bio-qtlHD 0.0.1.alpha.1

data/.document

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+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"
+  gem "bio", ">= 1.4.2"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.2)
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.9.2.2)
+    rcov (0.9.11)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.2)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.6.4)
+  rcov

data/LICENSE.txt

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+Copyright (c) 2011 Pjotr Prins
+
+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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+= bio-qtlHD
+
+Description goes here.
+
+== Contributing to bio-qtlHD
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2011 Pjotr Prins. 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 = "bio-qtlHD"
+  gem.homepage = "http://github.com/pjotrp/bioruby-qtlHD"
+  gem.license = "MIT"
+  gem.summary = %Q{Support for qtlHD}
+  gem.description = %Q{Ruby tools and scripts for QTL mapping, part of the qtlHD project}
+  gem.email = "pjotr.public01@thebird.nl"
+  gem.authors = ["Pjotr Prins", "Danny Arends", "Karl Broman"]
+  # 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 = "bio-qtlHD #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1.alpha.1

data/bin/biobio-qtlHD

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+#!/usr/bin/env ruby
+#
+# BioRuby bio-qtlHD Plugin
+# Version 0.0.0 
+# Author:: Pjotr Prins
+# Copyright:: 2011
+# License:: The Ruby License
+
+ USAGE = "Describe biobio-qtlHD"
+
+if ARGV.size == 0
+  print USAGE
+end
+
+require 'bio-qtlHD'
+require 'optparse'
+
+# Uncomment when using the bio-logger 
+# require 'bio-logger'
+# Bio::Log::CLI.logger('stderr')
+# Bio::Log::CLI.trace('info')
+
+options = {:example_switch=>false,:show_help=>false}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
+
+  o.on('--example_parameter [EXAMPLE_PARAMETER]', 'TODO: put a description for the PARAMETER') do |example_parameter|
+    # TODO: your logic here, below an example
+    options[:example_parameter] = 'this is a parameter'
+  end
+  
+  o.separator ""
+  o.on("--switch-example", 'TODO: put a description for the SWITCH') do
+    # TODO: your logic here, below an example
+    self[:example_switch] = true
+  end
+
+  # Uncomment the following when using the bio-logger 
+  # o.separator ""
+  # o.on("--logger filename",String,"Log to file (default stderr)") do | name |
+  #   Bio::Log::CLI.logger(name)
+  # end
+  #
+  # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
+  #   Bio::Log::CLI.trace(s)
+  # end
+  # 
+  # o.on("-q", "--quiet", "Run quietly") do |q|
+  #   Bio::Log::CLI.trace('error')
+  # end
+  # 
+  # o.on("-v", "--verbose", "Run verbosely") do |v|
+  #   Bio::Log::CLI.trace('info')
+  # end
+  # 
+  # o.on("--debug", "Show debug messages") do |v|
+  #   Bio::Log::CLI.trace('debug')
+  # end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+begin
+  opts.parse!(ARGV)
+
+  # Uncomment the following when using the bio-logger 
+  # Bio::Log::CLI.configure('bio-qtlHD')
+
+  # TODO: your code here
+  # use options for your logic
+rescue OptionParser::InvalidOption => e
+  options[:invalid_argument] = e.message
+end

data/bio-qtlHD.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 = %q{bio-qtlHD}
+  s.version = "0.0.1.alpha.1"
+
+  s.required_rubygems_version = Gem::Requirement.new("> 1.3.1") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Pjotr Prins", "Danny Arends", "Karl Broman"]
+  s.date = %q{2011-11-16}
+  s.default_executable = %q{biobio-qtlHD}
+  s.description = %q{Ruby tools and scripts for QTL mapping, part of the qtlHD project}
+  s.email = %q{pjotr.public01@thebird.nl}
+  s.executables = ["biobio-qtlHD"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/biobio-qtlHD",
+    "bio-qtlHD.gemspec",
+    "lib/bio-qtlHD.rb",
+    "test/helper.rb",
+    "test/test_bio-qtlHD.rb"
+  ]
+  s.homepage = %q{http://github.com/pjotrp/bioruby-qtlHD}
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{Support for qtlHD}
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    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"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+    else
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+    end
+  else
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+  end
+end
+

data/lib/bio-qtlHD.rb

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+# Please require your code below, respecting the bioruby directory tree. 
+# For instance, perhaps the only uncommented line in this file might 
+# be something like this:
+#
+#   require 'bio/sequence/awesome_sequence_plugin_thingy'
+#
+# and then create the ruby file 'lib/bio/sequence/awesome_sequence_thingy.rb'
+# and put your plugin's code there. It is bad practice to write other code 
+# directly into this file, because doing so causes confusion if this biogem 
+# was ever to get merged into the main bioruby tree.

data/test/helper.rb

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+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 'bio-qtlHD'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-qtlHD.rb

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+require 'helper'
+
+class TestBioQtlhd < Test::Unit::TestCase
+  def test_something_for_real
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-qtlHD
+version: !ruby/object:Gem::Version
+  version: 0.0.1.alpha.1
+  segments:
+  - 0
+  - 0
+  - 1
+  - alpha
+  - 1
+  prerelease: true
+  segments_generated: true
+platform: ruby
+authors:
+- Pjotr Prins
+- Danny Arends
+- Karl Broman
+autorequire: !!null 
+bindir: bin
+cert_chain: []
+date: 2011-11-16 00:00:00.000000000 +01:00
+default_executable: biobio-qtlHD
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &27481940 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+        segments:
+        - 1
+        - 0
+        - 0
+        segments_generated: true
+  type: :development
+  prerelease: false
+  version_requirements: *27481940
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &27481040 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+        segments:
+        - 1
+        - 6
+        - 4
+        segments_generated: true
+  type: :development
+  prerelease: false
+  version_requirements: *27481040
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &27480060 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+        segments:
+        - 0
+        segments_generated: true
+  type: :development
+  prerelease: false
+  version_requirements: *27480060
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &27479320 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+        segments:
+        - 1
+        - 4
+        - 2
+        segments_generated: true
+  type: :development
+  prerelease: false
+  version_requirements: *27479320
+description: Ruby tools and scripts for QTL mapping, part of the qtlHD project
+email: pjotr.public01@thebird.nl
+executables:
+- biobio-qtlHD
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/biobio-qtlHD
+- bio-qtlHD.gemspec
+- lib/bio-qtlHD.rb
+- test/helper.rb
+- test/test_bio-qtlHD.rb
+has_rdoc: true
+homepage: http://github.com/pjotrp/bioruby-qtlHD
+licenses:
+- MIT
+post_install_message: !!null 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      segments_generated: true
+      hash: -3806591435548056034
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>'
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+      segments:
+      - 1
+      - 3
+      - 1
+      segments_generated: true
+requirements: []
+rubyforge_project: !!null 
+rubygems_version: 1.3.7
+signing_key: !!null 
+specification_version: 3
+summary: Support for qtlHD
+test_files: []