bio::graphics(3pm) [debian man page]

Bio::Graphics(3pm)					User Contributed Perl Documentation					Bio::Graphics(3pm)

NAME

       Bio::Graphics - 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::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;

DESCRIPTION

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

SEE ALSO

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

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 http://bugzilla.open-bio.org/

AUTHOR

       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 v5.14.2							    2012-02-20							Bio::Graphics(3pm)