chipgps 0.1.1
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- data/.document +5 -0
- data/Gemfile +12 -0
- data/Gemfile.lock +18 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +7 -0
- data/Rakefile +53 -0
- data/VERSION +1 -0
- data/chipgps.gemspec +58 -0
- data/lib/chipgps.rb +79 -0
- data/sample/Demo_2_GPS_significant.txt +11 -0
- data/sample/gps2bet.rb +29 -0
- data/test/helper.rb +17 -0
- data/test/test_chipgps.rb +177 -0
- metadata +102 -0
data/.document
ADDED
data/Gemfile
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source "http://rubygems.org"
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# Add dependencies required to use your gem here.
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# Example:
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# gem "activesupport", ">= 2.3.5"
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# Add dependencies to develop your gem here.
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# Include everything needed to run rake, tests, features, etc.
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group :development do
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gem "bundler", "~> 1.0.0"
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gem "jeweler", "~> 1.6.4"
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gem "rcov", ">= 0"
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end
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data/Gemfile.lock
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GEM
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remote: http://rubygems.org/
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specs:
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git (1.2.5)
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jeweler (1.6.4)
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bundler (~> 1.0)
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git (>= 1.2.5)
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rake
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rake (0.9.2)
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rcov (0.9.11)
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PLATFORMS
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ruby
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DEPENDENCIES
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bundler (~> 1.0.0)
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jeweler (~> 1.6.4)
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rcov
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data/LICENSE.txt
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Copyright (c) 2011 Itoshi NIKAIDO
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.rdoc
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= chipgps
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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.
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== Copyright
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Copyright (c) 2011 Itoshi NIKAIDO <dritoshi@gmail.com>. See LICENSE.txt for further details.
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data/Rakefile
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# encoding: utf-8
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require 'rubygems'
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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end
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require 'rake'
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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# gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
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gem.name = "chipgps"
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gem.homepage = "http://github.com/dritoshi/chipgps"
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gem.license = "MIT"
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gem.summary = %Q{Parser for the Genome Positioning System}
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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.}
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gem.email = "dritoshi@gmail.com"
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gem.authors = ["Itoshi NIKAIDO"]
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# dependencies defined in Gemfile
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end
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Jeweler::RubygemsDotOrgTasks.new
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require 'rake/testtask'
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Rake::TestTask.new(:test) do |test|
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test.libs << 'lib' << 'test'
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test.pattern = 'test/**/test_*.rb'
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test.verbose = true
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end
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require 'rcov/rcovtask'
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Rcov::RcovTask.new do |test|
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test.libs << 'test'
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test.pattern = 'test/**/test_*.rb'
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test.verbose = true
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test.rcov_opts << '--exclude "gems/*"'
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end
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task :default => :test
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require 'rake/rdoctask'
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Rake::RDocTask.new do |rdoc|
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version = File.exist?('VERSION') ? File.read('VERSION') : ""
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "chipgps #{version}"
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rdoc.rdoc_files.include('README*')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/VERSION
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0.1.1
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data/chipgps.gemspec
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# Generated by jeweler
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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Gem::Specification.new do |s|
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s.name = "chipgps"
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s.version = "0.1.1"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Itoshi NIKAIDO"]
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s.date = "2011-10-20"
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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."
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s.email = "dritoshi@gmail.com"
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s.extra_rdoc_files = [
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"LICENSE.txt",
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"README.rdoc"
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]
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s.files = [
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".document",
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"Gemfile",
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"Gemfile.lock",
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"LICENSE.txt",
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"README.rdoc",
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"Rakefile",
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"VERSION",
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"chipgps.gemspec",
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"lib/chipgps.rb",
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"sample/Demo_2_GPS_significant.txt",
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"sample/gps2bet.rb",
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"test/helper.rb",
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"test/test_chipgps.rb"
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]
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s.homepage = "http://github.com/dritoshi/chipgps"
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s.licenses = ["MIT"]
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s.require_paths = ["lib"]
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s.rubygems_version = "1.8.11"
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s.summary = "Parser for the Genome Positioning System"
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if s.respond_to? :specification_version then
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s.specification_version = 3
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if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
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s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
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s.add_development_dependency(%q<rcov>, [">= 0"])
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else
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s.add_dependency(%q<bundler>, ["~> 1.0.0"])
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s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
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s.add_dependency(%q<rcov>, [">= 0"])
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end
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else
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s.add_dependency(%q<bundler>, ["~> 1.0.0"])
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s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
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s.add_dependency(%q<rcov>, [">= 0"])
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end
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end
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data/lib/chipgps.rb
ADDED
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class Chipgps
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class Event
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def initialize(line)
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@line = line
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end
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attr_reader :line
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attr_accessor :chr, :bp, :ip
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attr_accessor :ip_binding_present, :ip_binding_strength, :control_binding_strength,
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:fold_enrichment, :mlog10_qvalue, :mlog10_pvalue, :ipvsEMP_KLD, :ipvsCTR_KLD
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end # End of Event class
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class Search < Event
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def initialize(line, options = {})
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@line = line
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@event_number = options[:event]
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@condition_number = options[:condition]
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parse
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end
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def cleanup(line)
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new_line = line.strip
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new_line.chomp!
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new_line.gsub!(/ +/, "")
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return new_line
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end
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def parse
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# condition_number start from 0.
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line = cleanup(@line)
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f = line.split(/\t/)
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@chr = f[0].split(/:/)[0]
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@bp = f[0].split(/:/)[1].to_i
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@ip = f[1].to_f
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@ip_binding_present = f[(@condition_number * 9 + 2) + 0].to_i
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@ip_binding_strength = f[(@condition_number * 9 + 2) + 1].to_f
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@control_binding_strength = f[(@condition_number * 9 + 2) + 2].to_f
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@fold_enrichment = f[(@condition_number * 9 + 2) + 3].to_f
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@mlog10_qvalue = f[(@condition_number * 9 + 2) + 4].to_f
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@mlog10_pvalue = f[(@condition_number * 9 + 2) + 5].to_f
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@ipvsEMP_KLD = f[(@condition_number * 9 + 2) + 6].to_f
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@ipvsCTR_KLD = f[(@condition_number * 9 + 2) + 7].to_f
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end
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end # End of Search class
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def initialize(file)
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@gps_out_file = file
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@lines = File.open(@gps_out_file).readlines
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@header = @lines.shift
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@num_of_conditions = num_of_conditions
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@num_of_events = num_of_events
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end
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attr_reader :header
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def num_of_conditions
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f = @lines[0].split(/\t/)
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num_of_conditions = (f.size - 2) / 9 # each condition has 9 cols
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# pp f.size
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return num_of_conditions
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end
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def num_of_events
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return @lines.size
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end
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def each_by_condition(condition_id) # condition_id starts from 0
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@lines.each_with_index do |line, idx|
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yield Chipgps::Search.new(line, {:condition => condition_id, :event => idx})
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end
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end
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end
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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
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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
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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
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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
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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
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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
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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
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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
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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
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10
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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
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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
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data/sample/gps2bet.rb
ADDED
@@ -0,0 +1,29 @@
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#!/usr/bin/env ruby
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2
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+
|
3
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$LOAD_PATH.push("../lib")
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4
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|
5
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require 'pp'
|
6
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require 'chipgps'
|
7
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|
8
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#gps_out_file = ARGV.shift
|
9
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gps_out_file = "Demo_2_GPS_significant.txt"
|
10
|
+
gps = Chipgps.new(gps_out_file)
|
11
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+
|
12
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for condition_id in 0..(gps.num_of_conditions-1)
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13
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|
14
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exp_name = "Demo_Day" + condition_id.to_s
|
15
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+
header = "track name=#{exp_name} description=\"GPS: #{exp_name}\" useScore=0"
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16
|
+
puts header
|
17
|
+
gps.each_by_condition(condition_id) do |event|
|
18
|
+
|
19
|
+
# output (bed format)
|
20
|
+
puts [
|
21
|
+
"chr" + event.chr, # chr
|
22
|
+
event.bp, # start
|
23
|
+
event.bp + 1, # end
|
24
|
+
[exp_name, event.chr, event.bp.to_s].join(":"), # name
|
25
|
+
event.fold_enrichment # score
|
26
|
+
].join("\t")
|
27
|
+
|
28
|
+
end
|
29
|
+
end
|
data/test/helper.rb
ADDED
@@ -0,0 +1,17 @@
|
|
1
|
+
require 'rubygems'
|
2
|
+
require 'bundler'
|
3
|
+
begin
|
4
|
+
Bundler.setup(:default, :development)
|
5
|
+
rescue Bundler::BundlerError => e
|
6
|
+
$stderr.puts e.message
|
7
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
8
|
+
exit e.status_code
|
9
|
+
end
|
10
|
+
require 'test/unit'
|
11
|
+
|
12
|
+
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
13
|
+
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
14
|
+
require 'chipgps'
|
15
|
+
|
16
|
+
class Test::Unit::TestCase
|
17
|
+
end
|
@@ -0,0 +1,177 @@
|
|
1
|
+
require 'helper'
|
2
|
+
|
3
|
+
class Test_Chipgps < Test::Unit::TestCase
|
4
|
+
|
5
|
+
def setup
|
6
|
+
@gps_out_file = Dir.pwd + "/sample/Demo_2_GPS_significant.txt"
|
7
|
+
@gps = Chipgps.new(@gps_out_file)
|
8
|
+
|
9
|
+
@event_c0_e0 = nil
|
10
|
+
@gps.each_by_condition(0) do |event|
|
11
|
+
@event_c0_e0 = event
|
12
|
+
break
|
13
|
+
end
|
14
|
+
|
15
|
+
@event_c2_e0 = nil
|
16
|
+
@gps.each_by_condition(2) do |event|
|
17
|
+
@event_c2_e0 = event
|
18
|
+
break
|
19
|
+
end
|
20
|
+
end
|
21
|
+
|
22
|
+
def test_open_gps_out_file
|
23
|
+
assert(FileTest.exist?(@gps_out_file))
|
24
|
+
end
|
25
|
+
|
26
|
+
def test_gps_num_of_conditions
|
27
|
+
assert_equal(5, @gps.num_of_conditions)
|
28
|
+
end
|
29
|
+
|
30
|
+
def test_gps_num_of_events
|
31
|
+
assert_equal(11-1, @gps.num_of_events)
|
32
|
+
end
|
33
|
+
|
34
|
+
# event = 0, condition = 0
|
35
|
+
def test_gps_each_by_condition_with_c0_e0
|
36
|
+
assert_equal("1", @event_c0_e0.chr)
|
37
|
+
assert_equal(3390040, @event_c0_e0.bp)
|
38
|
+
assert_equal(19.0, @event_c0_e0.ip)
|
39
|
+
assert_equal(0, @event_c0_e0.ip_binding_present)
|
40
|
+
assert_equal(1.0, @event_c0_e0.ip_binding_strength)
|
41
|
+
assert_equal(1.4, @event_c0_e0.control_binding_strength)
|
42
|
+
assert_equal(0.7, @event_c0_e0.fold_enrichment)
|
43
|
+
assert_equal(-0.07, @event_c0_e0.mlog10_qvalue)
|
44
|
+
assert_equal(999.00, @event_c0_e0.mlog10_pvalue)
|
45
|
+
assert_equal(-4.00, @event_c0_e0.ipvsEMP_KLD)
|
46
|
+
assert_equal(0.00, @event_c0_e0.ipvsCTR_KLD)
|
47
|
+
end
|
48
|
+
|
49
|
+
# event = 0, condition = 2
|
50
|
+
def test_gps_each_by_condition_with_c2_e0
|
51
|
+
assert_equal("1", @event_c2_e0.chr)
|
52
|
+
assert_equal(3390040, @event_c2_e0.bp)
|
53
|
+
assert_equal(19.0, @event_c2_e0.ip)
|
54
|
+
assert_equal(0, @event_c2_e0.ip_binding_present)
|
55
|
+
assert_equal(2.0, @event_c2_e0.ip_binding_strength)
|
56
|
+
assert_equal(2.1, @event_c2_e0.control_binding_strength)
|
57
|
+
assert_equal(1.0, @event_c2_e0.fold_enrichment)
|
58
|
+
assert_equal(-0.06, @event_c2_e0.mlog10_qvalue)
|
59
|
+
assert_equal(999.00, @event_c2_e0.mlog10_pvalue)
|
60
|
+
assert_equal(-3.59, @event_c2_e0.ipvsEMP_KLD)
|
61
|
+
assert_equal(0.00, @event_c2_e0.ipvsCTR_KLD)
|
62
|
+
end
|
63
|
+
|
64
|
+
end
|
65
|
+
|
66
|
+
class Test_Chipgps::Event < Test::Unit::TestCase
|
67
|
+
def setup
|
68
|
+
@gps_out_file = Dir.pwd + "/sample/Demo_2_GPS_significant.txt"
|
69
|
+
@line = File.open(@gps_out_file).readlines[1]
|
70
|
+
@event = Chipgps::Event.new(@line)
|
71
|
+
end
|
72
|
+
end
|
73
|
+
|
74
|
+
class Test_Chipgps::Search < Test::Unit::TestCase
|
75
|
+
def setup
|
76
|
+
@gps_out_file = Dir.pwd + "/sample/Demo_2_GPS_significant.txt"
|
77
|
+
@line = File.open(@gps_out_file).readlines[1]
|
78
|
+
|
79
|
+
event_number = 0
|
80
|
+
condition_number = 0
|
81
|
+
@event = Chipgps::Search.new(@line, {:event => event_number, :condition => condition_number})
|
82
|
+
|
83
|
+
event_number = 0
|
84
|
+
condition_number = 2
|
85
|
+
@event_0_2 = Chipgps::Search.new(@line, {:event => event_number, :condition => condition_number})
|
86
|
+
end
|
87
|
+
|
88
|
+
# start: event = 0, condition = 0
|
89
|
+
def test_gps_search_search_chr
|
90
|
+
assert_equal("1", @event.chr)
|
91
|
+
end
|
92
|
+
def test_gps_search_search_bp
|
93
|
+
assert_equal(3390040, @event.bp)
|
94
|
+
end
|
95
|
+
def test_gps_search_search_ip
|
96
|
+
assert_equal(19.0, @event.ip)
|
97
|
+
end
|
98
|
+
|
99
|
+
def test_gps_search_search_ip_binding_present
|
100
|
+
assert_equal(0, @event.ip_binding_present)
|
101
|
+
end
|
102
|
+
|
103
|
+
def test_gps_search_search_ip_binding_strength
|
104
|
+
assert_equal(1.0, @event.ip_binding_strength)
|
105
|
+
end
|
106
|
+
|
107
|
+
def test_gps_search_search_control_binding_strength
|
108
|
+
assert_equal(1.4, @event.control_binding_strength)
|
109
|
+
end
|
110
|
+
|
111
|
+
def test_gps_search_search_fold_enrichment
|
112
|
+
assert_equal(0.7, @event.fold_enrichment)
|
113
|
+
end
|
114
|
+
|
115
|
+
def test_gps_search_search_mlog10_qvalue
|
116
|
+
assert_equal(-0.07, @event.mlog10_qvalue)
|
117
|
+
end
|
118
|
+
|
119
|
+
def test_gps_search_search_mlog10_pvalue
|
120
|
+
assert_equal(999.00, @event.mlog10_pvalue)
|
121
|
+
end
|
122
|
+
|
123
|
+
def test_gps_search_search_ipvsEMP_KLD
|
124
|
+
assert_equal(-4.00, @event.ipvsEMP_KLD)
|
125
|
+
end
|
126
|
+
|
127
|
+
def test_gps_search_search_ipvsCTR_KLD
|
128
|
+
assert_equal(0.00, @event.ipvsCTR_KLD)
|
129
|
+
end
|
130
|
+
# end: event = 0, condition = 0
|
131
|
+
|
132
|
+
|
133
|
+
# start: event = 0, condition = 2
|
134
|
+
def test_gps_search_search_chr_by_evnet_0_2
|
135
|
+
assert_equal("1", @event_0_2.chr)
|
136
|
+
end
|
137
|
+
def test_gps_search_search_bp_by_evnet_0_2
|
138
|
+
assert_equal(3390040, @event_0_2.bp)
|
139
|
+
end
|
140
|
+
def test_gps_search_search_ip_by_evnet_0_2
|
141
|
+
assert_equal(19.0, @event_0_2.ip)
|
142
|
+
end
|
143
|
+
|
144
|
+
def test_gps_search_search_ip_binding_present_by_evnet_0_2
|
145
|
+
assert_equal(0, @event_0_2.ip_binding_present)
|
146
|
+
end
|
147
|
+
|
148
|
+
def test_gps_search_search_ip_binding_strength_by_evnet_0_2
|
149
|
+
assert_equal(2.0, @event_0_2.ip_binding_strength)
|
150
|
+
end
|
151
|
+
|
152
|
+
def test_gps_search_search_control_binding_strength_by_evnet_0_2
|
153
|
+
assert_equal(2.1, @event_0_2.control_binding_strength)
|
154
|
+
end
|
155
|
+
|
156
|
+
def test_gps_search_search_fold_enrichment_by_evnet_0_2
|
157
|
+
assert_equal(1.0, @event_0_2.fold_enrichment)
|
158
|
+
end
|
159
|
+
|
160
|
+
def test_gps_search_search_mlog10_qvalue_by_evnet_0_2
|
161
|
+
assert_equal(-0.06, @event_0_2.mlog10_qvalue)
|
162
|
+
end
|
163
|
+
|
164
|
+
def test_gps_search_search_mlog10_pvalue_by_evnet_0_2
|
165
|
+
assert_equal(999.00, @event_0_2.mlog10_pvalue)
|
166
|
+
end
|
167
|
+
|
168
|
+
def test_gps_search_search_ipvsEMP_KLD_by_evnet_0_2
|
169
|
+
assert_equal(-3.59, @event_0_2.ipvsEMP_KLD)
|
170
|
+
end
|
171
|
+
|
172
|
+
def test_gps_search_search_ipvsCTR_KLD_by_evnet_0_2
|
173
|
+
assert_equal(0.00, @event_0_2.ipvsCTR_KLD)
|
174
|
+
end
|
175
|
+
# end: event = 0, condition = 2
|
176
|
+
|
177
|
+
end
|
metadata
ADDED
@@ -0,0 +1,102 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: chipgps
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
prerelease:
|
5
|
+
version: 0.1.1
|
6
|
+
platform: ruby
|
7
|
+
authors:
|
8
|
+
- Itoshi NIKAIDO
|
9
|
+
autorequire:
|
10
|
+
bindir: bin
|
11
|
+
cert_chain: []
|
12
|
+
|
13
|
+
date: 2011-10-20 00:00:00 Z
|
14
|
+
dependencies:
|
15
|
+
- !ruby/object:Gem::Dependency
|
16
|
+
name: bundler
|
17
|
+
requirement: &id001 !ruby/object:Gem::Requirement
|
18
|
+
none: false
|
19
|
+
requirements:
|
20
|
+
- - ~>
|
21
|
+
- !ruby/object:Gem::Version
|
22
|
+
version: 1.0.0
|
23
|
+
type: :development
|
24
|
+
prerelease: false
|
25
|
+
version_requirements: *id001
|
26
|
+
- !ruby/object:Gem::Dependency
|
27
|
+
name: jeweler
|
28
|
+
requirement: &id002 !ruby/object:Gem::Requirement
|
29
|
+
none: false
|
30
|
+
requirements:
|
31
|
+
- - ~>
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: 1.6.4
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: *id002
|
37
|
+
- !ruby/object:Gem::Dependency
|
38
|
+
name: rcov
|
39
|
+
requirement: &id003 !ruby/object:Gem::Requirement
|
40
|
+
none: false
|
41
|
+
requirements:
|
42
|
+
- - ">="
|
43
|
+
- !ruby/object:Gem::Version
|
44
|
+
version: "0"
|
45
|
+
type: :development
|
46
|
+
prerelease: false
|
47
|
+
version_requirements: *id003
|
48
|
+
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.
|
49
|
+
email: dritoshi@gmail.com
|
50
|
+
executables: []
|
51
|
+
|
52
|
+
extensions: []
|
53
|
+
|
54
|
+
extra_rdoc_files:
|
55
|
+
- LICENSE.txt
|
56
|
+
- README.rdoc
|
57
|
+
files:
|
58
|
+
- .document
|
59
|
+
- Gemfile
|
60
|
+
- Gemfile.lock
|
61
|
+
- LICENSE.txt
|
62
|
+
- README.rdoc
|
63
|
+
- Rakefile
|
64
|
+
- VERSION
|
65
|
+
- chipgps.gemspec
|
66
|
+
- lib/chipgps.rb
|
67
|
+
- sample/Demo_2_GPS_significant.txt
|
68
|
+
- sample/gps2bet.rb
|
69
|
+
- test/helper.rb
|
70
|
+
- test/test_chipgps.rb
|
71
|
+
homepage: http://github.com/dritoshi/chipgps
|
72
|
+
licenses:
|
73
|
+
- MIT
|
74
|
+
post_install_message:
|
75
|
+
rdoc_options: []
|
76
|
+
|
77
|
+
require_paths:
|
78
|
+
- lib
|
79
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
80
|
+
none: false
|
81
|
+
requirements:
|
82
|
+
- - ">="
|
83
|
+
- !ruby/object:Gem::Version
|
84
|
+
hash: 1295371598341010762
|
85
|
+
segments:
|
86
|
+
- 0
|
87
|
+
version: "0"
|
88
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
89
|
+
none: false
|
90
|
+
requirements:
|
91
|
+
- - ">="
|
92
|
+
- !ruby/object:Gem::Version
|
93
|
+
version: "0"
|
94
|
+
requirements: []
|
95
|
+
|
96
|
+
rubyforge_project:
|
97
|
+
rubygems_version: 1.8.11
|
98
|
+
signing_key:
|
99
|
+
specification_version: 3
|
100
|
+
summary: Parser for the Genome Positioning System
|
101
|
+
test_files: []
|
102
|
+
|