Lincoln D. Stein > Bio-Graphics-2.31 > Bio::Graphics



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Module Version: 2.31   Source   Latest Release: Bio-Graphics-2.37


Bio::Graphics - Generate GD images of Bio::Seq objects


 # 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:
 # > 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:
 # my_file.embl | display -

 use strict;
 use Bio::Graphics;
 use Bio::SeqFeature::Generic;
 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,
                  -glyph => 'arrow',
                  -bump => 0,
                  -tick => 2);

                  -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};
                    -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;


Please see Bio::Graphics::Panel for the full interface. Also try the script for quick help on glyphs and their options.


Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, Bio::DB::GFF::Feature, Ace::Sequence, GD


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Lincoln Stein <>.

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.

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