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Computer Language Benchmarks Game      [[ Play ]]

- all benchmarks - n-body fannkuch-redux meteor-contest fasta fasta-redux spectral-norm reverse-complement mandelbrot k-nucleotide regex-dna pidigits chameneos-redux thread-ring binary-trees-redux binary-trees - all languages - Ada 2005 GNAT ATS C CINT C gcc Clojure C# Mono C++ g++ Dart Erlang HiPE F# Mono Fortran Intel Go Haskell GHC Java 7 JavaScript V8 Lisp SBCL Lua OCaml Pascal Free Pascal Perl PHP Python 3 Racket Ruby 2.0 Ruby JRuby Scala Smalltalk VisualWorks x86 one core x64 quad-core x86 quad-core x64 one core

 performance measurements

Each table row shows performance measurements for this Racket program with a particular command-line input value N.

N	CPU secs	Elapsed secs	Memory KB	Code B	≈ CPU Load
250,000	2.53	2.53	53,676	542	0% 0% 0% 100%
2,500,000	21.92	21.99	157,112	542	0% 0% 0% 100%
25,000,000	225.97	226.51	1,419,356	542	0% 0% 0% 100%

Read the ↓ make, command line, and program output logs to see how this program was run.

Read k-nucleotide benchmark to see what this program should do.

 notes

Welcome to Racket v5.3.4.

 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)))

 make, command-line, and program output logs

Mon, 13 May 2013 05:18:57 GMT

COMMAND LINE:
/usr/local/src/racket-5.3.4/bin/racket  knucleotide.racket 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

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