The Computer Language
Benchmarks Game

k-nucleotide Racket program

source code

#lang racket/base

;;; The Computer Language Benchmarks Game
;;; http://benchmarksgame.alioth.debian.org/

;;; contributed by Matthew Flatt

(define (all-counts len dna)
  (let ([table (make-hasheq)]
        [seq (make-string len)])
    (for ([s (in-range (- (string-length dna) len) -1 -1)])
      (string-copy! seq 0 dna s (+ s len))
      (let ([key (string->symbol seq)])
        (let ([cnt (hash-ref table key 0)])
          (hash-set! table key (add1 cnt)))))
    table))

(define (write-freqs table)
  (let* ([content (hash-map table cons)]
         [total (exact->inexact (apply + (map cdr content)))])
    (for ([a (sort content > #:key cdr)])
      (printf "~a ~a\n" 
              (car a) 
              (real->decimal-string (* 100 (/ (cdr a) total)) 3)))))

(define (write-one-freq table key)
  (let ([cnt (hash-ref table key 0)])
    (printf "~a\t~a\n" cnt key)))

(define dna
  (let ([in (current-input-port)])
    ;; Skip to ">THREE ..."
    (regexp-match #rx#"(?m:^>THREE.*$)" in)
    (let ([s (open-output-string)])
      ;; Copy everything but newlines to s:
      (for ([l (in-bytes-lines in)])
        (write-bytes l s))
      ;; Extract the string from s:
      (string-upcase (get-output-string s)))))

;; 1-nucleotide counts:
(write-freqs (all-counts 1 dna))
(newline)

;; 2-nucleotide counts:
(write-freqs (all-counts 2 dna))
(newline)

;; Specific sequences:
(for ([seq '("GGT" "GGTA" "GGTATT" "GGTATTTTAATT" "GGTATTTTAATTTATAGT")]) 
  (write-one-freq (all-counts (string-length seq) dna)
                  (string->symbol seq)))
    

notes, command-line, and program output

NOTES:
64-bit Ubuntu quad core
Welcome to Racket v6.8.


Sun, 16 Apr 2017 03:32:31 GMT

MAKE:
/usr/local/src/racket-6.8/bin/raco make knucleotide.racket
0.49s to complete and log all make actions

COMMAND LINE:
/usr/local/src/racket-6.8/bin/racket ./compiled/knucleotide_racket.zo 0 < knucleotide-input25000000.txt

PROGRAM OUTPUT:
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
893	GGTATTTTAATT
893	GGTATTTTAATTTATAGT