rraxml 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 "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.8.3"
+  gem "rcov", ">= 0"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    git (1.2.5)
+    jeweler (1.8.3)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+      rdoc
+    json (1.6.6)
+    rake (0.9.2.2)
+    rcov (1.0.0)
+    rdoc (3.12)
+      json (~> 1.4)
+    shoulda (3.0.1)
+      shoulda-context (~> 1.0.0)
+      shoulda-matchers (~> 1.0.0)
+    shoulda-context (1.0.0)
+    shoulda-matchers (1.0.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0.0)
+  jeweler (~> 1.8.3)
+  rcov
+  rdoc (~> 3.12)
+  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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+= rraxml
+
+Description goes here.
+
+== Contributing to rraxml
+ 
+* 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 '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 = "rraxml"
+  gem.homepage = "http://github.com/fizquierdo/rraxml"
+  gem.license = "MIT"
+  gem.summary = "RAxML wrappers for ruby"
+  gem.description = "desc"
+  gem.email = "fer.izquierdo@gmail.com"
+  gem.authors = ["Fernando Izquierdo-Carrasco"]
+  # 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 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "rraxml #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/lib/rraxml.rb

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+#!/usr/bin/env ruby
+require 'rphylip'
+require 'rnewick'
+require 'fileutils'
+
+def binary_available(name)
+    available = false
+    ENV['PATH'].split(':').each do |folder|
+      available = true if File.exists?(File.join folder, name)
+    end
+    available
+end
+
+class Raxml
+  attr_reader :stdout, :stderr, :infofile, :name, :outdir, :phylip, :binary, :ops
+  def initialize(opts)
+    raise "No alignment in #{opts[:phylip]}" if opts[:phylip].nil? or not File.exist?(opts[:phylip])
+    @phylip = opts[:phylip]
+    @name = opts[:name] || "RUN_NAME"
+    @seed = opts[:seed] || "12345"
+    @outdir = opts[:outdir] || "test/outdir/#{@name}"
+    @stderr = opts[:stderr] || File.join(@outdir, 'stderr')
+    @stdout = opts[:stdout] || File.join(@outdir, 'stdout')
+    @binary = ""
+    @flags = opts[:flags] || ""
+    @ops = "-s #{@phylip} -n #{@name} #{@flags}"
+  end
+  def before_run
+    FileUtils.mkdir_p @outdir unless File.exist?(@outdir) 
+    self.complete_call
+  end
+  def after_run
+    @infofile = File.join Dir.pwd, "RAxML_info.#{@name}" 
+    @outfiles = [@stdout, @stderr, @infofile]
+    self.gather_outfiles
+    @outfiles.each do |f| 
+      unless f.nil? or not File.exist?(f)
+        FileUtils.move(f, @outdir) unless File.join(@outdir, File.basename(f)) == f
+      end
+    end
+  end
+  def run
+    self.before_run
+    raise "#{@binary} not found" unless binary_available(@binary)
+    puts "#{@binary} #{@ops} "
+    system "(#{@binary} #{@ops} 2> #{@stderr}) > #{@stdout}"
+    self.after_run
+  end
+end
+
+module TreeCheck
+  def check_fulltree
+    newick_taxa = NewickFile.new(@starting_newick).newickStrings[0].numtaxa
+    alignment_taxa = Phylip.new(@phylip).numtaxa
+    if alignment_taxa != newick_taxa
+      raise "Tree #{@starting_newick} includes #{newick_taxa} taxa, #{alignment_taxa} expected"
+    end
+  end
+  def check_correctAlignment
+    rexec = RaxmlAlignmentChecker.new(:phylip => @phylip)
+    rexec.run
+    lastline =  File.open(rexec.stdout).readlines.last.chomp.strip
+    if lastline != "Alignment format can be read by RAxML"
+      raise "File #{@phylip} does not seem to be a correct alignment"
+      ret = false
+    else
+      FileUtils.rm_rf rexec.outdir
+      ret = true
+    end
+  end
+end
+class Parsimonator < Raxml
+  include TreeCheck
+  attr_reader :seed, :num_trees, :newick
+  def initialize(opts)
+    super(opts)
+    check_correctAlignment
+    @num_trees = opts[:num_trees] || 1
+    @newick = opts[:newick] || ""
+    @binary = 'parsimonator-SSE3'
+  end
+  def complete_call
+    @ops += " -N #{@num_trees} -p #{@seed}"
+    unless @newick.empty? then
+      raise "No newick starting tree?" unless File.exists?(@newick)
+      @ops += " -t #{@newick}"
+    end
+  end
+  def gather_outfiles
+    @num_trees.times{|i| @outfiles <<  "RAxML_parsimonyTree.#{name}.#{i}"}
+  end
+end
+class RaxmlLight < Raxml
+  include TreeCheck
+  attr_reader :starting_newick
+  def initialize(opts)
+    super(opts)
+    check_correctAlignment
+    if opts[:starting_newick].nil? or not File.exists?(opts[:starting_newick])
+      raise "Raxml Light requires a starting tree" 
+    end
+    @starting_newick = opts[:starting_newick] 
+    check_fulltree # makes sure the tree is comprenhensive in relation to the phylip file
+    #@name = @starting_newick.split(".").last 
+    if opts[:num_threads].nil? 
+      @binary = 'raxmlLight'
+      @num_threads = 0
+    else
+      @binary = 'raxmlLight-PTHREADS'
+      @num_threads = opts[:num_threads].to_i
+    end
+  end
+  def complete_call
+    @ops += " -m GTRCAT -t #{@starting_newick} "
+    @ops += " -T #{@num_threads} " if @num_threads > 0
+  end
+  def resultfilename
+    "RAxML_result.#{@name}"
+  end
+  def logfilename
+    "RAxML_log.#{@name}"
+  end
+  def gather_outfiles
+    @outfiles += [self.resultfilename, self.logfilename]
+    Dir.entries(Dir.pwd).select{|f| f=~ /^RAxML_binaryCheckpoint.#{@name}_/}.each{ |f| @outfiles << f}
+    @outfiles
+  end
+end
+class GammaScorer < Raxml
+  #TODO no tests for the gamma scorer class :(
+  include TreeCheck
+  def initialize(opts)
+    super(opts)
+    check_correctAlignment
+    if opts[:starting_newick].nil? or not File.exists?(opts[:starting_newick])
+      raise "Scorer requires a starting bunch of trees to score" 
+    end
+    @starting_newick = opts[:starting_newick]
+    check_fulltree # makes sure the tree is comprenhensive in relation to the phylip file
+    if opts[:num_threads].nil? 
+      @binary = 'raxmlHPC-SSE3'
+      @num_threads = 0
+    else
+      @binary = 'raxmlHPC-PTHREADS-SSE3'
+      @num_threads = opts[:num_threads].to_i
+    end
+  end
+  def complete_call
+    @ops += " -m GTRGAMMA -z #{@starting_newick} -f n"
+    @ops += " -T #{@num_threads} " if @num_threads > 0
+  end
+  def gather_outfiles
+    @outfiles += ["RAxML_result.#{@name}"]
+  end
+end
+class RaxmlAlignmentChecker < Raxml
+  def initialize(phylipfile)
+    super(phylipfile)
+    @binary = 'raxmlHPC-SSE3'
+  end
+  def complete_call
+    @ops += " -m GTRCAT -f c"
+  end
+  def gather_outfiles
+  end
+end
+
+class RaxmlGammaSearch < Raxml
+  #TODO no tests for the gamma search class :(
+  include TreeCheck
+  def initialize(opts)
+    super(opts)
+    check_correctAlignment
+    @num_trees = opts[:num_gamma_trees] 
+    if opts[:num_threads].nil? 
+      @binary = 'raxmlHPC-SSE3'
+      @num_threads = 0
+    else
+      @binary = 'raxmlHPC-PTHREADS-SSE3'
+      @num_threads = opts[:num_threads].to_i
+    end
+  end
+  def complete_call
+    @ops += " -m GTRCAT -p #{@seed} -N #{@num_trees}"
+    @ops += " -T #{@num_threads} " if @num_threads > 0
+  end
+  def gather_outfiles
+    @outfiles += ["RAxML_bestTree.#{@name}"]
+    other_files = ["result", "log", "parsimonyTree"]
+    if @num_trees > 1
+      @num_trees.times{|num| @outfiles += other_files.map{|n| "RAxML_" + n + ".#{@name}.RUN.#{num.to_s}"} }
+    else
+      @outfiles += other_files.map{|n| "RAxML_" + n + ".#{@name}"}
+    end
+  end
+end

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

data/test/test_rraxml.rb

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+require 'helper'
+
+class TestRraxml < 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: rraxml
+version: !ruby/object:Gem::Version 
+  hash: 27
+  prerelease: 
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- Fernando Izquierdo-Carrasco
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2012-03-27 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id001
+  name: shoulda
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 31
+        segments: 
+        - 3
+        - 12
+        version: "3.12"
+  version_requirements: *id002
+  name: rdoc
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 23
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  version_requirements: *id003
+  name: bundler
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 49
+        segments: 
+        - 1
+        - 8
+        - 3
+        version: 1.8.3
+  version_requirements: *id004
+  name: jeweler
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id005
+  name: rcov
+  prerelease: false
+description: desc
+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
+- lib/rraxml.rb
+- test/helper.rb
+- test/test_rraxml.rb
+homepage: http://github.com/fizquierdo/rraxml
+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: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.6
+signing_key: 
+specification_version: 3
+summary: RAxML wrappers for ruby
+test_files: []
+