Lincoln D. Stein > Bio-Graphics-2.34 > Bio::Graphics

Download:
Bio-Graphics-2.34.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  12
Open  1
View/Report Bugs
Module Version: 2.34   Source   Latest Release: Bio-Graphics-2.39

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.

syntax highlighting: