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  • Committer: Bazaar Package Importer
  • Author(s): Stephan Hermann
  • Date: 2008-01-24 11:42:29 UTC
  • mfrom: (1.1.9 upstream)
  • Revision ID: james.westby@ubuntu.com-20080124114229-jw2f87rdxlq6gp11
Tags: 1.9.0.0-2ubuntu1
* Merge from debian unstable, remaining changes:
  - Robustify check for target_os, fixing build failure on lpia.

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benchmark/bm_so_fasta.rb
 
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# The Computer Language Shootout
 
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# http://shootout.alioth.debian.org/
 
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# Contributed by Sokolov Yura
 
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$last = 42.0
 
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def gen_random (max,im=139968,ia=3877,ic=29573)
 
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    (max * ($last = ($last * ia + ic) % im)) / im
 
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end
 
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alu =
 
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   "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG"+
 
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   "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA"+
 
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   "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT"+
 
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   "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA"+
 
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   "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG"+
 
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   "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC"+
 
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   "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"
 
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iub = [
 
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    ["a", 0.27],
 
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    ["c", 0.12],
 
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    ["g", 0.12],
 
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    ["t", 0.27],
 
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    ["B", 0.02],
 
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    ["D", 0.02],
 
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    ["H", 0.02],
 
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    ["K", 0.02],
 
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    ["M", 0.02],
 
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    ["N", 0.02],
 
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    ["R", 0.02],
 
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    ["S", 0.02],
 
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    ["V", 0.02],
 
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    ["W", 0.02],
 
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    ["Y", 0.02],
 
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]
 
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homosapiens = [
 
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    ["a", 0.3029549426680],
 
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    ["c", 0.1979883004921],
 
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    ["g", 0.1975473066391],
 
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    ["t", 0.3015094502008],
 
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]
 
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def make_repeat_fasta(id, desc, src, n)
 
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    puts ">#{id} #{desc}"
 
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    v = nil
 
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    width = 60
 
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    l = src.length
 
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    s = src * ((n / l) + 1)
 
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    s.slice!(n, l)
 
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    puts(s.scan(/.{1,#{width}}/).join("\n"))
 
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end
 
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def make_random_fasta(id, desc, table, n)
 
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    puts ">#{id} #{desc}"
 
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    rand, v = nil,nil
 
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    width = 60
 
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    chunk = 1 * width
 
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    prob = 0.0
 
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    table.each{|v| v[1]= (prob += v[1])}
 
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    for i in 1..(n/width)
 
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        puts((1..width).collect{
 
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            rand = gen_random(1.0)
 
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            table.find{|v| v[1]>rand}[0]
 
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        }.join)
 
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    end
 
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    if n%width != 0
 
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        puts((1..(n%width)).collect{
 
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            rand = gen_random(1.0)
 
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            table.find{|v| v[1]>rand}[0]
 
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        }.join)
 
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    end
 
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end
 
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n = (ARGV[0] or 250_000).to_i
 
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make_repeat_fasta('ONE', 'Homo sapiens alu', alu, n*2)
 
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make_random_fasta('TWO', 'IUB ambiguity codes', iub, n*3)
 
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make_random_fasta('THREE', 'Homo sapiens frequency', homosapiens, n*5)
 
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