chipgps 0.1.1

data/.document

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

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+end

data/Gemfile.lock

@@ -0,0 +1,18 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.9.2)
+    rcov (0.9.11)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0.0)
+  jeweler (~> 1.6.4)
+  rcov

data/LICENSE.txt

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+Copyright (c) 2011 Itoshi NIKAIDO
+
+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.rdoc

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+= chipgps
+
+ChIPgps is an open source Ruby library for parsing result files of the Genome Positioning System which is a software tool to study protein-DNA interaction using ChIP-Seq data. 
+
+== Copyright
+
+Copyright (c) 2011 Itoshi NIKAIDO <dritoshi@gmail.com>. See LICENSE.txt for further details.

data/Rakefile

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+# 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 = "chipgps"
+  gem.homepage = "http://github.com/dritoshi/chipgps"
+  gem.license = "MIT"
+  gem.summary = %Q{Parser for the Genome Positioning System}
+  gem.description = %Q{ChIPgps is an open source Ruby library for parsing result files of the Genome Positioning System which is a software tool to study protein-DNA interaction using ChIP-Seq data.}
+  gem.email = "dritoshi@gmail.com"
+  gem.authors = ["Itoshi NIKAIDO"]
+  # 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
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "chipgps #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.1

data/chipgps.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "chipgps"
+  s.version = "0.1.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Itoshi NIKAIDO"]
+  s.date = "2011-10-20"
+  s.description = "ChIPgps is an open source Ruby library for parsing result files of the Genome Positioning System which is a software tool to study protein-DNA interaction using ChIP-Seq data."
+  s.email = "dritoshi@gmail.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "chipgps.gemspec",
+    "lib/chipgps.rb",
+    "sample/Demo_2_GPS_significant.txt",
+    "sample/gps2bet.rb",
+    "test/helper.rb",
+    "test/test_chipgps.rb"
+  ]
+  s.homepage = "http://github.com/dritoshi/chipgps"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.11"
+  s.summary = "Parser for the Genome Positioning System"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+    else
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+  end
+end
+

data/lib/chipgps.rb

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+class Chipgps
+
+  class Event
+    def initialize(line)
+      @line = line
+    end
+    attr_reader   :line
+    attr_accessor :chr, :bp, :ip
+    attr_accessor :ip_binding_present, :ip_binding_strength, :control_binding_strength,
+      :fold_enrichment, :mlog10_qvalue, :mlog10_pvalue, :ipvsEMP_KLD, :ipvsCTR_KLD
+
+  end  # End of Event class
+
+  class Search < Event
+    def initialize(line, options = {})
+      @line = line
+      @event_number     = options[:event]
+      @condition_number = options[:condition]
+
+      parse
+    end
+
+    def cleanup(line)
+      new_line = line.strip
+      new_line.chomp!
+      new_line.gsub!(/ +/, "")
+      return new_line
+    end
+
+    def parse
+      # condition_number start from 0.
+
+      line = cleanup(@line)
+      f = line.split(/\t/)
+
+      @chr = f[0].split(/:/)[0]
+      @bp  = f[0].split(/:/)[1].to_i
+      @ip  = f[1].to_f
+
+      @ip_binding_present       = f[(@condition_number * 9 + 2) + 0].to_i 
+      @ip_binding_strength      = f[(@condition_number * 9 + 2) + 1].to_f  
+      @control_binding_strength = f[(@condition_number * 9 + 2) + 2].to_f  
+      @fold_enrichment          = f[(@condition_number * 9 + 2) + 3].to_f  
+      @mlog10_qvalue            = f[(@condition_number * 9 + 2) + 4].to_f  
+      @mlog10_pvalue            = f[(@condition_number * 9 + 2) + 5].to_f  
+      @ipvsEMP_KLD              = f[(@condition_number * 9 + 2) + 6].to_f  
+      @ipvsCTR_KLD              = f[(@condition_number * 9 + 2) + 7].to_f  
+    end
+
+  end  # End of Search class
+
+  def initialize(file)
+    @gps_out_file = file
+    @lines = File.open(@gps_out_file).readlines
+    @header = @lines.shift
+
+    @num_of_conditions = num_of_conditions
+    @num_of_events     = num_of_events
+  end
+  attr_reader :header
+
+  def num_of_conditions
+    f = @lines[0].split(/\t/)
+    num_of_conditions = (f.size - 2) / 9  # each condition has 9 cols
+    # pp f.size
+    return num_of_conditions
+  end
+
+  def num_of_events
+    return @lines.size
+  end
+
+  def each_by_condition(condition_id) # condition_id starts from 0
+    @lines.each_with_index do |line, idx|
+      yield Chipgps::Search.new(line, {:condition => condition_id, :event => idx})
+    end
+  end
+
+end

data/sample/Demo_2_GPS_significant.txt

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+Position	     IP	Demo_Day0_Present	Demo_Day0_IP	Demo_Day0_Control	Demo_Day0_   Fold	Demo_Day0_Q_-lg10	Demo_Day0_P_-lg10	IPvsEMP	Demo_Day0_IPvsCTR		Demo_Day1_Present	Demo_Day1_IP	Demo_Day1_Control	Demo_Day1_   Fold	Demo_Day1_Q_-lg10	Demo_Day1_P_-lg10	IPvsEMP	Demo_Day1_IPvsCTR		Demo_Day2_Present	Demo_Day2_IP	Demo_Day2_Control	Demo_Day2_   Fold	Demo_Day2_Q_-lg10	Demo_Day2_P_-lg10	IPvsEMP	Demo_Day2_IPvsCTR		Demo_Day3_Present	Demo_Day3_IP	Demo_Day3_Control	Demo_Day3_   Fold	Demo_Day3_Q_-lg10	Demo_Day3_P_-lg10	IPvsEMP	Demo_Day3_IPvsCTR		Demo_Day4_Present	Demo_Day4_IP	Demo_Day4_Control	Demo_Day4_   Fold	Demo_Day4_Q_-lg10	Demo_Day4_P_-lg10	IPvsEMP	Demo_Day4_IPvsCTR	
+1:3390040	   19.0	0	    1.0	    1.4	    0.7	  -0.07	 999.00	  -4.00	   0.00		1	   10.0	    1.6	    6.3	   2.78	 999.00	  -1.07	   0.00		0	    2.0	    2.1	    1.0	  -0.06	 999.00	  -3.59	   0.00		0	    5.0	    2.7	    1.8	   0.17	 999.00	  -0.84	   0.00		0	    1.0	    2.1	    0.5	  -0.06	 999.00	  -4.00	   0.00	
+1:3667860	   16.2	0	    2.0	    1.4	    1.4	  -0.02	 999.00	  -0.71	   0.00		0	    2.0	    1.6	    1.3	  -0.02	 999.00	  -2.45	   0.00		0	    2.0	    1.3	    1.6	  -0.01	 999.00	  -3.21	   0.00		1	    9.2	    1.9	    4.8	   2.21	 999.00	  -0.91	   0.00		0	    1.0	    2.2	    0.4	  -0.05	 999.00	  -4.00	   0.00	
+1:3722075	   33.0	0	    7.0	    1.4	    4.8	   1.37	 999.00	  -0.94	   0.00		1	    9.0	    1.5	    6.2	   2.40	 999.00	  -0.83	   0.00		0	    7.0	    1.3	    5.5	   1.39	 999.00	  -0.93	   0.00		0	    5.0	    2.1	    2.4	   0.33	 999.00	  -0.82	   0.00		0	    5.0	    1.8	    2.8	   0.44	 999.00	  -1.60	   0.00	
+1:3985092	   26.0	0	    2.0	    1.4	    1.4	  -0.02	 999.00	  -2.98	   0.00		0	    5.0	    1.6	    3.1	   0.52	 999.00	  -0.70	   0.00		1	    9.0	    1.5	    6.1	   2.17	 999.00	  -1.42	   0.00		0	    5.0	    1.6	    3.1	   0.53	 999.00	  -0.81	   0.00		0	    5.0	    1.4	    3.5	   0.61	 999.00	  -0.84	   0.00	
+1:4005442	   24.0	0	    6.0	    1.4	    4.2	   0.96	 999.00	  -0.72	   0.00		0	    4.0	    2.1	    1.9	   0.13	 999.00	  -0.92	   0.00		0	    2.0	    1.6	    1.3	  -0.03	 999.00	  -0.72	   0.00		0	    2.0	    2.1	    0.9	  -0.04	 999.00	  -0.83	   0.00		1	   10.0	    1.4	    7.0	   3.03	 999.00	  -0.77	   0.00	
+1:4083105	   39.6	0	   10.0	    2.7	    3.6	   1.46	 999.00	  -1.16	   0.00		1	   12.8	    2.2	    5.8	   3.64	 999.00	  -0.97	   0.00		0	    4.0	    3.0	    1.3	  -0.02	 999.00	  -1.52	   0.00		0	    5.9	    3.5	    1.7	   0.17	 999.00	  -1.34	   0.00		0	    6.9	    2.1	    3.3	   0.85	 999.00	  -0.79	   0.00	
+1:4367903	   19.0	1	    9.0	    1.4	    6.2	   2.49	 999.00	  -1.17	   0.00		0	    4.0	    1.5	    2.8	   0.32	 999.00	  -0.79	   0.00		0	    1.0	    1.3	    0.8	  -0.07	 999.00	  -4.00	   0.00		0	    4.0	    1.5	    2.6	   0.30	 999.00	  -1.07	   0.00		0	    1.0	    1.4	    0.7	  -0.07	 999.00	  -4.00	   0.00	
+1:4373820	   30.0	0	    7.0	    1.4	    4.8	   1.37	 999.00	  -0.80	   0.00		0	    5.0	    1.5	    3.4	   0.58	 999.00	  -0.96	   0.00		0	    4.0	    1.3	    3.1	   0.34	 999.00	  -0.86	   0.00		0	    5.0	    1.5	    3.3	   0.56	 999.00	  -1.06	   0.00		1	    9.0	    1.4	    6.3	   2.40	 999.00	  -1.18	   0.00	
+1:4443835	   31.0	0	    6.0	    2.1	    2.9	   0.57	 999.00	  -0.86	   0.00		0	    1.0	    1.8	    0.6	  -0.05	 999.00	  -4.00	   0.00		0	    8.0	    1.4	    5.7	   1.73	 999.00	  -0.75	   0.00		1	   10.0	    1.9	    5.2	   2.21	 999.00	  -0.90	   0.00		0	    6.0	    1.4	    4.2	   0.95	 999.00	  -1.23	   0.00	
+1:4527690	   22.0	0	    3.9	    5.4	    0.7	  -0.06	 999.00	  -0.71	   0.00		0	    2.0	    2.7	    0.8	  -0.06	 999.00	  -2.07	   0.00		0	    3.7	    2.1	    1.8	   0.12	 999.00	  -0.99	   0.00		1	   10.6	    2.2	    4.7	   2.31	 999.00	  -1.17	   0.00		0	    1.8	    3.7	    0.5	  -0.06	 999.00	  -1.32	   0.00	

data/sample/gps2bet.rb

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+#!/usr/bin/env ruby
+
+$LOAD_PATH.push("../lib")
+
+require 'pp'
+require 'chipgps'
+
+#gps_out_file = ARGV.shift
+gps_out_file = "Demo_2_GPS_significant.txt"
+gps = Chipgps.new(gps_out_file)
+
+for condition_id in 0..(gps.num_of_conditions-1)
+
+  exp_name = "Demo_Day" + condition_id.to_s
+  header = "track name=#{exp_name} description=\"GPS: #{exp_name}\" useScore=0"
+  puts header
+  gps.each_by_condition(condition_id) do |event|
+
+    # output (bed format)
+    puts [
+      "chr" + event.chr,                # chr
+      event.bp,                         # start
+      event.bp + 1,                     # end
+      [exp_name, event.chr, event.bp.to_s].join(":"),  # name
+      event.fold_enrichment             # score
+    ].join("\t")
+
+  end
+end

data/test/helper.rb

@@ -0,0 +1,17 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'chipgps'
+
+class Test::Unit::TestCase
+end

data/test/test_chipgps.rb

@@ -0,0 +1,177 @@
+require 'helper'
+
+class Test_Chipgps < Test::Unit::TestCase
+
+  def setup
+    @gps_out_file = Dir.pwd + "/sample/Demo_2_GPS_significant.txt"
+    @gps = Chipgps.new(@gps_out_file)
+
+    @event_c0_e0 = nil
+    @gps.each_by_condition(0) do |event|
+      @event_c0_e0 = event
+      break
+    end
+
+    @event_c2_e0 = nil
+    @gps.each_by_condition(2) do |event|
+      @event_c2_e0 = event
+      break
+    end
+  end
+
+  def test_open_gps_out_file
+    assert(FileTest.exist?(@gps_out_file))
+  end
+
+  def test_gps_num_of_conditions
+    assert_equal(5, @gps.num_of_conditions)
+  end
+
+  def test_gps_num_of_events
+    assert_equal(11-1, @gps.num_of_events)
+  end
+
+  # event = 0, condition = 0
+  def test_gps_each_by_condition_with_c0_e0
+    assert_equal("1",     @event_c0_e0.chr)
+    assert_equal(3390040, @event_c0_e0.bp)
+    assert_equal(19.0,    @event_c0_e0.ip)
+    assert_equal(0,       @event_c0_e0.ip_binding_present)
+    assert_equal(1.0,     @event_c0_e0.ip_binding_strength)
+    assert_equal(1.4,     @event_c0_e0.control_binding_strength)
+    assert_equal(0.7,     @event_c0_e0.fold_enrichment)
+    assert_equal(-0.07,   @event_c0_e0.mlog10_qvalue) 
+    assert_equal(999.00,  @event_c0_e0.mlog10_pvalue)
+    assert_equal(-4.00,   @event_c0_e0.ipvsEMP_KLD)
+    assert_equal(0.00,    @event_c0_e0.ipvsCTR_KLD)
+  end
+
+  # event = 0, condition = 2
+  def test_gps_each_by_condition_with_c2_e0
+    assert_equal("1",     @event_c2_e0.chr)
+    assert_equal(3390040, @event_c2_e0.bp)
+    assert_equal(19.0,    @event_c2_e0.ip)
+    assert_equal(0,       @event_c2_e0.ip_binding_present)
+    assert_equal(2.0,     @event_c2_e0.ip_binding_strength)
+    assert_equal(2.1,     @event_c2_e0.control_binding_strength)
+    assert_equal(1.0,     @event_c2_e0.fold_enrichment)
+    assert_equal(-0.06,   @event_c2_e0.mlog10_qvalue) 
+    assert_equal(999.00,  @event_c2_e0.mlog10_pvalue)
+    assert_equal(-3.59,   @event_c2_e0.ipvsEMP_KLD)
+    assert_equal(0.00,    @event_c2_e0.ipvsCTR_KLD)
+  end
+
+end
+
+class Test_Chipgps::Event < Test::Unit::TestCase
+  def setup
+    @gps_out_file = Dir.pwd + "/sample/Demo_2_GPS_significant.txt"
+    @line = File.open(@gps_out_file).readlines[1]
+    @event = Chipgps::Event.new(@line)
+  end
+end
+
+class Test_Chipgps::Search < Test::Unit::TestCase
+  def setup
+    @gps_out_file = Dir.pwd + "/sample/Demo_2_GPS_significant.txt"
+    @line  = File.open(@gps_out_file).readlines[1]
+
+    event_number     = 0
+    condition_number = 0
+    @event = Chipgps::Search.new(@line, {:event => event_number, :condition => condition_number})
+
+    event_number     = 0
+    condition_number = 2
+    @event_0_2 = Chipgps::Search.new(@line, {:event => event_number, :condition => condition_number})
+  end
+
+  # start: event = 0, condition = 0
+  def test_gps_search_search_chr
+    assert_equal("1", @event.chr)
+  end
+  def test_gps_search_search_bp
+    assert_equal(3390040, @event.bp)
+  end
+  def test_gps_search_search_ip
+    assert_equal(19.0, @event.ip)
+  end
+
+  def test_gps_search_search_ip_binding_present
+    assert_equal(0,      @event.ip_binding_present)
+  end
+
+  def test_gps_search_search_ip_binding_strength
+    assert_equal(1.0,    @event.ip_binding_strength)
+  end
+
+  def test_gps_search_search_control_binding_strength
+    assert_equal(1.4,    @event.control_binding_strength)
+  end
+
+  def test_gps_search_search_fold_enrichment
+    assert_equal(0.7,    @event.fold_enrichment)
+  end
+
+  def test_gps_search_search_mlog10_qvalue 
+    assert_equal(-0.07,  @event.mlog10_qvalue) 
+  end
+
+  def test_gps_search_search_mlog10_pvalue
+    assert_equal(999.00, @event.mlog10_pvalue)
+  end
+
+  def test_gps_search_search_ipvsEMP_KLD
+    assert_equal(-4.00,  @event.ipvsEMP_KLD)
+  end
+
+  def test_gps_search_search_ipvsCTR_KLD
+    assert_equal(0.00,   @event.ipvsCTR_KLD)
+  end
+  # end: event = 0, condition = 0
+
+
+  # start: event = 0, condition = 2
+  def test_gps_search_search_chr_by_evnet_0_2
+    assert_equal("1", @event_0_2.chr)
+  end
+  def test_gps_search_search_bp_by_evnet_0_2
+    assert_equal(3390040, @event_0_2.bp)
+  end
+  def test_gps_search_search_ip_by_evnet_0_2
+    assert_equal(19.0, @event_0_2.ip)
+  end
+
+  def test_gps_search_search_ip_binding_present_by_evnet_0_2
+    assert_equal(0,      @event_0_2.ip_binding_present)
+  end
+
+  def test_gps_search_search_ip_binding_strength_by_evnet_0_2
+    assert_equal(2.0,    @event_0_2.ip_binding_strength)
+  end
+
+  def test_gps_search_search_control_binding_strength_by_evnet_0_2
+    assert_equal(2.1,    @event_0_2.control_binding_strength)
+  end
+
+  def test_gps_search_search_fold_enrichment_by_evnet_0_2
+    assert_equal(1.0,    @event_0_2.fold_enrichment)
+  end
+
+  def test_gps_search_search_mlog10_qvalue_by_evnet_0_2
+    assert_equal(-0.06,  @event_0_2.mlog10_qvalue) 
+  end
+
+  def test_gps_search_search_mlog10_pvalue_by_evnet_0_2
+    assert_equal(999.00, @event_0_2.mlog10_pvalue)
+  end
+
+  def test_gps_search_search_ipvsEMP_KLD_by_evnet_0_2
+    assert_equal(-3.59,  @event_0_2.ipvsEMP_KLD)
+  end
+
+  def test_gps_search_search_ipvsCTR_KLD_by_evnet_0_2
+    assert_equal(0.00,   @event_0_2.ipvsCTR_KLD)
+  end
+  # end: event = 0, condition = 2
+
+end

metadata

@@ -0,0 +1,102 @@
+--- !ruby/object:Gem::Specification 
+name: chipgps
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.1.1
+platform: ruby
+authors: 
+- Itoshi NIKAIDO
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-10-20 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.6.4
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+description: ChIPgps is an open source Ruby library for parsing result files of the Genome Positioning System which is a software tool to study protein-DNA interaction using ChIP-Seq data.
+email: dritoshi@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- chipgps.gemspec
+- lib/chipgps.rb
+- sample/Demo_2_GPS_significant.txt
+- sample/gps2bet.rb
+- test/helper.rb
+- test/test_chipgps.rb
+homepage: http://github.com/dritoshi/chipgps
+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: 1295371598341010762
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.11
+signing_key: 
+specification_version: 3
+summary: Parser for the Genome Positioning System
+test_files: []
+