Render features

From BioPerl

#!/usr/bin/perl
 
# file: render_features.pl
# This is code example 5 in the Graphics-HOWTO
# Author: Lincoln Stein
 
use strict;
use lib "$ENV{HOME}/projects/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 @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(
				      -length    => $seq->length,
				      -key_style => 'between',
				      -width     => 800,
				      -pad_left  => 10,
				      -pad_right => 10,
				      );
$panel->add_track($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 $panel->png;
exit 0;