database.rb

require 'rubygems'
require 'datamapper'
require 'bio'

DataMapper.setup(:default,{
  :adapter => 'sqlite3',
  :database => 'db.sqlite3'
})

class Gene
  include DataMapper::Resource

  property :id,       Serial
  property :name,     String
  property :sequence, Text,  :format => /^M[\w\n]+\*$/m
end

class Count
  include DataMapper::Resource

  property :id,    Serial
  property :acid,  String
  property :count, Integer
end

Rakefile.rb

task :environment do
  require 'database'
  require 'logger'
  @log = Logger.new('log/analysis.log')
end

namespace :db do

  desc 'Create database'
  task :create => :environment do
    DataMapper.auto_migrate!
  end

  desc 'Delete database'
  task :delete do
    system 'rm db.sqlite3'
  end
end

namespace :load do
  desc 'Loads protein sequences'
  task :proteins => :environment do
    Gene.all.destroy!

    Zlib::GzipReader.open('data/cerevisiae.fasta.gz') do |file|
      Bio::FlatFile.auto(file).each do |entry|
        gene = Gene.create(
          :name     => entry.definition.split(' ').first,
          :sequence => entry.data.strip
        )
        @log.warn("#{gene.name} not included") unless gene.valid?
      end
    end
    @log.info "#{Gene.count}"
  end
end

namespace :analyse do
  desc 'Count amino acids in proteins'
  task :count_acids => :environment do
    Count.all.destroy!

    # Count amino acids across all proteins
    counts = Gene.all.inject(Hash.new) do |hash, gene|
      composition = Bio::Sequence.auto(gene.sequence).composition
      hash.merge!(composition) {|acid,one,two| one + two}
    end

    @log.info "#{counts['*']} stop codons skipped"
    counts.delete('*')

    counts.each do |acid,count|
      Count.create(:acid => acid, :count => count)
      @log.info "#{count} instances of #{acid}"
    end
  end
end