js/src/t/string-fasta.js

   1 // The Great Computer Language Shootout
   2 //  http://shootout.alioth.debian.org
   3 //
   4 //  Contributed by Ian Osgood
   5
   6 var last = 42, A = 3877, C = 29573, M = 139968;
   7
   8 function rand(max) {
   9   last = (last * A + C) % M;
  10   return max * last / M;
  11 }
  12
  13 var ALU =
  14   "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
  15   "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
  16   "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
  17   "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
  18   "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
  19   "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
  20   "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
  21
  22 var IUB = {
  23   a:0.27, c:0.12, g:0.12, t:0.27,
  24   B:0.02, D:0.02, H:0.02, K:0.02,
  25   M:0.02, N:0.02, R:0.02, S:0.02,
  26   V:0.02, W:0.02, Y:0.02
  27 }
  28
  29 var HomoSap = {
  30   a: 0.3029549426680,
  31   c: 0.1979883004921,
  32   g: 0.1975473066391,
  33   t: 0.3015094502008
  34 }
  35
  36 function makeCumulative(table) {
  37   var last = null;
  38   for (var c in table) {
  39     if (last) table[c] += table[last];
  40     last = c;
  41   }
  42 }
  43
  44 function fastaRepeat(n, seq) {
  45   var seqi = 0, lenOut = 60;
  46   while (n>0) {
  47     if (n<lenOut) lenOut = n;
  48     if (seqi + lenOut < seq.length) {
  49       ret = seq.substring(seqi, seqi+lenOut);
  50       seqi += lenOut;
  51     } else {
  52       var s = seq.substring(seqi);
  53       seqi = lenOut - s.length;
  54       ret = s + seq.substring(0, seqi);
  55     }
  56     n -= lenOut;
  57   }
  58 }
  59
  60 function fastaRandom(n, table) {
  61   var line = new Array(60);
  62   makeCumulative(table);
  63   while (n>0) {
  64     if (n<line.length) line = new Array(n);
  65     for (var i=0; i<line.length; i++) {
  66       var r = rand(1);
  67       for (var c in table) {
  68         if (r < table[c]) {
  69           line[i] = c;
  70           break;
  71         }
  72       }
  73     }
  74     ret = line.join('');
  75     n -= line.length;
  76   }
  77 }
  78
  79 var ret;
  80
  81 var count = 7;
  82 ret = fastaRepeat(2*count*100000, ALU);
  83 ret = fastaRandom(3*count*1000, IUB);
  84 ret = fastaRandom(5*count*1000, HomoSap);
  85