rphylip 0.1.0 → 0.2.0

data/Gemfile

@@ -8,7 +8,7 @@ source "http://rubygems.org"
 group :development do
   gem "shoulda", ">= 0"
   gem "rdoc", "~> 3.12"
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.8.3"
-  gem "rcov", ">= 0"
+  gem "bundler", "~> 1.1.3"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", "0.9.9"
 end

data/Gemfile.lock

@@ -2,14 +2,13 @@ GEM
   remote: http://rubygems.org/
   specs:
     git (1.2.5)
-    jeweler (1.8.3)
+    jeweler (1.6.4)
       bundler (~> 1.0)
       git (>= 1.2.5)
       rake
-      rdoc
     json (1.6.6)
     rake (0.9.2.2)
-    rcov (1.0.0)
+    rcov (0.9.9)
     rdoc (3.12)
       json (~> 1.4)
     shoulda (3.0.1)
@@ -22,8 +21,8 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  bundler (~> 1.0.0)
-  jeweler (~> 1.8.3)
-  rcov
+  bundler (~> 1.1.3)
+  jeweler (~> 1.6.4)
+  rcov (= 0.9.9)
   rdoc (~> 3.12)
   shoulda

data/Rakefile

@@ -1,6 +1,5 @@
 # encoding: utf-8
 
-require 'rubygems'
 require 'bundler'
 begin
   Bundler.setup(:default, :development)

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/example.rb

@@ -0,0 +1,18 @@
+#!/usr/bin/env ruby
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), "lib")
+
+require 'rphylip'
+
+p = Phylip.new("testdata/7")
+
+names =  p.names
+puts "Names #{names.to_s}"
+
+puts "Prune the first two"
+list_to_prune = []
+2.times{list_to_prune.push names.pop}
+p list_to_prune
+
+pruned_phylip = "testdata/7.pruned"
+p.remove_taxa(list_to_prune, pruned_phylip)
+

data/lib/rphylip.rb

@@ -95,6 +95,15 @@ class Phylip
     end
     i
   end
+  def remove_taxa(taxa, pruned_phylip)
+    puts "Original size #{@seqs.size}, after removal expect #{@seqs.size - taxa.size}"
+    raise "empty list of taxa to prune" if not taxa or taxa.empty?
+    taxa.each do |taxon|
+      @seqs.delete_if{|l| l.split.first.strip == taxon}
+    end
+    self.save_as(pruned_phylip)
+    puts "Final size #{@seqs.size} saved in #{pruned_phylip}"
+  end
   def save_as(newfile)
     self.save_seqs_as(@seqs, newfile)
   end

data/rphylip.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{rphylip}
-  s.version = "0.1.0"
+  s.version = "0.2.0"
 
   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.date = %q{2012-06-08}
   s.description = %q{Build fake phylip alignments, extract names form a given alignment}
   s.email = %q{fer.izquierdo@gmail.com}
   s.extra_rdoc_files = [
@@ -24,10 +24,12 @@ Gem::Specification.new do |s|
     "README.rdoc",
     "Rakefile",
     "VERSION",
+    "example.rb",
     "lib/rphylip.rb",
     "rphylip.gemspec",
     "test/helper.rb",
-    "test/test_rphylip.rb"
+    "test/test_rphylip.rb",
+    "testdata/7"
   ]
   s.homepage = %q{http://github.com/fizquierdo/rphylip}
   s.licenses = [%q{MIT}]
@@ -41,22 +43,22 @@ Gem::Specification.new do |s|
     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"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.1.3"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, ["= 0.9.9"])
     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"])
+      s.add_dependency(%q<bundler>, ["~> 1.1.3"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, ["= 0.9.9"])
     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"])
+    s.add_dependency(%q<bundler>, ["~> 1.1.3"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, ["= 0.9.9"])
   end
 end
 

data/testdata/7

@@ -0,0 +1,8 @@
+7 1200
+Seq1 ATGACCAACATTCGAAAATCACACCCCCTTATCAAAATCGTTAATCACTCATTCATCGATTTACCCACCCCACCTAACATTTCAGCATGATGAAACTTCGGCTCCCTACTAGGAGTCTGCCTAGTCCTACAGATCCTAACCGGCCTTTTCCTAGCCATACACTACACATCAGACACAATAACCGCCTTTTCATCAGTTACTCACATCTGCCGCGACGTCAACTACGGCTGAATTATTCGATACATGCACGCCAACGGAGCCTCTATATTCTTTATCTGCCTATACATGCATGTAGGACGAGGAATATACTACGGCTCCTACACCTTCTCAGAAACATGAAATATTGGAATCATACTACTACTCACAGTCATAGCCACAGCCTTCATAGGATATGTCTTACCATGAGGTCAAATATCTTTCTGAGGAGCAACTGTAATTACCAACCTCCTATCAGCAATTCCTTACATCGGCACTAATCTAGTAGAGTGAATTTGAGGAGGTTTCTCGGTAGACAAAGCTACCCTGACACGATTCTTTGCCTTCCACTTTATCCTTCCATTCATCATCTCAGCCCTAGCAGCAGTACACCTCTTATTTCTCCACGAGACAGGATCCAATAACCCCTCAGGAATCACATCCGACTCAGACAAAATTCCATTCCACCCATACTACATAATCAAGGACATTCTAGGTCTCCTAATACTAATTTTAATACTCACACTACTCGTCCTCTTCTCACCAGACCTGTTAGGAGATCCAGACAACTACATCCCCGCCAACCCCCTAAACACTCCTCCCCATATTAAACCCGAATGATATTTTTTATTCGCATACGCAATCCTCCGATCCATCCCTAACAAATTAGGAGGAGTCCTAGCCCTAATATTCTCCATCCTAATCCTAGCAATCATTCCAATTTTCCACACCTCCAAACAACGAGGAATAATATTTCGACCACTAAGCCAATGCTTATTCTGACTCCTAGTAGCAGACCTCCTCACCCTAACATGAATTGGCGGCCAACCTGTAGAACACCCCTTTATTACCATCGGCCAACTAGCCTCCATTCTATACTTCTCAACCCTCCTAGTTCTAATACCTATTTCAGGCATCATCGAAAACCGCCTCCTA------AAATGA------------------------------------------------------AGA
+Seq2 ATGAAAATTATACGAAAAACACACCCACTCCTAAAAATCATTAACCATGCATTCGTCGACCTCCCTGCACCCTCCAACATCTCATCATGATGAAACTTCGGCTCTCTATTAGGAGTATGCCTAATAATCCAAATCCTCACAGGACTGTTTCTAGCAATACACTACACCTCAGACACTATAACAGCATTCTCATCCGTAACCCACATCTGCCGAGACGTAAATTACGGTTGACTGATTCGATACCTCCATGCAAACGGAGCCTCCATGTTCTTCATGTGCTTATTCATACACGTAGGACGAGGCATCTACTATGGGTCCTACACCTTTATAGAGACATGAAACCTTGGTATTATTCTACTGTTTGCCGTAATAGCAACTGCATTTATAGGATATGTCCTCCCATGGGGGCAAATATCCTTCTGAGGGGCCACAGTCATCACAAACCTACTTTCAGCCATCCCCTACATCGGTACTAACCTAGTAGAATGAATCTGAGGCGGATTTTCAGTAGACAAAGCCACCCTTACACGCTTCTTCGCATTCCACTTTATCCTCCCCTTTATTATTGCAGCTCTGGCCATGGTACACCTACTTTTTCTCCACGAAACAGGCTCTAATAACCCCACAGGAATGAACTCCGATGCAGACAAAATCCCCTTCCACCCCTACTACACAATCAAAGACCTCTTAGGTGTATTCCTCATACTGTCAGTCCTCCTCCTATTAGTACTTTTCTCCCCAGACCTATTAGGAGACCCCGACAACTATACACCAGCTAACCCCCTAAACACCCCTCCTCACATTAAGCCAGAATGATACTTTCTATTTGCATATGCTATCCTACGCTCTATCCCCAACAAACTAGGAGGCGTATTAGCCCTAGTACTATCCATCCTAATCCTAGCTTTTATACCTCTCACCTACACCTTAAAACAACGAATCTTAATATTCCGCCCAATCAGCCAGACCATATTCTGAATCCTAGCAGCCAACCTACTTATCCTAACCTGAATCGGAGGACAACCCGTAGAACACCCCTTCATCATTATTGGCCAACTAGCTTCAATCAGCTACTTCTCCATCATTTTAATTCTAATACCAATCTCAGGACTAATCGAAAACAAAATACTAAAACTA------AAC---------------------------------------------------T--
+Seq3 ATGAAAATTATACGAAAAACACACCCACTCCTAAAAATCATTAATCACGCATTCGTCGACCTCCCTGCACCCTCTAACATCTCATCATGATGAAACTTCGGCTCCCTATTAGGAGTATGCCTAATAATCCAAATCCTCACAGGACTATTTCTAGCAATACACTACACCTCCGACACTACAACAGCATTCTCATCCGTAACCCACATCTGCCGAGACGTAAACTACGGCTGATTAATTCGATACCTCCATGCAAATGGGGCTTCCATATTCTTCATGTGCTTATTCATACACGTAGGACGAGGCATTTATTATGGGTCTTACACCTTCACAGAGACATGAAACCTTGGTATCATTCTACTGTTTGCCGTAATAGCAACTGCATTTATAGGATATGTCCTTCCATGGGGACAAATATCCTTCTGAGGGGCCACAGTCATTACAAACCTACTCTCAGCCATCCCCTACATCGGCACTGACCTGGTAGAGTGAATCTGAGGCGGGTTTTCAGTAGACAAAGCCACCCTTACACGCTTCTTCGCATTCCACTTTATTCTCCCCTTTATCATTGCAGCCCTAGCCATAGTACACCTACTCTTTCTACACGAAACAGGCTCTAATAACCCCACAGGAGTGAACTCCGATGCAGACAAAATCCCCTTCCACCCCTACTACACAATCAAAGACCTTTTAGGTGTATTCCTCATACTATTAGTCCTCCTCCTATTAGTACTATTCTCCCCAGACCTACTAGGAGACCCCGACAACTACACACCAGCTAACCCCCTGAACACCCCTCCTCACATTAAACCAGAATGATATTTCCTATTCGCATATGCTATTCTACGCTCCATCCCCAACAAACTCGGAGGCGTACTAGCTCTAGTAATATCTATCCTAATCCTAATTTTCATACCCCTCACCCACACCTCAAAACAACGAAGCTTAATATTCCGCCCAATCAGTCAGGCTATATTCTGAATCCTAACAGCTAACCTACTTATCCTAACCTGAATCGGAGGACAACCCGTAGAACACCCCTTTATCATTATCGGCCAACTAGCTTCAATCAGCTATTTCTCCATCATTTTAATCCTAATACCAATCTCAGGACTAATTGAAAACAAAATACTAAAATTA------AAC---------------------------------------------------T--
+Seq4 ATGAAAATTATACGAAAAACACACCCACTCATAAAAATTATCAACCACGCATTCATCGATCTCCCTGCACCCTCCAACATCTCATCATGATGAAACTTTGGTTCTCTATTAGGAGTATGCCTAATAGTCCAAATCCTCACAGGCCTATTCTTAGCAATACACTACACCTCCGACACTATAACAGCATTCACATCCGTAACCCACATCTGCCGAGACGTAAACTACGGCTGATTAATTCGATATCTCCATGCAAACGGAGCCTCCATATTCTTCGTATGCTTGTTTATACACGTAGGACGAGGAATCTACTATGGATCTTACACCTTTACAGAAACATGAAATCTTGGTGTTATTCTACTATTTGCCGTAATAGCAACTGCATTTATAGGATATGTACTTCCATGAGGACAAATATCCTTCTGAGGAGCCACAGTCATTACAAACCTTCTCTCAGCTATTCCCTACATCGGTACTAACCTAGTAGAATGAATTTGAGGGGGGTTCTCAGTAGACAAAGCCACCCTCACACGCTTCTTCGCATTCCACTTTATCCTTCCATTTATCATTGCAGCCCTAGCCATAGTACACCTACTATTCCTCCACGAAACAGGCTCTAATAACCCCACAGGAATGAACTCTGACGCAGATAAAATTCCCTTTCACCCCTACTATACAATCAAAGACCTCTTAGGCGTATTTCTCATACTACTAGTTCTCCTACTATTAGTACTATTTTCCCCAGACTTATTAGGAGACCCCGACAACTACACACCAGCCAACCCCCTAAATACCCCTCCCCACATTAAACCAGAGTGATATTTTCTATT-GCATACGCTATCCTACGCTCTATCCCCAATAAACTTGGAGGCGTACTAGCCCTAGTACTATCTATCCTAATCCTAATTCTCATACCCTTAATCCATACCTCAAAACAACGAAGCTTAATATTCCGTCCAATTAGCCAAATCATATTCTGAATCCTAACAGCTAACCTACTCATCCTGACCTGAATCGGAGGACAACCCGTAGAACATCCCTTTATCATTATCGGCCAACTAGCTTCAATCAGCTATTTCTCCATTATTCTAATCCTAATACCGATCTCAGGACTAATTGAAAATAAAATACTAAAATTA------AAC---------------------------------------------------T--
+Seq5 ATGAAAAACATACGAAAAACGCAACCACTCCTAAAAATTATTAACCACGAATTCATTGA-TTTCCTGAAACATCCAA-ATCTCATCATGATGAAACTTTGGCTCTCTACTAGGCATCTGCCTAGTAATCCAGATCCTAACAGGCTTATTCCTAGCAATACACTATACCTCCGACACCACCACAGCATTTTCATCTGTAACCCACATTTGCCGAGACGTAAACTACGGCTGACTGATTCGTTACCTCCATGCAAATGGAGCCTCCATATTCTTCATGTGCCTGTTCATACATGTAGGACGGGGAATCTACTACGGATCTTATACCTTCATAGAAACCTGAAATCTCGGCATTATTCTACTGTTCGCCGTAATAGCAACTGCATTTATAGGATATGTACTCCCATGAGGACAGATATCCTTCTGAGGGGCCACAGTCATTACAAATCTACTCTCAGCTATCCCCTACATCGGAACTAATCTAGTAGAGTGAATTTGAGGAGGCTTCTCAGTAGACAAAGCCACTCTAACACGCTTTTTCGCATTCCACTTTATCCTACCCTTTATCATTGCAGCCCTAGCTATAGTCCACCTACTATTCCTCCACGAAACAGGATCTAACAA-CCCACCGGGATAAACTCTGACGCAGATAAAATCCCCTTTCATCCCTACTACACAATTAAAGATCTCCTAGGAGTATTCCTAATATTAACAGCCCTACTCTTATTAGTCCTCTTCTCCCCAGACTTATTAGGAGACCCCGACAACTACACACCAGCCAACCCCCTAAACACCCCTCCCCACATCAAACCAGAATGATATTTCCTATTTGCATACGCCATCCTACGCTCTATTCCTAACAAACTCGGAGGAGTACTAGCCCTAGTGCTATCAATCCTAATCCTAATTTTTTTACCCTTCATCCACACTTCCAAACAACGAAGCCTAATATTCCGCCCAATCAGCCAAACCATATTTTGAATCCTAGCAGCAAATCTTCTTGTCCTAACCTGAATCGGAGGACAACCTGTAGAATACCCCTTCACCATTATTGGCCAACTAGCCTCAATCAGTTATTTCTCTATTATCCTAATCCTACTACCAATCTCAGGTCTAATC-AAAATAAAATAATAAAAATA------AAC---------------------------------------------------T--
+Seq6 ATGAAAATTATACGAAAAACACACCCACTCCTAAAAATCATTAATCACGCATTCGTCGACCTCCCTGCACCCTCTAACATCTCATCATGATGAAACTTCGGCTCCCTATTAGGAGTATGCCTAATAATCCAAATCCTCACAGGACTATTTCTAGCAATACACTACACCTCCGACACTACAACAGCATTCTCATCCGTAACCCACATCTGCCGAGACGTAAACTACGGCTGATTAATTCGATACCTCCATGCAAATGGGGCTTCCATATTCTTCATGTGCTTATTCATACACGTAGGACGAGGCATTTATTATGGGTCTTACACCTTCACAGAGACATGAAACCTTGGTATCATTCTACTGTTTGCCGTAATAGCAACTGCATTTATAGGATATGTCCTTCCATGGGGACAAATATCCTTCTGAGGGGCCACAGTCATTACAAACCTACTCTCAGCCATCCCCTACATCGGCACTGACCTGGTAGAGTGAATCTGAGGCGGGTTTTCAGTAGACAAAGCCACCCTTACACGCTTCTTCGCATTCCACTTTATTCTCCCCTTTATCATTGCAGCCCTAGCCATAGTACACCTACTCTTTCTACACGAAACAGGCTCTAATAACCCCACAGGAGTGAACTCCGATGCAGACAAAATCCCCTTCCACCCCTACTACACAATCAAAGACCTTTTAGGTGTATTCCTCATACTATTAGCCCTCCTCCTATTAGTACTATTCTCCCCAGACCTACTAGGAGACCCCGACAACTACACACCAGCTAACCCCCTGAACACCCCTCCTCACATTAAACCAGAATGATATTTCCTATTCGCATATGCTATTCTACGCTCCATCCCCAACAAACTCGGAGGCGTACTAGCTCTAGTAATATCTATCCTAATCCTAATTTTCATACCCCTCACCCACACCTCAAAACAACGAAGCTTAATATTCCGCCCAATCAGTCAGGCTATATTCTGAATCCTAACAGCTAACCTACTTATCCTAACCTGAATCGGAGGACAACCCGTAGAACACCCCTTTATCATTATCGGCCAACTAGCTTCAATCAGCTATTTCTCCATCATTTTAATCCTAATACCAATCTCAGGACTAATTGAAAACAAAATACTAAAATTA------AAC---------------------------------------------------T--
+Seq7 ATGAAAATTATACGAAAAACACACCCACTCCTAAAAATCATTAATCACGCATTCGTCGACCTCCCTGCACCCTCTAATATCTCATCATGATGAAACTTCGGCTCCCTATTAGGAGTATGCCTAGTAATCCAAATCCTCACAGGATTATTTCTAGCAATACACTACACCTCCGACACTATAACAGCATTCTCATCCGTAACCCACATCTGCCGAGACGTAAACTACGGCTGATTAATTCGATACCTCCATGCAAATGGGGCTTCCATATTCTTCGTGTGCTTATTCATACACGTAGGACGAGGCATTTATTATGGATCTTACACCTTCACAGAGACATGAAACCTTGGTATCATTCTACTGTTTGCCGTAATAGCAACTGCATTTATAGGGTATGTCCTTCCATGGGGACAAATATCCTTCTGAGGGGCCACAGTCATTACAAACCTACTCTCAGCCATCCCCTACATCGGCACTGACCTGGTAGAGTGAATCTGAGGCGGGTTTTCAGTAGACAAAGCCACCCTTACACGCTTCTTCGCATTCCACTTTATTCTCCCCTTTATCATTGCAGCCCTAGCCATAGTACACCTACTCTTTCTACACGAAACAGGCTCTAATAACCCCACAGGAGTAAACTCCGATGCAGACAAAATCCCCTTCCACCCCTACTACACAATCAAAGACCTTTTAGGTGTTTTCCTCATACTATTAGTCCTCCTCCTACTAGTACTATTCTCCCCAGATCTACTAGGAGACCCCGACAACTACACACCAGCTAACCCCCTGAACACCCCTCCTCACATTAAACCAGAATGGTATTTCCTATTCGCATATGCTATTCTACGCTCCATCCCCAACAAACTCGGAGGTGTACTAGCTCTAGTAATATCTATCCTAATCCTAATTTTCATACCCCTCACCCACACCTCAAAACAACGAAGCTTAATATTCCGCCCAATCAGTCAGGCTATATTCTGAATCCTAACAGCTAACCTACTTATCCTAACCTGAATCGGAGGACAACCCGTAGAACACCCCTTTATCATTATCGGCCAACTAGCTTCAATCAGCTACTTCTCCATTATTTTAATCCTAATACCAATCTCAGGACTAATTGAAAACAAAATACTAAAATTA------AAC---------------------------------------------------T--

metadata

@@ -1,107 +1,79 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: rphylip
-version: !ruby/object:Gem::Version 
-  hash: 27
+version: !ruby/object:Gem::Version
+  version: 0.2.0
   prerelease: 
-  segments: 
-  - 0
-  - 1
-  - 0
-  version: 0.1.0
 platform: ruby
-authors: 
+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
+date: 2012-06-08 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: shoulda
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+  requirement: &14769180 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *14769180
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &14768660 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 31
-        segments: 
-        - 3
-        - 12
-        version: "3.12"
-  version_requirements: *id002
-  name: rdoc
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+      - !ruby/object:Gem::Version
+        version: '3.12'
   type: :development
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *14768660
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &14768120 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    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 
+      - !ruby/object:Gem::Version
+        version: 1.1.3
   type: :development
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *14768120
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &14767600 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    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 
+      - !ruby/object:Gem::Version
+        version: 1.6.4
   type: :development
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id005
+  prerelease: false
+  version_requirements: *14767600
+- !ruby/object:Gem::Dependency
   name: rcov
+  requirement: &14767060 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - =
+      - !ruby/object:Gem::Version
+        version: 0.9.9
+  type: :development
   prerelease: false
+  version_requirements: *14767060
 description: Build fake phylip alignments, extract names form a given alignment
 email: fer.izquierdo@gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - .document
 - Gemfile
 - Gemfile.lock
@@ -109,42 +81,38 @@ files:
 - README.rdoc
 - Rakefile
 - VERSION
+- example.rb
 - lib/rphylip.rb
 - rphylip.gemspec
 - test/helper.rb
 - test/test_rphylip.rb
+- testdata/7
 homepage: http://github.com/fizquierdo/rphylip
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: 198981227287080683
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      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: []
-