[Bioperl-l] Graphics/Panel problem

[Jason Stajich]

http://bioperl.org/pipermail/bioperl-l/2003-January/010973.html

The HOWTO is updated on how to do this.
http://www.bioperl.org/HOWTOs/html/Graphics-HOWTO.html

You need to create a feature rather than adding the sequence directly.

On Fri, 9 May 2003, Thomas Keller wrote:

> 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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://pw600a.bioperl.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu