cwords 0.1.9 → 0.1.10

data/lib/wordRS-lib.rb

@@ -1,6 +1,44 @@
 
 class Array
+  
+  # threaded each
+  def threach(n = 1, &b)
+    return [] if n == 0 or size == 0
+    result = Array.new(size)
+    self.send(:each,&b) if n == 1
+    
+    n = [n,size].min
+    
+    part_size, part_remainder = size/n, size % n
+    threads = []
+
+    pstart = 0
+    n.times do |pi|
+      pend = pstart + part_size - 1
+      pend += 1 if pi<part_remainder
+      threads << Thread.new(pstart,pend) do |a,b|
+        for j in a..b
+          yield(slice(j))
+        end
+      end
+      pstart = pend+1
+    end
+    
+    threads.each { |t| t.join }
+    self
+  end
+  
+  # unit tests for threach
+  #Array.send(:include, Threach)
+  #a=(0..4).to_a
+  #res = a.map{|x| x*10}
+  #a.size.times do |pn|
+  #  b=Array.new(a.size)
+  #  a.threach(pn+1) {|x| b[x]=x*10}
+  #  puts b == beach
+  #end
 
+  
   def shuffle()
     arr = self.dup
     arr.size.downto 2 do |j|

data/scripts/cwords.rb

@@ -9,7 +9,6 @@ require 'wordRS-lib.rb'
 require 'rubygems'
 require 'progressbar'
 require 'optparse'
-require 'peach'
 require 'java'
 require libdir + 'ushuffle.jar'
 java_import 'UShuffle'
@@ -188,7 +187,7 @@ if sequences
   puts "\n>> Enumerating words in sequences"
   wordscores = Array.new(all.size) {Array.new(wids.size,0)} # {Java::short[wids.size].new}
   pbar = ProgressBar.new("progress",sequences.size)
-  all.peach(threads) do |seqid,val|
+  all.threach(threads) do |seqid,val|
     us = UShuffle.new
     seq=sequences[seqid]
     seqidx=allorder[seqid]
@@ -286,7 +285,7 @@ analyze.each do |set,nm|
   options[:permutations].times{|i| perms << (0..set.size-1).to_a.shuffle}
   
   pbar = ProgressBar.new("progress",nwords)
-  wids.to_a.sort_by{|x| x[1]}.peach(threads) do |word,wid|
+  wids.to_a.sort_by{|x| x[1]}.threach(threads) do |word,wid|
     pbar.inc
     next if options[:onlyanno] and not word_annotation.key?(word) #only process annotated words
     next if options[:plot_words] and !options[:plot_words].include?(word)

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 9
-  version: 0.1.9
+  - 10
+  version: 0.1.10
 platform: ruby
 authors: 
 - Anders Jacobsen
@@ -32,20 +32,6 @@ dependencies:
         version: 0.9.0
   type: :runtime
   version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: peach
-  prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        - 2
-        - 0
-        version: 0.2.0
-  type: :runtime
-  version_requirements: *id002
 description: Word correlation analysis in ranked nucleotide sequences (bioinformatics)
 email: andersmbj@gmail.com
 executables: