diff options
Diffstat (limited to 'benchmark/bm_so_fasta.rb')
-rw-r--r-- | benchmark/bm_so_fasta.rb | 81 |
1 files changed, 0 insertions, 81 deletions
diff --git a/benchmark/bm_so_fasta.rb b/benchmark/bm_so_fasta.rb deleted file mode 100644 index dcc6b39507..0000000000 --- a/benchmark/bm_so_fasta.rb +++ /dev/null @@ -1,81 +0,0 @@ -# The Computer Language Shootout -# http://shootout.alioth.debian.org/ -# Contributed by Sokolov Yura - -$last = 42.0 -def gen_random(max, im=139968, ia=3877, ic=29573) - (max * ($last = ($last * ia + ic) % im)) / im -end - -alu = - "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG"+ - "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA"+ - "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT"+ - "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA"+ - "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG"+ - "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC"+ - "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA" - -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], -] -homosapiens = [ - ["a", 0.3029549426680], - ["c", 0.1979883004921], - ["g", 0.1975473066391], - ["t", 0.3015094502008], -] - -def make_repeat_fasta(id, desc, src, n) - puts ">#{id} #{desc}" - v = nil - width = 60 - l = src.length - s = src * ((n / l) + 1) - s.slice!(n, l) - puts(s.scan(/.{1,#{width}}/).join("\n")) -end - -def make_random_fasta(id, desc, table, n) - puts ">#{id} #{desc}" - rand, v = nil,nil - width = 60 - chunk = 1 * width - prob = 0.0 - table.each{|v| v[1]= (prob += v[1])} - for i in 1..(n/width) - puts((1..width).collect{ - rand = gen_random(1.0) - table.find{|v| v[1]>rand}[0] - }.join) - end - if n%width != 0 - puts((1..(n%width)).collect{ - rand = gen_random(1.0) - table.find{|v| v[1]>rand}[0] - }.join) - end -end - - -n = (ARGV[0] or 250_000).to_i - -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) - |