Raw content of Bio::Graphics
<![CDATA[package Bio::Graphics;
use Bio::Graphics::Panel;
use strict;
use vars '$VERSION';
$VERSION = 1.2003;
1;
=head1 NAME
Bio::Graphics - Generate GD images of Bio::Seq objects
=head1 SYNOPSIS
# This script generates a PNG picture of a 10K region containing a
# set of red features and a set of blue features. Call it like this:
# red_and_blue.pl > redblue.png
# you can now view the picture with your favorite image application
# This script parses a GenBank or EMBL file named on the command
# line and produces a PNG rendering of it. Call it like this:
# render.pl my_file.embl | display -
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 "could not create Bio::SeqIO";
my $seq = $io->next_seq or die "could not 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 $wholeseq = Bio::SeqFeature::Generic->new(-start=>1,-end=>$seq->length);
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);
$panel->add_track($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;
=head1 DESCRIPTION
Please see L<Bio::Graphics::Panel> for the full interface.
=head1 SEE ALSO
L<Bio::Graphics::Panel>,
L<Bio::Graphics::Glyph>,
L<Bio::SeqI>,
L<Bio::SeqFeatureI>,
L<Bio::Das>,
L<Bio::DB::GFF::Feature>,
L<Ace::Sequence>,
L<GD>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
]]>