Bio::Graphics Generate GD images of Bio::Seq objects
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Perl module perl images GD GD images

Bio::Graphics Description

Generate GD images of Bio::Seq objects Bio::Graphics is a Perl module to generate GD images of Bio::Seq objects.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); $panel->add_track($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 => $colors, -fgcolor => 'black', -font2color => 'red', -key => "${tag}s", -bump => +1, -height => 8, -label => 1, -description => 1, ); } print $panel->png; exit 0; Requirements: · Perl

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