michaelbarton

(defproject resolve-contig-one "1.0.0-SNAPSHOT"
  :dependencies [[org.clojure/clojure         "1.2.0"]
                 [org.clojure/clojure-contrib "1.2.0"]
                 [clj-redis                   "0.0.12"]])

michaelbarton

(use '[clojure.java.io :only [reader]])
(use '[clojure.string  :only [split]])

(def read-keys [:id :status :pos-contig :pos-position :pos-strand :neg-contig :neg-position :neg-strand])

(defn split-line [x]
  (split x #"\t"))

(defn create-read [x]
  (with-meta 

michaelbarton

(use '[clojure.java.io :only [reader]])
(use '[clojure.string  :only [split]])

(defrecord Read
  [id status
   pos-contig pos-position pos-strand
   neg-contig neg-position neg-strand])

(defn split-line [x]

michaelbarton

#!/usr/bin/env Rscript

library('plyr')
library('ggplot2')

source('lib/r/drop.levels.r')
source('lib/r/find.replace.R')

options(stringsAsFactors = FALSE)

michaelbarton

#!/usr/bin/env ruby
require 'fastercsv'
require 'pp'

map = FCSV.open('addition.csv',:headers => true).inject(Hash.new) do |hash,row|
  if row['Gene ']
    hash['250327' + row['R124#']] = row['Gene ']
  end
  hash
end

michaelbarton

out
tmp

michaelbarton

class Git < Thor

  desc "branch", "Name of current branch"
  def branch
    puts branch_name
  end

  private

  def git(command,args)

michaelbarton

out

michaelbarton

require 'bio'

task :map_ids do
  mappings = YAML.load(File.read('data/mapping.yml'))
  v2_ids = File.readlines('data/v2_gene_ids.txt').map{|a| a.to_i}
end

task :select do
  v2_ids = File.readlines('data/v2_gene_ids.txt').map{|a| a.to_i}
  entries = Bio::FlatFile.auto('data/proteins.faa')

michaelbarton

Dir['content/markup/*/*'].each do |file|
  file =~ /\d+-\d+-\d+/
  date = Regexp.last_match(0) + ' 00:00 GMT'

  file =~ /\d+-\d+-\d+-(.+).markdown$/
  title = Regexp.last_match(1)
  english_title = title.gsub('-',' ').capitalize

  content = File.open(file) do |pipe|
    pipe.readline