michaelbarton

# Reasons to use rails approach for bioinformatics

## Generic Ruby

* Modules like enumerable are great for sorting data

## Activerecord

* Simple to add indexes to enforce uniqueness of data

michaelbarton

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

namespace :db do

  desc 'Create database'
  task :create => :environment do

michaelbarton

require 'database'

gene = Gene.find(2)

gene.alignment_sequences.each do |a|
  puts "#{a.species.letter}#{gene.name}   #{a.protein}"
end

michaelbarton

Can I over-ride task :environment in test_helper.rb to test rake tasks?

I have a series of rake tasks in a Rakefile which I'd like to test as part of my specs etc. Each task is defined in the form:

    task :do_somthing => :environment do
      # Do something with the database here
    end

Where the :environment task sets up an ActiveRecord/DataMapper database connection and classes. I'm not using this as part of Rails but I have a series of tests which I like to run as part of BDD.

michaelbarton

BEGIN { FS = OFS = "," 
	print "gene", "cost", "cost-type"}
/yeast-carbon|weight/ && /0\.1/ && /nitrogen/{
	gsub(/"/,"")
	gsub(/yeast-carbon-/,"")
	printf "%s,%3.4f,%s\n", $2, $3, $13
}

michaelbarton

*.swp

michaelbarton

module NavigationHelpers
  # Maps a name to a path. Used by the
  #
  #   When /^I go to (.+)$/ do |page_name|
  #
  # step definition in webrat_steps.rb
  #
  def path_to(page_name)
    "http://0.0.0.0:3000" + case page_name
    

michaelbarton

require 'www/mechanize'

# Patches WWW::Mechanize for Cucumber + Webrat

module WWW
  class Mechanize
    def self.log_disabled
      @@log ||= Logger.new(STDOUT)
    end

michaelbarton

#! /usr/local/bin/ruby

require 'rubygems'
require 'fastercsv'

layout = Hash.new

FasterCSV.open(ARGV.first, :headers => true).each do |row|
  row.headers.each do |header|
    layout[header] ||= Hash.new

michaelbarton

\documentclass[12pt,PhD]{muthesis}

\usepackage{verbatim}
\usepackage{graphicx}
\usepackage{url} % typeset URL's reasonably
\usepackage{listings}
\usepackage{phdthesis}
\usepackage{rotating}
\usepackage{subfig}
\usepackage{psfrag}