rbbt 1.2.2 → 1.2.5

data/install_scripts/classifier/Rakefile

@@ -9,12 +9,12 @@ require 'rbbt/util/misc'
 require 'progress-monitor'
 require 'rand'
 
-$hi      = ENV['hi']  || 0.8
-$low     = ENV['low'] || 0.01
-$max     = ENV['max'] || 3000
-$bigrams = ENV['bigrams'] == 'true' || false
+$hi      ||= ENV['hi']  || 0.8
+$low     ||= ENV['low'] || 0.01
+$max     ||= ENV['max'] || 3000
+$bigrams ||= ENV['bigrams'] == 'true' 
 
-$ndocs   = ENV['ndocs'] || 5000
+$ndocs   ||= ENV['ndocs'] || 5000
 
 desc "Bilds Dictionary and Features for an organism"
 rule(/data\/(.*)/) do |t|
@@ -34,7 +34,7 @@ rule(/data\/(.*)/) do |t|
  
 
   chunks = all.chunk(50)
-  Progress.monitor("Building Dictionary for #{ org }: -",1000)
+  Progress.monitor("Building Dictionary for #{ org }: -")
   chunks.each{|chunk|
     PubMed.get_article(chunk).each{|pmid, article|
       words = BagOfWords.terms(article.text,$bigrams)
@@ -43,7 +43,7 @@ rule(/data\/(.*)/) do |t|
   }
 
   chunks = go.chunk(50)
-  Progress.monitor("Building Dictionary for #{ org }: +",1000)
+  Progress.monitor("Building Dictionary for #{ org }: +")
   chunks.each{|chunk|
     PubMed.get_article(chunk).each{|pmid, article|
       words = BagOfWords.terms(article.text,$bigrams)
@@ -59,7 +59,7 @@ rule(/data\/(.*)/) do |t|
   fout = File.open(t.name, 'w')
   fout.puts((['Name','Class'] + terms).join("\t"))
   
-  Progress.monitor("Building Features for #{ org }", 1000)
+  Progress.monitor("Building Features for #{ org }")
   all.each{|pmid|
     text = PubMed.get_article(pmid).text
     fout.puts(([pmid, :-] + BagOfWords.features(text, terms)).join("\t"))
@@ -83,14 +83,9 @@ rule (/results\/(.*)/) => lambda{|n| n.sub(/results/,'model')} do |t|
   features    = t.name.sub(/results/,'data')
   org = File.basename(t.name)
 
-  ndocs    = 100
+  ndocs    = 1000
 
-  used = []
-  if "".respond_to? :collect
-    used = Open.read(features).collect{|l| l.chomp.split(/\t/).first}[1..-1]
-  else
-    used = Open.read(features).lines.collect{|l| l.chomp.split(/\t/).first}[1..-1]
-  end
+  used = Open.read(features).read.split(/\n/).collect{|l| l.chomp.split(/\t/).first}[1..-1]
 
   classifier = Classifier.new(model)
   go  = Organism.gene_literature_go(org).collect{|gene, pmids| pmids}.flatten.uniq - used
@@ -104,12 +99,12 @@ rule (/results\/(.*)/) => lambda{|n| n.sub(/results/,'model')} do |t|
   raise "Not enogh unused articles to evaluate" if  go.empty? || all.empty?
 
   features_go = PubMed.get_article(go).collect{|pmid, article|
-    article = article.text
+    article.text
   }
   pos = classifier.classify(features_go).select{|v| v == '+'}.length
 
   features_all = PubMed.get_article(all).collect{|pmid, article|
-    article = article.text
+    article.text
   }
   neg = classifier.classify(features_all).select{|v| v == '-'}.length
 

data/install_scripts/norm/config/cue_default.rb

@@ -1,6 +1,6 @@
 equal    do |w| [w] end
 standard do |w| [w.downcase.split(/\s+/).sort.join("")] end
-cleaned  do |w| [w.downcase.sub(/,.*/,'').sub(/\(.*\)/,'')] end
+cleaned  do |w| [w.downcase.sub(/,.*/,'').sub(/\(.*\)/,'').gsub(/s(?:=\W)/,'')] end
 special  do |w| s = w.split.select{|w| w.is_special?}.collect{|w| w.downcase.sub(/p$/,'')} end
 words    do |w| 
   w.sub(/(.*)I$/,'\1I \1').

data/install_scripts/norm/config/tokens_default.rb

@@ -1,4 +1,8 @@
 require 'rbbt/util/misc'
+
+
+plural = Proc.new do |t| t.sub(/s$/,'') end
+
 tokens do
 
   # Some (possible) single letters first
@@ -70,6 +74,9 @@ comparisons do
   miss.special    -3 
   extr.special    -3 
 
+  transform.receptor plural
+  transform.protein plural
+
   transform.roman do |t| [t.arabic, :number] end
   transform.greek_letter do |t| [$inverse_greek[t.downcase], :greek] end
   transform.ase do |t| [t, :special] end

data/install_scripts/organisms/Ath.Rakefile

@@ -13,7 +13,7 @@ $entrez2native = {
 
 $lexicon = {
   :file => {
-    :url => "ftp://ftp.arabidopsis.org/home/tair/Genes/gene_aliases.20090313",
+    :url => "ftp://ftp.arabidopsis.org/home/tair/Genes/gene_aliases.20100413",
     :native => 0,
     :extra => [1,2],
   },

data/install_scripts/organisms/Hsa.Rakefile

@@ -37,7 +37,6 @@ $identifiers = {
       [ 'Protein ID', "protein_id"  ],
       [ 'RefSeq Protein ID', "refseq_peptide"  ],
       [ 'Unigene ID', "unigene"  ],
-      [ 'UniProt/SwissProt ID', "uniprot_swissprot"  ],
       [ 'UniProt/SwissProt Accession', "uniprot_swissprot_accession"  ],
       [ 'HGNC ID', "hgnc_id", 'HGNC'],
       ['EMBL (Genbank) ID' , "embl"] , 

data/install_scripts/organisms/Sce.Rakefile

@@ -6,7 +6,7 @@ $name = "Saccharomyces cerevisiae"
 $native_id = "SGD DB Id"
 
 $entrez2native = {
-  :tax =>  4932,
+  :tax => 559292,
   :fix => proc{|code| code.sub(/SGD:S0/,'S0') },
   :check => proc{|code| code.match(/^S0/)},
 }

data/install_scripts/organisms/rake-include.rb

@@ -107,18 +107,18 @@ file 'identifiers' do
     if $entrez2native
       translations = {}
       Entrez.entrez2native(*$entrez2native.values_at(:tax,:native,:fix,:check)).
-        each{|k,v|
-          translations[k] = [v.join("|")]
-      }
+        each{|k,v| translations[k] = [v.join("|")] }
+
       if translations.keys.any?
         translations_data = ArrayHash.new(translations,'Entrez Gene ID', [$native_id])
         if data
-          data.merge(translations_data)
+          data.merge(translations_data, $native_id)
         else
           data = translations_data
         end
+      else
+        puts "No translations from Entrez to #{ $native_id }"
       end
-
     end
 
 
@@ -174,8 +174,6 @@ file 'identifiers' do
       end
     end
 
-
-
     # Write ids to file
     fout = File.open('identifiers', 'w')
     fout.puts "##{$native_id}\t" + data.fields.join("\t")

data/lib/rbbt/bow/bow.rb

@@ -17,7 +17,7 @@ module BagOfWords
   # 'rbbt/util/misc'.
   def self.words(text)
     return [] if text.nil?
-    raise "Stopword list not loaded. Have you installed the wordlists? (rbbt_config install wordlists)" if $stopwords.nil?
+    raise "Stopword list not loaded. Have you installed the wordlists? (rbbt_config prepare wordlists)" if $stopwords.nil?
     text.scan(/\w+/).
       collect{|word| word.downcase.stem}.
       select{|word|  

data/lib/rbbt/ner/dictionaryNER.rb

@@ -3,7 +3,7 @@
 class DictionaryNER
 
   A_INT   = "a"[0]
-  DOWNCASE_OFFSET = "A"[0] - "a"[0]
+  DOWNCASE_OFFSET = "A"[0].bytes.first - "a"[0].bytes.first
 
   require 'rbbt/bow/bow'
   # Divides a string of text into words. A slash separates words, only if the

data/lib/rbbt/ner/rnorm/tokens.rb

@@ -102,7 +102,11 @@ class Tokenizer < SimpleDSL
     end
     def method_missing(name, *args, &block)
       @token = name.to_sym
-      @block = block
+      if block_given?
+        @block = block
+      else
+        @block = args.first
+      end
       self
     end
 

data/lib/rbbt/sources/organism.rb

@@ -72,7 +72,7 @@ module Organism
   def self.norm(org, to_entrez = nil)
     require 'rbbt/ner/rnorm'
     if to_entrez.nil?
-      to_entrez = id_index(org, :native => 'Entrez Gene ID', :other => [supported_ids(org).first])
+      to_entrez = id_index(org, :native => 'Entrez Gene Id', :other => [supported_ids(org).first])
     end
     
     token_file = File.join(Rbbt.datadir, 'norm','config',org.to_s + '.config')
@@ -216,7 +216,7 @@ module Organism
       first = nil
       if native
         first = id_position(supported,native,options)
-        raise "No match for native format '#{ native }'"
+        raise "No match for native format '#{ native }'" if first.nil?
       else
         first = 0
       end

data/lib/rbbt/sources/pubmed.rb

@@ -24,7 +24,7 @@ module PubMed
     
     @@last = Time.now
 
-    articles = xml.scan(/(<PubmedArticle>.*?<\/PubmedArticle>)/sm).flatten
+    articles = xml.scan(/(<PubmedArticle>.*?<\/PubmedArticle>)/smu).flatten
 
     if pmids.is_a? Array
       list = {}
@@ -53,6 +53,7 @@ module PubMed
       [:volume   , "Journal/JournalIssue/Volume"],
       [:issn     , "Journal/ISSN"],
       [:year     , "Journal/JournalIssue/PubDate/Year"],
+      [:month    , "Journal/JournalIssue/PubDate/Month"],
       [:pages    , "Pagination/MedlinePgn"],
       [:abstract , "Abstract/AbstractText"],
     ]
@@ -63,6 +64,15 @@ module PubMed
       title.gsub(/(\w*[A-Z][A-Z]+\w*)/, '{\1}')
     end
 
+    def self.make_bibentry(lastname, year, title)
+      words = title.downcase.scan(/\w+/)
+      if words.first.length > 3
+        abrev = words.first
+      else
+        abrev = words[0..2].collect{|w| w.chars.first} * ""
+      end
+      [lastname.gsub(/\s/,'_'), year || "NOYEAR", abrev] * ""
+    end
     def self.parse_xml(xml)
       parser  = LibXML::XML::Parser.string(xml)
       pubmed  = parser.parse.find("/PubmedArticle").first
@@ -84,17 +94,20 @@ module PubMed
 
       bibentry = nil
       info[:author] = article.find("AuthorList/Author").collect do |author|
-        lastname = author.find("LastName").first.content
-        if author.find("ForeName").first.nil?
-          forename = nil
-        else
-          forename = author.find("ForeName").first.content.split(/\s/).collect{|word| if word.length == 1; then word + '.'; else word; end} * " "
+        begin
+          lastname = author.find("LastName").first.content
+          if author.find("ForeName").first.nil?
+            forename = nil
+          else
+            forename = author.find("ForeName").first.content.split(/\s/).collect{|word| if word.length == 1; then word + '.'; else word; end} * " "
+          end
+          bibentry ||= make_bibentry lastname, info[:year], info[:title]
+        rescue
         end
-        bibentry ||= [lastname, (info[:year] || "NOYEAR"), info[:title].scan(/\w+/)[0]] * ""
         [lastname, forename] * ", "
       end * " and "
 
-      info[:bibentry] = bibentry.downcase
+      info[:bibentry] = bibentry.downcase if bibentry
 
       info[:pmc_pdf] = pubmed.find("PubmedData/ArticleIdList/ArticleId").select{|id| id[:IdType] == "pmc"}.first
 
@@ -122,6 +135,23 @@ module PubMed
       @gscholar_pdf ||= GoogleScholar::full_text_url title
     end
 
+    def full_text
+      return nil if pdf_url.nil?
+
+      text = nil
+      TmpFile.with_file do |pdf|
+
+        # Change user-agent, oh well...
+        `wget --user-agent=firefox #{ pdf_url } -O #{ pdf }`
+        TmpFile.with_file do |txt|
+          `pdftotext #{ pdf } #{ txt }`
+          text = Open.read(txt) if File.exists? txt
+        end
+      end
+
+      text
+    end
+
     def bibtex
       keys = [:author] + XML_KEYS.collect{|p| p.first } - [:bibentry]
       bibtex = "@article{#{bibentry},\n"

data/lib/rbbt/util/arrayHash.rb

@@ -1,6 +1,20 @@
 
 class ArrayHash
 
+  def self.make_case_insensitive(hash)
+    new = {}
+    hash.each{|k,v|
+      new[k.to_s.downcase] = v
+    }
+
+    class << new; self; end.instance_eval{
+      alias_method :old_get, :[]
+      define_method(:[], proc{|key| old_get(key.to_s.downcase)})
+    }
+
+    new
+  end
+
   # Take two strings of elements separated by the character sep_char and join them
   # into one, removing repetitions.
   def self.merge_values_string(list1, list2, sep_char ='|')
@@ -33,8 +47,8 @@ class ArrayHash
 
   
   # Take an hash of arrays and a position and use the value at that position
-  # of the arrays and build a new hash with that value as key, and the original
-  # key prepended to the arrays. The options hash appcepts the following keys
+  # of the arrays to build a new hash with that value as key, and the original
+  # key prepended to the arrays. The options hash accepts the following keys
   # :case_insensitive, which defaults to true, and :index, which indicates that
   # the original key should be the value of the hash entry, instead of the
   # complete array of values.
@@ -60,69 +74,63 @@ class ArrayHash
       }
     }
 
-    if case_insensitive
-      class << new; self; end.instance_eval{
-        alias_method :old_get, :[]
-        define_method(:[], proc{|key| old_get(key.to_s.downcase)})
-      }
-    end
+    new = make_case_insensitive new if case_insensitive
 
     new
   end
 
-  # Merge to hashes of arrays. Each hash contains a number of fields for each
+  # Merge one hash of arrays into another. Each hash contains a number of fields for each
   # entry. The pos1 and pos2 indicate what fields should be used to match
   # entries, the values for pos1 and pos2 can be an integer indicating the
   # position in the array or the symbol :main to refer to the key of the hash.
   # The options hash accepts the key :case_insensitive, which defaults to true.
   def self.merge(hash1, hash2, pos1 = :main, pos2 = :main, options = {})
-
     case_insensitive = options[:case_insensitive]; case_insensitive = true if case_insensitive.nil?
+
+    raise "Key #{ pos1 } should be an Interger or :main" unless Fixnum === pos1 || pos1.to_s.downcase == 'main'
+    raise "Key #{ pos2 } should be an Interger or :main" unless Fixnum === pos2 || pos2.to_s.downcase == 'main'
+
+
+    # Pullout if pos2 is not :main
+    hash2 = pullout(hash2, pos2) unless pos2.to_s.downcase == 'main'
+
+    # Translate if pos1 is not :main
     if pos1.to_s.downcase != 'main'
-      index1 = pullout(hash1, pos1, options.merge(:index => true))
-    elsif options[:case_insensitive]
+      index = pullout(hash1, pos1, options.merge(:index => true))
       new = {}
-      hash1.each{|k,v|
-        new[k.to_s.downcase] = v
-      }
-      class << new; self; end.instance_eval{
-        alias_method :old_get, :[]
-        define_method(:[], proc{|key| old_get(key.to_s.downcase)})
-      }
-      hash1 = new
+      hash2.each do |key, list|
+        next unless index[key]
+        new[index[key]] = list
+      end
+      hash2 = new
     end
 
+    # Get the lengths of the arrays on each hash (they should
+    # be the same for every entry)
     length1 = hash1.values.first.length
     length2 = hash2.values.first.length
+    
+    if case_insensitive
+      hash1 = make_case_insensitive hash1
+      hash2 = make_case_insensitive hash2
+    end
 
     new = {}
-    hash2.each{|key, values|
-      case
-      when pos2.to_s.downcase == 'main'
-        k = key
-        v = values
-      when Fixnum === pos2
-        k = values[pos2]
-        v = values
-        v.delete_at(pos2)
-        v.unshift(key)
+    (hash1.keys + hash2.keys).uniq.each do |key|
+      if hash2[key].nil?
+        list2 = [''] * length2
       else
-        raise "Format of second index not understood"
+        list2 = hash2[key]
       end
 
-      code = (index1.nil? ? k : index1[k])
-      if code
-        code.split('|').each{|c|
-          c = c.to_s.downcase if options[:case_insensitive]
-          new[c] = hash1[c] || [''] * length1
-          new[c] += v
-        }
+      if hash1[key].nil?
+        list1 = [''] * length1
+      else
+        list1 = hash1[key]
       end
-    }
 
-    hash1.each{|key, values|
-      new[key] ||= values + [''] * length2 
-    }
+      new[key] = list1 + list2
+    end
 
     new
   end
@@ -139,7 +147,7 @@ class ArrayHash
     new
   end
 
-  # Clean structure for repeated values. If the same value apear two times use
+  # Clean structure for repeated values. If the same value appears two times 
   # eliminate the one that appears latter on the values list (columns of the
   # ArrayHash are assumed to be sorted for importance) if the appear on the
   # same position, remove the one with the smaller vale of the code after
@@ -188,7 +196,7 @@ class ArrayHash
     @data = hash
     @main = main.to_s
     
-    if fields.nil?
+    if fields.nil? || fields.empty?
       l = hash.values.first.length
       fields = []
       l.times{|i| fields << "F#{i}"}
@@ -207,10 +215,10 @@ class ArrayHash
   # Returns the position of a given field in the value arrays
   def field_pos(field)
     return :main if field == :main
-    if field.downcase == self.main.downcase
+    if field.to_s.downcase == self.main.to_s.downcase
       return :main
     else
-      @fields.collect{|f| f.downcase}.index(field.to_s.downcase)
+      @fields.collect{|f| f.downcase }.index(field.to_s.downcase)
     end
   end
 
@@ -222,6 +230,9 @@ class ArrayHash
     pos1 = self.field_pos(field)
     pos2 = other.field_pos(field)
 
+    raise "Field #{ field } not found in target hash" if pos1.nil?
+    raise "Field #{ field } not found in added hash" if pos2.nil?
+
     new = ArrayHash.merge(self.data, other.data, pos1, pos2, options)
     @data = new
     if pos2 == :main

data/lib/rbbt/util/index.rb

@@ -8,7 +8,7 @@ module Index
   # where each element points to the first element in the row. +lexicon+
   # is the file containing the data.
   def self.index(lexicon, options = {}) 
-    options = {:sep => "\t|\\|", :case_sensitive => true}.merge(options)
+    options = {:sep => "\t", :sep2 => '\|', :case_sensitive => true}.merge(options)
 
 
     data = Open.to_hash(lexicon, options)

data/lib/rbbt/util/open.rb

@@ -17,10 +17,13 @@ module Open
   end
 
   def self.fields(line, sep = "\t")
-    chunks = line.chomp.split(/(#{sep})/).select{|c| c !~ /^#{sep}$/ }
+    line << sep
+    line << "PLACEHOLDER"
+    chunks = line.split(/(#{sep})/).select{|c| c !~ /^#{sep}$/ }
     if line =~ /#{sep}$/
       chunks << ""
     end
+    chunks.pop
     chunks
   end
 
@@ -101,7 +104,7 @@ module Open
 
       wait(options[:nice]) if options[:nice]
       tmp = TmpFile.tmp_file("open-")
-      `wget -O #{tmp} '#{url}' #{options[:quiet] ? '-q' : '' }`
+      `wget --user-agent=firefox -O #{tmp} '#{url}' #{options[:quiet] ? '-q' : '' }`
 
       if $?.success?
         if gziped(url)
@@ -197,7 +200,7 @@ module Open
     sep2    = options[:sep2]    || "|"
     single  = options[:single]  
     single  = false if single.nil?
-    flatten = options[:flatten] || single
+    flatten = options[:flatten]
     flatten = single if flatten.nil?
 
     extra = [extra] if extra && ! extra.is_a?( Array)
@@ -214,7 +217,7 @@ module Open
       next if exclude and exclude.call(l)
       next if select  and ! select.call(l)
 
-      row_fields = self.fields(l, sep)
+      row_fields = self.fields(l.chomp, sep)
       id = row_fields[native]
       next if id.nil? || id == ""
 

data/test/rbbt/sources/test_pubmed.rb

@@ -19,11 +19,21 @@ class TestPubMed < Test::Unit::TestCase
     pmids = ['16438716', 17204154]
     assert(PubMed.get_article(pmids)[pmid].title == "Discovering semantic features in the literature: a foundation for building functional associations.")
   end
-
+ 
+  def test_full_text
+    pmid = '16438716'
+    assert(PubMed.get_article(pmid).full_text =~ /Discovering/)
+  end
+ 
   def test_query
     assert(PubMed.query('chagoyen[All Fields] AND ("loattrfull text"[sb] AND hasabstract[text])').include? '16438716')
   end
 
+  def test_bibentry
+    assert("vazquez2008sent", PubMed::Article.make_bibentry('vazquez', 2008, "SENT: Semantic features in text"))
+    assert("vazquez2008aes", PubMed::Article.make_bibentry('vazquez', 2008, "An Example System"))
+  end
+
 end
 
 

data/test/rbbt/util/test_arrayHash.rb

@@ -89,7 +89,7 @@ class TestArrayHash < Test::Unit::TestCase
   end
 
   def test_case_insensitive
-     hash1 = {
+    hash1 = {
       'c' => ['A','B'],
       'd' => ['a','b'],
     }

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 1
   - 2
-  - 2
-  version: 1.2.2
+  - 5
+  version: 1.2.5
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -14,13 +14,14 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-05-27 00:00:00 +02:00
+date: 2010-10-22 00:00:00 +02:00
 default_executable: rbbt_config
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: rake
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -35,6 +36,7 @@ dependencies:
   name: simpleconsole
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -47,6 +49,7 @@ dependencies:
   name: stemmer
   prerelease: false
   requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -59,6 +62,7 @@ dependencies:
   name: progress-monitor
   prerelease: false
   requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -71,6 +75,7 @@ dependencies:
   name: simpleconsole
   prerelease: false
   requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -150,6 +155,33 @@ files:
 - tasks/install.rake
 - LICENSE
 - README.rdoc
+- test/test_rbbt.rb
+- test/rbbt/bow/test_bow.rb
+- test/rbbt/bow/test_classifier.rb
+- test/rbbt/bow/test_dictionary.rb
+- test/rbbt/sources/test_organism.rb
+- test/rbbt/sources/test_biomart.rb
+- test/rbbt/sources/test_pubmed.rb
+- test/rbbt/sources/test_polysearch.rb
+- test/rbbt/sources/test_biocreative.rb
+- test/rbbt/sources/test_entrez.rb
+- test/rbbt/sources/test_go.rb
+- test/rbbt/ner/test_rner.rb
+- test/rbbt/ner/test_dictionaryNER.rb
+- test/rbbt/ner/test_banner.rb
+- test/rbbt/ner/test_rnorm.rb
+- test/rbbt/ner/test_regexpNER.rb
+- test/rbbt/ner/test_abner.rb
+- test/rbbt/ner/rnorm/test_cue_index.rb
+- test/rbbt/ner/rnorm/test_tokens.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/test_arrayHash.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_index.rb
+- test/test_helper.rb
 has_rdoc: true
 homepage: http://github.com/mikisvaz/rbbt
 licenses: []
@@ -160,6 +192,7 @@ rdoc_options:
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
@@ -167,6 +200,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
@@ -176,7 +210,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.6
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: Bioinformatics and text mining toolbox