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(ns sandbox.cipher
  (:require [clojure.string :as str]))

(def alphabet "abcdefghijklmnopqrstuvwxyz")

(defn rotate [n coll]
  (concat (drop n coll) (take n coll)))

(defn caeser-cipher [offset]
  (-> (zipmap alphabet (rotate offset alphabet))

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(defn levenshtein [thr str1 str2]
        "Clojure Levenshtein distance which short circuits when the distance is > thr"
        (let [n (count str1) 
              m (count str2)]
          (cond 
            (= 0 n) m
            (= 0 m) n
            :else
            (last
             (reduce (fn [prev-col i]

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(defn bar [input]
  (let [xf1 (partial re-seq #"[-\w]+")
        xf2 (fn [[x & ys]]
              [x
               (->> ys
                    (map-indexed #(if (odd? %1)
                                    (read-string %2)
                                    %2))
                    (apply assoc {}))])]
    (transduce (comp (map xf1)

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// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

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(-> (identity 12)
    ((fn [the-threaded-var] (* the-threaded-var 3)))
    (/ 3))

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(let [sqs {"AUGUGGAAAG" 4, "CGACCUCGUC" 2, "CCAGCGAACC" 2, "GGGCGAAGCU" 5, "GUUUACUUCA" 1, 
           "UACCAUAGUA" 1, "CGACCAGCAU" 2, "UGAAUUUCGA" 2, "GGUCUUUCUU" 2, "UGAAAUACAU" 1}]
                                 (prn :>>)
                                 (r/fold (fn ([] {})
                                           ([l r] (merge-with + l r)))
                                         (fn [M sq cs]
                                           (->> (take 2 sq)
                                                frequencies
                                                (merge-with + M)))
                                         sqs))

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(ns mysql-test
  (:require [clojure.java.jdbc :as jdbc])
  (:use [edu.bc.bio.sequtils.files]))




(def mysql-ds
  {:classname "com.mysql.jdbc.Driver"
   :subprotocol "mysql"

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(require '[clojure.java.jdbc :as jdbc]
         '[korma.db :as kdb]
         '[korma.core :as kcore]
         '[sqlingvo.core :as sql]
         '[sqlingvo.vendor :as v]))

;;;examples here are directly from the sqlingvo, jdbc, korma websites
;;;in order to provide a concrete example of using a SQL DSL with jdbc
;;;to execute mysql commands

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(ns sudoku
  (:require [clojure.contrib.io :as io]
            [clojure.contrib.string :as str]
            [clojure.set :as sets]))

;;;example input for testing
(def grid01
  (list "003020600"
        "900305001"
        "001806400"

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;;; init.el --- Where all the magic begins
;;
;; Part of the Emacs Starter Kit
;;
;; This is the first thing to get loaded.
;;
;; "Emacs outshines all other editing software in approximately the
;; same way that the noonday sun does the stars. It is not just bigger
;; and brighter; it simply makes everything else vanish."
;; -Neal Stephenson, "In the Beginning was the Command Line"