cwords 0.1.4-jruby → 0.1.6-jruby

data/README

@@ -6,10 +6,17 @@ Cwords is a software tool that measure correlations of short oligonucleotide seq
 All software components require Ruby (>=1.8.6, http://www.ruby-lang.org/) and JRuby (>=1.4.0, http://jruby.org/).
 The software has only been tested on a Unix platform.
 
-The following Ruby gems are required (install with JRuby gem command)
 
-* jgem install progressbar
-* jgem install schleyfox-peach --source=http://gems.github.com
+2. INSTALL
+
+* Install Ruby (www.ruby-lang.org, check if it is already installed: 'ruby -v')
+* Install JRruby (www.jruby.org, check if it is already installed: 'jruby -v'),
+  make sure that you have the 'jruby' command in your path.
+* Install Rubygems (www.rubygems.org, check if it is already installed: 'gem -v')
+* Install cwords:
+
+> gem install cwords
+> cwords --help
 
 2. USAGE
 

data/bin/cwords

@@ -2,10 +2,16 @@
 
 scriptdir = File.dirname(__FILE__) + "/../scripts/"
 
+helps = ARGV.join(" ").match(/--help/)
+if (helps) 
+  # start lightweight
+  exec "jruby --client " + scriptdir + "cwords.rb " + ARGV.join(" ")
+end
+
 mems = ARGV.join(" ").match(/M=(\w+)/)
 mem = mems ? mems[1] : '4096m'
 argv = ARGV.select{|x| not x=~ /^M=\w+$/}.join(' ')
 puts "Starting cwords with max heap size " + mem + " ...\n"
 
-cmd = "jruby --server --fast -J-Xmx#{mem} " + scriptdir + "cwords.rb " + argv
+cmd = "jruby --1.9 --server --fast -J-Xmx#{mem} " + scriptdir + "cwords.rb " + argv
 exec cmd

data/bin/cwords_mkdb

@@ -1,10 +1,16 @@
 #!/usr/bin/env ruby
 scriptdir = File.dirname(__FILE__) + "/../scripts/"
 
+helps = ARGV.join(" ").match(/--help/)
+if (helps) 
+  # start lightweight
+  exec "jruby --client " + scriptdir + "cwords_mkdb.rb " + ARGV.join(" ")
+end
+
 mems = ARGV.join(" ").match(/M=(\w+)/)
 mem = mems ? mems[1] : '4096m'
 argv = ARGV.select{|x| not x=~ /^M=\w+$/}.join(' ')
-puts "Starting cwords with max heap size " + mem + " ..."
+puts "Starting cwords with max heap size " + mem + " ...\n"
 
-cmd = "jruby --server --fast -J-Xmx#{mem} " + scriptdir + "cwords_mkdb.rb " + argv
+cmd = "jruby --1.9 --server --fast -J-Xmx#{mem} " + scriptdir + "cwords_mkdb.rb " + argv
 exec cmd

data/scripts/cwords.rb

@@ -1,13 +1,5 @@
 #!/usr/bin/env jruby
 
-### Requires jruby, www.jruby.org
-
-###
-### Running sum analysis for 5 different measures of word enrichment in a sequence:
-###  obs     : use the observed word count
-###  bin     : use presence/absence of word
-###  pval    : use the p-value of the expected occurrences being >= the observed occurence
-
 srcdir = File.dirname(__FILE__)
 basedir = srcdir + "/../"
 libdir = basedir + '/lib/'
@@ -80,7 +72,14 @@ def show_help(msg="", code=0, io=STDOUT)
   exit(code)
 end
 
-$coptions.parse!(ARGV)
+begin
+  $coptions.parse!(ARGV)
+rescue OptionParser::ParseError => error
+  puts error.message
+  puts $coptions
+  exit
+end
+
 # mandatory parameters
 [:rankfile].each{|p| show_help("option '#{p}' mandatory") if options[p].nil?}
 show_help("db or seqfile required") if !(options[:db] or options[:seqfile])
@@ -116,7 +115,7 @@ IO.readlines(annofile).each{|l| word_annotation[l.split("\t")[0]] = l.split("\t"
 
 # read optional sequences
 if options[:seqfile]
-  puts ">> reading sequences ..."
+  puts "\n>> reading sequences ..."
   sequences = Hash.new
   IO.readlines(options[:seqfile],">")[1..-1].each do |entry|
     ls = entry.split("\n").map{|x| x.chomp}
@@ -141,7 +140,7 @@ options[:wordsize].each{|ws| ['a','g','c','t'].rep_perm(ws) {|seqa| wids[seqa.jo
 # sequence file:
 #  take intersection of rank and sequence IDs
 
-puts ">> Mapping and filtering IDs ..."
+puts "\n>> Mapping and filtering IDs ..."
 
 all = []
 begin
@@ -186,7 +185,7 @@ all.each_with_index{|x,i| allorder[x[0]] = i}
 
 wordscores = []
 if sequences
-  puts ">> Enumerating words in 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|
@@ -270,7 +269,7 @@ end
 ### Correlation analysis
 ###
 
-puts ">> Analyzing sequence sets: " + analyze.map{|x| x[1]}.join(", ")
+puts "\n>> Analyzing sequence sets: " + analyze.map{|x| x[1]}.join(", ")
 
 analyze.each do |set,nm|
   ngenes = set.size

data/scripts/cwords_mkdb.rb

@@ -1,11 +1,12 @@
-#!/usr/bin/ruby
+#!/usr/bin/env jruby
 
 srcdir = File.dirname(__FILE__)
-basedir = srcdir + "../"
+basedir = srcdir + "/../"
 libdir = basedir + 'lib/'
 $LOAD_PATH << libdir
 
 require 'wordRS-lib.rb'
+require 'rubygems'
 require 'progressbar'
 require 'optparse'
 require 'fileutils'
@@ -42,7 +43,14 @@ def show_help(msg="", code=0, io=STDOUT)
   exit(code)
 end
 
-$coptions.parse!(ARGV)
+begin
+  $coptions.parse!(ARGV)
+rescue OptionParser::ParseError => error
+  puts error.message
+  puts $coptions
+  exit
+end
+
 #mandatory parameters
 [:seqfile].each{  |p| show_help("option '#{p}' mandatory") if options[p].nil?}
 

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 4
-  version: 0.1.4
+  - 6
+  version: 0.1.6
 platform: jruby
 authors: 
 - Anders Jacobsen