scaffolder 0.4.4 → 0.5.0

checksums.yaml

@@ -0,0 +1,15 @@
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data/.gitignore

@@ -0,0 +1,22 @@
+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+doc
+.yardoc
+pkg
+
+## PROJECT::SPECIFIC

data/.travis.yml

@@ -1,3 +1,5 @@
 rvm:
   - 1.8.7
   - 1.9.2
+  - 1.9.3
+  - 2.0.0

data/Gemfile

@@ -1,17 +1,2 @@
-source "http://rubygems.org"
-
-group :default do
-  gem "bio", "~> 1.4"
-end
-
-group :development do
-  gem "bundler",         "~> 1.0"
-  gem "shoulda",         "~> 2.11"
-  gem "rspec",           "~> 2.4"
-  gem "mocha",           "~> 0.9"
-  gem "yard",            "~> 0.6"
-  gem "cucumber",        "~> 0.9"
-  gem "aruba",           "~> 0.2"
-  gem "jeweler",         "~> 1.5"
-  gem "mynyml-redgreen", "~> 0.7.1", :require => 'redgreen'
-end
+source "https://rubygems.org"
+gemspec

data/README.rdoc

@@ -15,8 +15,12 @@ repeatability.
 
 == Installing
 
-Ruby and RubyGems are required to use scaffolder. Scaffolder is installed on
-the command line using:
+Ruby and RubyGems are required to use scaffolder. Scaffolder is compatible with
+at least Ruby versions 1.8.7 and 1.9.2. The {last stable version of the
+RubyGems package manager}[https://rubygems.org/pages/download] is recommended
+for installing scaffolder.
+
+Scaffolder is installed on the command line using:
 
   $ gem install scaffolder
 
@@ -27,10 +31,12 @@ getting started with Scaffolder.
 
 == Contact
 
-Scaffolder was developed by Michael Barton (www.michaelbarton.me.uk). Pull
-requests, patches and bug reports are welcome. The source code is available on
-github[http://github.com/scaffolder/scaffolder]. Bug reports and feature
-requests may also be made there.
+Scaffolder was developed by Michael Barton (www.michaelbarton.me.uk). The
+website for scaffolder is at http://next.gs and a {twitter feed for
+updates}[http://twitter.com/nxtgs] is available. There is a {Google
+group}[http://groups.google.com/group/scaffolder] for questions and comments.
+The source code is available on github[http://github.com/scaffolder]. Bug
+reports and feature requests may also be made there.
 
 == Copyright
 

data/Rakefile

@@ -7,32 +7,21 @@ rescue Bundler::BundlerError => e
   $stderr.puts "Run `bundle install` to install missing gems"
   exit e.status_code
 end
-require 'rake'
-
-require 'jeweler'
-Jeweler::Tasks.new do |gem|
-  gem.name = "scaffolder"
-  gem.homepage = "http://next.gs"
-  gem.license = "MIT"
-  gem.summary = %Q{Genome scaffolding for human beings.}
-  gem.description = %Q{Organise sequence contigs into genome scaffolds using simple human-readable YAML files.}
-  gem.email = "mail@next.gs"
-  gem.authors = ["Michael Barton"]
-  gem.test_files = Dir['test/**/*.rb']
-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 'rake/dsl_definition'
+require 'rspec/core'
+require 'rspec/core/rake_task'
 require 'cucumber/rake/task'
-Cucumber::Rake::Task.new(:features)
+
+Bundler::GemHelper.install_tasks
 
 require 'yard'
 YARD::Rake::YardocTask.new
 
-task :default => :test
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+Cucumber::Rake::Task.new(:features)
+
+task :default => :spec

data/lib/scaffolder.rb

@@ -1,4 +1,5 @@
-require 'delegate'
+require 'scaffolder/version'
+
 require 'bio'
 
 # == Quick start
@@ -148,7 +149,7 @@ require 'bio'
 # Inserts with overlapping *open* and *close* regions in the same sequence will
 # cause unexpected behaviour and should be avoided.
 #
-class Scaffolder < DelegateClass(Array)
+class Scaffolder
   require 'scaffolder/errors'
   require 'scaffolder/region'
 

data/lib/scaffolder/version.rb

@@ -0,0 +1,5 @@
+require 'delegate'
+
+class Scaffolder < DelegateClass(Array)
+  VERSION = "0.5.0"
+end

data/scaffolder.gemspec

@@ -1,93 +1,35 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
-# -*- encoding: utf-8 -*-
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'scaffolder/version'
 
 Gem::Specification.new do |s|
-  s.name = %q{scaffolder}
-  s.version = "0.4.4"
+  s.name        = "scaffolder"
+  s.version     = Scaffolder::VERSION
+  s.platform    = Gem::Platform::RUBY
+  s.authors     = ["Michael Barton"]
+  s.email       = %q{mail@next.gs}
+  s.homepage    = "http://next.gs"
+  s.summary     = %Q{Build genome output files}
+  s.description = %Q{Turns scaffolded contigs and annotations into a genome.}
+  s.license     = "MIT"
 
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Michael Barton"]
-  s.date = %q{2011-08-11}
-  s.description = %q{Organise sequence contigs into genome scaffolds using simple human-readable YAML files.}
-  s.email = %q{mail@next.gs}
-  s.extra_rdoc_files = [
-    "LICENSE",
-    "README.rdoc"
-  ]
-  s.files = [
-    ".document",
-    ".travis.yml",
-    "Gemfile",
-    "LICENSE",
-    "README.rdoc",
-    "Rakefile",
-    "VERSION",
-    "cucumber.yml",
-    "features/insert.feature",
-    "features/sequence.feature",
-    "features/step_definitions/scaffolder_steps.rb",
-    "features/support/env.rb",
-    "lib/scaffolder.rb",
-    "lib/scaffolder/errors.rb",
-    "lib/scaffolder/region.rb",
-    "lib/scaffolder/region/insert.rb",
-    "lib/scaffolder/region/sequence.rb",
-    "lib/scaffolder/region/unresolved.rb",
-    "scaffolder.gemspec",
-    "test/helper.rb",
-    "test/test_insert.rb",
-    "test/test_region.rb",
-    "test/test_scaffolder.rb",
-    "test/test_sequence.rb",
-    "test/test_unresolved.rb",
-    "yard/attribute_handler.rb"
-  ]
-  s.homepage = %q{http://next.gs}
-  s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.6.2}
-  s.summary = %q{Genome scaffolding for human beings.}
-  s.test_files = ["test/helper.rb", "test/test_insert.rb", "test/test_region.rb", "test/test_scaffolder.rb", "test/test_sequence.rb", "test/test_unresolved.rb"]
+  s.required_rubygems_version = ">= 1.8.0"
+  s.rubyforge_project         = "scaffolder"
 
-  if s.respond_to? :specification_version then
-    s.specification_version = 3
+  s.add_dependency "rake"   , "~> 10.1.0"
+  s.add_dependency "bundler", "~> 1.3.0"
+  s.add_dependency "bio",     "~> 1.4.0"
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<bio>, ["~> 1.4"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.0"])
-      s.add_development_dependency(%q<shoulda>, ["~> 2.11"])
-      s.add_development_dependency(%q<rspec>, ["~> 2.4"])
-      s.add_development_dependency(%q<mocha>, ["~> 0.9"])
-      s.add_development_dependency(%q<yard>, ["~> 0.6"])
-      s.add_development_dependency(%q<cucumber>, ["~> 0.9"])
-      s.add_development_dependency(%q<aruba>, ["~> 0.2"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.5"])
-      s.add_development_dependency(%q<mynyml-redgreen>, ["~> 0.7.1"])
-    else
-      s.add_dependency(%q<bio>, ["~> 1.4"])
-      s.add_dependency(%q<bundler>, ["~> 1.0"])
-      s.add_dependency(%q<shoulda>, ["~> 2.11"])
-      s.add_dependency(%q<rspec>, ["~> 2.4"])
-      s.add_dependency(%q<mocha>, ["~> 0.9"])
-      s.add_dependency(%q<yard>, ["~> 0.6"])
-      s.add_dependency(%q<cucumber>, ["~> 0.9"])
-      s.add_dependency(%q<aruba>, ["~> 0.2"])
-      s.add_dependency(%q<jeweler>, ["~> 1.5"])
-      s.add_dependency(%q<mynyml-redgreen>, ["~> 0.7.1"])
-    end
-  else
-    s.add_dependency(%q<bio>, ["~> 1.4"])
-    s.add_dependency(%q<bundler>, ["~> 1.0"])
-    s.add_dependency(%q<shoulda>, ["~> 2.11"])
-    s.add_dependency(%q<rspec>, ["~> 2.4"])
-    s.add_dependency(%q<mocha>, ["~> 0.9"])
-    s.add_dependency(%q<yard>, ["~> 0.6"])
-    s.add_dependency(%q<cucumber>, ["~> 0.9"])
-    s.add_dependency(%q<aruba>, ["~> 0.2"])
-    s.add_dependency(%q<jeweler>, ["~> 1.5"])
-    s.add_dependency(%q<mynyml-redgreen>, ["~> 0.7.1"])
-  end
-end
+  # Specs
+  s.add_development_dependency "rspec",   "~> 2.14.0"
+  s.add_development_dependency "mocha",   "~> 0.14.0"
+  s.add_development_dependency "yard",    "~> 0.8.0"
+  
+  # Features
+  s.add_development_dependency "cucumber", "~> 1.3.0"
+  s.add_development_dependency "aruba",    "~> 0.5.3"
 
+  s.files        = `git ls-files`.split("\n")
+  s.require_path = 'lib'
+end

data/spec/helper.rb

@@ -0,0 +1,8 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'rspec'
+require 'mocha/api'
+require 'scaffolder'
+
+RSpec.configure do |config|
+  config.mock_with :mocha
+end

data/spec/insert_spec.rb

@@ -0,0 +1,75 @@
+require 'helper'
+
+describe Scaffolder::Region::Insert do
+
+  describe "attributes" do
+
+    its(:class){ should respond_to(:attribute)}
+    it{ should respond_to :source, :open, :close}
+
+    let(:length){ 15 }
+
+    before do
+      subject.raw_sequence('N' * length)
+    end
+
+    it "should return open plus sequence length as default close" do
+      subject.open 5
+      subject.close.should == (subject.open + length - 1)
+    end
+
+    it "should return close minus sequence length as default open" do
+      subject.close 20
+      subject.open.should == (subject.close - length - 1)
+    end
+
+    it "should include the insert position" do
+      subject.open  5
+      subject.close 10
+      subject.position.should == (4..9)
+    end
+
+    it "should throw an error when neither open or close are provided" do
+      lambda{subject.position}.should raise_error(Scaffolder::Errors::CoordinateError)
+    end
+
+  end
+
+  describe "#size_diff" do
+
+    before do
+      subject.open  3
+      subject.close 5
+    end
+
+    it "should return a negative diff for a sequence smaller than insert site" do
+      subject.raw_sequence 'TT'
+      subject.size_diff.should == -1
+    end
+
+    it "should return 0 for a sequence equal to the insert site" do
+      subject.raw_sequence 'TTT'
+      subject.size_diff.should == 0
+    end
+
+    it "should return a positive diff for a sequence larger than insert site" do
+      subject.raw_sequence 'TTTT'
+      subject.size_diff.should == 1
+    end
+
+  end
+
+  it "should be comparable by close position" do
+    a = subject
+    a.close 1
+
+    b = subject.clone
+    b.close 2
+
+    c = subject.clone
+    c.close 3
+
+    [c,a,b].sort.should == [a,b,c]
+  end
+
+end

data/spec/region_spec.rb

@@ -0,0 +1,148 @@
+require 'helper'
+
+describe Scaffolder::Region do
+
+  describe "adding instance methods with attribute method" do
+
+    let(:attr){ :some_attribute }
+
+    it "should create a single accessor attribute" do
+      Scaffolder::Region.attribute attr
+      methods = Scaffolder::Region.instance_methods.map{|m| m.to_s}
+      expect(methods).to include(attr.to_s)
+    end
+
+    it "should return nil until attribute value is stored" do
+      Scaffolder::Region.attribute attr
+      region = Scaffolder::Region.new
+      region.send(attr).should be_nil
+      region.send(attr,5)
+      region.send(attr).should == 5
+    end
+
+    it "should allow specification of default value" do
+      Scaffolder::Region.attribute attr, :default => 1
+      region = Scaffolder::Region.new
+      region.send(attr).should == 1
+      region.send(attr,5)
+      region.send(attr).should == 5
+    end
+
+    it "should allow specification of default value using a block" do
+      Scaffolder::Region.attribute attr, :default => lambda{|s| s.entry_type }
+      region = Scaffolder::Region.new
+      region.send(attr).should == region.entry_type
+      region.send(attr,5)
+      region.send(attr).should == 5
+    end
+
+  end
+
+  describe "passing the yaml hash to the generate method" do
+
+    let(:tags) do
+      {'one' => 1, 'two' => 2}
+    end
+
+    before do
+      Scaffolder::Region.attribute(:one)
+      Scaffolder::Region.attribute(:two)
+    end
+
+    it "should should call each tag in the hash as a method to store the value" do
+      Scaffolder::Region.any_instance.expects(:one).with(1)
+      Scaffolder::Region.any_instance.expects(:two).with(2)
+      Scaffolder::Region.generate(tags)
+    end
+
+    it "should return an instantiated region object" do
+      region = Scaffolder::Region.generate(tags)
+      region.one.should == 1
+      region.two.should == 2
+    end
+
+    it "should throw UnknownAttributeError for an unknown attribute" do
+        lambda{ Scaffolder::Region.generate({:three => 3}) }.should \
+          raise_error(Scaffolder::Errors::UnknownAttributeError)
+    end
+
+  end
+
+  context "attributes" do
+
+    it{ should respond_to :start, :stop, :reverse, :raw_sequence }
+
+    it "should return the class name as the entry type" do
+      Scaffolder::Region::NewRegion = Class.new(Scaffolder::Region)
+      Scaffolder::Region::NewRegion.new.entry_type.should == :newregion
+    end
+
+    it "should return 1 as default value for start attribute" do
+      sequence = Scaffolder::Region.new
+      sequence.start.should == 1
+    end
+
+    it "should return #raw_sequence length as default value for stop attribute" do
+      length = 5
+      subject.raw_sequence('N' * length)
+      subject.stop.should == length
+    end
+
+  end
+
+  describe "generating the processed sequence" do
+
+    [:sequence_hook, :raw_sequence].each do |method|
+
+      context "using the #{method} method" do
+
+        let(:region) do
+          # Test class to prevent interference with other tests
+          s = Class.new(Scaffolder::Region).new
+          s.class.send(:define_method,method,lambda{'ATGCCAGATAACTGACTAGCATG'})
+          s
+        end
+
+        it "should return the sequence when no other options are passed" do
+          region.sequence.should == 'ATGCCAGATAACTGACTAGCATG'
+        end
+
+        it "should reverse complement sequence when passed the reverse option" do
+          region.reverse true
+          region.sequence.should == 'CATGCTAGTCAGTTATCTGGCAT'
+        end
+
+        it "should create subsequence when passed sequence coordinates" do
+          region.start 5
+          region.stop 20
+          region.sequence.should == 'CAGATAACTGACTAGC'
+        end
+
+        it "should raise a CoordinateError when start is less than 1" do
+          region.start 0
+          lambda{ region.sequence }.should raise_error(Scaffolder::Errors::CoordinateError)
+        end
+
+        it "should raise a CoordinateError when stop is greater than sequence " do
+          region.stop 24
+          lambda{region.sequence}.should raise_error(Scaffolder::Errors::CoordinateError)
+        end
+
+        it "should raise a CoordinateError when stop is greater than start " do
+          region.start 6
+          region.stop 5
+          lambda{ region.sequence }.should raise_error(Scaffolder::Errors::CoordinateError)
+        end
+
+      end
+
+    end
+
+  end
+
+  it "should instantiate return corresponding region subclass when requested" do
+    Scaffolder::Region::Type = Class.new
+    Scaffolder::Region['type'].should == Scaffolder::Region::Type
+  end
+
+end