Bio::Graphics and rails

As a follow up to my post on Bio::Graphics, I tried integrating this library in a rails application. After all, you'd get your data either from a file (like GFF) or a database. And let me tell you: it took me just 30 minutes or so to get a proof-of-concept running. This included installing rails itself, creating the rails app, creating the database, loading dummy data, and doing the coding itself. That 30 minutes was interrupted for a couple of hours, because I needed some advice from Kouhei Sutou, the author of rcairo, on how to write PNG images in memory instead of to a file.

So how do you do it? The proof-of-concept little database I created contained 3 tables:

• chromosomes (columns: id, name, length)
• tracks (columns: id, name, glyph, colour)
• features (columns: id, chromosome_id, track_id, name, location, url)

Create some features for a couple of different tracks for a particular chromosome.

In views/chromosomes/show.rhtml, add the following line:

<%= @chromosome.to_png %>

My models/chromosome.rb looks like this:

require 'stringio'
require 'base64'
require_gem 'bio-graphics'

class Chromosome < through =""> :features

def to_png(width = 800, start = 1, stop = self.length)
 return %{}
end

def draw(width, start, stop)
 panel = Bio::Graphics::Panel.new(self.length, width, false, start, stop)
 track_container = Hash.new
 self.tracks.each do |track|
   if ! track_container.has_key?(track.name)
     track_container[track.name] = panel.add_track(track.name, track.colour.split(',').collect{|i| i.to_i}, track.glyph)
   end
 end

 self.features.each do |feature|
   track_container[feature.track.name].add_feature(feature.name, feature.location)
 end

 output = StringIO.new
 panel.draw(output)
 return output.string
end
end

UPDATE: Apparently, Blogger does not allow me to paste the correct code above. In the to_png method, replace the following ascii codes:

• %7B with {


• %28 with (


• %29 with )


• %7D with }

And that's it. I leave the integration of my ensembl-api, bio-graphics and rails as an exercise for the reader. We could make a ruby version of the Ensembl browser... and then: world domination. Mwahaha.