[Bioperl-l] Graphics/Panel problem

Thomas Keller kellert at ohsu.edu
Fri May 9 14:15:14 EDT 2003


Greetings,
I'm just following the example in doc.bioperl.org for 
Bio::Graphics::Panel, called render.pl in the Synopsis.
but I get the following error:
% render.pl AE014076.genbank
Can't locate object method "start" via package "Bio::Seq::RichSeq" at 
/Library/Perl/Bio/Graphics/Panel.pm line 45, <DATA> line 141.

I'm stumped. I'd greatly appreciate your help bioperlers.
Thanks,
Tom K
## here's the script ##
  #! /usr/bin/perl
  ## render.pl from 
http://doc.bioperl.org/releases/bioperl-1.2/Graphics/Panel.html

  use strict;
  use Bio::Graphics;
  use Bio::SeqIO;
  my $file = shift                       or die "provide a sequence file 
as the argument";
  my $io = Bio::SeqIO->new(-file=>$file) or die "couldn't create 
Bio::SeqIO";
  my $seq = $io->next_seq                or die "couldn't find a 
sequence in the file";
  my @features = $seq->all_SeqFeatures;
  # sort features by their primary tags
  my %sorted_features;
  for my $f (@features) {
    my $tag = $f->primary_tag;
    push @{$sorted_features{$tag}},$f;
  }
  my $panel = Bio::Graphics::Panel->new(
  				      -segment   => $seq,
  				      -key_style => 'between',
  				      -width     => 800,
  				      -pad_left  => 10,
  				      -pad_right => 10,
  				      );
  $panel->add_track($seq,
  		  -glyph => 'arrow',
  		  -bump => 0,
  		  -double=>1,
  		  -tick => 2);
  $panel->add_track($seq,
  		  -glyph  => 'generic',
  		  -bgcolor => 'blue',
  		  -label  => 1,
  		 );
  # general case
  my @colors = qw(cyan orange blue purple green chartreuse magenta 
yellow aqua);
  my $idx    = 0;
  for my $tag (sort keys %sorted_features) {
    my $features = $sorted_features{$tag};
    $panel->add_track($features,
  		    -glyph    =>  'generic',
  		    -bgcolor  =>  $colors[$idx++ % @colors],
  		    -fgcolor  => 'black',
  		    -font2color => 'red',
  		    -key      => "${tag}s",
  		    -bump     => +1,
  		    -height   => 8,
  		    -label    => 1,
  		    -description => 1,
  		   );
  }
  print $panel->png;
  exit 0;
__END__
Tom Keller, Ph.D.
http://www.ohsu.edu/core
kellert at ohsu.edu
503-494-2442



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