Bio::Graphics::Util - non-object-oriented utilities used in Bio::Graphics modules

Bio-Graphics documentation Contained in the Bio-Graphics distribution.

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Bio::Graphics::Util - non-object-oriented utilities used in Bio::Graphics modules

($frame,$offset) = frame_and_offset($pos,$strand,$phase)

Calculate the reading frame for a given genomic position, strand and phase. The offset is the offset from $pos to the first nucleotide of the reading frame.

In a scalar context, returns the frame only.

Bio-Graphics documentation Contained in the Bio-Graphics distribution. 
package Bio::Graphics::Util;

# $Id: Util.pm,v 1.1 2008-12-08 23:15:57 lstein Exp $
# Non object-oriented utilities used here-and-there in Bio::Graphics modules


use strict;
require Exporter;
use base qw(Exporter);
use vars '@EXPORT','@EXPORT_OK';
@EXPORT = 'frame_and_offset';
use Bio::Root::Version;


sub frame_and_offset {
  my ($pos,$strand,$phase) = @_;
  $strand ||= +1;
  $phase  ||= 0;
  my $codon_start =  $strand >= 0
                   ? $pos + $phase
	           : $pos - $phase;  # probably wrong
  my $frame  = ($codon_start-1) % 3;
  my $offset = $strand >= 0 ? $phase : -$phase;
  return wantarray ? ($frame,$offset) : $frame;
}


1;