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1 package Bio::Graphics;
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2
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3 use Bio::Graphics::Panel;
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4 use strict;
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5
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6 use vars '$VERSION';
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7 $VERSION = 1.2003;
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8
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9 1;
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10
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11 =head1 NAME
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12
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13 Bio::Graphics - Generate GD images of Bio::Seq objects
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14
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15 =head1 SYNOPSIS
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16
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17 # This script generates a PNG picture of a 10K region containing a
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18 # set of red features and a set of blue features. Call it like this:
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19 # red_and_blue.pl > redblue.png
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20 # you can now view the picture with your favorite image application
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21
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22
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23 # This script parses a GenBank or EMBL file named on the command
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24 # line and produces a PNG rendering of it. Call it like this:
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25 # render.pl my_file.embl | display -
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26
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27 use strict;
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28 use Bio::Graphics;
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29 use Bio::SeqIO;
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30
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31 my $file = shift or die "provide a sequence file as the argument";
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32 my $io = Bio::SeqIO->new(-file=>$file) or die "could not create Bio::SeqIO";
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33 my $seq = $io->next_seq or die "could not find a sequence in the file";
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34
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35 my @features = $seq->all_SeqFeatures;
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36
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37 # sort features by their primary tags
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38 my %sorted_features;
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39 for my $f (@features) {
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40 my $tag = $f->primary_tag;
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41 push @{$sorted_features{$tag}},$f;
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42 }
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43
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44 my $wholeseq = Bio::SeqFeature::Generic->new(-start=>1,-end=>$seq->length);
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45
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46 my $panel = Bio::Graphics::Panel->new(
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47 -length => $seq->length,
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48 -key_style => 'between',
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49 -width => 800,
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50 -pad_left => 10,
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51 -pad_right => 10,
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52 );
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53 $panel->add_track($wholeseq,
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54 -glyph => 'arrow',
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55 -bump => 0,
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56 -double=>1,
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57 -tick => 2);
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58
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59 $panel->add_track($seq,
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60 -glyph => 'generic',
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61 -bgcolor => 'blue',
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62 -label => 1,
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63 );
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64
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65 # general case
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66 my @colors = qw(cyan orange blue purple green chartreuse magenta yellow aqua);
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67 my $idx = 0;
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68 for my $tag (sort keys %sorted_features) {
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69 my $features = $sorted_features{$tag};
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70 $panel->add_track($features,
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71 -glyph => 'generic',
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72 -bgcolor => $colors[$idx++ % @colors],
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73 -fgcolor => 'black',
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74 -font2color => 'red',
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75 -key => "${tag}s",
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76 -bump => +1,
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77 -height => 8,
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78 -label => 1,
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79 -description => 1,
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80 );
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81 }
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82
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83 print $panel->png;
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84 exit 0;
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85
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86 =head1 DESCRIPTION
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87
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88 Please see L<Bio::Graphics::Panel> for the full interface.
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89
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90 =head1 SEE ALSO
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91
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92 L<Bio::Graphics::Panel>,
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93 L<Bio::Graphics::Glyph>,
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94 L<Bio::SeqI>,
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95 L<Bio::SeqFeatureI>,
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96 L<Bio::Das>,
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97 L<Bio::DB::GFF::Feature>,
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98 L<Ace::Sequence>,
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99 L<GD>
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100
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101 =head1 AUTHOR
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102
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103 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
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104
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105 Copyright (c) 2001 Cold Spring Harbor Laboratory
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106
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107 This library is free software; you can redistribute it and/or modify
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108 it under the same terms as Perl itself. See DISCLAIMER.txt for
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109 disclaimers of warranty.
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110
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111 =cut
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112
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