Skip to content


Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
tree: 0b078bfa2c
Fetching contributors…

Cannot retrieve contributors at this time

244 lines (202 sloc) 9.008 kb
;; The Computer Language Benchmarks Game
;; contributed by Andy Fingerhut
;; modified by Marko Kocic
;; modified by Mike Anderson to make better use of primitive operations
(ns knucleotide
(set! *warn-on-reflection* true)
(defmacro key-type [num]
`(long ~num))
(definterface IFragment
(set_key_BANG_ [^long k])
(^long get_key [])
(inc_BANG_ [])
(^int get_count []))
(deftype Fragment [^{:unsynchronized-mutable true :tag long} key
^{:unsynchronized-mutable true :tag int} cnt]
;; TBD: Is there a way to return an int hashCode that is a truncated
;; version of the long value key without using bit-and? Simply
;; using (int key) throws an exception if key is larger than
;; Integer/MAX_VALUE, e.g. (int Long/MAX_VALUE).
(^int hashCode [this]
(int (bit-and key Integer/MAX_VALUE)))
(^boolean equals [this ^Object o]
(let [^Fragment f o]
(== key (.key f))))
(set-key! [this ^long k]
(set! key k))
(get-key [this] key)
(inc! [this]
(set! cnt (unchecked-inc-int cnt)))
(get-count [this] cnt))
;; 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-map {\A 0, \C 1, \T 2, \G 3})
(def code-val-to-dna-char {0 \A, 1 \C, 2 \T, 3 \G})
(defmacro dna-char-to-code-val [ch]
`(case ~ch
~@(flatten (seq dna-char-to-code-val-map))))
;; 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 ^:static dna-str-to-key
(^long [^String s] (dna-str-to-key s 0 (count s)))
(^long [^String s ^long start ^long length]
;; Accessing a local let binding is much faster than accessing a var
(loop [key (long 0)
offset (int (+ start length -1))]
(if (< offset start)
(let [c (.charAt 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 [^Fragment f len]
(let [k (.get-key f)]
(apply str (map code-val-to-dna-char
(map (fn [pos] (bit-and 3 (bit-shift-right k pos)))
(range 0 (* 2 len) 2))))))
;; required function : "to update a hashtable of k-nucleotide keys and
;; count values, for a particular reading-frame"
(defn tally-dna-subs-with-len [len dna-str start-offset end-offset]
(let [len (int len)
start-offset (int start-offset)
dna-str ^String dna-str
mask-width (* 2 len)
mask (key-type (dec (bit-shift-left 1 mask-width)))]
(loop [offset (int end-offset)
key (key-type (dna-str-to-key dna-str offset len))
tally (let [h (java.util.HashMap.)
one (Fragment. (long key) (int 1))]
(.put h one one)
fragment (Fragment. (long 0) (int 1))]
(if (<= offset start-offset)
(let [new-offset (unchecked-dec offset)
new-first-char-code (dna-char-to-code-val
(.charAt dna-str new-offset))
new-key (key-type (bit-and mask (unchecked-add (bit-shift-left key 2)
(.set-key! fragment new-key)
(if-let [^Fragment cur-fragment (get tally fragment)]
(.inc! cur-fragment)
(recur new-offset new-key tally fragment))
(let [new-fragment (Fragment. (long 0) (int 1))]
(.put tally fragment fragment)
(recur new-offset new-key tally new-fragment)))))))))
(defn ^:static getcnt ^long [^Fragment tc]
(.get-count tc))
(defn ^:static tally-total [tally]
(loop [acc (long 0)
s (vals tally)]
(if-let [v (first s)]
(recur (+ acc (getcnt v)) (next s))
(defn all-tally-to-str [tally fn-key-to-str]
(let [total (tally-total 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 (Fragment. 0 0)
^Fragment f (Fragment. (long (dna-str-to-key dna-str)) 0)]
(format "%d\t%s" (getcnt (get tally f zerotc))
(defn compute-one-part [dna-str part]
(let [len (count dna-str)]
(condp = part
0 (all-tally-to-str (tally-dna-subs-with-len 1 dna-str 0 (- len 1))
(fn [k] (key-to-dna-str k 1)))
1 (all-tally-to-str (tally-dna-subs-with-len 2 dna-str 0 (- len 2))
(fn [k] (key-to-dna-str k 2)))
2 (one-tally-to-str "GGT"
(tally-dna-subs-with-len 3 dna-str 0 (- len 3)))
3 (one-tally-to-str "GGTA"
(tally-dna-subs-with-len 4 dna-str 0 (- len 4)))
4 (one-tally-to-str "GGTATT"
(tally-dna-subs-with-len 6 dna-str 0 (- len 6)))
5 (one-tally-to-str "GGTATTTTAATT"
(tally-dna-subs-with-len 12 dna-str 0 (- len 12)))
6 (one-tally-to-str "GGTATTTTAATTTATAGT"
(tally-dna-subs-with-len 18 dna-str 0 (- len 18))))]))
(defn run [br]
(let [dna-str (fasta-dna-str-with-desc-beginning "THREE" (line-seq br))
;; Due to the peculiarities of how pmap works, the amount of
;; parallelism you achieve may not equal the number of
;; processors you have. In the future it would be better to
;; use something more "eager" like medusa-pmap in the Medusa
;; library.
results (map second
(sort #(< (first %1) (first %2))
#(compute-one-part dna-str %)
;; '(0 5 6 1 2 3 4)
'(0 1 4 5 6 2 3)
(doseq [r results]
(println r)
(defn -main [& args]
(with-open [br ( *in*)]
(run br))
Jump to Line
Something went wrong with that request. Please try again.