acnfp-trans-counter 0.1.0

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 "bio", ">=1.4.1"
+  gem "thor", ">=0.14.6"
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.5.2"
+  gem "rcov", ">= 0"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.1.5000)
+    git (1.2.5)
+    jeweler (1.5.2)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.8.7)
+    rcov (0.9.9)
+    shoulda (2.11.3)
+    thor (0.14.6)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.1)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.5.2)
+  rcov
+  shoulda
+  thor (>= 0.14.6)

data/LICENSE.txt

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+Copyright (c) 2011 Robert Syme
+
+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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+= acnfp-trans-counter
+
+Description goes here.
+
+== Contributing to acnfp-trans-counter
+ 
+* 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 Robert Syme. See LICENSE.txt for
+further details.
+

data/Rakefile

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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 '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 = "acnfp-trans-counter"
+  gem.homepage = "http://github.com/robsyme/acnfp-trans-counter"
+  gem.license = "MIT"
+  gem.summary = %Q{A quick and dirty tool for analysis of transition and transversion frequency aross and alignment}
+  gem.description = %Q{A quick and dirty tool for analysis of transition and transversion frequency aross and alignment}
+  gem.email = "rob.syme@gmail.com"
+  gem.authors = ["Robert Syme"]
+  # Include your dependencies below. Runtime dependencies are required when using your gem,
+  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
+  #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
+  gem.add_runtime_dependency 'bio', '>= 1.4.1'
+  gem.add_runtime_dependency 'thor', '>= 0.14.6'
+  #  gem.add_development_dependency 'rspec', '> 1.2.3'
+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
+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 = "acnfp-trans-counter #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/acnfp-trans-counter.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{acnfp-trans-counter}
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Robert Syme"]
+  s.date = %q{2011-04-04}
+  s.default_executable = %q{acnfp-trans-counter}
+  s.description = %q{A quick and dirty tool for analysis of transition and transversion frequency aross and alignment}
+  s.email = %q{rob.syme@gmail.com}
+  s.executables = ["acnfp-trans-counter"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "acnfp-trans-counter.gemspec",
+    "bin/acnfp-trans-counter",
+    "lib/acnfp-trans-counter.rb",
+    "test/helper.rb",
+    "test/test_acnfp-trans-counter.rb"
+  ]
+  s.homepage = %q{http://github.com/robsyme/acnfp-trans-counter}
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.5.0}
+  s.summary = %q{A quick and dirty tool for analysis of transition and transversion frequency aross and alignment}
+  s.test_files = [
+    "test/helper.rb",
+    "test/test_acnfp-trans-counter.rb"
+  ]
+
+  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<bio>, [">= 1.4.1"])
+      s.add_development_dependency(%q<thor>, [">= 0.14.6"])
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_runtime_dependency(%q<thor>, [">= 0.14.6"])
+    else
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<thor>, [">= 0.14.6"])
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<thor>, [">= 0.14.6"])
+    end
+  else
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<thor>, [">= 0.14.6"])
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<thor>, [">= 0.14.6"])
+  end
+end
+

data/bin/acnfp-trans-counter

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+#!/usr/bin/env ruby
+require "bio"
+require "thor"
+
+
+class AcnfpTransCounter < Thor
+  desc "analyse FILENAME", "Run acnfp-trans-counter on a given alignment"
+  def analyse(filename)
+    alignments = Bio::FlatFile.open(filename)
+    
+    alignments.to_a.combination(2) do |a,b|
+      transition_count = 0
+      transversion_count = 0
+      indel_count = 0
+      
+      alignment = Bio::Alignment::OriginalAlignment.new([a,b])
+      alignment.each_site do |site|
+        next if site[0] == site[1]
+        next if site.has_gap?
+        next if site.include? "N"
+
+        case site.sort.map{|char| char.upcase}
+        when %w{C T}, %w{A G}
+          transition_count += 1
+        when %w{A C}, %w{A T}, %w{C G}, %w{G T}
+          transversion_count += 1
+        else
+          raise "Unknown pairing: #{site}"
+        end
+      end
+
+      mutation_count = transversion_count + transition_count.to_f
+      
+      header = "%s vs %s" % [a.definition, b.definition]
+      puts header
+      puts "=" * header.length
+
+      puts "Transversions: %d (%.2f%%)" % [transversion_count, 100 * transversion_count / mutation_count]
+      puts "Transitions:   %d (%.2f%%)" % [transition_count, 100 * transition_count / mutation_count]
+
+      puts "Transversions / Transitions: %.2f" % [transversion_count.to_f / transition_count]
+      puts
+    end
+  end
+end
+
+
+AcnfpTransCounter.start

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
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'acnfp-trans-counter'
+
+class Test::Unit::TestCase
+end

data/test/test_acnfp-trans-counter.rb

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+require 'helper'
+
+class TestAcnfpTransCounter < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    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: acnfp-trans-counter
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.1.0
+platform: ruby
+authors: 
+- Robert Syme
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-04-04 00:00:00 +08:00
+default_executable: acnfp-trans-counter
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: bio
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.4.1
+  type: :development
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: thor
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.14.6
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id006
+- !ruby/object:Gem::Dependency 
+  name: bio
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.4.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *id007
+- !ruby/object:Gem::Dependency 
+  name: thor
+  requirement: &id008 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.14.6
+  type: :runtime
+  prerelease: false
+  version_requirements: *id008
+description: A quick and dirty tool for analysis of transition and transversion frequency aross and alignment
+email: rob.syme@gmail.com
+executables: 
+- acnfp-trans-counter
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- acnfp-trans-counter.gemspec
+- bin/acnfp-trans-counter
+- lib/acnfp-trans-counter.rb
+- test/helper.rb
+- test/test_acnfp-trans-counter.rb
+has_rdoc: true
+homepage: http://github.com/robsyme/acnfp-trans-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: 492392011685652161
+      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: 1.5.0
+signing_key: 
+specification_version: 3
+summary: A quick and dirty tool for analysis of transition and transversion frequency aross and alignment
+test_files: 
+- test/helper.rb
+- test/test_acnfp-trans-counter.rb