bio-kmer_counter 0.0.2

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

@@ -0,0 +1,12 @@
+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

@@ -0,0 +1,18 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem 'bio', ">= 1.4.2"
+gem 'progressbar', '>=0.11.0'
+gem 'parallel', '>=0.5.17'
+gem 'bio-logger', '>=1.0.1'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "jeweler", "~> 1.8.3"
+  gem "bundler", ">= 1.0.21"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2012 Ben J Woodcroft
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -0,0 +1,55 @@
+# bio-kmer_counter
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-kmer_counter.png)](http://travis-ci.org/wwood/bioruby-kmer_counter)
+
+bio-kmer_counter is a simple [biogem](http://biogem.info) for fingerprinting
+nucleotide sequences by counting the occurences of particular kmers in the
+sequence. The methodology is not new, for references see [Teeling et. al. 2004](http://www.biomedcentral.com/1471-2105/5/163). The default parameters are derived from the methods section of [Dick et. al. 2009](http://genomebiology.com/content/10/8/R85).
+
+This methodology is quite different to that of other software that counts
+kmer content with longer kmers, e.g. [khmer](https://github.com/ged-lab/khmer).
+Here only small kmers are intended (e.g. 1mer or 4mer).
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-kmer_counter
+```
+
+## Usage
+
+To analyse a fasta file (that contains one or more sequences in it) for 4-mer (tetranucleotide)
+content, reporting the fingerprint of 5kb windows in each sequence separately,
+plus the leftover part if it is longer than 2kb:
+
+```sh
+    kmer_counter.rb <fasta_file> >tetranucleotide_content.csv
+```
+
+The fingerprints are reported in percentages. Well, between 0 and 1, that is.
+From there it is up to you how to use the fingerprints, sorry.
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wwood/bioruby-kmer_counter
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+This software is currently unpublished, so please just cite the homepage (thanks!).
+
+Please also cite the tools upon which it is based, one of:
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Copyright
+
+Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
+

data/README.rdoc

@@ -0,0 +1,48 @@
+= bio-kmer_counter
+
+{<img
+src="https://secure.travis-ci.org/wwood/bioruby-kmer_counter.png"
+/>}[http://travis-ci.org/#!/wwood/bioruby-kmer_counter]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-kmer_counter
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-kmer_counter'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/wwood/bioruby-kmer_counter
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-kmer_counter
+
+== Copyright
+
+Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
+

data/Rakefile

@@ -0,0 +1,45 @@
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-kmer_counter"
+  gem.homepage = "http://github.com/wwood/bioruby-kmer_counter"
+  gem.license = "MIT"
+  gem.summary = %Q{A biogem for counting small kmers for fingerprinting nucleotide sequences}
+  gem.description = %Q{A biogem for counting small kmers for fingerprinting nucleotide sequences. See README for details.}
+  gem.email = "gmail.com after donttrustben"
+  gem.authors = ["Ben J Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-kmer_counter #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

@@ -0,0 +1 @@
+0.0.2

data/bin/kmer_counter.rb

@@ -0,0 +1,166 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'progressbar'
+require 'parallel'
+
+gempath = File.dirname(File.dirname(__FILE__))
+$: << File.join(gempath,'lib')
+require 'bio-kmer_counter'
+
+# Parse cmd line options
+USAGE = "Usage: kmer_counter.rb [-w window_size] [-W window_offset] [-m minimum_window_size] [--window-length] [-k kmer_length] [--contig-name] <fasta_filename>"
+options = {
+  :window_size => 5000,
+  :minimum_window_size => 2000,
+  :window_offset => 5000,
+  :kmer => 4,
+  :contig_name => false,
+  :sequence_length => false,
+  :logger => 'stderr',
+  :threads => 1,
+  :processes => 1,
+  :progressbar => true,
+}
+
+OptionParser.new do |opts|
+  opts.banner = USAGE
+
+  opts.on("-w", "--window-size SIZE", "Length of the window to be used [default #{options[:window_size]}]") do |v|
+    window = v.to_i
+    unless window > 0
+      raise Exception, "Unexpected window size specified: #{v} - it must be greater than 0 residues long!"
+    end
+    options[:window_size] = window
+    options[:window_offset] = window
+  end
+
+  opts.on("-W", "--window-offset SIZE", "Length of the offset between windows [default #{options[:window_offset]}]") do |v|
+    offset = v.to_i
+    unless offset > 0
+      offset = options[:window_isze]
+    end
+    options[:window_offset] = offset
+  end
+
+  opts.on("-m", "--minimum-window-size SIZE", "Length of the minimum window to be used [default #{options[:minimum_window_size]}]") do |v|
+    window = v.to_i
+    unless window > 0
+      raise Exception, "Unexpected minimum window size specified: #{v} - it must be greater than 0 residues long!"
+    end
+    options[:minimum_window_size] = window
+  end
+
+  opts.on("-k", "--kmer-length SIZE", "Length of the kmer to be used [default #{options[:kmer]}]") do |v|
+    window = v.to_i
+    unless window > 0
+      raise Exception, "Unexpected minimum window size specified: #{v} - it must be greater than 0 residues long!"
+    end
+    options[:kmer] = window
+  end
+
+  opts.on("-n", "--contig-name", "Output the contig name, on top of the default contig chunk name [default: #{options[:contig_name]}]") do |v|
+    options[:contig_name] = true
+  end
+
+  opts.on("-l", "--window-length", "print the length of the window in the output [default #{options[:sequence_length]}]") do |v|
+    options[:sequence_length] = true
+  end
+  
+  opts.on("-p", "--processes NUM_PROCESSES", "Use this many processes. Currently setting multiple processes means there is no progress bar [default #{options[:processes]}]") do |v|
+    options[:processes] = v.to_i
+    if options[:processes] < 1
+      raise "Unexpected number of processes specified (after converting to integer) - '#{options[:processes]}'"
+    end
+  end
+  
+  opts.on("-t", "--threads NUM_THREADS", "Use this many threads. This currently only makes sense if you are running on JRuby, since the standard MRI ruby 1.9 can't use multiple cores. Maybe use --processes instead? [default #{options[:threads]}]") do |v|
+    options[:threads] = v.to_i
+    if options[:threads] < 1
+      raise "Unexpected number of threads specified (after converting to integer) - '#{options[:threads]}'"
+    end
+  end
+  
+  
+  # logger options
+  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") do |q|
+    Bio::Log::CLI.trace('error')
+  end
+  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") do | name |
+    options[:logger] = name
+  end
+  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG") do | s |
+    Bio::Log::CLI.trace(s)
+  end
+end.parse!
+if ARGV.length != 1
+  $stderr.puts o
+  exit 1
+end
+# multiple processes doesn't work well with ProgressBar
+options[:progressbar] = false if options[:processes] != 1
+
+LOG_NAME = 'bio-kmer_counter'
+Bio::Log::CLI.logger(options[:logger]) #bio-logger defaults to STDERR not STDOUT, I disagree
+log = Bio::Log::LoggerPlus.new(LOG_NAME)
+Bio::Log::CLI.configure(LOG_NAME)
+
+
+# Print headers
+print "ID\t"
+print Bio::Sequence::Kmer.merge_down_to_lowest_lexigraphical_form(Bio::Sequence::Kmer.empty_full_kmer_hash(options[:kmer])).keys.join("\t")
+print "\tWindowLength" if options[:sequence_length]
+print "\tcontig" if options[:contig_name]
+puts
+
+orig = Bio::Sequence::Kmer.empty_full_kmer_hash(options[:kmer])
+process_window = lambda do |window,kmer,sequence_name,contig_name|
+  counts = orig.dup
+  num_kmers_counted = 0
+  
+  window.window_search(options[:kmer],1) do |tetranucleotide|
+    str = tetranucleotide.to_s
+    next unless str.gsub(/[ATGC]+/,'') == ''
+    num_kmers_counted += 1
+    counts[str]+=1
+    #counts[Bio::Sequence::NA.new(tetranucleotide).lowest_lexigraphical_form.to_s.upcase] += 1
+  end
+  
+  # Merge everything into lowest lexigraphical form
+  new_counts = Bio::Sequence::Kmer.merge_down_to_lowest_lexigraphical_form counts
+  
+  if num_kmers_counted == 0
+    log.warn "Skipping window #{sequence_name} because few/none ATGC's were detected (was it all N's?)"
+  else
+    print "#{sequence_name}"
+    new_counts.keys.sort.each do |tetramer|
+      print "\t#{new_counts[tetramer].to_f/num_kmers_counted}"
+    end
+    print "\t#{window.length}" if options[:sequence_length]
+    print "\t#{contig_name}" if options[:contig_name]
+    puts
+  end
+end
+
+fasta_filename = ARGV[0]
+progress = nil
+progress = ProgressBar.new('kmer_counter', `grep -c '>' '#{fasta_filename}'`.to_i) if options[:progressbar]
+ff = Bio::FlatFile.open(fasta_filename) 
+Parallel.each(ff, :in_processes => options[:processes], :threads => options[:threads]) do |sequence|
+#ff.each do |sequence|
+  window_counter = 0
+  sequence.seq.window_search(options[:window_size],options[:window_offset]) do |window|
+    process_window.call(window, options[:kmer], "#{sequence.definition}_#{window_counter}",sequence.definition)
+    window_counter += 1
+  end
+  leftover_length = sequence.seq.length % options[:window_size]
+  if leftover_length >= options[:minimum_window_size]
+    process_window.call(
+    sequence.seq[sequence.seq.length-leftover_length..sequence.seq.length],
+    options[:kmer], "#{sequence.definition}_leftover_#{window_counter}",sequence.definition)
+  end
+  progress.inc if options[:progressbar]
+end
+progress.finish if options[:progressbar]
+
+

data/lib/bio-kmer_counter.rb

@@ -0,0 +1,16 @@
+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-logger'
+Bio::Log::LoggerPlus.new('bio-kmer_counter')
+
+require 'bio'
+require 'bio-kmer_counter/kmer_counter.rb'
+

data/lib/bio-kmer_counter/kmer_counter.rb

@@ -0,0 +1,45 @@
+# Initialise the hash of the different
+module Bio
+  class Sequence
+    class NA
+      # Return the current object or its reverse complement, whichever
+      # has the sequence that comes first in lexigraphical (alphabetical)
+      # order
+      def lowest_lexigraphical_form
+        rev = self.reverse_complement
+        to_s < rev.to_s ? self : rev
+      end
+    end
+
+    class Kmer
+      def self.empty_full_kmer_hash(k=4)
+        return @empty_full_hash.dup unless @empty_full_hash.nil?
+        
+        counts = {}
+                
+        ordered_possibilities = %w(A T C G)
+        keys = ordered_possibilities
+        (k-1).times do
+          keys = keys.collect{|k| ordered_possibilities.collect{|n| "#{k}#{n}"}.flatten}.flatten
+        end
+        
+        keys.each do |key|
+          counts[key] = 0
+        end
+        counts
+      end
+      
+      def self.merge_down_to_lowest_lexigraphical_form(hash)
+        keys = empty_full_kmer_hash.keys
+        
+        new_hash = {}
+        hash.each do |kmer, count|
+          key = Bio::Sequence::NA.new(kmer).lowest_lexigraphical_form.to_s.upcase
+          new_hash[key] ||= 0
+          new_hash[key] += count
+        end
+        return new_hash
+      end
+    end
+  end
+end

data/test/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-kmer_counter'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-kmer_counter.rb

@@ -0,0 +1,98 @@
+require 'helper'
+require 'tempfile'
+require 'open3'
+
+class TestBioKmerCounter < Test::Unit::TestCase
+  should 'test_lowest_lexigraphical_form' do
+    assert_equal Bio::Sequence::NA.new('AA'), Bio::Sequence::NA.new('AA').lowest_lexigraphical_form
+    assert_equal Bio::Sequence::NA.new('AA'), Bio::Sequence::NA.new('TT').lowest_lexigraphical_form
+    assert_equal Bio::Sequence::NA.new('AG'), Bio::Sequence::NA.new('CT').lowest_lexigraphical_form
+  end
+  
+  should 'test_empty_full_kmer_hash' do
+    answer = {}; %w(A C G T).each{|k| answer[k] = 0}
+    assert_equal answer, Bio::Sequence::Kmer.empty_full_kmer_hash(1)
+  end
+  
+  should 'test merge down' do
+    answer = {}; %w(A C).each{|k| answer[k] = 0}
+    full = Bio::Sequence::Kmer.empty_full_kmer_hash(1)
+    assert_equal answer, Bio::Sequence::Kmer.merge_down_to_lowest_lexigraphical_form(full)
+    full = Bio::Sequence::Kmer.empty_full_kmer_hash #defaults to kmer hash length 4
+    assert_equal 136, Bio::Sequence::Kmer.merge_down_to_lowest_lexigraphical_form(full).length
+  end
+  
+  def script_path
+    File.join(File.dirname(__FILE__),'..','bin','kmer_counter.rb')
+  end
+  
+  should 'test_running1' do
+    Tempfile.open('one') do |tempfile|
+      tempfile.puts '>one'
+      tempfile.puts 'ACAGT'
+      tempfile.close
+
+      assert_equal "ID\tA\tC\none_0\t0.6\t0.4\n", `#{script_path} -w 5 -k 1 #{tempfile.path}`
+    end
+  end
+  
+  should 'not whack out when there isnt any sequence to count' do
+    Tempfile.open('one') do |tempfile|
+      tempfile.puts '>one'
+      tempfile.puts 'NNNNN'
+      tempfile.close
+
+      assert_equal "ID\tA\tC\n", `#{script_path} -w 5 -k 1 #{tempfile.path}`
+    end
+  end
+  
+  should 'give correct increments in window numbering' do
+    Tempfile.open('one') do |tempfile|
+      tempfile.puts '>one'
+      tempfile.puts 'ATGCATGCAT' #10 letters long
+      tempfile.close
+      
+      expected = "ID\tA\tC\n"+
+      "one_0\t0.5\t0.5\n"+
+      "one_1\t0.5\t0.5\n"+
+      "one_leftover_2\t1.0\t0.0\n"
+
+      assert_equal expected, `#{script_path} -w 4 -k 1 -m 2 #{tempfile.path}`
+    end
+  end
+  
+  should "not give a progressbar with multiple processes" do
+    Tempfile.open('one') do |tempfile|
+      tempfile.puts '>one'
+      tempfile.puts 'ATGCATGCAT' #10 letters long
+      tempfile.close
+      
+      expected = ["ID\tA\tC\n",
+      "one_0\t0.5\t0.5\n",
+      "one_1\t0.5\t0.5\n",
+      "one_leftover_2\t1.0\t0.0\n"]
+
+      # execute command and capture both stdout, and stderr
+      # no extra processes
+      command = "#{script_path} -w 4 -k 1 -m 2 #{tempfile.path}"
+      Open3.popen3(command) do |stdin, stdout, stderr|
+        result = stdout.readlines # convert to string?
+        error  = stderr.readlines
+        
+        assert_not_equal [], error
+        assert_equal expected, result
+      end
+      
+      # execute command and capture both stdout, and stderr
+      # extra processes
+      command = "#{script_path} -p 2 -w 4 -k 1 -m 2 #{tempfile.path}"
+      Open3.popen3(command) do |stdin, stdout, stderr|
+        result = stdout.readlines # convert to string?
+        error  = stderr.readlines
+        
+        assert_equal [], error
+        assert_equal expected, result
+      end
+    end
+  end
+end

metadata

@@ -0,0 +1,218 @@
+--- !ruby/object:Gem::Specification 
+name: bio-kmer_counter
+version: !ruby/object:Gem::Version 
+  hash: 27
+  prerelease: 
+  segments: 
+  - 0
+  - 0
+  - 2
+  version: 0.0.2
+platform: ruby
+authors: 
+- Ben J Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2012-06-08 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 1
+        - 4
+        - 2
+        version: 1.4.2
+  version_requirements: *id001
+  name: bio
+  prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency 
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 51
+        segments: 
+        - 0
+        - 11
+        - 0
+        version: 0.11.0
+  version_requirements: *id002
+  name: progressbar
+  prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency 
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 41
+        segments: 
+        - 0
+        - 5
+        - 17
+        version: 0.5.17
+  version_requirements: *id003
+  name: parallel
+  prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency 
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 21
+        segments: 
+        - 1
+        - 0
+        - 1
+        version: 1.0.1
+  version_requirements: *id004
+  name: bio-logger
+  prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency 
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id005
+  name: shoulda
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency 
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 31
+        segments: 
+        - 3
+        - 12
+        version: "3.12"
+  version_requirements: *id006
+  name: rdoc
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency 
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 49
+        segments: 
+        - 1
+        - 8
+        - 3
+        version: 1.8.3
+  version_requirements: *id007
+  name: jeweler
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency 
+  requirement: &id008 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 61
+        segments: 
+        - 1
+        - 0
+        - 21
+        version: 1.0.21
+  version_requirements: *id008
+  name: bundler
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency 
+  requirement: &id009 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 31
+        segments: 
+        - 3
+        - 12
+        version: "3.12"
+  version_requirements: *id009
+  name: rdoc
+  prerelease: false
+  type: :development
+description: A biogem for counting small kmers for fingerprinting nucleotide sequences. See README for details.
+email: gmail.com after donttrustben
+executables: 
+- kmer_counter.rb
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.md
+- README.rdoc
+files: 
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/kmer_counter.rb
+- lib/bio-kmer_counter.rb
+- lib/bio-kmer_counter/kmer_counter.rb
+- test/helper.rb
+- test/test_bio-kmer_counter.rb
+homepage: http://github.com/wwood/bioruby-kmer_counter
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: A biogem for counting small kmers for fingerprinting nucleotide sequences
+test_files: []
+