rnewick 0.1.0

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

@@ -0,0 +1,14 @@
+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

@@ -0,0 +1,29 @@
+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

@@ -0,0 +1,20 @@
+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

@@ -0,0 +1,19 @@
+= rnewick
+
+Description goes here.
+
+== Contributing to rnewick
+ 
+* 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

@@ -0,0 +1,53 @@
+# 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 = "rnewick"
+  gem.homepage = "http://github.com/fizquierdo/rnewick"
+  gem.license = "MIT"
+  gem.summary = "newick utilities"
+  gem.description = "newick utilities" 
+  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 = "rnewick #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

@@ -0,0 +1 @@
+0.1.0

data/lib/rnewick.rb

@@ -0,0 +1,83 @@
+#!/usr/bin/env ruby
+class NewickString
+  attr_reader :str
+  def initialize(str)
+    @str=String.new(str)
+  end
+  def support_values
+    @str.gsub("0.0;","").scan(/\[([0-9]+)\]/).map{|n| n[0].to_i}
+  end
+  def multifurcations
+    # TODO find the multifurcations and show their support (guess it is 100 cause bifurcations were lower than 50)
+    # maybe try to resolve them on the fly?
+  end
+  def branch_lengths
+    @str.gsub("0.0;","").scan(/:([0-9]+\.[0-9]+)/).map{|n| n[0].to_f}
+  end
+  def str_with_scaled_branch_lengths(factor)
+    newt = @str.gsub(/:([0-9]+\.[0-9]+)/) do |bl|
+      newval = bl.gsub(":","").to_f * factor
+      ":" + "%.9f" % newval 
+    end
+    newt
+  end
+  def str_with_numeric_branch_lengths
+    newt = @str.gsub(/:([0-9]+\.[0-9]+)e-([0-9]+)/) do |bl|
+      newval = bl.gsub(":","").to_f  
+      ":" + "%.9f" % newval 
+    end
+    newt
+  end
+  def treelength
+    self.branch_lengths.inject(0){|acc,i| acc+i}
+  end
+  def rawtopology
+    @str.gsub(/[0-9]+\.[0-9]+/,'').gsub(':','')
+  end
+  def taxanames
+    self.rawtopology.gsub("(", " ").gsub(")", " ").gsub(",", " ").gsub(";", " ").strip.split
+  end
+  def numtaxa
+    @str.count(",").to_i + 1
+  end
+  def clean
+    newstr = @str.gsub('(,)',"").gsub('(,(','((').gsub('),)','))')
+    newstr = newstr.gsub('(,)',"").gsub('(,(','((').gsub('),)','))')
+    newstr.gsub(',)',")").gsub('(,','(').gsub("e-06","")
+  end
+end
+class NewickFile
+  attr_reader :newickStrings
+  def initialize(filename)
+    @newickStrings = File.open(filename).readlines.map{|line| NewickString.new(line)}
+    @filename = filename 
+  end
+  def size
+    @newickStrings.size
+  end
+  def save_each_newick_as(newfile_basename, ending)
+    @newickStrings.each_with_index do |newick, i|
+      File.open(newfile_basename + "_#{i}.#{ending}" , "w") do |f|
+        f.puts newick.str
+      end
+    end
+  end
+  def remove_taxa(taxa, pruned_tree, verbose = false)
+    nw_pruner = File.join ConfigData.bin_dir, "nw_prune"
+    nw_unrooter = File.join ConfigData.bin_dir, "nw_reroot"
+    [nw_pruner, nw_unrooter].each do |nw_util|
+      raise "#{nw_util} from newick utilities not available" unless File.exist?(nw_util)
+    end
+    # prune a list of taxa and unroot resulting tree with these nice and fast newick utilities
+    system "#{nw_pruner} #{@filename} #{taxa.join ' '} | #{nw_unrooter} -d - > #{pruned_tree}"
+    puts "removed #{taxa.join ','} and saved in #{pruned_tree}, use #{nw_pruner}" if verbose
+  end
+end
+
+=begin
+if __FILE__ == $0 then
+  # test usage
+  tree = NewickFile.new(tree_topology).newickStrings[0]
+  puts tree.numtaxa
+end
+=end

data/test/helper.rb

@@ -0,0 +1,18 @@
+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 'rnewick'
+
+class Test::Unit::TestCase
+end

data/test/test_rnewick.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestRnewick < 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

@@ -0,0 +1,149 @@
+--- !ruby/object:Gem::Specification 
+name: rnewick
+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: newick utilities
+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/rnewick.rb
+- test/helper.rb
+- test/test_rnewick.rb
+homepage: http://github.com/fizquierdo/rnewick
+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: newick utilities
+test_files: []
+