genomer-plugin-summary 0.0.1

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in genomer-plugin-summary.gemspec
+gemspec

data/LICENSE

@@ -0,0 +1,22 @@
+Copyright (c) 2012 Michael Barton
+
+MIT License
+
+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.md

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+# Genomer::Plugin::Summary
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'genomer-plugin-summary'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install genomer-plugin-summary
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Added some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+#!/usr/bin/env rake
+require "bundler/gem_tasks"
+require 'rspec/core/rake_task'
+
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+task :default => :spec

data/VERSION

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+0.0.1

data/features/gaps.feature

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+Feature: Producing a summary of the scaffold gaps
+  In order to have an overview of the gaps in a scaffold
+  A user can use the "gaps" command
+  to generate the a tabular output of the scaffold gaps
+
+  @disable-bundler
+  Scenario: A single contig scaffold
+    Given I create a new genomer project
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGGC
+      """
+     When I run `genomer summary gaps`
+     Then the exit status should be 0
+      And the output should contain:
+      """
+      +----------+----------+----------+----------+--------------+
+      |                      Scaffold Gaps                       |
+      +----------+----------+----------+----------+--------------+
+      |  Number  |  Length  |  Start   |   End    |     Type     |
+      +----------+----------+----------+----------+--------------+
+      +----------+----------+----------+----------+--------------+
+      """
+
+  @disable-bundler
+  Scenario: A single contig with an internal gap
+    Given I create a new genomer project
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGNNNATG
+      """
+     When I run `genomer summary gaps`
+     Then the exit status should be 0
+      And the output should contain:
+      """
+      +----------+----------+----------+----------+--------------+
+      |                      Scaffold Gaps                       |
+      +----------+----------+----------+----------+--------------+
+      |  Number  |  Length  |  Start   |   End    |     Type     |
+      +----------+----------+----------+----------+--------------+
+      |        1 |        3 |        4 |        6 |    contig    |
+      +----------+----------+----------+----------+--------------+
+      """
+
+  @disable-bundler
+  Scenario: Two contigs separated by an unresolved region
+    Given I create a new genomer project
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      -
+        unresolved:
+          length: 10
+      -
+        sequence:
+          source: "contig00001"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGCC
+      """
+     When I run `genomer summary gaps`
+     Then the exit status should be 0
+      And the output should contain:
+      """
+      +----------+----------+----------+----------+--------------+
+      |                      Scaffold Gaps                       |
+      +----------+----------+----------+----------+--------------+
+      |  Number  |  Length  |  Start   |   End    |     Type     |
+      +----------+----------+----------+----------+--------------+
+      |        1 |       10 |        6 |       15 |  unresolved  |
+      +----------+----------+----------+----------+--------------+
+      """
+
+  @disable-bundler
+  Scenario: A mixture of contig gaps and unresolved regions
+    Given I create a new genomer project
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+      -
+        unresolved:
+          length: 10
+      -
+        sequence:
+          source: "contig00002"
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGNNNATG
+      >contig00002
+      ANG
+      """
+     When I run `genomer summary gaps`
+     Then the exit status should be 0
+      And the output should contain:
+      """
+      +----------+----------+----------+----------+--------------+
+      |                      Scaffold Gaps                       |
+      +----------+----------+----------+----------+--------------+
+      |  Number  |  Length  |  Start   |   End    |     Type     |
+      +----------+----------+----------+----------+--------------+
+      |        1 |        3 |        4 |        6 |    contig    |
+      |        2 |       10 |       10 |       19 |  unresolved  |
+      |        3 |        1 |       21 |       21 |    contig    |
+      +----------+----------+----------+----------+--------------+
+      """
+
+  @disable-bundler
+  Scenario: A single contig with an internal gap filled by an insert
+    Given I create a new genomer project
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+          inserts:
+          -
+            source: "insert_1"
+            open: 4
+            close: 6
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGNNNATG
+      >insert_1
+      AAA
+      """
+     When I run `genomer summary gaps`
+     Then the exit status should be 0
+      And the output should contain:
+      """
+      +----------+----------+----------+----------+--------------+
+      |                      Scaffold Gaps                       |
+      +----------+----------+----------+----------+--------------+
+      |  Number  |  Length  |  Start   |   End    |     Type     |
+      +----------+----------+----------+----------+--------------+
+      +----------+----------+----------+----------+--------------+
+      """
+
+  @disable-bundler
+  Scenario: A single contig with an internal gap partially filled by an insert
+    Given I create a new genomer project
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+          inserts:
+          -
+            source: "insert_1"
+            open: 4
+            close: 5
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGNNNATG
+      >insert_1
+      AAA
+      """
+     When I run `genomer summary gaps`
+     Then the exit status should be 0
+      And the output should contain:
+      """
+      +----------+----------+----------+----------+--------------+
+      |                      Scaffold Gaps                       |
+      +----------+----------+----------+----------+--------------+
+      |  Number  |  Length  |  Start   |   End    |     Type     |
+      +----------+----------+----------+----------+--------------+
+      |        1 |        1 |        7 |        7 |    contig    |
+      +----------+----------+----------+----------+--------------+
+      """
+
+  @disable-bundler
+  Scenario: A partially filled contig internal gap followed by an unresolved region
+    Given I create a new genomer project
+      And I write to "assembly/scaffold.yml" with:
+      """
+      ---
+      -
+        sequence:
+          source: "contig00001"
+          inserts:
+          -
+            source: "insert_1"
+            open: 4
+            close: 5
+      -
+        unresolved:
+          length: 5
+      """
+      And I write to "assembly/sequence.fna" with:
+      """
+      >contig00001
+      ATGNNNATG
+      >insert_1
+      AAA
+      """
+     When I run `genomer summary gaps`
+     Then the exit status should be 0
+      And the output should contain:
+      """
+      +----------+----------+----------+----------+--------------+
+      |                      Scaffold Gaps                       |
+      +----------+----------+----------+----------+--------------+
+      |  Number  |  Length  |  Start   |   End    |     Type     |
+      +----------+----------+----------+----------+--------------+
+      |        1 |        1 |        7 |        7 |    contig    |
+      |        2 |        5 |       11 |       15 |  unresolved  |
+      +----------+----------+----------+----------+--------------+
+      """

data/features/support/env.rb

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+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../spec')
+
+require 'aruba/cucumber'

data/features/support/genomer_steps.rb

@@ -0,0 +1,5 @@
+When /^I create a new genomer project$/ do
+  step 'I successfully run `genomer init project`'
+  step 'I cd to "project"'
+  step 'I append to "Gemfile" with "gem \'genomer-plugin-summary\', :path =>\'../../../\'"'
+end

data/genomer-plugin-summary.gemspec

@@ -0,0 +1,29 @@
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |gem|
+  gem.authors       = ["Michael Barton"]
+  gem.email         = ["mail@michaelbarton.me.uk"]
+  gem.description   = %q{Genomer plugin for generating reports}
+  gem.summary       = %q{Generates reports on the status of the genomer project}
+  gem.homepage      = ""
+
+  gem.files         = `git ls-files`.split($\)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.name          = "genomer-plugin-summary"
+  gem.require_paths = ["lib"]
+  gem.version       = File.read 'VERSION'
+
+  gem.add_dependency "genomer",        ">= 0.0.4"
+  gem.add_dependency "terminal-table", "~> 1.4.5"
+
+  gem.add_development_dependency 'rake', '~> 0.9.0'
+
+  gem.add_development_dependency 'rspec',            '~> 2.9.0'
+  gem.add_development_dependency "heredoc_unindent", "~> 1.1.2"
+  gem.add_development_dependency "rr",               "~> 1.0.4"
+
+  gem.add_development_dependency 'cucumber', '~> 1.1.9'
+  gem.add_development_dependency 'aruba',    '~> 0.4.11'
+
+end

data/lib/genomer-plugin-summary/gaps.rb

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+require 'genomer'
+require 'terminal-table'
+
+class GenomerPluginSummary::Gaps < Genomer::Plugin
+
+  def run
+    tabulate determine_gaps scaffold
+  end
+
+  def headings
+    ['Number'.center(8),
+     'Length'.center(8),
+     'Start'.center(8),
+     'End'.center(8),
+     'Type'.center(12)]
+  end
+
+  def title
+    'Scaffold Gaps'
+  end
+
+  def tabulate(contigs)
+    table = Terminal::Table.new(:title => title) do |t|
+      t << headings
+      t << :separator
+      contigs.each do |ctg|
+        t << [ctg[:number],
+              ctg[:length],
+              ctg[:start],
+              ctg[:end],
+              ctg[:type]]
+      end
+    end
+
+    table.style = {:width => 60}
+    table.align_column 0, :right
+    table.align_column 1, :right
+    table.align_column 2, :right
+    table.align_column 3, :right
+    table.align_column 4, :center
+
+    table
+  end
+
+  def gap_locations(seq)
+    seq.upcase.enum_for(:scan, /(N+)/).map do
+      (Regexp.last_match.begin(0)+1)..(Regexp.last_match.end(0))
+    end
+  end
+
+  def determine_gaps(scaffold)
+    count  = 0
+    length = 0
+
+    scaffold.map do |entry|
+      gaps = case entry.entry_type
+             when :sequence then
+               gap_locations(entry.sequence).map do |gap|
+                 count += 1
+                 {:number => count,
+                  :length => (gap.end - gap.begin) + 1,
+                  :start  => gap.begin + length,
+                  :end    => gap.end   + length,
+                  :type   => :contig}
+               end
+             when :unresolved then
+               count += 1
+               {:number => count,
+                :length => entry.sequence.length,
+                :start  => length + 1,
+                :end    => length + entry.sequence.length,
+                :type   => :unresolved}
+             end
+      length += entry.sequence.length
+      gaps
+    end.flatten
+  end
+
+end

data/lib/genomer-plugin-summary.rb

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+require "genomer"
+
+class GenomerPluginSummary < Genomer::Plugin
+
+  def self.fetch(name)
+    require 'genomer-plugin-summary/' + name
+    const_get(name.capitalize)
+  end
+
+  def run
+    self.class.fetch(arguments.shift).new(arguments,flags).run
+  end
+
+end

data/man/genomer-summary-gaps.ronn

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+genomer-summary-gaps(1) -- summarise the gaps in the scaffold
+=============================================================
+
+## SYNOPSIS
+
+`genomer summary gaps`
+
+## DESCRIPTION
+
+Generates a summary of the gaps (regions of N characters) in the scaffolded 
+output sequence. This summary command lists these gaps with the following 
+attributes:
+
+  * Number:
+    Incremental gap number from the start of the sequence.
+
+  * Length:
+    The length of the gap sequence.
+
+  * Start:
+    The start of the gap sequence in the output sequence.
+
+  * End:
+    The end of the gap sequence in the output sequence.
+
+  * Type:
+    Whether the gap is **specified** in the scaffold file as an unresolved 
+    region or is a **contig** gaps which appears in one of the contigs used to 
+    build the scaffold.
+
+## BUGS
+
+**Genomer-summary** is written in Ruby and uses several RubyGem dependencies. 
+See the .gemspec file in the install directory for version details.
+
+## COPYRIGHT
+
+**Genomer** is Copyright (C) 2011 Michael Barton <http://michaelbarton.me.uk>

data/man/genomer-summary.ronn

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+genomer-summary(1) -- generate summaries of genomer projects
+============================================================
+
+## SYNOPSIS
+
+`genomer summary` <summary-type> [<options>...]
+
+## DESCRIPTION
+
+Generates different summary types for genomer projects. Each **summary-type** 
+has a corresponding man page which can be accessed using:
+
+`genome man summary <summary-type>`
+
+The following **summary-type** are available:
+
+  * `gaps`:
+    Summarises the gaps in the genome scaffold.
+
+## BUGS
+
+**Genomer-summary** is written in Ruby and uses several RubyGem dependencies. 
+See the .gemspec file in the install directory for version details.
+
+## COPYRIGHT
+
+**Genomer** is Copyright (C) 2011 Michael Barton <http://michaelbarton.me.uk>

data/spec/genomer-plugin-summary_spec/gaps_spec.rb

@@ -0,0 +1,197 @@
+require 'spec_helper'
+require 'genomer-plugin-summary/gaps'
+
+describe GenomerPluginSummary::Gaps do
+
+  describe "#tabulate" do
+
+    subject do
+      described_class.new([],{}).tabulate(contigs).to_s + "\n"
+    end
+
+    context "passed an empty array" do
+
+      let(:contigs) do
+        []
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+          +----------+----------+----------+----------+--------------+
+          |                      Scaffold Gaps                       |
+          +----------+----------+----------+----------+--------------+
+          |  Number  |  Length  |  Start   |   End    |     Type     |
+          +----------+----------+----------+----------+--------------+
+          +----------+----------+----------+----------+--------------+
+        EOS
+      end
+
+    end
+
+    context "passed an array with one entry" do
+
+      let(:contigs) do
+        [{:number => 1, :length => 1, :start => 1, :end => 1, :type => :contig}]
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+          +----------+----------+----------+----------+--------------+
+          |                      Scaffold Gaps                       |
+          +----------+----------+----------+----------+--------------+
+          |  Number  |  Length  |  Start   |   End    |     Type     |
+          +----------+----------+----------+----------+--------------+
+          |        1 |        1 |        1 |        1 |    contig    |
+          +----------+----------+----------+----------+--------------+
+        EOS
+      end
+
+    end
+
+    context "passed an array with two entries" do
+
+      let(:contigs) do
+        [{:number => 1, :length => 1, :start => 1, :end => 1, :type => :contig},
+         {:number => 2, :length => 2, :start => 2, :end => 2, :type => :unresolved}]
+      end
+
+      it do
+        should ==<<-EOS.unindent!
+          +----------+----------+----------+----------+--------------+
+          |                      Scaffold Gaps                       |
+          +----------+----------+----------+----------+--------------+
+          |  Number  |  Length  |  Start   |   End    |     Type     |
+          +----------+----------+----------+----------+--------------+
+          |        1 |        1 |        1 |        1 |    contig    |
+          |        2 |        2 |        2 |        2 |  unresolved  |
+          +----------+----------+----------+----------+--------------+
+        EOS
+      end
+
+    end
+
+  end
+
+  describe "#determine_gaps" do
+
+    def sequence(seq)
+      s = mock!
+      stub(s).sequence{ seq }
+      stub(s).entry_type{ :sequence }
+      s
+    end
+
+    def unresolved(seq)
+      s = mock!
+      stub(s).sequence{ seq }
+      stub(s).entry_type{ :unresolved }
+      s
+    end
+
+    subject do
+      described_class.new([],{}).determine_gaps(scaffold)
+    end
+
+    context "an empty scaffold" do
+      let(:scaffold) do
+        []
+      end
+
+      it{ should == []}
+    end
+
+    context "a scaffold with a single contig" do
+      let(:scaffold) do
+        [sequence('AAATTT')]
+      end
+
+      it{ should == []}
+    end
+
+    context "a scaffold with a single contig containing a gap" do
+      let(:scaffold) do
+        [sequence('AANNTT')]
+      end
+
+      it do
+        should == [{:number => 1, :length => 2, :start => 3, :end => 4, :type => :contig}]
+      end
+    end
+
+    context "a scaffold with a two contigs containing gaps" do
+      let(:scaffold) do
+        [sequence('AANNTT'), sequence('AANNTT')]
+      end
+
+      it do
+        should == [
+          {:number => 1, :length => 2, :start => 3,  :end => 4,  :type => :contig},
+          {:number => 2, :length => 2, :start => 9, :end => 10, :type => :contig}]
+      end
+    end
+
+    context "a scaffold with two contigs separated by an unresolved region" do
+      let(:scaffold) do
+        [sequence('AAT'),
+         unresolved('NNNNNNNNNN'),
+         sequence('AAT')]
+      end
+
+      it do
+        should == [
+          {:number => 1, :length => 10, :start => 4,  :end => 13,  :type => :unresolved}]
+      end
+    end
+
+    context "a scaffold with a mixture of gapped contigs and unresolved regions" do
+      let(:scaffold) do
+        [sequence('AAANNNTTT'),
+         unresolved('NNNNNNNNNN'),
+         sequence('AAANT'),
+         unresolved('NNNNNNNNNN')]
+      end
+
+      it do
+        should == [
+          {:number => 1, :length => 3,  :start => 4,   :end => 6,  :type => :contig},
+          {:number => 2, :length => 10, :start => 10,  :end => 19, :type => :unresolved},
+          {:number => 3, :length => 1,  :start => 23,  :end => 23, :type => :contig},
+          {:number => 4, :length => 10, :start => 25,  :end => 34, :type => :unresolved}]
+      end
+    end
+  end
+
+  describe "#gap_locations" do
+
+    subject do
+      described_class.new([],{}).gap_locations(sequence)
+    end
+
+    context "an empty string" do
+      let(:sequence){ "" }
+      it{ should == []}
+    end
+
+    context "a sequence with no gaps" do
+      let(:sequence){ "ATGC" }
+      it{ should == []}
+    end
+
+    context "a sequence with a single gap" do
+      let(:sequence){ "ATGCNNNATGC" }
+      it{ should == [5..7]}
+    end
+
+    context "a sequence with a single character gap" do
+      let(:sequence){ "ANC" }
+      it{ should == [2..2]}
+    end
+
+    context "a sequence with two gaps" do
+      let(:sequence){ "ATGCNNNATGCNNNNATGC" }
+      it{ should == [5..7, 12..15]}
+    end
+
+  end
+
+end

data/spec/genomer-plugin-summary_spec.rb

@@ -0,0 +1,31 @@
+require 'spec_helper'
+
+describe GenomerPluginSummary do
+
+  example = described_class::Example = Class.new(described_class)
+
+  before do
+    mock(described_class).require 'genomer-plugin-summary/example'
+  end
+
+  describe "#fetch" do
+
+    it "should return the required view plugin class" do
+      described_class.fetch('example').should == example
+    end
+
+  end
+
+  describe "#run" do
+
+    it "should initialize and run the required summary plugin" do
+      mock.proxy(example).new([:arg],:flags) do |instance|
+        mock(instance).run
+      end
+
+      described_class.new(['example',:arg],:flags).run
+    end
+
+  end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,15 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+
+require 'rspec'
+require 'heredoc_unindent'
+require 'genomer-plugin-summary'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each do |f|
+  require File.expand_path(f)
+end
+
+RSpec.configure do |config|
+  config.mock_with :rr
+end

metadata

@@ -0,0 +1,202 @@
+--- !ruby/object:Gem::Specification
+name: genomer-plugin-summary
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Michael Barton
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-05-28 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: genomer
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.4
+- !ruby/object:Gem::Dependency
+  name: terminal-table
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.5
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.9.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.9.0
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.9.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.9.0
+- !ruby/object:Gem::Dependency
+  name: heredoc_unindent
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.2
+- !ruby/object:Gem::Dependency
+  name: rr
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.4
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.9
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.9
+- !ruby/object:Gem::Dependency
+  name: aruba
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.11
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.11
+description: Genomer plugin for generating reports
+email:
+- mail@michaelbarton.me.uk
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- VERSION
+- features/gaps.feature
+- features/support/env.rb
+- features/support/genomer_steps.rb
+- genomer-plugin-summary.gemspec
+- lib/genomer-plugin-summary.rb
+- lib/genomer-plugin-summary/gaps.rb
+- man/genomer-summary-gaps.ronn
+- man/genomer-summary.ronn
+- spec/genomer-plugin-summary_spec.rb
+- spec/genomer-plugin-summary_spec/gaps_spec.rb
+- spec/spec_helper.rb
+homepage: ''
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -2942156995405587810
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -2942156995405587810
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Generates reports on the status of the genomer project
+test_files:
+- features/gaps.feature
+- features/support/env.rb
+- features/support/genomer_steps.rb
+- spec/genomer-plugin-summary_spec.rb
+- spec/genomer-plugin-summary_spec/gaps_spec.rb
+- spec/spec_helper.rb