The Computer Language
Benchmarks Game

k-nucleotide Clojure #4 program

source code

;;   The Computer Language Benchmarks Game

;; contributed by Andy Fingerhut

(ns knucleotide

(set! *warn-on-reflection* true)

;; Handle slight difference in function name between Clojure 1.2.0 and
;; 1.3.0-alpha* ability to use type hints to infer fast bit
;; operations.
(defmacro my-unchecked-inc-int [& args]
  (if (and (== (*clojure-version* :major) 1)
           (== (*clojure-version* :minor) 2))
    `(unchecked-inc ~@args)
    `(unchecked-inc-int ~@args)))

(defmacro key-type [num]
  (if (and (== (*clojure-version* :major) 1)
           (== (*clojure-version* :minor) 2))
    `(long ~num)))

(definterface ITallyCounter
  (^int get_count [])
  (inc_BANG_ []))

(deftype TallyCounter [^{:unsynchronized-mutable true :tag int} cnt]
  (get-count [this] cnt)
  (inc! [this]
    (set! cnt (my-unchecked-inc-int cnt))))

(defn my-lazy-map [f coll]
    (when-let [s (seq coll)]
      (cons (f (first s)) (my-lazy-map f (rest s))))))

;; modified-pmap is like pmap from Clojure 1.1, but with only as much
;; parallelism as specified by the parameter num-threads.  Uses
;; my-lazy-map instead of map from core.clj, since that version of map
;; can use unwanted additional parallelism for chunked collections,
;; like ranges.

(defn modified-pmap
  ([num-threads f coll]
     (if (== num-threads 1)
       (map f coll)
       (let [n (if (>= num-threads 2) (dec num-threads) 1)
             rets (my-lazy-map #(future (f %)) coll)
             step (fn step [[x & xs :as vs] fs]
                      (if-let [s (seq fs)]
                        (cons (deref x) (step xs (rest s)))
                        (map deref vs))))]
         (step rets (drop n rets)))))
  ([num-threads f coll & colls]
     (let [step (fn step [cs]
                    (let [ss (my-lazy-map seq cs)]
                      (when (every? identity ss)
                        (cons (my-lazy-map first ss)
			      (step (my-lazy-map rest ss)))))))]
       (modified-pmap num-threads #(apply f %) (step (cons coll colls))))))

;; Return true when the line l is a FASTA description line

(defn fasta-description-line [l]
  (= \> (first (seq l))))

;; Return true when the line l is a FASTA description line that begins
;; with the string desc-str.

(defn fasta-description-line-beginning [desc-str l]
  (and (fasta-description-line l)
       (= desc-str (subs l 1 (min (count l) (inc (count desc-str)))))))

;; Take a sequence of lines from a FASTA format file, and a string
;; desc-str.  Look for a FASTA record with a description that begins
;; with desc-str, and if one is found, return its DNA sequence as a
;; single (potentially quite long) string.  If input file is big,
;; you'll save lots of memory if you call this function in a with-open
;; for the file, and don't hold on to the head of the lines parameter.

(defn fasta-dna-str-with-desc-beginning [desc-str lines]
  (when-let [x (drop-while
		(fn [l] (not (fasta-description-line-beginning desc-str l)))
    (when-let [x (seq x)]
      (let [y (take-while (fn [l] (not (fasta-description-line l)))
                          (map (fn [#^java.lang.String s] (.toUpperCase s))
                               (rest x)))]
        (apply str y)))))

(def dna-char-to-code-val {\A 0, \C 1, \T 2, \G 3})
(def code-val-to-dna-char {0 \A, 1 \C, 2 \T, 3 \G})

;; In the hash map 'tally' in tally-dna-subs-with-len, it is more
;; straightforward to use a Clojure string (same as a Java string) as
;; the key, but such a key is significantly bigger than it needs to
;; be, increasing memory and time required to hash the value.  By
;; converting a string of A, C, T, and G characters down to an integer
;; that contains only 2 bits for each character, we make a value that
;; is significantly smaller and faster to use as a key in the map.

;;    most                 least
;; significant          significant
;; bits of int          bits of int
;;  |                         |
;;  V                         V
;; code code code ....  code code
;;  ^                         ^
;;  |                         |
;; code for               code for
;; *latest*               *earliest*
;; char in                char in
;; sequence               sequence

;; Note: Given Clojure 1.2's implementation of bit-shift-left/right
;; operations, when the value being shifted is larger than a 32-bit
;; int, they are faster when the shift amount is a compile time
;; constant.

(defn dna-str-to-key [s]
  ;; Accessing a local let binding is much faster than accessing a var
  (let [dna-char-to-code-val dna-char-to-code-val]
    (loop [key 0
	   offset (int (dec (count s)))]
      (if (neg? offset)
	(let [c (nth s offset)
              code (int (dna-char-to-code-val c))
	      new-key (+ (bit-shift-left key 2) code)]
	  (recur new-key (dec offset)))))))

(defn key-to-dna-str [k len]
  (apply str (map code-val-to-dna-char
		  (map (fn [pos] (bit-and 3 (bit-shift-right k pos)))
		       (range 0 (* 2 len) 2)))))

(defn tally-dna-subs-with-len [len dna-str]
  (let [mask-width (* 2 len)
	mask (key-type (dec (bit-shift-left 1 mask-width)))
	dna-char-to-code-val dna-char-to-code-val]
    (loop [offset (int (- (count dna-str) len))
	   key (key-type (dna-str-to-key (subs dna-str offset (+ offset len))))
           tally (let [h (java.util.HashMap.)
                       one (TallyCounter. (int 1))]
                   (.put h key one)
      (if (zero? offset)
	(let [new-offset (dec offset)
	      new-first-char-code (dna-char-to-code-val
                                   (nth dna-str new-offset))
	      new-key (key-type (bit-and mask (+ (bit-shift-left key 2)
          (if-let [^TallyCounter cur-count (get tally new-key)]
            (.inc! cur-count)
            (let [one (TallyCounter. (int 1))]
              (.put tally new-key one)))
	  (recur new-offset new-key tally))))))

(defn getcnt [^TallyCounter tc]
  (.get-count tc))

(defn all-tally-to-str [tally fn-key-to-str]
    (let [total (reduce + (map getcnt (vals tally)))
          cmp-keys (fn [k1 k2]
                     ;; Return negative integer if k1 should come earlier
                     ;; in the sort order than k2, 0 if they are equal,
                     ;; otherwise a positive integer.
                     (let [cnt1 (int (getcnt (get tally k1)))
                           cnt2 (int (getcnt (get tally k2)))]
                       (if (not= cnt1 cnt2)
                         (- cnt2 cnt1)
                         (let [^String s1 (fn-key-to-str k1)
                               ^String s2 (fn-key-to-str k2)]
                           (.compareTo s1 s2)))))]
      (doseq [k (sort cmp-keys (keys tally))]
        (printf "%s %.3f\n" (fn-key-to-str k)
                (double (* 100 (/ (getcnt (get tally k)) total))))))))

(defn one-tally-to-str [dna-str tally]
  (let [zerotc (TallyCounter. 0)]
    (format "%d\t%s" (getcnt (get tally (dna-str-to-key dna-str) zerotc))

(defn compute-one-part [dna-str part]
   (condp = part
       0 (all-tally-to-str (tally-dna-subs-with-len 1 dna-str)
                           (fn [k] (key-to-dna-str k 1)))
       1 (all-tally-to-str (tally-dna-subs-with-len 2 dna-str)
                           (fn [k] (key-to-dna-str k 2)))
       2 (one-tally-to-str "GGT"
                           (tally-dna-subs-with-len 3 dna-str))
       3 (one-tally-to-str "GGTA"
                           (tally-dna-subs-with-len 4 dna-str))
       4 (one-tally-to-str "GGTATT"
                           (tally-dna-subs-with-len 6 dna-str))
       5 (one-tally-to-str "GGTATTTTAATT"
                           (tally-dna-subs-with-len 12 dna-str))
       6 (one-tally-to-str "GGTATTTTAATTTATAGT"
                           (tally-dna-subs-with-len 18 dna-str)))])

(def +default-modified-pmap-num-threads+
     (+ 2 (.. Runtime getRuntime availableProcessors)))

(defn -main [& args]
  (def num-threads
       (if (and (>= (count args) 1)
		(re-matches #"^\d+$" (nth args 0)))
	 (let [n (. Integer valueOf (nth args 0) 10)]
	   (if (== n 0)
  (with-open [br ( *in*)]
    (let [dna-str (fasta-dna-str-with-desc-beginning "THREE" (line-seq br))
          ;; Select the order of computing parts such that it is
          ;; unlikely that parts 5 and 6 will be computed concurrently.
          ;; Those are the two that take the most memory.  It would be
          ;; nice if we could specify a DAG for which jobs should finish
          ;; before others begin -- then we could prevent those two
          ;; parts from running simultaneously.
          results (map second
                       (sort #(< (first %1) (first %2))
                             (modified-pmap num-threads
                                            #(compute-one-part dna-str %)
                                            '(0 5 6 1 2 3 4)
      (doseq [r results]
        (println r)

notes, command-line, and program output

64-bit Ubuntu quad core
Clojure 1.8.0
java version "1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)

Sat, 27 Feb 2016 17:47:22 GMT

mv knucleotide.clojure-4.clojure knucleotide.clj
/usr/local/src/jdk1.8.0_45/bin/java -Dclojure.compile.path=. -cp .:/usr/local/src/clojure/clojure-1.8.0.jar clojure.lang.Compile knucleotide
Compiling knucleotide to .
1.30s to complete and log all make actions

/usr/local/src/jdk1.8.0_45/bin/java -server -XX:+TieredCompilation -XX:+AggressiveOpts -Xmx1024m -cp .:/usr/local/src/clojure/clojure-1.8.0.jar knucleotide 0 < knucleotide-input25000000.txt

A 30.295
T 30.151
C 19.800
G 19.754

AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902

1471758	GGT
446535	GGTA
47336	GGTATT