Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils IntronUtils
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Summary
Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::IntronUtils - utilities for transcript objects
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils qw ( coord_string id )
Bio::EnsEMBL::Analysis::Tools::Logger qw ( logger_info )
Bio::EnsEMBL::Utils::Exception qw ( verbose throw warning stack_trace_dump )
Exporter
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
Intron_infoDescriptionCode
get_splice_sitesDescriptionCode
intron_length_less_than_maximumDescriptionCode
print_IntronDescriptionCode
Methods description
Intron_infocode    nextTop
  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 :
get_splice_sitescodeprevnextTop
  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 :
intron_length_less_than_maximumcodeprevnextTop
  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 :
print_IntroncodeprevnextTop
  Arg [1]   : Bio::EnsEMBL::Intron
Arg [2] : string, indent
Function : print out info about given Intron
Returntype: none
Exceptions: n/a
Example :
Methods code
Intron_infodescriptionprevnextTop
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;
}
get_splice_sitesdescriptionprevnextTop
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, $acceptor_seq;
}
intron_length_less_than_maximumdescriptionprevnextTop
sub intron_length_less_than_maximum {
  my ($intron, $max_length) = @_;
  if($intron->length >= $max_length){
    warning("This intron is longer than ".$max_length);
    return 0;
  }
  return 1;
}

1;
}
print_IntrondescriptionprevnextTop
sub print_Intron {
  my ($intron, $indent) = @_;
  print Intron_info($intron, $indent)."\n";
}
General documentation
CONTACTTop
please send any questions to ensembl-dev@ebi.ac.uk