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Summary

Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::IntronUtils - utilities for transcript objects

Package variables

Included modules

Inherit

Exporter

Synopsis

  use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::IntronUtils qw(get_splice_sites);

  or 

  use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::IntronUtils 

  to get all methods

Description

All methods in this class should take a Bio::EnsEMBL::Intron
object as their first argument.
The methods provided should carry out some standard
functionality for said objects such as printing info or
getting splice sites

Methods

Methods description

  Arg [1]   : Bio::EnsEMBL::Intron
  Arg [2]   : string, indent of \ts to put infrount of string
  Function  : return a string with coords or intron
  Returntype: string
  Exceptions: throw is not given an argument
  Example   :

  Arg [1]   : Bio::EnsEMBL::Intron
  Function  : get the donor and acceptor splice sites for the
  given intron
  Returntype: array, (two strings in an array the donor and
                      acceptor splice sites)
  Exceptions: none
  Example   :

  Arg [1]   : Bio::EnsEMBL::Intron
  Arg [2]   : Int, max length of intron
  Function  : check intron length against specificed maximum
  Returntype: boolean 0 for longer than max, 1 for less than
  Exceptions: none
  Example   :

  Arg [1]   : Bio::EnsEMBL::Intron
  Arg [2]   : string, indent
  Function  : print out info about given Intron
  Returntype: none
  Exceptions: n/a
  Example   :

Methods code

sub Intron_info {

  my ($intron, $indent) = @_;
  throw("Must be passed an intron") if(!$intron);
  $indent = '' if(!$indent);
  my $coord_string = coord_string($intron);
  my $id = id($intron);
  return $indent."INTRON: ".$coord_string;

}

sub get_splice_sites {

  my ($intron) = @_;
  my $intron_slice = $intron->feature_Slice;
  my $donor_seq    = uc($intron_slice->subseq(1,2));
  my $acceptor_seq = uc($intron_slice->subseq($intron->length-1,$intron->length));
  return $donor_seq, $acceptor_seq;

}

sub intron_length_less_than_maximum {

  my ($intron, $max_length) = @_;
  if($intron->length >= $max_length){
    warning("This intron is longer than ".$max_length);
    return 0;
  }
  return 1;
}

1;

}

sub print_Intron {

  my ($intron, $indent) = @_;
  print Intron_info($intron, $indent)."\n";

}

General documentation

please send any questions to ensembl-dev@ebi.ac.uk