which arm of the hairpin precursor this miRNA comes
                        from. Returns 3 and 5 for 3' and 5', respectively.
  Arg [...]           : Named arguments to superclass constructor
                        (see Bio::EnsEMBL::RNAProduct)
  Example    : my $miR = Bio::EnsEMBL::MicroRNA->new(
                 -SEQ_START => 36,
                 -SEQ_END   => 58,
                 -ARM       => 3
               );
  Description: Constructor.  Creates a new MicroRNA object
  Returntype : Bio::EnsEMBL::MicroRNA
  Exceptions : throw if ARM value is out of bounds
  Caller     : general
  Status     : In Development

arm

    Arg [1]     : (optional) int $arm which arm of the hairpin precursor
                  this miRNA comes from
    Example     : $mirna_arm = $mirna->arm();
                  $mirna->arm(3);
    Description : Sets or returns the arm of the hairpin this miRNA comes
                  from. Accepted values are 3 and 5 for 3' and 5',
                  respectively.
    Return type : Integer
    Exceptions  : throw if setter is passed an incorrect value
                  or if multiple 'mirna_arm' attributes exist.
    Caller      : General
    Status      : Stable

summary_as_hash

  Example       : $mirna_summary = $mirna->summary_as_hash();
  Description   : Retrieves a textual summary of this MicroRNA.
                  Built on top of generic implementation in RNAProduct.
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use

_validate_arm_value Arg [1] : int $arm which arm of the hairpin precursor this miRNA comes from Description: PRIVATE validates if its argument has one of the accepted values for specifying the miRNA hairpin arm. Returntype : none Exceptions : throw if the argument is out of bounds Caller : internal Status : Stable