expetable 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"
+gem "rphylip", "~> 0.1.0"
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.1.3"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.9.2.2)
+    rcov (0.9.9)
+    rphylip (0.1.0)
+    shoulda (2.11.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.1.3)
+  jeweler (~> 1.6.4)
+  rcov
+  rphylip (~> 0.1.0)
+  shoulda

data/LICENSE.txt

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+Copyright (c) 2012 Fernando Izquierdo-Carrasco
+
+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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+= expetable
+
+Description goes here.
+
+== Contributing to expetable
+ 
+* 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) 2012 Fernando Izquierdo-Carrasco. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+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 = "expetable"
+  gem.homepage = "http://github.com/fizquierdo/expetable"
+  gem.license = "MIT"
+  gem.summary = %Q{Tables to persist experimental data in Yaml format}
+  gem.description = %Q{}
+  gem.email = "fer.izquierdo@gmail.com"
+  gem.authors = ["Fernando Izquierdo-Carrasco"]
+  # dependencies defined in Gemfile
+  gem.add_dependency "rphylip", "~> 0.1.0"
+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 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "expetable #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/expetable.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{expetable}
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = [%q{Fernando Izquierdo-Carrasco}]
+  s.date = %q{2012-05-08}
+  s.description = %q{}
+  s.email = %q{fer.izquierdo@gmail.com}
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "expetable.gemspec",
+    "lib/experiment.rb",
+    "lib/expetable.rb",
+    "test/helper.rb",
+    "test/test_expetable.rb"
+  ]
+  s.homepage = %q{http://github.com/fizquierdo/expetable}
+  s.licenses = [%q{MIT}]
+  s.require_paths = [%q{lib}]
+  s.rubygems_version = %q{1.8.6}
+  s.summary = %q{Tables to persist experimental data in Yaml format}
+
+  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_runtime_dependency(%q<rphylip>, ["~> 0.1.0"])
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.1.3"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_runtime_dependency(%q<rphylip>, ["~> 0.1.0"])
+    else
+      s.add_dependency(%q<rphylip>, ["~> 0.1.0"])
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.1.3"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<rphylip>, ["~> 0.1.0"])
+    end
+  else
+    s.add_dependency(%q<rphylip>, ["~> 0.1.0"])
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.1.3"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<rphylip>, ["~> 0.1.0"])
+  end
+end
+

data/lib/experiment.rb

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+#!/usr/bin/env ruby
+#require 'rphylip'
+require 'fileutils'
+require 'yaml'
+
+class Experiment
+  def initialize(name, basedir)
+    @name = name
+    @base_dir = basedir
+  end
+  def dirname(a)
+    File.join @base_dir, 'experiments', @name, a
+  end
+  def last_bunch_dir
+    dirs = Dir.entries(dirname("output")).select{|f| f =~ /^bunch/}
+    dirs.sort_by{|s| s.split("_").last.to_i}.last
+  end
+  def setup_dirs
+    setup_ready = true
+    %w(alignment output).map{|n| self.dirname n}.each do |dir|
+      if File.exist?(dir)
+        puts "Exists #{dir}"
+        setup_ready = false # to avoid overwrite
+      else
+        FileUtils.mkdir_p dir
+      end
+    end
+    setup_ready
+  end
+  def expand_with_updates(opts, updates_are_full_alignments = true)
+    ali = self.dirname("alignment")
+    phy = opts[:phylip]
+    raise "phylip file not available" if phy.nil? or not File.exist?(phy)
+    FileUtils.copy phy, ali 
+    p = Phylip.new(File.join ali, File.basename(phy))
+    p.subdivide_random opts 
+  end
+end
+
+class ExperimentList
+  # Persistent storage in .yml file of the experiment status
+  attr_accessor :name, :date
+  def initialize(expfile)
+    @expfile = expfile
+    File.open(expfile, "w"){|f| f.puts "---"} unless File.exist?(expfile)
+    @list = YAML.load_file(expfile) || Array.new
+  end
+  def add(opts)
+    name_available = self.name_available?(opts[:name]) 
+    if name_available
+      #newexp = {:name => opts[:name], :date => Time.now, :fake_phy => opts[:fake_phy]}
+      newexp = {:name => opts[:name], :date => Time.now}
+      newexp.merge!({:fake_phy => opts[:fake_phy]}) unless opts[:fake_phy].nil?
+      newexp.merge!({:initial_phy => opts[:initial_phy]}) unless opts[:initial_phy].nil?
+      @list.push newexp
+      self.save
+      true
+    end
+  end
+  def update(name, step, state)
+    e = self.find_by_name(name) 
+    unless e.nil?
+      @list.each do |item|
+        if item[:name] == name
+          if item[step].nil?
+            item[step] = state
+          else
+            item[step] += " " + state
+          end
+        end
+      end
+    end
+    self.save
+  end
+  def show
+    puts "Current Experiments"
+    puts "ID\tname"
+    @list.each_with_index  do |item, i|
+      fake_name = item[:fake_phy].nil? ? "-" : File.basename(item[:fake_phy]) 
+      initial_name = item[:initial_phy].nil? ? "-" : File.basename(item[:initial_phy]) 
+      puts "#{i}\t#{item[:name]}\t fake: #{fake_name} \t init: #{initial_name} Best LH: #{item["bestLH"]}"
+      item.keys.select{|k| k =~ /^u\d+$/}.sort.each do |update_key|
+        puts "  #{update_key}: #{item[update_key]}"
+      end
+    end
+  end
+  def remove(name)
+    item = find_by_name(name)
+    unless item.nil?
+      @list.delete(item) 
+      self.save
+    end
+  end
+  def save
+    File.open(@expfile, "w"){|f| f.write @list.to_yaml}
+    puts "Experiment list updated"
+  end
+  def name_available?(name)
+    existing_items = find_by_name(name)
+    unless existing_items.nil?
+       if existing_items.size >= 1
+         puts "A expremient with this name exists already"
+         p existing_items
+         return false
+       end
+    end
+    return true
+  end
+  protected
+  def find_by_name(name)
+    @list.find{|e| e[:name] == name}
+  end
+end

data/lib/expetable.rb

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+#!/usr/bin/env ruby
+require 'experiment'

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 'expetable'
+
+class Test::Unit::TestCase
+end

data/test/test_expetable.rb

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+require 'helper'
+
+class TestExpetable < 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: expetable
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- Fernando Izquierdo-Carrasco
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-05-08 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rphylip
+  requirement: &11398640 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *11398640
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &11398040 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *11398040
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &11397440 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.3
+  type: :development
+  prerelease: false
+  version_requirements: *11397440
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &11396860 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+  type: :development
+  prerelease: false
+  version_requirements: *11396860
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &11396240 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *11396240
+- !ruby/object:Gem::Dependency
+  name: rphylip
+  requirement: &11395700 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *11395700
+description: ''
+email: fer.izquierdo@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- expetable.gemspec
+- lib/experiment.rb
+- lib/expetable.rb
+- test/helper.rb
+- test/test_expetable.rb
+homepage: http://github.com/fizquierdo/expetable
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -76775336940039374
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.6
+signing_key: 
+specification_version: 3
+summary: Tables to persist experimental data in Yaml format
+test_files: []