[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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