benchmarks_game/fasta.fz

# https://benchmarksgame-team.pages.debian.net/benchmarksgame/description/fasta.html#fasta
# this is a port of https://benchmarksgame-team.pages.debian.net/benchmarksgame/program/fasta-java-2.html
# thus it is still rough around the edges

fasta =>
  im := f64 139968
  ia := f64 3877
  ic := f64 29573
  last := mut f64 42
  line_length := 60

  random(max f64) =>
    last <- (last.get * ia + ic) % im
    max * last.get / im

  alu := ("GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
    "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
    "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
    "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
    "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
    "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC"+
    "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA")

  frequency(c String, p f64) is

  iub := [
             frequency("a", 0.27),
             frequency("c", 0.12),
             frequency("g", 0.12),
             frequency("t", 0.27),

             frequency("B", 0.02),
             frequency("D", 0.02),
             frequency("H", 0.02),
             frequency("K", 0.02),
             frequency("M", 0.02),
             frequency("N", 0.02),
             frequency("R", 0.02),
             frequency("S", 0.02),
             frequency("V", 0.02),
             frequency("W", 0.02),
             frequency("Y", 0.02)
    ]

  homo_sapiens := [
             frequency("a", 0.3029549426680),
             frequency("c", 0.1979883004921),
             frequency("g", 0.1975473066391),
             frequency("t", 0.3015094502008)
    ]

  make_cumulative(a array frequency) =>
    a.map frequency (freq ->
      cp := a.take_while(f -> !(freq.c = f.c))
        .map f64 (f -> f.p)
        .fold(f64.type.sum) + freq.p
      frequency freq.c cp)

  select_random(a array frequency) =>
    r := random 1.0
    for i := 0, i+1
    while i < a.length
    until r < a[i].p
      a[i].c
    else
      a.last().c

  random_fasta(id, desc String, a array frequency, n i32) =>
    m := 0
    say (">" + id + " " + desc)
    (1..line_length)
      .for_each(_ ->
        b := (0..line_length-1)
          .map String (_ -> select_random(a))
          .fold(String.type.concat)
        say b
        )

  repeat_fasta(id, desc, alu String, n i32) =>
    m := 0
    k := mut 0
    kn := alu.byte_length
    say (">" + id + " " + desc)
    (1..line_length)
      .for_each(_ ->
        (0..line_length-1)
          .for_each(_ ->
            if (k.get = kn) then k <- 0
            yak alu.substring(k.get, k.get+1)
            k <- k.get + 1
            )
        say
        )

  homo := make_cumulative homo_sapiens
  iub := make_cumulative iub

  n := 2500000

  repeat_fasta "ONE" "Homo sapiens alu" alu (n * 2)
  random_fasta "TWO" "iub ambiguity codes" iub (n * 3)
  random_fasta "THREE" "Homo sapiens frequency" homo (n * 5)