[Bioperl-l] Bio::Graphics - Here is the program in a better format

[Janet Smith]

#!/usr/bin/perl -w

use strict;
use Bio::Graphics;
use Bio::SeqFeature::Generic;

chomp (my $file = shift(@ARGV));
open(INPUT, "<$file") or die "Cannot open \"$file\": $!\n";
my @data = <INPUT>;
close INPUT;
my $panel;
				
my $flag = 1;

my ($feature, $track);

foreach(@data) {
	chomp;
	next if /^\#/; # ignore comments
	my ($name, $length, $domain, $score, $start, $end) = split /\t+/;
	
	if($flag == 1) {
		
		# draw panel
		$panel = Bio::Graphics::Panel->new(-length => $length,
									  -width => 800,
									  -pad_left => 10,
									  -pad_right => 10,
									  );
		
		# draw reference ruler of size sequence
		my $full_length = Bio::SeqFeature::Generic->new(-start=>1, 
-end=>$length);
		$panel->add_track($full_length,
					      -glyph => 'arrow',
					      -tick => 2,
					      -fgcolor => 'black',
					      -double => 1,
						  -label => "$name",
						  );
		$flag = 0;
		
		$track = $panel -> add_track(-glyph => 'rndrect',
								-label => 1,
								-bgcolor => 'blue',
								-min_score => 0,
								-max_score => 1000,
								-font2color => 'red',
								-sort_order => 'high_score',
								-description => sub {
									my $feature = shift;
									my $score = $feature->score;
									if ($score =~ /E/) {
										return "e-value=$score";
									}
									else {
										return "score=$score";
									}
									});

		$feature = Bio::SeqFeature::Generic->new(-display_name=>$domain, 
-score=>$score, -start=>$start, -end=>$end);
		
	
	}			

	
	my $subfeature = Bio::SeqFeature::Generic->new(-label =>$domain, 
-display_name=>$domain, -score=>$score, -start=>$start, -end=>$end);
	$feature->add_SeqFeature($subfeature, 'EXPAND');

}
$track -> add_feature($feature);

print $panel -> png;

exit;