scaffolder-tools 0.1.2 → 0.1.3

data/spec/scaffolder/tool/sequence_spec.rb

@@ -1,4 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__),'..','..','spec_helper'))
+require 'spec_helper'
 
 describe Scaffolder::Tool::Sequence do
 
@@ -11,29 +11,68 @@ describe Scaffolder::Tool::Sequence do
     described_class.description.should == desc
   end
 
-  describe "execution when correctly instantiated" do
+  describe "command line argument" do
 
-    before(:each) do
-      entries = [{:name => 'seq1', :nucleotides => 'ATGC'}]
+    before do
+      cntg = Sequence.new(:name => 'seq1', :sequence => 'ATGC')
+      @scf_file, @seq_file = generate_scaffold_files([cntg])
+    end
+
+    subject do
+      Bio::FastaFormat.new(
+        StringIO.new(
+          described_class.new(
+            MockSettings.new(
+              @scf_file.path,
+              @seq_file.path,
+              settings)).execute).string)
+    end
 
-      @scaffold_file = File.new("scaffold",'w').path
-      @sequence_file = File.new("sequence",'w').path
+    describe "empty" do
 
-      write_scaffold_file(entries,@scaffold_file)
-      write_sequence_file(entries,@sequence_file)
-      settings = mock_command_line_settings(@scaffold_file,@sequence_file,{
-        :definition => nil,:no => nil})
+      let(:settings) do
+        {}
+      end
+
+      it "should set the fasta definition" do
+        subject.definition.should == ""
+      end
+
+      it "should return the expected sequence" do
+        subject.seq.should == 'ATGC'
+      end
 
-      tool = described_class.new(settings)
-      @output = StringIO.new(tool.execute)
     end
 
-    after(:each) do
-      File.delete @scaffold_file, @sequence_file
+    describe "--definition" do
+
+      let(:settings) do
+        {:definition => 'name'}
+      end
+
+      it "should set the fasta definition" do
+        subject.definition.should == "name"
+      end
+
+      it "should return the expected sequence" do
+        subject.seq.should == 'ATGC'
+      end
+
     end
 
-    it "should return the expected sequence" do
-      Bio::FlatFile.auto(@output).first.seq.should == 'ATGC'
+    describe "--with-sequence-digest" do
+      let(:settings) do
+        {:"with-sequence-digest" => true}
+      end
+
+      it "should set the fasta definition" do
+        header = "[sha1=627a3d8eb465be91696114803b3410ca92f59cc7]"
+        subject.definition.should == header
+      end
+
+      it "should return the expected sequence" do
+        subject.seq.should == 'ATGC'
+      end
     end
 
   end

data/spec/scaffolder/tool/validate_spec.rb

@@ -1,4 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__),'..','..','spec_helper'))
+require 'spec_helper'
 
 describe Scaffolder::Tool::Validate do
 
@@ -63,7 +63,7 @@ describe Scaffolder::Tool::Validate do
     end
 
     subject do
-      described_class.new(mock_command_line_settings)
+      described_class.new(MockSettings.new)
     end
 
     it "should return an empty array when scaffold is valid" do
@@ -87,7 +87,7 @@ describe Scaffolder::Tool::Validate do
   describe "scaffold validation with no overlapping inserts" do
 
     subject do
-      validate = described_class.new(mock_command_line_settings)
+      validate = described_class.new(MockSettings.new)
       validate.stubs(:errors).returns([])
       validate
     end
@@ -105,7 +105,7 @@ describe Scaffolder::Tool::Validate do
   describe "returning errors using the errors method" do
 
     subject do
-      validate = described_class.new(mock_command_line_settings)
+      validate = described_class.new(MockSettings.new)
 
       sequence = stub(:source => :seq1)
       validate.stubs(:errors).returns([sequence])
@@ -133,7 +133,7 @@ describe Scaffolder::Tool::Validate do
   describe "the attributes of the error data" do
 
     subject do
-      validate = described_class.new(mock_command_line_settings)
+      validate = described_class.new(MockSettings.new)
       @err = {:open => 1,:close => 2,:source => 'some_insert'}
 
       sequence = stub(:source => 'seq1')

data/spec/scaffolder/tool_index_spec.rb

@@ -1,4 +1,4 @@
-require File.join(File.dirname(__FILE__),'..','spec_helper')
+require 'spec_helper'
 
 describe Scaffolder::ToolIndex do
 

data/spec/scaffolder/tool_spec.rb

@@ -1,26 +1,26 @@
-require File.join(File.dirname(__FILE__),'..','spec_helper')
+require 'spec_helper'
 
 describe Scaffolder::Tool do
 
   describe "initialisation with attributes" do
 
     before(:each) do
-      @settings = mock_command_line_settings
+      @settings = MockSettings.new(:fake_scf,:fake_seq)
     end
 
     subject do
       Scaffolder::Tool.new(@settings)
     end
 
-    its(:scaffold_file){ should ==  @settings.scaffold_file }
-    its(:sequence_file){ should ==  @settings.sequence_file }
+    its(:scaffold_file){ should ==  @settings.scaf_file }
+    its(:sequence_file){ should ==  @settings.seq_file }
     its(:settings){ should ==  @settings }
   end
 
   describe "the run method" do
 
     before(:all) do
-      @settings = mock_command_line_settings
+      @settings = MockSettings.new
     end
 
     before(:each) do
@@ -88,28 +88,28 @@ describe Scaffolder::Tool do
     end
 
     it "should raise an error if the sequence file is missing" do
-      settings = mock_command_line_settings(@scaffold_file,@missing_file)
+      settings = MockSettings.new(@scaffold_file,@missing_file)
       tool = Scaffolder::Tool.new(settings)
       lambda{ tool.scaffold }.should raise_error(ArgumentError,
         "Sequence file not found: #{@missing_file}")
     end
 
     it "should raise an error if the sequence file is empty" do
-      settings = mock_command_line_settings(@scaffold_file,@empty_file)
+      settings = MockSettings.new(@scaffold_file,@empty_file)
       tool = Scaffolder::Tool.new(settings)
       lambda{ tool.scaffold }.should raise_error(ArgumentError,
         "Sequence file is empty: #{@empty_file}")
     end
 
     it "should raise an error if the scaffold file is missing" do
-      settings = mock_command_line_settings(@missing_file,@sequence_file)
+      settings = MockSettings.new(@missing_file,@sequence_file)
       tool = Scaffolder::Tool.new(settings)
       lambda{ tool.scaffold }.should raise_error(ArgumentError,
         "Scaffold file not found: #{@missing_file}")
     end
 
     it "should raise an error if the scaffold file is empty" do
-      settings = mock_command_line_settings(@empty_file,@sequence_file)
+      settings = MockSettings.new(@empty_file,@sequence_file)
       tool = Scaffolder::Tool.new(settings)
       lambda{ tool.scaffold }.should raise_error(ArgumentError,
         "Scaffold file is empty: #{@empty_file}")
@@ -119,21 +119,12 @@ describe Scaffolder::Tool do
   describe "creating the scaffold with the scaffold method" do
 
     before(:each) do
-      entries = [{:name => 'seq1', :nucleotides => 'ATGC'}]
-
-      @scaffold_file = File.new('scaffold','w').path
-      @sequence_file = File.new('sequence','w').path
-      write_scaffold_file(entries,@scaffold_file)
-      write_sequence_file(entries,@sequence_file)
-    end
-
-    after(:each) do
-      File.delete @scaffold_file, @sequence_file
+      contig = Sequence.new(:name => 'seq1', :sequence => 'ATGC')
+      @scf_file, @seq_file = generate_scaffold_files([contig])
     end
 
     subject do
-      Scaffolder::Tool.new(
-        mock_command_line_settings(@scaffold_file,@sequence_file))
+      Scaffolder::Tool.new(MockSettings.new(@scf_file.path,@seq_file.path))
     end
 
     it "should produce the expected sequence scaffold" do

data/spec/spec_helper.rb

@@ -4,7 +4,6 @@ $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'tempfile'
 require 'ostruct'
 
-require 'hashie'
 require 'rspec'
 require 'fakefs/safe'
 require 'mocha'
@@ -26,6 +25,7 @@ end
 RSpec.configure do |config|
   config.mock_with :mocha
 
+  include Scaffolder::Test
   include Scaffolder::Test::Helpers
 
   def tool_subclasses
@@ -34,18 +34,24 @@ RSpec.configure do |config|
     end
   end
 
-  def mock_command_line_settings(scaf_file = mock, seq_file = mock, hash_args={})
-    settings = mock
+  class MockSettings
 
-    settings.stubs(:rest).returns([scaf_file,seq_file])
-    settings.stubs(:sequence_file).returns(seq_file)
-    settings.stubs(:scaffold_file).returns(scaf_file)
+    attr :scaf_file
+    attr :seq_file
 
-    hash_args.each do |key,value|
-      settings.expects(:[]).with(key).returns(value)
+    def initialize(scaf_file = nil, seq_file = nil, command_args = {})
+      @scaf_file, @seq_file, = scaf_file, seq_file
+      @args = command_args
+    end
+
+    def rest
+      [scaf_file,seq_file]
+    end
+
+    def [](arg)
+      @args[arg]
     end
 
-    settings
   end
 
 end

data/spec/support/exit_code_matcher.rb

@@ -21,6 +21,6 @@ module ExitCodeMatchers
     end
     description do
       "expect block to call exit(#{code})"
-    end    
-  end  
+    end
+  end
 end

metadata

@@ -1,267 +1,178 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: scaffolder-tools
-version: !ruby/object:Gem::Version 
-  hash: 31
-  prerelease: false
-  segments: 
-  - 0
-  - 1
-  - 2
-  version: 0.1.2
+version: !ruby/object:Gem::Version
+  version: 0.1.3
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Michael Barton
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-01-28 00:00:00 -05:00
-default_executable: scaffolder
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  requirement: &id001 !ruby/object:Gem::Requirement 
+date: 2011-08-13 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: configliere
+  requirement: &2173650600 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 9
-        segments: 
-        - 0
-        - 1
-        version: "0.1"
+      - !ruby/object:Gem::Version
+        version: '0.1'
   type: :runtime
-  name: configliere
   prerelease: false
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: *2173650600
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &2173650020 !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: *id002
-- !ruby/object:Gem::Dependency 
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: *2173650020
+- !ruby/object:Gem::Dependency
+  name: scaffolder
+  requirement: &2173649540 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        - 4
-        version: "0.4"
+      - !ruby/object:Gem::Version
+        version: '0.4'
   type: :runtime
-  name: scaffolder
   prerelease: false
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  version_requirements: *2173649540
+- !ruby/object:Gem::Dependency
+  name: ronn
+  requirement: &2173649060 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 0
-        - 7
-        version: "0.7"
+      - !ruby/object:Gem::Version
+        version: '0.7'
   type: :runtime
-  name: ronn
   prerelease: false
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 15
-        segments: 
-        - 1
-        - 0
-        version: "1.0"
-  type: :development
+  version_requirements: *2173649060
+- !ruby/object:Gem::Dependency
   name: bundler
-  prerelease: false
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  requirement: &2173648520 !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: '1.0'
   type: :development
-  name: jeweler
   prerelease: false
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  version_requirements: *2173648520
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &2173647960 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 2
-        - 3
-        - 3
-        version: 2.3.3
+      - !ruby/object:Gem::Version
+        version: '1.5'
   type: :development
-  name: gherkin
   prerelease: false
-  version_requirements: *id007
-- !ruby/object:Gem::Dependency 
-  requirement: &id008 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 11
-        segments: 
-        - 2
-        - 4
-        version: "2.4"
-  type: :development
+  version_requirements: *2173647960
+- !ruby/object:Gem::Dependency
   name: rspec
-  prerelease: false
-  version_requirements: *id008
-- !ruby/object:Gem::Dependency 
-  requirement: &id009 !ruby/object:Gem::Requirement 
+  requirement: &2173647360 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 31
-        segments: 
-        - 0
-        - 10
-        version: "0.10"
+      - !ruby/object:Gem::Version
+        version: '2.4'
   type: :development
-  name: cucumber
   prerelease: false
-  version_requirements: *id009
-- !ruby/object:Gem::Dependency 
-  requirement: &id010 !ruby/object:Gem::Requirement 
+  version_requirements: *2173647360
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: &2173646840 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 15
-        segments: 
-        - 0
-        - 2
-        version: "0.2"
+      - !ruby/object:Gem::Version
+        version: '0.10'
   type: :development
-  name: fakefs
   prerelease: false
-  version_requirements: *id010
-- !ruby/object:Gem::Dependency 
-  requirement: &id011 !ruby/object:Gem::Requirement 
+  version_requirements: *2173646840
+- !ruby/object:Gem::Dependency
+  name: fakefs
+  requirement: &2173646340 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 15
-        segments: 
-        - 0
-        - 2
-        version: "0.2"
+      - !ruby/object:Gem::Version
+        version: '0.2'
   type: :development
-  name: aruba
   prerelease: false
-  version_requirements: *id011
-- !ruby/object:Gem::Dependency 
-  requirement: &id012 !ruby/object:Gem::Requirement 
+  version_requirements: *2173646340
+- !ruby/object:Gem::Dependency
+  name: aruba
+  requirement: &2173645780 !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: '0.2'
   type: :development
-  name: mocha
   prerelease: false
-  version_requirements: *id012
-- !ruby/object:Gem::Dependency 
-  requirement: &id013 !ruby/object:Gem::Requirement 
+  version_requirements: *2173645780
+- !ruby/object:Gem::Dependency
+  name: mocha
+  requirement: &2173645240 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        - 4
-        version: "0.4"
+      - !ruby/object:Gem::Version
+        version: '0.9'
   type: :development
-  name: hashie
   prerelease: false
-  version_requirements: *id013
-- !ruby/object:Gem::Dependency 
-  requirement: &id014 !ruby/object:Gem::Requirement 
+  version_requirements: *2173645240
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: &2173644660 !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: '0.6'
   type: :development
-  name: yard
   prerelease: false
-  version_requirements: *id014
-- !ruby/object:Gem::Dependency 
-  requirement: &id015 !ruby/object:Gem::Requirement 
+  version_requirements: *2173644660
+- !ruby/object:Gem::Dependency
+  name: scaffolder-test-helpers
+  requirement: &2173644100 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 9
-        segments: 
-        - 0
-        - 1
-        version: "0.1"
+      - !ruby/object:Gem::Version
+        version: '0.4'
   type: :development
-  name: scaffolder-test-helpers
   prerelease: false
-  version_requirements: *id015
+  version_requirements: *2173644100
 description: Binary to use with scaffolder genome scaffolds
-email: mail@michaelbarton.me.uk
-executables: 
+email: mail@next.gs
+executables:
 - scaffolder
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - .document
 - .rspec
+- .travis.yml
 - Gemfile
 - LICENSE.txt
 - README.rdoc
 - Rakefile
 - VERSION
 - bin/scaffolder
+- features/error_checking.feature
 - features/help.feature
 - features/sequence.feature
 - features/step_definitions/scaffolder-tools.rb
@@ -273,6 +184,7 @@ files:
 - lib/scaffolder/tool/sequence.rb
 - lib/scaffolder/tool/validate.rb
 - lib/scaffolder/tool_index.rb
+- man/scaffolder-format.7.ronn
 - man/scaffolder-help.1.ronn
 - man/scaffolder-sequence.1.ronn
 - man/scaffolder-validate.1.ronn
@@ -285,41 +197,35 @@ files:
 - spec/scaffolder/tool_spec.rb
 - spec/spec_helper.rb
 - spec/support/exit_code_matcher.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: 2501104196888492226
+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: 1.8.6
 signing_key: 
 specification_version: 3
 summary: Tools for manipulating genome scaffolds
-test_files: 
+test_files:
 - spec/scaffolder/binary_helper_spec.rb
 - spec/scaffolder/tool/help_spec.rb
 - spec/scaffolder/tool/sequence_spec.rb