diff variant_effect_predictor/Bio/Graphics.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,112 @@
+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>[e-mail]<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
+