Rakefile

require 'open-uri'

FILE = 'SBW25.fna'
URL = "ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Pseudomonas_fluorescens_SBW25/AM181176.fna"

READS = [200_000]
N_SIMULATIONS = 5
METASIM = 'metasim'

desc "Fetches SBW25 genome sequence"
task :fetch do
  unless File.exists?(FILE)
    File.open(FILE,'w') do |f|
      open(URL) do |url|
        url.each_line { |line| f.write(line) }
      end
    end
  end
end

desc "Simulates genome sequencing"
task :sequence => :fetch do
  READS.each do |reads|
    dir = mkdir(reads)
    0.upto(N_SIMULATIONS - 1) do
      `#{METASIM} cmd --reads #{reads} --454 --output-dir #{dir} #{FILE}`
    end
  end
end

private

def mkdir(reads)
  dir = "#{reads/1_000}k"
  Dir.mkdir(dir) unless File.exists?(dir)
  dir
end