rphylip 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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+= rphylip
+
+Description goes here.
+
+== Contributing to rphylip
+ 
+* 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 = "rphylip"
+  gem.homepage = "http://github.com/fizquierdo/rphylip"
+  gem.license = "MIT"
+  gem.summary = "Helper functions to handle phylogenetic phylip formatted alignments" 
+  gem.description = "Build fake phylip alignments, extract names form a given alignment"
+  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 = "rphylip #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/lib/rphylip.rb

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+#!/usr/bin/env ruby
+def fisher_yates_shuffle(a)
+    (a.size-1).downto(1) do |i|
+      j = rand(i+1)
+      a[i], a[j] = a[j], a[i] if i != j
+    end
+end
+def pseudonormal(x,y)
+    num = 0
+    reps = 4
+    reps.times do
+     num += rand(y - x + 1) + x
+    end
+    num / reps
+end
+
+class Phylip
+  attr_reader :numtaxa, :seqlen, :seqs
+  def initialize(phylipfile)
+    raise "File #{phylipfile} does not exist" unless File.exists?(phylipfile)
+    @filename = phylipfile
+    @seqs = File.open(phylipfile).readlines
+    @numtaxa, @seqlen = @seqs[0].split.map{|w| w.to_i}
+    @seqs.delete_at(0)
+    @seqs.delete_if{|l| l=~ /^\s+$/}
+    raise "wrong number of seqs,parsed #{@seqs.size} expected ntaxa #{@numtaxa}" unless @seqs.size == @numtaxa
+  end
+  def names
+    ali_names = []
+    @seqs.each do |seq|
+      ali_names << seq.split.first.strip 
+    end
+    raise "unexpected #names" unless ali_names.size == @numtaxa
+    ali_names
+  end
+  def generate_base_alignment(numseqs_base)
+      seqs = @seqs[0...numseqs_base].select{|s| s.split.last.split(//).uniq.size > 1}
+      basename = @filename + "_initial"
+      puts "Saving base alignment as #{basename} with #{seqs.size} seqs"
+      raise "too few seqs" unless seqs.size > 4
+      self.save_seqs_as(seqs, basename)
+  end
+  def generate_update(seqs, update_filename)
+      # remove from seqs single char stuff
+      seqs = seqs.select{|s| s.split.last.split(//).uniq.size > 1}
+      puts "Saving update alignment as #{update_filename} with #{seqs.size} seqs"
+      raise "too few seqs" unless seqs.size > 4
+      self.save_seqs_as(seqs, update_filename)
+  end
+  def subdivide(numseqs_base, num_subalignments)
+    # Subdivides the present alignemnt in a file base.phy and num_subalignments (i) subi.phy 
+    # iterarions generated are of equal size
+    if numseqs_base.to_i + num_subalignments.to_i > @numtaxa then
+      raise "Wrong input to subdivide phylip file"
+    else
+      fisher_yates_shuffle(@seqs)
+      generate_base_alignment(numseqs_base)
+      # Generaute pseudo-new subsets of sequences
+      rest = @seqs[numseqs_base...@seqs.size]
+      subset_size = rest.size / num_subalignments 
+      update_sequences = [] 
+      rest.each_slice(subset_size) do |subset|
+        # Note the last slice may be shorter unless rest.size % num_subalignments == 0
+        if update_sequences.size < num_subalignments
+          update_sequences << subset # a new subset
+        else
+          update_sequences[num_subalignments - 1] += subset # appends to the last subset
+        end
+      end
+      update_sequences.each_with_index do |seqs, i|
+        generate_update(seqs, @filename + "_sequpdate_#{i}.phy")
+      end
+    end
+    return update_sequences.size 
+  end
+  def subdivide_random(conf)
+    numseqs_base = conf[:initial_seqs]
+    raise "too many seqs" if numseqs_base > @numtaxa
+    fisher_yates_shuffle(@seqs)
+    generate_base_alignment(numseqs_base)
+    n = numseqs_base
+    i = 0 #iteration id
+    srand(12345) # be deterministic
+    while n < @seqs.size
+      num_newseqs = pseudonormal(conf[:min_size_update], conf[:max_size_update])
+      num_newseqs = @seqs.size - n if (@seqs.size - n - num_newseqs < conf[:min_size_update])
+      if conf[:updates_as_full_alignments].nil? or not conf[:updates_as_full_alignments]
+        start = n
+      else
+        start = 0
+      end
+      generate_update(@seqs[start...n+num_newseqs], @filename + "_sequpdate_#{i}.phy")
+      n += num_newseqs 
+      i += 1
+    end
+    i
+  end
+  def save_as(newfile)
+    self.save_seqs_as(@seqs, newfile)
+  end
+  def save_seqs_as(seqs, newfile)
+    File.open(newfile, "w") do |f|
+      f.puts "#{seqs.size} #{@seqlen}"
+      seqs.each{|seq| f.puts seq}
+    end
+  end
+  def expand_with(phylipfile)
+    additional_phylip = Phylip.new(phylipfile)
+    if additional_phylip.seqlen == self.seqlen then
+      additional_phylip.seqs.each do |newseq|
+        @seqs << newseq
+        @numtaxa += 1
+      end
+    else
+      raise "different sequence lengths for new #{phylipfile}, cannot be expanded"
+    end
+  end
+  def extract_partition(from_pos, to_pos)
+    @seqlen = to_pos - from_pos  + 1
+    newseqs = []
+    from = from_pos - 1
+    to = to_pos - 1
+    @seqs.each do |seq|
+      name, info = seq.split
+      newseqs << name + " " + info.slice!(from..to) 
+    end
+    @seqs = newseqs
+    self.save_as(@filename + "_from#{from_pos}_to#{to_pos}")
+  end
+end

data/rphylip.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{rphylip}
+  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{2012-03-27}
+  s.description = %q{Build fake phylip alignments, extract names form a given alignment}
+  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",
+    "lib/rphylip.rb",
+    "rphylip.gemspec",
+    "test/helper.rb",
+    "test/test_rphylip.rb"
+  ]
+  s.homepage = %q{http://github.com/fizquierdo/rphylip}
+  s.licenses = [%q{MIT}]
+  s.require_paths = [%q{lib}]
+  s.rubygems_version = %q{1.8.6}
+  s.summary = %q{Helper functions to handle phylogenetic phylip formatted alignments}
+
+  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<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+  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 'rphylip'
+
+class Test::Unit::TestCase
+end

data/test/test_rphylip.rb

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+require 'helper'
+
+class TestRphylip < 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: rphylip
+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: Build fake phylip alignments, extract names form a given alignment
+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/rphylip.rb
+- rphylip.gemspec
+- test/helper.rb
+- test/test_rphylip.rb
+homepage: http://github.com/fizquierdo/rphylip
+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: Helper functions to handle phylogenetic phylip formatted alignments
+test_files: []
+