scaffolder 0.4.3 → 0.4.4

data/.travis.yml

@@ -0,0 +1,3 @@
+rvm:
+  - 1.8.7
+  - 1.9.2

data/Gemfile

@@ -5,11 +5,13 @@ group :default do
 end
 
 group :development do
-  gem "bundler", "~> 1.0"
-  gem "shoulda", "~> 2.11"
-  gem "mocha", "~> 0.9"
-  gem "yard", "~> 0.6"
-  gem "cucumber", "~> 0.9"
-  gem "jeweler", "~> 1.5"
-  gem "redgreen", "~> 1.2"
+  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

data/README.rdoc

@@ -22,13 +22,14 @@ the command line using:
 
 == Documentation
 
-See the Scaffolder class for getting started with Scaffolder.
+See the Scaffolder[http://rubydoc.info/gems/scaffolder/Scaffolder] class for
+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/michaelbarton/scaffolder]. Bug reports and feature
+github[http://github.com/scaffolder/scaffolder]. Bug reports and feature
 requests may also be made there.
 
 == Copyright

data/Rakefile

@@ -12,11 +12,11 @@ require 'rake'
 require 'jeweler'
 Jeweler::Tasks.new do |gem|
   gem.name = "scaffolder"
-  gem.homepage = "http://www.michaelbarton.me.uk/projects/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@michaelbarton.me.uk"
+  gem.email = "mail@next.gs"
   gem.authors = ["Michael Barton"]
   gem.test_files = Dir['test/**/*.rb']
 end

data/VERSION

@@ -1 +1 @@
-0.4.3
+0.4.4

data/features/insert.feature

@@ -3,13 +3,26 @@ Feature: The insert keyword
   A user can use the insert keyword
 
   Scenario: A scaffold with a single insert keyword
-    Given the scaffold file has the sequences:
-      | name | nucleotides |
-      | seq  | ATGCCGCGTAA |
-    And the first scaffold sequence has the inserts:
-      | name | nucleotides | open | close |
-      | ins  | AAAA        | 4    | 6     |
-    When creating a scaffolder object
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      TTTTTTTTT
+      >insert
+      AAA
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+            inserts:
+            -
+              source: "insert"
+              open: 4
+              close: 6
+      """
+    When creating a scaffold with the files "scaffold.yml" and "sequence.fna"
     Then the scaffold should contain 1 sequence entries
     Then the scaffold should contain 1 insert entries
-    And the scaffold sequence should be ATGAAAACGTAA
+    And the scaffold sequence should be TTTAAATTT

data/features/sequence.feature

@@ -3,18 +3,40 @@ Feature: The sequence keyword
   A user can use the sequence keyword
 
   Scenario: A scaffold with a single sequence keyword
-    Given the scaffold file has the sequences:
-      | name | nucleotides |
-      | seq  | ATGCC       |
-    When creating a scaffolder object
+    Given a file named "sequence.fna" with:
+      """
+      >seq
+      TTTTT
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq"
+      """
+    When creating a scaffold with the files "scaffold.yml" and "sequence.fna"
     Then the scaffold should contain 1 sequence entries
-    And the scaffold sequence should be ATGCC
+    And the scaffold sequence should be TTTTT
 
   Scenario: A scaffold with a two sequence keywords
-    Given the scaffold file has the sequences:
-      | name | nucleotides |
-      | seq1 | ATGCC       |
-      | seq2 | ATGCC       |
-    When creating a scaffolder object
+    Given a file named "sequence.fna" with:
+      """
+      >seq1
+      TTT
+      >seq2
+      AAA
+      """
+    Given a file named "scaffold.yml" with:
+      """
+      ---
+        -
+          sequence:
+            source: "seq1"
+        -
+          sequence:
+            source: "seq2"
+      """
+    When creating a scaffold with the files "scaffold.yml" and "sequence.fna"
     Then the scaffold should contain 2 sequence entries
-    And the scaffold sequence should be ATGCCATGCC
+    And the scaffold sequence should be TTTAAA

data/features/step_definitions/scaffolder_steps.rb

@@ -1,33 +1,7 @@
-Given /^the scaffold file has the sequences:$/ do |sequences|
-  @entries   ||= Array.new
-  @sequences ||= Array.new
-
-  sequences.hashes.each do |seq|
-    @entries << {'sequence' => {'source' => seq['name']}}
-  end
-  sequences.hashes.map do |seq|
-    @sequences << {:name => seq['name'], :sequence => seq['nucleotides']}
-  end
-end
-
-Given /^the first scaffold sequence has the inserts:$/ do |inserts|
-  sequence = @entries.detect{|s| s.keys.first == 'sequence' }
-  sequence['sequence']['inserts'] = (inserts.hashes.map do |insert|
-    i = {'source' => insert['name']}
-    i['open']  = insert['open'].to_i  if insert['open']
-    i['close'] = insert['close'].to_i if insert['close']
-    i
-  end)
-  inserts.hashes.map do |insert|
-    @sequences << {:name => insert['name'], :sequence => insert['nucleotides']}
-  end
-end
-
-When /^creating a scaffolder object$/ do
-  @scf_file = write_scaffold_file(@entries)
-  @seq_file = write_sequence_file(@sequences)
-
-  @scaffold = Scaffolder.new(YAML.load(File.read(@scf_file)),@seq_file)
+When /^creating a scaffold with the files "([^"]*)" and "([^"]*)"$/ do |x, y|
+  scf_file = File.join(TMP,x)
+  seq_file = File.join(TMP,y)
+  @scaffold = Scaffolder.new( YAML.load(File.read(scf_file)), seq_file)
 end
 
 Then /^the scaffold should contain (.*) sequence entries$/ do |n|

data/features/support/env.rb

@@ -7,24 +7,14 @@ rescue Bundler::BundlerError => e
   exit e.status_code
 end
 
-require 'tempfile'
+require 'rspec/expectations'
+require 'aruba/cucumber'
 
 $LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
 require 'scaffolder'
 
-def write_sequence_file(*sequences)
-  file = Tempfile.new("sequence").path
-  File.open(file,'w') do |tmp|
-    sequences.flatten.each do |sequence|
-      seq = Bio::Sequence.new(sequence[:sequence])
-      tmp.print(seq.output(:fasta,:header => sequence[:name]))
-    end
-  end
-  file
-end
+TMP = "/tmp"
 
-def write_scaffold_file(scaffold)
-  file = Tempfile.new("scaffold").path
-  File.open(file,'w'){|tmp| tmp.print(YAML.dump(scaffold))}
-  file
+Before do
+  @dirs = [TMP]
 end

data/scaffolder.gemspec

@@ -5,19 +5,20 @@
 
 Gem::Specification.new do |s|
   s.name = %q{scaffolder}
-  s.version = "0.4.3"
+  s.version = "0.4.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Michael Barton"]
-  s.date = %q{2011-06-03}
+  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@michaelbarton.me.uk}
+  s.email = %q{mail@next.gs}
   s.extra_rdoc_files = [
     "LICENSE",
     "README.rdoc"
   ]
   s.files = [
     ".document",
+    ".travis.yml",
     "Gemfile",
     "LICENSE",
     "README.rdoc",
@@ -43,45 +44,50 @@ Gem::Specification.new do |s|
     "test/test_unresolved.rb",
     "yard/attribute_handler.rb"
   ]
-  s.homepage = %q{http://www.michaelbarton.me.uk/projects/scaffolder/}
+  s.homepage = %q{http://next.gs}
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.7}
+  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"]
 
   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>, ["~> 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<redgreen>, ["~> 1.2"])
+      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<redgreen>, ["~> 1.2"])
+      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<redgreen>, ["~> 1.2"])
+    s.add_dependency(%q<mynyml-redgreen>, ["~> 0.7.1"])
   end
 end
 

data/test/test_insert.rb

@@ -45,17 +45,17 @@ class TestInsert < Test::Unit::TestCase
 
       should "return a negative diff for a sequence smaller than insert site" do
         @insert.raw_sequence 'TT'
-        assert(@insert.size_diff,-1)
+        assert_equal(@insert.size_diff,-1)
       end
 
       should "return 0 for a sequence equal to the insert site" do
-        @insert.raw_sequence 'TT'
-        assert(@insert.size_diff,0)
+        @insert.raw_sequence 'TTT'
+        assert_equal(@insert.size_diff,0)
       end
 
       should "return a positive diff for a sequence larger than insert site" do
         @insert.raw_sequence 'TTTT'
-        assert(@insert.size_diff,1)
+        assert_equal(@insert.size_diff,1)
       end
 
     end

data/test/test_region.rb

@@ -11,7 +11,8 @@ class TestScaffolder < Test::Unit::TestCase
 
       should "create a single accessor attribute" do
         Scaffolder::Region.attribute @attr
-        assert(Scaffolder::Region.instance_methods.include? @attr.to_s)
+        methods = Scaffolder::Region.instance_methods.map{|m| m.to_s}
+        assert(methods.include?(@attr.to_s))
       end
 
       should "return nil until attribute value is stored" do

metadata

@@ -1,154 +1,138 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: scaffolder
-version: !ruby/object:Gem::Version 
-  hash: 9
-  prerelease: false
-  segments: 
-  - 0
-  - 4
-  - 3
-  version: 0.4.3
+version: !ruby/object:Gem::Version
+  version: 0.4.4
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Michael Barton
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-06-03 00:00:00 -04:00
+date: 2011-08-11 00:00:00.000000000 -04:00
 default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  requirement: &id001 !ruby/object:Gem::Requirement 
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &2153752620 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 7
-        segments: 
-        - 1
-        - 4
-        version: "1.4"
+      - !ruby/object:Gem::Version
+        version: '1.4'
   type: :runtime
-  name: bio
   prerelease: false
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: *2153752620
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &2153750940 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 15
-        segments: 
-        - 1
-        - 0
-        version: "1.0"
+      - !ruby/object:Gem::Version
+        version: '1.0'
   type: :development
-  name: bundler
   prerelease: false
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: *2153750940
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &2153748000 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 21
-        segments: 
-        - 2
-        - 11
-        version: "2.11"
+      - !ruby/object:Gem::Version
+        version: '2.11'
   type: :development
-  name: shoulda
   prerelease: false
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  version_requirements: *2153748000
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &2153746760 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 25
-        segments: 
-        - 0
-        - 9
-        version: "0.9"
+      - !ruby/object:Gem::Version
+        version: '2.4'
   type: :development
-  name: mocha
   prerelease: false
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: *2153746760
+- !ruby/object:Gem::Dependency
+  name: mocha
+  requirement: &2153746240 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 7
-        segments: 
-        - 0
-        - 6
-        version: "0.6"
+      - !ruby/object:Gem::Version
+        version: '0.9'
   type: :development
-  name: yard
   prerelease: false
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  version_requirements: *2153746240
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: &2153743100 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 25
-        segments: 
-        - 0
-        - 9
-        version: "0.9"
+      - !ruby/object:Gem::Version
+        version: '0.6'
   type: :development
+  prerelease: false
+  version_requirements: *2153743100
+- !ruby/object:Gem::Dependency
   name: cucumber
+  requirement: &2153742480 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.9'
+  type: :development
   prerelease: false
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  version_requirements: *2153742480
+- !ruby/object:Gem::Dependency
+  name: aruba
+  requirement: &2153741780 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 1
-        - 5
-        version: "1.5"
+      - !ruby/object:Gem::Version
+        version: '0.2'
   type: :development
+  prerelease: false
+  version_requirements: *2153741780
+- !ruby/object:Gem::Dependency
   name: jeweler
+  requirement: &2153741080 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :development
   prerelease: false
-  version_requirements: *id007
-- !ruby/object:Gem::Dependency 
-  requirement: &id008 !ruby/object:Gem::Requirement 
+  version_requirements: *2153741080
+- !ruby/object:Gem::Dependency
+  name: mynyml-redgreen
+  requirement: &2153740340 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 11
-        segments: 
-        - 1
-        - 2
-        version: "1.2"
+      - !ruby/object:Gem::Version
+        version: 0.7.1
   type: :development
-  name: redgreen
   prerelease: false
-  version_requirements: *id008
-description: Organise sequence contigs into genome scaffolds using simple human-readable YAML files.
-email: mail@michaelbarton.me.uk
+  version_requirements: *2153740340
+description: Organise sequence contigs into genome scaffolds using simple human-readable
+  YAML files.
+email: mail@next.gs
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE
 - README.rdoc
-files: 
+files:
 - .document
+- .travis.yml
 - Gemfile
 - LICENSE
 - README.rdoc
@@ -174,40 +158,35 @@ files:
 - test/test_unresolved.rb
 - yard/attribute_handler.rb
 has_rdoc: true
-homepage: http://www.michaelbarton.me.uk/projects/scaffolder/
-licenses: 
+homepage: http://next.gs
+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: -4011958643952341412
+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: 1.3.7
+rubygems_version: 1.6.2
 signing_key: 
 specification_version: 3
 summary: Genome scaffolding for human beings.
-test_files: 
+test_files:
 - test/helper.rb
 - test/test_insert.rb
 - test/test_region.rb