[Bioperl-l] chromatogram

[Lee Katz]

Thank you Scott.  I know that this message is really late, but I got really side
tracked and want to follow through with this.  My code so far is a mutt between
everything I found online.  It only produces a generic track though; however, I
want to produce a chromatogram image, as shown on the gbrowse tutorial I found
at http://wheat.pw.usda.gov/gbrowse/tutorial/tutorial.html (section 15:
Displaying Trace Data, where a semantic zoom is shown).  Can you guys help me
finish it off?  Thanks.

use Bio::Graphics;
 use Bio::Seq;
 use Bio::SeqFeature::Generic;

my @scfFile=qw(1.scf 2.scf);

 my $bsg = 'Bio::SeqFeature::Generic';

 my $seq    = Bio::Seq->new(-length=>900);

 my $whole  = $bsg->new(-display_name => 'Clone82',
                        -start        => 1,
                        -end          => $seq->length);

 my $trace1 = $bsg->new(-start        => 1,
                        -end          => 500,
                        -display_name => 'Trace',
                        -tag=>{
                              trace=>"$scfFile[0]"
                              }
                       );

 my $panel = Bio::Graphics::Panel->new(-length    => $seq->length,
                                       -width     => 800,
                                       -truecolor => 1,
                                       -key_style => 'between',
                                       -pad_left  => 10,
                                       -pad_right => 10,
                                      );

 $panel->add_track($whole,
                   -glyph    => 'arrow',
                   -double   => 1,
                   -tick     => 2,
                   -label    => 1,
                   );

 $panel->add_track([$trace1],
		   -feature=>'read',
		   -strand_arrow=>1,
                   -glyph    => 'trace',
		   -a_color=>'green',
		   -c_color=>'blue',
		   -g_color=>'black',
		   -t_color=>'red',
		   -trace_height=>80,
		   -description=>1,
                   -label    => 1,
                   -key       => 'Traces');

 binmode STDOUT;
 print $panel->png;