michaelbarton

  desc 'Loads all the alignment codon data'
  task :load_alignment_codons => :clear_alignment_codons do
    starfish = %x|which starfish|.strip
    loader = PROJECT_ROOT + '/model/starfish/load_alignment_codons.rb'
    p = lambda{ system( "qsub -cwd -j y -V #{starfish} #{loader}") }

    p.call
    sleep(120)
    16.times { p.call }
  end

michaelbarton

BLAST protein YDL177C
BLAST dna YDL177C

michaelbarton

# Given the location of an SQL query file, this method will
# execute the query on the database, and print each line to 
# the supplied target file.
# This method relies on the MySQL adapter for the fetch_fields 
# method, but should not suffer in performance from pulling 
# large amounts of data into memory.

public

def export_csv_from_sql(sql_file,target_file)

michaelbarton

# Example activerecord interator based on using an indexed 'id' column.
# See http://schuerig.de/michael/blog/index.php/2007/02/03/ar-enumerable/
# and http://weblog.jamisbuck.org/2007/4/6/faking-cursors-in-activerecord

class << ActiveRecord::Base
  def each(chunk_size=1000)
    (0..self.last.id / chunk_size).each do |offset|
      self.find(:all,
        :limit => chunk_size,
        :conditions => ["id > ?", offset * chunk_size]).each do |i|

michaelbarton

require 'fileutils'
require 'find'

class Latex < Thor

  desc "build","builds thesis document"
  method_options :src  => 'src',
                 :dest => 'out',
                 :tmp  => 'tmp'
  def build(file)

michaelbarton

- Example where
  - cost of alanine is being considered
  - in glucose limitation
  - at biomass flux of 0.5

- Set all exchange fluxes to have a lower bound of -10000.
  - Effectively unlimited nutrients with respect to biomass flux

- Set biomass flux reaction rate to have upper and lower bounds of 0.05

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.