diff options
| author | ko1 <ko1@b2dd03c8-39d4-4d8f-98ff-823fe69b080e> | 2007-09-28 13:42:36 +0000 |
|---|---|---|
| committer | ko1 <ko1@b2dd03c8-39d4-4d8f-98ff-823fe69b080e> | 2007-09-28 13:42:36 +0000 |
| commit | fbebfdf23db958e3bb06dc0d4ccadca48d748dff (patch) | |
| tree | 6e5ef2d8e4b3b913524839cc1f2c37bb3f3f0c30 /benchmark/bm_so_fasta.rb | |
| parent | d6c43c45eaf5a6813ba5c2b3a68df154a69bdf9b (diff) | |
* benchmark/bm_so_fasta.rb: added.
* benchmark/bm_so_k_nucleotide.rb: added.
* benchmark/bm_so_reverse_complement.rb: added.
* benchmark/make_fasta_output.rb: added.
* benchmark/prepare_so_k_nucleotide.rb: added.
* benchmark/prepare_so_reverse_complement.rb: added.
git-svn-id: svn+ssh://ci.ruby-lang.org/ruby/trunk@13550 b2dd03c8-39d4-4d8f-98ff-823fe69b080e
Diffstat (limited to 'benchmark/bm_so_fasta.rb')
| -rw-r--r-- | benchmark/bm_so_fasta.rb | 81 |
1 files changed, 81 insertions, 0 deletions
diff --git a/benchmark/bm_so_fasta.rb b/benchmark/bm_so_fasta.rb new file mode 100644 index 0000000000..b95f5e9f10 --- /dev/null +++ b/benchmark/bm_so_fasta.rb @@ -0,0 +1,81 @@ +# 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)
+
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