samples/shootout/fasta.io

   1 #!/usr/bin/env io
   2
   3 /* The Great Computer Language Shootout
   4    http://shootout.alioth.debian.org
   5
   6    Contributed by Ian Osgood */
   7
   8 ALU := Sequence with(
   9        "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG",
  10        "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA",
  11        "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT",
  12        "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA",
  13        "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG",
  14        "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC",
  15        "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA")
  16
  17 # probabilities for symbols in Fasta codes
  18
  19 IUB := list(0.27, 0.12, 0.12, 0.27)
  20 11 repeatTimes( IUB append(0.02) )
  21
  22 HomoSap := list(0.3029549426680, 0.1979883004921, 0.1975473066391, 0.3015094502008)
  23
  24 Fasta := Object clone do(
  25     last := 42
  26
  27     gen_random := method(
  28         (last = ((last * 3877 + 29573) % 139968)) / 139968
  29     )
  30
  31     repeat := method(n,seq, i := li := 0
  32         line := Sequence clone setSize(60)
  33         n repeatTimes(
  34             line atPut(li, seq at(i))
  35             li = li + 1
  36             if (li == line size, line println; li = 0)
  37             i = ((i+1) % seq size)
  38         )
  39         if (li != 0, line setSize(li) println)
  40     )
  41
  42     codes := "acgtBDHKMNRSVWY"
  43
  44     random := method(n, probs, sum := li := 0
  45         line := Sequence clone setSize(60)
  46         probs mapInPlace(prob, sum = sum + prob)
  47         n repeatTimes(
  48             r := gen_random; i := 0
  49             while (r > probs at(i), i = i + 1)
  50             line atPut(li, codes at(i))
  51             li = li + 1
  52             if (li == line size, line println; li = 0)
  53         )
  54         if (li != 0, line setSize(li) println)
  55     )
  56 )
  57
  58 n := System args at(1) asNumber
  59
  60 ">ONE Homo sapiens alu" println
  61 Fasta repeat(2*n, ALU)
  62
  63 ">TWO IUB ambiguity codes" println
  64 Fasta random(3*n, IUB)
  65
  66 ">THREE Homo sapiens frequency" println
  67 Fasta random(5*n, HomoSap)