scaffolder 0.2.6

data/.document

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

data/.gitignore

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+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+doc
+.yardoc
+pkg
+
+## PROJECT::SPECIFIC

data/LICENSE

@@ -0,0 +1,20 @@
+Copyright (c) 2009 Michael Barton
+
+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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+= scaffolder
+
+Description goes here.
+
+== Note on Patches/Pull Requests
+ 
+* Fork the project.
+* Make your feature addition or bug fix.
+* Add tests for it. This is important so I don't break it in a
+  future version unintentionally.
+* Commit, do not mess with rakefile, version, or history.
+  (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)
+* Send me a pull request. Bonus points for topic branches.
+
+== Copyright
+
+Copyright (c) 2010 Michael Barton. See LICENSE for details.
+
+== Notes
+
+Inserts processed are processed in reverse order according to end position. Last insert added up until first insert. Done to preserve insert coordinates.
+
+Overlapping inserts may cause unexpected behaviour
+
+Sequence reversed after inserts have been added.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "scaffolder"
+    gem.summary = %Q{Scaffolder for genome sequence data}
+    gem.description = %Q{Organise genome sequence data into scaffolds using YAML configuration files.}
+    gem.email = "mail@michaelbarton.me.uk"
+    gem.homepage = "http://github.com/michaelbarton/scaffolder"
+    gem.authors = ["Michael Barton"]
+    gem.add_dependency "bio", ">= 0"
+    gem.add_development_dependency "rr", ">= 0.10.11"
+    gem.add_development_dependency "shoulda", ">= 0"
+    gem.add_development_dependency "redgreen", ">= 0"
+    gem.add_development_dependency "yard", ">= 0"
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+  Jeweler::GemcutterTasks.new
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
+end
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+begin
+  require 'rcov/rcovtask'
+  Rcov::RcovTask.new do |test|
+    test.libs << 'test'
+    test.pattern = 'test/**/test_*.rb'
+    test.verbose = true
+  end
+rescue LoadError
+  task :rcov do
+    abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
+  end
+end
+
+task :test => :check_dependencies
+
+task :default => :test
+
+begin
+  require 'yard'
+  YARD::Rake::YardocTask.new
+rescue LoadError
+  task :yardoc do
+    abort "YARD is not available. In order to run yardoc, you must: sudo gem install yard"
+  end
+end

data/VERSION

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+0.2.6

data/lib/scaffolder.rb

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+require 'delegate'
+require 'bio'
+
+class Scaffolder < DelegateClass(Array)
+  autoload :Region,   'scaffolder/region'
+  autoload :Insert,   'scaffolder/insert'
+  autoload :Sequence, 'scaffolder/sequence'
+
+  def initialize(assembly,sequence)
+    @sequences = Hash[ *Bio::FlatFile::auto(sequence).collect { |s|
+      [s.definition.split.first,s.seq]
+    }.flatten]
+
+    super(assembly.map do |entry|
+      type, data = entry.keys.first, entry.values.first
+
+      case type
+      when 'unresolved'
+        Scaffolder::Region.new(:unresolved,'N'*data['length'])
+      when 'sequence'
+        sequence = Scaffolder::Sequence.new(
+          :name     => data['source'],
+          :start    => data['start'],
+          :end      => data['end'],
+          :reverse  => data['reverse'],
+          :sequence => fetch_sequence(data['source'])
+        )
+        if data['inserts']
+          sequence.add_inserts(data['inserts'].map do |insert|
+            Scaffolder::Insert.new(
+              :start    => insert['start'],
+              :stop     => insert['stop'],
+              :reverse  => insert['reverse'],
+              :sequence => fetch_sequence(insert['source'])
+            )
+          end)
+        end
+        sequence
+      else
+        raise ArgumentError.new("Unknown tag: #{type}")
+      end
+    end)
+  end
+
+  def fetch_sequence(name)
+    sequence = @sequences[name]
+    raise ArgumentError.new("Missing sequence: #{name}") unless sequence
+    sequence
+  end
+
+end

data/lib/scaffolder/insert.rb

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+class Scaffolder
+  class Insert
+    include Comparable
+
+    attr_accessor :start, :stop, :sequence
+
+    def initialize(options)
+      @sequence = options[:sequence]
+      @start    = options[:start]
+      @stop     = options[:stop]
+
+      m = "Either insert start or stop must be provided"
+      raise ArgumentError.new(m) if @start.nil? and @stop.nil?
+
+      @start ||= (@stop  - @sequence.length - 1)
+      @stop  ||= (@start + @sequence.length - 1)
+
+      if options[:reverse]
+        @sequence = Bio::Sequence::NA.new(@sequence).reverse_complement.seq.upcase
+      end
+    end
+
+    def position
+      @start-1..@stop-1
+    end
+
+    def <=>(other)
+      self.stop <=> other.stop
+    end
+
+  end
+end

data/lib/scaffolder/region.rb

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+Scaffolder::Region = Struct.new(:entry_type,:sequence)

data/lib/scaffolder/sequence.rb

@@ -0,0 +1,50 @@
+class Scaffolder
+  class Sequence
+
+    attr_accessor :entry_type, :start, :end, :name, :inserts, :raw_sequence
+
+    def initialize(options)
+      @entry_type   = :sequence
+      @name         = options[:name]
+      @start        = options[:start] || 1
+      @end          = options[:end]   || options[:sequence].length
+      @sequence     = options[:sequence]
+      @raw_sequence = @sequence.clone
+      @reverse      = options[:reverse]
+      @inserts      = []
+
+      raise ArgumentError.new("Sequence end greater than length") if @end > @raw_sequence.length
+      raise ArgumentError.new("Sequence start less than 0") if @start < 1
+      raise ArgumentError.new("Sequence start greater than end") if @start > @end
+
+    end
+
+    def add_inserts(inserts)
+      @inserts = inserts.sort.reverse
+      @inserts.each do |insert|
+        if insert.start > @sequence.length
+          raise ArgumentError.new("Insert start greater than length")
+        end
+        if insert.stop < 1
+          raise ArgumentError.new("Insert end less than 1")
+        end
+        if insert.stop <= insert.start
+          raise ArgumentError.new("Insert end less than start")
+        end
+
+        before_size = @sequence.length
+        @sequence[insert.position] = insert.sequence
+
+        # Update sequence end after adding inserts
+        diff = @sequence.length - before_size
+        @end += diff
+      end
+    end
+
+    def sequence
+      seq = @sequence[(@start-1)..(@end-1)]
+      seq = Bio::Sequence::NA.new(seq).reverse_complement if @reverse
+      seq.to_s.upcase
+    end
+  end
+end

data/scaffolder.gemspec

@@ -0,0 +1,76 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{scaffolder}
+  s.version = "0.2.6"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Michael Barton"]
+  s.date = %q{2010-10-10}
+  s.description = %q{Organise genome sequence data into scaffolds using YAML configuration files.}
+  s.email = %q{mail@michaelbarton.me.uk}
+  s.extra_rdoc_files = [
+    "LICENSE",
+     "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+     ".gitignore",
+     "LICENSE",
+     "README.rdoc",
+     "Rakefile",
+     "VERSION",
+     "lib/scaffolder.rb",
+     "lib/scaffolder/insert.rb",
+     "lib/scaffolder/region.rb",
+     "lib/scaffolder/sequence.rb",
+     "scaffolder.gemspec",
+     "test/data/sequences.fna",
+     "test/helper.rb",
+     "test/test_insert.rb",
+     "test/test_region.rb",
+     "test/test_scaffolder.rb",
+     "test/test_sequence.rb"
+  ]
+  s.homepage = %q{http://github.com/michaelbarton/scaffolder}
+  s.rdoc_options = ["--charset=UTF-8"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{Scaffolder for genome sequence data}
+  s.test_files = [
+    "test/helper.rb",
+     "test/test_insert.rb",
+     "test/test_region.rb",
+     "test/test_scaffolder.rb",
+     "test/test_sequence.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<bio>, [">= 0"])
+      s.add_development_dependency(%q<rr>, [">= 0.10.11"])
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<redgreen>, [">= 0"])
+      s.add_development_dependency(%q<yard>, [">= 0"])
+    else
+      s.add_dependency(%q<bio>, [">= 0"])
+      s.add_dependency(%q<rr>, [">= 0.10.11"])
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<redgreen>, [">= 0"])
+      s.add_dependency(%q<yard>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<bio>, [">= 0"])
+    s.add_dependency(%q<rr>, [">= 0.10.11"])
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<redgreen>, [">= 0"])
+    s.add_dependency(%q<yard>, [">= 0"])
+  end
+end
+

data/test/data/sequences.fna

@@ -0,0 +1,4 @@
+> sequence1
+ATGCCAGATAACTGACTAGCATG
+> insert1
+GGTAGTA

data/test/helper.rb

@@ -0,0 +1,15 @@
+require 'rubygems'
+require 'test/unit'
+require 'shoulda'
+require 'redgreen'
+require 'rr'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+require 'scaffolder'
+
+class Test::Unit::TestCase
+  require 'tempfile'
+  include RR::Adapters::TestUnit
+end

data/test/test_insert.rb

@@ -0,0 +1,60 @@
+require 'helper'
+
+class TestInsert < Test::Unit::TestCase
+  context Scaffolder::Insert do
+
+    setup do
+      @options = {
+        :start    => 5,
+        :stop     => 10,
+        :sequence => "ATGCGGGC"
+      }
+    end
+
+    should "correctly store the passed options" do
+      i = Scaffolder::Insert.new @options
+      assert_equal(i.start, @options[:start])
+      assert_equal(i.stop, @options[:stop])
+      assert_equal(i.sequence, @options[:sequence])
+    end
+
+    should "reverse the sequence when passed the reverse tag" do
+      i = Scaffolder::Insert.new @options.merge(:reverse => true)
+      rev = Bio::Sequence::NA.new(@options[:sequence]).reverse_complement
+      assert_equal(i.sequence, rev.upcase)
+    end
+
+    should "correctly generate the position" do
+      i = Scaffolder::Insert.new @options
+      assert_equal(i.position, (@options[:start]-1)..(@options[:stop]-1))
+    end
+
+    should "estimate the sequence end position" do
+      @options.delete(:stop)
+      i = Scaffolder::Insert.new @options
+      assert_equal(i.stop, @options[:start] + @options[:sequence].length - 1)
+    end
+
+    should "estimate the sequence start position" do
+      @options.delete(:start)
+      i = Scaffolder::Insert.new @options
+      assert_equal(i.start, @options[:stop] - @options[:sequence].length - 1)
+    end
+
+    should "throw error when neither start or stop are provided" do
+      @options.delete(:start)
+      @options.delete(:stop)
+      assert_raise ArgumentError do
+        Scaffolder::Insert.new @options
+      end
+    end
+
+    should "be comparable by end position" do
+      a = Scaffolder::Insert.new @options
+      b = Scaffolder::Insert.new @options.merge(:stop => @options[:stop] + 1)
+      c = Scaffolder::Insert.new @options.merge(:stop => @options[:stop] + 2)
+      assert_equal([c,a,b].sort, [a,b,c])
+    end
+
+  end
+end

data/test/test_region.rb

@@ -0,0 +1,11 @@
+require 'helper'
+
+class TestScaffolder < Test::Unit::TestCase
+  context Scaffolder::Region do
+    should "be created from parameters" do
+      region = Scaffolder::Region.new(:unresolved,'NNNN')
+      assert_equal(region.entry_type,:unresolved)
+      assert_equal(region.sequence,'NNNN')
+    end
+  end
+end

data/test/test_scaffolder.rb

@@ -0,0 +1,85 @@
+require 'helper'
+
+class TestScaffolder < Test::Unit::TestCase
+  context Scaffolder do
+    
+    setup do
+      @sequence = File.join(File.dirname(__FILE__),'data','sequences.fna')
+        @assembly = [ {"sequence" => { "source" => "sequence1" } } ]
+        @expect = {:name => 'sequence1', :start => nil, :end => nil,
+          :sequence => 'ATGCCAGATAACTGACTAGCATG', :reverse => nil}
+    end
+
+    context "when parsing a sequence tag" do
+
+      should "create sequence" do
+        mock(Scaffolder::Sequence).new(@expect)
+        Scaffolder.new @assembly, @sequence
+      end
+
+      should "create sequence with coordinates" do
+        @assembly.first['sequence'].update('start' => 2, 'end' => 5)
+        mock(Scaffolder::Sequence).new(@expect.update({:start => 2, :end => 5 }))
+        Scaffolder.new @assembly, @sequence
+      end
+
+      should "create sequence with reverse" do
+        @assembly.first['sequence'].update('reverse' => true)
+        mock(Scaffolder::Sequence).new(@expect.update({:reverse => true }))
+        Scaffolder.new @assembly, @sequence
+      end
+
+      should "throw an error when source doesn't have a matching sequence" do
+        @assembly.first['sequence'].update('source' => 'sequence3')
+        assert_raise(ArgumentError){ Scaffolder.new @assembly, @sequence }
+      end
+    end
+
+    context "parsing an assembly with sequence inserts" do
+
+      setup do
+        @assembly.first['sequence'].update({"inserts" => [{
+          "source" => "insert1", "start" => 5, "stop" => 10, "reverse" => true
+        }]})
+      end
+
+      should "pass inserts to sequence object" do
+        params = {:start => 5, :stop => 10,
+          :sequence => 'GGTAGTA', :reverse => true}
+
+        insert = Scaffolder::Insert.new(params)
+
+        mock.instance_of(Scaffolder::Sequence).add_inserts([insert])
+        mock(Scaffolder::Insert).new(params){insert}
+
+        Scaffolder.new @assembly, @sequence
+      end
+
+      should "throw and error when insert does not have a matching sequence" do
+        @assembly.first['sequence']['inserts'].first.update({
+          "source" => "missing"})
+        assert_raise(ArgumentError){ Scaffolder.new @assembly, @sequence }
+      end
+
+    end
+
+    context "when parsing an assembly with an unresolved region" do
+
+      setup{ @assembly = [ {"unresolved" => { "length" => 5 } } ] }
+
+      should 'create an unresolved region' do
+        mock(Scaffolder::Region).new(:unresolved,'N'*5)
+        Scaffolder.new @assembly, @sequence
+      end
+
+    end
+
+    context "when parsing an unknown tag" do
+      setup{ @assembly = [{'non_standard_tag' => []}] }
+      should "throw an argument error" do
+        assert_raise(ArgumentError){ Scaffolder.new @assembly, @sequence }
+      end
+    end
+
+  end
+end

data/test/test_sequence.rb

@@ -0,0 +1,124 @@
+require 'helper'
+
+class TestScaffolder < Test::Unit::TestCase
+  context Scaffolder::Sequence do
+
+    setup do
+      @options = { :name => "sequence1",
+        :sequence => 'ATGCCAGATAACTGACTAGCATG' }
+    end
+
+    context "processing a simple sequence tag" do
+
+      should "create sequence object" do
+        sequence = Scaffolder::Sequence.new @options
+        assert_equal(sequence.entry_type,:sequence)
+        assert_equal(sequence.start,1)
+        assert_equal(sequence.end,23)
+        assert_equal(sequence.name,'sequence1')
+        assert_equal(sequence.sequence,'ATGCCAGATAACTGACTAGCATG')
+        assert_equal(sequence.raw_sequence,'ATGCCAGATAACTGACTAGCATG')
+      end
+
+      should "reverse sequence when passed the reverse option" do
+        sequence = Scaffolder::Sequence.new @options.merge(:reverse => true)
+        assert_equal(sequence.sequence,'CATGCTAGTCAGTTATCTGGCAT')
+        assert_equal(sequence.raw_sequence,'ATGCCAGATAACTGACTAGCATG')
+      end
+
+      should "create subsequence object when passed sequence coordinates" do
+        sequence = Scaffolder::Sequence.new @options.merge(:start => 5,:end => 20)
+        assert_equal(sequence.start,5)
+        assert_equal(sequence.end,20)
+        assert_equal(sequence.sequence,'CAGATAACTGACTAGC')
+      end
+
+      should "throw an error when the start position is outside the sequence length" do
+        begin
+          Scaffolder::Sequence.new @options.merge(:start => 0)
+          flunk "Should throw an argument error"
+        rescue ArgumentError
+        end
+      end
+
+      should "throw an error when the end position is outside the sequence length" do
+        begin
+          Scaffolder::Sequence.new @options.merge(:end => 24)
+          flunk "Should throw an argument error"
+        rescue ArgumentError
+        end
+      end
+
+      should "throw an error when the start is greater than the end" do
+        begin
+          Scaffolder::Sequence.new @options.merge(:end => 5,:start => 10)
+          flunk "Should throw an argument error"
+        rescue ArgumentError
+        end
+      end
+
+    end
+
+    context "processing a sequence tag with inserts" do
+
+      setup do
+        @insert = {:start => 5, :stop => 10, :sequence => 'GGTAGTA'}
+        @sequence = Scaffolder::Sequence.new @options
+      end
+
+      should "raise when the insert start is after the sequence end" do
+        @insert.update(:start => 24,:stop => nil)
+        assert_raise(ArgumentError) do
+          @sequence.add_inserts([Scaffolder::Insert.new @insert])
+        end
+      end
+
+      should "raise when the insert stop is before the sequence start" do
+        @insert.update(:start => -5,:stop => 0)
+        assert_raise(ArgumentError) do
+          @sequence.add_inserts([Scaffolder::Insert.new @insert])
+        end
+      end
+
+      should "raise when insert start is greater than end" do
+        @insert.update(:start => 11)
+        assert_raise(ArgumentError) do
+          @sequence.add_inserts([Scaffolder::Insert.new @insert])
+        end
+      end
+
+      should "update the sequence" do
+        @sequence.add_inserts([Scaffolder::Insert.new @insert])
+        assert_equal(@sequence.sequence,'ATGCGGTAGTAACTGACTAGCATG')
+        assert_equal(@sequence.end,24)
+        assert_equal(@sequence.raw_sequence,'ATGCCAGATAACTGACTAGCATG')
+      end
+
+      should "return added insert as an attribute" do
+        inserts = [Scaffolder::Insert.new @insert]
+        @sequence.add_inserts(inserts)
+        assert_equal(@sequence.inserts,inserts)
+      end
+
+      should "return empty array when no inserts and inserts method called" do
+        assert_equal(@sequence.inserts,[])
+      end
+
+      should "update the sequence when reversed" do
+        @sequence = Scaffolder::Sequence.new @options.update(:reverse => true)
+        @sequence.add_inserts([Scaffolder::Insert.new @insert])
+        assert_equal(@sequence.sequence,"CATGCTAGTCAGTTACTACCGCAT")
+        assert_equal(@sequence.raw_sequence,'ATGCCAGATAACTGACTAGCATG')
+      end
+
+      should "update the sequence with two inserts" do
+        @sequence.add_inserts([Scaffolder::Insert.new(@insert),
+          Scaffolder::Insert.new(@insert.update(:start => 12, :stop => 15))])
+        assert_equal(@sequence.sequence,"ATGCGGTAGTAAGGTAGTACTAGCATG")
+        assert_equal(@sequence.end,27)
+        assert_equal(@sequence.raw_sequence,'ATGCCAGATAACTGACTAGCATG')
+      end
+    end
+
+  end
+end

metadata

@@ -0,0 +1,159 @@
+--- !ruby/object:Gem::Specification 
+name: scaffolder
+version: !ruby/object:Gem::Version 
+  hash: 27
+  prerelease: false
+  segments: 
+  - 0
+  - 2
+  - 6
+  version: 0.2.6
+platform: ruby
+authors: 
+- Michael Barton
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-10-10 00:00:00 -04:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: bio
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: rr
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 33
+        segments: 
+        - 0
+        - 10
+        - 11
+        version: 0.10.11
+  type: :development
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: redgreen
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: yard
+  prerelease: false
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id005
+description: Organise genome sequence data into scaffolds using YAML configuration files.
+email: mail@michaelbarton.me.uk
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- .document
+- .gitignore
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/scaffolder.rb
+- lib/scaffolder/insert.rb
+- lib/scaffolder/region.rb
+- lib/scaffolder/sequence.rb
+- scaffolder.gemspec
+- test/data/sequences.fna
+- test/helper.rb
+- test/test_insert.rb
+- test/test_region.rb
+- test/test_scaffolder.rb
+- test/test_sequence.rb
+has_rdoc: true
+homepage: http://github.com/michaelbarton/scaffolder
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+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: 1.3.7
+signing_key: 
+specification_version: 3
+summary: Scaffolder for genome sequence data
+test_files: 
+- test/helper.rb
+- test/test_insert.rb
+- test/test_region.rb
+- test/test_scaffolder.rb
+- test/test_sequence.rb