ruby-changes:2059
From: ko1@a...
Date: 28 Sep 2007 22:42:51 +0900
Subject: [ruby-changes:2059] ko1 - Ruby:r13550 (trunk): * benchmark/bm_so_fasta.rb: added.
ko1 2007-09-28 22:42:36 +0900 (Fri, 28 Sep 2007)
New Revision: 13550
Added files:
trunk/benchmark/bm_so_fasta.rb
trunk/benchmark/bm_so_k_nucleotide.rb
trunk/benchmark/bm_so_reverse_complement.rb
trunk/benchmark/make_fasta_output.rb
trunk/benchmark/prepare_so_k_nucleotide.rb
trunk/benchmark/prepare_so_reverse_complement.rb
Modified files:
trunk/ChangeLog
Log:
* 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.
http://svn.ruby-lang.org/cgi-bin/viewvc.cgi/trunk/benchmark/bm_so_reverse_complement.rb?revision=13550&view=markup
http://svn.ruby-lang.org/cgi-bin/viewvc.cgi/trunk/benchmark/bm_so_fasta.rb?revision=13550&view=markup
http://svn.ruby-lang.org/cgi-bin/viewvc.cgi/trunk/ChangeLog?r1=13550&r2=13549
http://svn.ruby-lang.org/cgi-bin/viewvc.cgi/trunk/benchmark/prepare_so_reverse_complement.rb?revision=13550&view=markup
http://svn.ruby-lang.org/cgi-bin/viewvc.cgi/trunk/benchmark/bm_so_k_nucleotide.rb?revision=13550&view=markup
http://svn.ruby-lang.org/cgi-bin/viewvc.cgi/trunk/benchmark/make_fasta_output.rb?revision=13550&view=markup
http://svn.ruby-lang.org/cgi-bin/viewvc.cgi/trunk/benchmark/prepare_so_k_nucleotide.rb?revision=13550&view=markup
Index: ChangeLog
===================================================================
--- ChangeLog (revision 13549)
+++ ChangeLog (revision 13550)
@@ -1,3 +1,17 @@
+Fri Sep 28 22:33:47 2007 Koichi Sasada <ko1@a...>
+
+ * 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.
+
Fri Sep 28 19:14:51 2007 Koichi Sasada <ko1@a...>
* benchmark/driver.rb: fix notations.
Index: benchmark/bm_so_reverse_complement.rb
===================================================================
--- benchmark/bm_so_reverse_complement.rb (revision 0)
+++ benchmark/bm_so_reverse_complement.rb (revision 13550)
@@ -0,0 +1,30 @@
+#!/usr/bin/ruby
+# The Great Computer Language Shootout
+# http://shootout.alioth.debian.org/
+#
+# Contributed by Peter Bjarke Olsen
+# Modified by Doug King
+
+seq=Array.new
+
+def revcomp(seq)
+ seq.reverse!.tr!('wsatugcyrkmbdhvnATUGCYRKMBDHVN','WSTAACGRYMKVHDBNTAACGRYMKVHDBN')
+ stringlen=seq.length
+ 0.step(stringlen-1,60) {|x| print seq.slice(x,60) , "\n"}
+end
+
+input = open(File.join(File.dirname($0), 'fasta.output.2500000'), 'rb')
+
+while input.gets
+ if $_ =~ />/
+ if seq.length != 0
+ revcomp(seq.join)
+ seq=Array.new
+ end
+ puts $_
+ else
+ $_.sub(/\n/,'')
+ seq.push $_
+ end
+end
+revcomp(seq.join)
Index: benchmark/bm_so_fasta.rb
===================================================================
--- benchmark/bm_so_fasta.rb (revision 0)
+++ benchmark/bm_so_fasta.rb (revision 13550)
@@ -0,0 +1,81 @@
+# The Computer Language Shootout
+# http://shootout.alioth.debian.org/
+# Contributed by Sokolov Yura
+
+$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)
+
Index: benchmark/make_fasta_output.rb
===================================================================
--- benchmark/make_fasta_output.rb (revision 0)
+++ benchmark/make_fasta_output.rb (revision 13550)
@@ -0,0 +1,19 @@
+# prepare 'fasta.output'
+
+def prepare_fasta_output n
+ filebase = File.join(File.dirname($0), 'fasta.output')
+ script = File.join(File.dirname($0), 'bm_so_fasta.rb')
+ file = "#{filebase}.#{n}"
+
+ unless FileTest.exist?(file)
+ STDERR.puts "preparing #{file}"
+
+ open(file, 'w'){|f|
+ ARGV[0] = n
+ $stdout = f
+ load script
+ $stdout = STDOUT
+ }
+ end
+end
+
Index: benchmark/prepare_so_reverse_complement.rb
===================================================================
--- benchmark/prepare_so_reverse_complement.rb (revision 0)
+++ benchmark/prepare_so_reverse_complement.rb (revision 13550)
@@ -0,0 +1,2 @@
+require File.join(File.dirname(__FILE__), 'make_fasta_output')
+prepare_fasta_output(2_500_000)
Index: benchmark/bm_so_k_nucleotide.rb
===================================================================
--- benchmark/bm_so_k_nucleotide.rb (revision 0)
+++ benchmark/bm_so_k_nucleotide.rb (revision 13550)
@@ -0,0 +1,48 @@
+# The Computer Language Shootout
+# http://shootout.alioth.debian.org
+#
+# contributed by jose fco. gonzalez
+# modified by Sokolov Yura
+
+seq = String.new
+
+def frecuency( seq,length )
+ n, table = seq.length - length + 1, Hash.new(0)
+ f, i = nil, nil
+ (0 ... length).each do |f|
+ (f ... n).step(length) do |i|
+ table[seq[i,length]] += 1
+ end
+ end
+ [n,table]
+
+end
+
+def sort_by_freq( seq,length )
+ n,table = frecuency( seq,length )
+ a, b, v = nil, nil, nil
+ table.sort{|a,b| b[1] <=> a[1]}.each do |v|
+ puts "%s %.3f" % [v[0].upcase,((v[1]*100).to_f/n)]
+ end
+ puts
+end
+
+def find_seq( seq,s )
+ n,table = frecuency( seq,s.length )
+ puts "#{table[s].to_s}\t#{s.upcase}"
+end
+
+input = open(File.join(File.dirname($0), 'fasta.output.100000'), 'rb')
+
+line = input.gets while line !~ /^>THREE/
+line = input.gets
+
+while (line !~ /^>/) & line do
+ seq << line.chomp
+ line = input.gets
+end
+
+[1,2].each {|i| sort_by_freq( seq,i ) }
+
+%w(ggt ggta ggtatt ggtattttaatt ggtattttaatttatagt).each{|s| find_seq( seq,s) }
+
Index: benchmark/prepare_so_k_nucleotide.rb
===================================================================
--- benchmark/prepare_so_k_nucleotide.rb (revision 0)
+++ benchmark/prepare_so_k_nucleotide.rb (revision 13550)
@@ -0,0 +1,2 @@
+require File.join(File.dirname(__FILE__), 'make_fasta_output')
+prepare_fasta_output(100_000)
--
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