The Computer Language
Benchmarks Game

fasta OCaml #3 program

(* The Computer Language Benchmarks Game
 * http://benchmarksgame.alioth.debian.org/
 *
 * contributed by Troestler Christophe
 * modified by Mauricio Fernandez
 *)

(* Random number generator *)
let im = 139968
and ia = 3877
and ic = 29573

let last = ref 42 and im_f = float im
let gen_random  max =
  let n = (!last * ia + ic) mod im in
    last := n;
    max *. float n /. im_f

module Cumul_tbl =
struct
  type t = { probs : float array; chars : char array }

  let make a = let p = ref 0.0 in
    {
      probs = Array.map (fun (_, p1) -> p := !p +. p1; !p) a;
      chars = Array.map fst a;
    }

  let rand_char t =
    let p = gen_random 1.0 in
    let i = ref 0 and ps = t.probs in
      while p >= ps.(!i) do incr i done;
      t.chars.(!i)
end

let width = 60

let make_random_fasta id desc table n =
  Printf.printf ">%s %s\n" id desc;
  let table = Cumul_tbl.make table in
  let line = String.make (width+1) '\n' in
  for i = 1 to n / width do
    for j = 0 to width - 1 do line.[j] <- Cumul_tbl.rand_char table done;
    print_string line;
  done;
  let w = n mod width in
  if w > 0 then (
    for j = 1 to w do print_char(Cumul_tbl.rand_char table); done;
    print_char '\n'
  )

(* [write s i0 l w] outputs [w] chars of [s.[0 .. l]], followed by a
   newline, starting with [s.[i0]] and considering the substring [s.[0
   .. l]] as a "circle".
   One assumes [0 <= i0 <= l <= String.length s].
   @return [i0] needed for subsequent writes.  *)
let rec write s i0 l w =
  let len = l - i0 in
  if w <= len then (output stdout s i0 w; print_char '\n'; i0 + w)
  else (output stdout s i0 len; write s 0 l (w - len))

let make_repeat_fasta id desc src n =
  Printf.printf ">%s %s\n" id desc;
  let l = String.length src
  and i0 = ref 0 in
  for i = 1 to n / width do
    i0 := write src !i0 l width;
  done;
  let w = n mod width in
  if w > 0 then ignore(write src !i0 l w)


let alu = "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG\
GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA\
CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT\
ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA\
GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG\
AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC\
AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"

let iub = [| ('a', 0.27);  ('c', 0.12);  ('g', 0.12);  ('t', 0.27);
	     ('B', 0.02);  ('D', 0.02);  ('H', 0.02);  ('K', 0.02);
	     ('M', 0.02);  ('N', 0.02);  ('R', 0.02);  ('S', 0.02);
	     ('V', 0.02);  ('W', 0.02);  ('Y', 0.02);  |]

let homosapiens = [| ('a', 0.3029549426680);    ('c', 0.1979883004921);
		     ('g', 0.1975473066391);    ('t', 0.3015094502008);  |]

let () =
  let n = try int_of_string(Array.get Sys.argv 1) with _ -> 1000 in
  make_repeat_fasta "ONE" "Homo sapiens alu" alu (n*2);
  make_random_fasta "TWO" "IUB ambiguity codes" iub (n*3);
  make_random_fasta "THREE" "Homo sapiens frequency" homosapiens (n*5)
    

NOTES:
64-bit Ubuntu quad core
The OCaml native-code compiler, version 4.06.0


Sun, 05 Nov 2017 22:19:25 GMT

MAKE:
mv fasta.ocaml-3.ocaml fasta.ocaml-3.ml
/opt/src/ocaml-4.06.0/bin/ocamlopt -noassert -unsafe -fPIC -nodynlink -inline 100 -O3 unix.cmxa fasta.ocaml-3.ml -o fasta.ocaml-3.ocaml_run
File "fasta.ocaml-3.ml", line 43, characters 30-67:
Warning 3: deprecated: String.unsafe_set
File "fasta.ocaml-3.ml", line 43, characters 30-34:
Error: This expression has type string but an expression was expected of type
         bytes
/home/dunham/benchmarksgame/nanobench/makefiles/u64q.programs.Makefile:417: recipe for target 'fasta.ocaml-3.ocaml_run' failed
make: [fasta.ocaml-3.ocaml_run] Error 2 (ignored)
rm fasta.ocaml-3.ml

0.03s to complete and log all make actions

COMMAND LINE:
./fasta.ocaml-3.ocaml_run 250000

MAKE ERROR