[Bioperl-l] Error for Bio::Graphics in the HOWTO script for rendering EMBL features

[Joshua Steele]

Dear All,

I'm getting an error (warning) message when I try to run examples 5 and 6 in
the Graphics HOWTO.

Error: Can't locate object method "has_tag" via package
"Bio::Location::Simple" at
/opt/local/lib/perl5/site_perl/5.12.3/Bio/Graphics/Glyph.pm line 704, <GEN0>
line 323.

This error occurs whether I'm using a genbank file or whether I'm using the
suggested EMBL file ( http://www.bioperl.org/wiki/Factor7 ).  The
Bio::Graphics package seems to work fine to render BLAST outputs, I was able
to get both the BLAST examples and a BLAST output to work.

I'm using (macports)Perl 5.12.3, Bioperl 1.0069, and Bio::Graphics 2.24 on
Mac OS 10.6.7.

If there is something obvious that I could do to fix it I'd be quite
grateful.

Cheers,
Josh

Here is the script as I tried to run it:


#!/opt/local/bin/perl

# file: embl2picture.pl
# This is code example 5 in the Graphics-HOWTO
# Author: Lincoln Stein

use strict;
use lib '$ENV{HOME}/src/bioperl-live';
use Bio::Graphics;
use Bio::SeqIO;
use Bio::SeqFeature::Generic;

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 $wholeseq = Bio::SeqFeature::Generic->new(
                                             -start        => 1,
                                             -end          => $seq->length,
                                             -display_name =>
$seq->display_name
                                            );
my $seqname = $seq->display_name;
my @features = $seq->get_SeqFeatures;

# partition 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(
                                      -length    => $seq->length,
                                      -key_style => 'between',
                                      -width     => 10000,
                                      -pad_left  => 50,
                                      -pad_right => 50,
                                     );
$panel->add_track($wholeseq,
                  -glyph  => 'arrow',
                  -bump   => 0,
                  -double => 1,
                  -tick   => 2);

$panel->add_track($wholeseq,
                  -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 PNG
open OUT, ">$seqname.png";
print OUT $panel->png;
close OUT;
exit 0;