scaffolder 0.4.4 → 0.5.0

data/spec/scaffolder_spec.rb

@@ -0,0 +1,112 @@
+require 'helper'
+
+describe Scaffolder do
+
+  Scaffolder::Region::Mock = Class.new(Scaffolder::Region)
+
+  before do
+    @sequence = nil
+    @data = [{'mock' => Hash.new}]
+  end
+
+  describe 'parsing a scaffold file' do
+
+    before do
+      Bio::FlatFile.stubs(:auto).with(@sequence).returns({})
+    end
+
+    it "should fetch correct region class type" do
+      Scaffolder::Region.expects(:'[]').with('mock').returns(Scaffolder::Region::Mock)
+      Scaffolder.new(@data,@sequence)
+    end
+
+    it "should pass data to region object" do
+      Scaffolder::Region::Mock.expects(:generate).with(@data.first['mock'])
+      Scaffolder.new(@data,@sequence)
+    end
+
+  end
+
+  context 'parsing a scaffold file with a source keyword' do
+
+    before do
+      Bio::FlatFile.stubs(:auto).with(@sequence).returns([
+                                                         stub(:definition => 'seq1', :seq => 'ATGC')])
+    end
+
+    it "should should also pass raw_sequence from flat file" do
+      @data.first['mock']['source'] = 'seq1'
+      Scaffolder::Region::Mock.any_instance.expects(:source).with('seq1')
+      Scaffolder::Region::Mock.any_instance.expects(:raw_sequence).with('ATGC')
+      Scaffolder.new(@data,@sequence)
+    end
+
+  end
+
+  context 'updating each data hash with raw_sequence attributes' do
+
+    before do
+      @seqs = {'seq1' => 'AAA'}
+      @expected = {'source' => 'seq1', 'raw_sequence' => @seqs['seq1']}
+    end
+
+    it "should do nothing when no source keyword" do
+      test = {'something' => 'nothing'}
+      Scaffolder.update_with_sequence(test,@seqs).should == test
+    end
+
+    it "should add raw_sequence to simple hash" do
+      test = {'source' => 'seq1'}
+      Scaffolder.update_with_sequence(test,@seqs).should == @expected
+    end
+
+    it "should add raw_sequence to a nested hash" do
+      test     = {'something' => {'source' => 'seq1'}}
+      expected = {'something' => @expected}
+      Scaffolder.update_with_sequence(test,@seqs).should == expected
+    end
+
+    it "should add raw_sequence to a twice nested hash" do
+      test     = {'something' => {'other' => {'source' => 'seq1'}}}
+      expected = {'something' => {'other' => @expected}}
+      Scaffolder.update_with_sequence(test,@seqs).should == expected
+    end
+
+    it "should add raw_sequence to simple hash inside an array" do
+      test     = [{'source' => 'seq1'}]
+      expected = [@expected]
+      Scaffolder.update_with_sequence(test,@seqs).should == expected
+    end
+
+    it "should add raw_sequence to a nested hash inside an array" do
+      test     = {'something' => [{'source' => 'seq1'}]}
+      expected = {'something' => [@expected]}
+      Scaffolder.update_with_sequence(test,@seqs).should == expected
+    end
+
+    it "should add raw_sequence to two nested hashes inside an array" do
+      test     = {'something' => [{'source' => 'seq1'},{'source' => 'seq1'}]}
+      expected = {'something' => [@expected,@expected]}
+      Scaffolder.update_with_sequence(test,@seqs).should == expected
+    end
+
+    it "should add raw_sequence to a hash inside a hash inside an array" do
+      test     = {'something' => [{'else' => {'source' => 'seq1'}}]}
+      expected = {'something' => [{'else' => @expected}]}
+      Scaffolder.update_with_sequence(test,@seqs).should == expected
+    end
+
+    it "should add raw_sequence to a twice nested (hash inside an array)" do
+      test     = {'something' => [{'else' => [{'source' => 'seq1'}]}]}
+      expected = {'something' => [{'else' => [@expected]}]}
+      Scaffolder.update_with_sequence(test,@seqs).should == expected
+    end
+
+    it "should throw an UnknownSequenceError when no matching sequence" do
+      test = {'source' => 'non_existent_sequence'}
+      lambda{ Scaffolder.update_with_sequence(test,@seqs)}.should raise_error(Scaffolder::Errors::UnknownSequenceError)
+    end
+
+  end
+
+end

data/spec/sequences_spec.rb

@@ -0,0 +1,110 @@
+require 'helper'
+
+describe Scaffolder::Region::Sequence do
+
+  its(:class){ should respond_to(:attribute)}
+  it{ should respond_to :source, :inserts}
+  
+  describe "insert attribute method" do
+
+    let(:coordinates) do
+      {'open' => 2, 'close' => 3}
+    end
+
+    let(:insert) do
+      i = Scaffolder::Region::Insert.new
+      i.open  coordinates['open']
+      i.close coordinates['close']
+      i
+    end
+
+    it "should return empty array as default value" do
+      subject.inserts.should be_empty
+    end
+
+    it "should allow array of inserts to be set as value" do
+      subject.inserts [insert]
+      subject.inserts.first.should == insert
+    end
+
+    it "should process insert data hash into an array of inserts" do
+      subject.inserts [coordinates]
+      ins = subject.inserts.first
+      ins.should be_instance_of Scaffolder::Region::Insert
+
+      ins.close.should == coordinates['close']
+      ins.open.should == coordinates['open']
+    end
+
+    it "should process mixed insert data into an array of inserts" do
+      subject.inserts [coordinates,insert]
+
+      subject.inserts.each do |ins|
+        ins.should be_instance_of Scaffolder::Region::Insert
+        ins.close.should == coordinates['close']
+        ins.open.should == coordinates['open']
+      end
+    end
+
+  end
+
+  describe "with inserts added" do
+
+    before do
+      subject.raw_sequence 'ATGCCAGATAACTGACTAGCATG'
+    end
+
+    let(:insert) do
+      ins = Scaffolder::Region::Insert.new
+      ins.raw_sequence 'GGTAGTA'
+      ins.open  5
+      ins.close 10
+      ins
+    end
+
+    it "should raise when the insert open is after the sequence stop" do
+      insert.open 24
+      insert.close 25
+      subject.inserts [insert]
+      lambda{subject.sequence}.should raise_error(Scaffolder::Errors::CoordinateError)
+    end
+
+    it "should raise when the insert close is before the sequence start" do
+      insert.open -5
+      insert.close 0
+      subject.inserts [insert]
+      lambda{subject.sequence}.should raise_error(Scaffolder::Errors::CoordinateError)
+    end
+
+    it "should raise when the insert open is greater than the insert close" do
+      insert.open 11
+      subject.inserts [insert]
+      lambda{subject.sequence}.should raise_error(Scaffolder::Errors::CoordinateError)
+    end
+
+    it "should update the sequence with a simple insert" do
+      subject.inserts [insert]
+      subject.sequence.should == 'ATGCGGTAGTAACTGACTAGCATG'
+    end
+
+    it "should update the sequence with a simple insert with repeated method calls" do
+      subject.inserts [insert]
+      subject.sequence.should == 'ATGCGGTAGTAACTGACTAGCATG'
+      subject.sequence.should == 'ATGCGGTAGTAACTGACTAGCATG'
+    end
+
+    it "should update the sequence stop position after adding a simple insert" do
+      subject.inserts [insert]
+      subject.stop.should == 24
+    end
+
+    it "should update the sequence with inserts in reverse order" do
+      insert_two = insert.clone
+      insert_two.open 12
+      insert_two.close 15
+      subject.inserts [insert,insert_two]
+      subject.sequence.should == "ATGCGGTAGTAAGGTAGTACTAGCATG"
+    end
+  end
+
+end

data/spec/unresolved_spec.rb

@@ -0,0 +1,17 @@
+require 'helper'
+
+describe Scaffolder::Region::Unresolved do
+
+  its(:class){ should respond_to(:attribute)}
+  it{ should respond_to :length}
+  
+  it "should return unresolved sequence when given length" do
+    subject.length 5
+    subject.sequence.should == ('N' * 5)
+  end
+
+  it "raise an error if length is unspecified" do
+    lambda{ subject.sequence }.should raise_error(Scaffolder::Errors::CoordinateError)
+  end
+
+end

metadata

@@ -1,137 +1,135 @@
 --- !ruby/object:Gem::Specification
 name: scaffolder
 version: !ruby/object:Gem::Version
-  version: 0.4.4
-  prerelease: 
+  version: 0.5.0
 platform: ruby
 authors:
 - Michael Barton
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-08-11 00:00:00.000000000 -04:00
-default_executable: 
+date: 2013-08-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: bio
-  requirement: &2153752620 !ruby/object:Gem::Requirement
-    none: false
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: 10.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *2153752620
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 10.1.0
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2153750940 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.0'
-  type: :development
+        version: 1.3.0
+  type: :runtime
   prerelease: false
-  version_requirements: *2153750940
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.0
 - !ruby/object:Gem::Dependency
-  name: shoulda
-  requirement: &2153748000 !ruby/object:Gem::Requirement
-    none: false
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '2.11'
-  type: :development
+        version: 1.4.0
+  type: :runtime
   prerelease: false
-  version_requirements: *2153748000
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.0
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2153746760 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '2.4'
+        version: 2.14.0
   type: :development
   prerelease: false
-  version_requirements: *2153746760
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.14.0
 - !ruby/object:Gem::Dependency
   name: mocha
-  requirement: &2153746240 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.9'
+        version: 0.14.0
   type: :development
   prerelease: false
-  version_requirements: *2153746240
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.14.0
 - !ruby/object:Gem::Dependency
   name: yard
-  requirement: &2153743100 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: 0.8.0
   type: :development
   prerelease: false
-  version_requirements: *2153743100
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.8.0
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &2153742480 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.9'
+        version: 1.3.0
   type: :development
   prerelease: false
-  version_requirements: *2153742480
-- !ruby/object:Gem::Dependency
-  name: aruba
-  requirement: &2153741780 !ruby/object:Gem::Requirement
-    none: false
+  version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.2'
-  type: :development
-  prerelease: false
-  version_requirements: *2153741780
+        version: 1.3.0
 - !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: &2153741080 !ruby/object:Gem::Requirement
-    none: false
+  name: aruba
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.5'
+        version: 0.5.3
   type: :development
   prerelease: false
-  version_requirements: *2153741080
-- !ruby/object:Gem::Dependency
-  name: mynyml-redgreen
-  requirement: &2153740340 !ruby/object:Gem::Requirement
-    none: false
+  version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.7.1
-  type: :development
-  prerelease: false
-  version_requirements: *2153740340
-description: Organise sequence contigs into genome scaffolds using simple human-readable
-  YAML files.
+        version: 0.5.3
+description: Turns scaffolded contigs and annotations into a genome.
 email: mail@next.gs
 executables: []
 extensions: []
-extra_rdoc_files:
-- LICENSE
-- README.rdoc
+extra_rdoc_files: []
 files:
 - .document
+- .gitignore
 - .travis.yml
 - Gemfile
 - LICENSE
@@ -149,47 +147,38 @@ files:
 - lib/scaffolder/region/insert.rb
 - lib/scaffolder/region/sequence.rb
 - lib/scaffolder/region/unresolved.rb
+- lib/scaffolder/version.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
+- spec/helper.rb
+- spec/insert_spec.rb
+- spec/region_spec.rb
+- spec/scaffolder_spec.rb
+- spec/sequences_spec.rb
+- spec/unresolved_spec.rb
 - yard/attribute_handler.rb
-has_rdoc: true
 homepage: http://next.gs
 licenses:
 - MIT
+metadata: {}
 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: -4011958643952341412
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.8.0
 requirements: []
-rubyforge_project: 
-rubygems_version: 1.6.2
+rubyforge_project: scaffolder
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
-summary: Genome scaffolding for human beings.
-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
+specification_version: 4
+summary: Build genome output files
+test_files: []
+has_rdoc: