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

       Lincoln Stein <lstein@cshl.org>.

       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.

perl v5.30.0                                       2019-11-25                                 Bio::Graphics(3pm)

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

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

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

        # 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::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,
                                             );
        $panel->add_track($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;