genomer-plugin-view 0.0.2

data/spec/genomer-view-plugin/table_spec.rb

@@ -0,0 +1,279 @@
+require 'spec_helper'
+require 'genomer-plugin-view/table'
+
+describe GenomerPluginView::Table do
+
+  describe "#run" do
+
+    let(:annotations){ [] }
+
+    let(:flags){ {} }
+
+    before(:each) do
+      stub(subject).annotations do
+        annotations
+      end
+      stub(subject).flags do
+        flags
+      end
+    end
+
+    subject do
+      described_class.new([],{})
+    end
+
+    describe "with no annotations or flags" do
+
+      it "should return an empty header line" do
+        subject.run.should == ">Feature\t\tannotation_table\n"
+      end
+
+    end
+
+    describe "with no annotations and the identifier flag" do
+
+      let(:flags){ {:identifier => 'id'} }
+
+      it "should add ID to the header line" do
+        subject.run.should == ">Feature\tid\tannotation_table\n"
+      end
+
+    end
+
+    describe "with one gene annotation" do
+
+      let(:annotations){ [gene] }
+
+      it "should call the to_genbank_features method " do
+        subject.run.should == <<-EOS.unindent
+        >Feature\t\tannotation_table
+        1\t3\tgene
+        EOS
+      end
+
+    end
+
+    describe "with one gene annotation and the CDS flag" do
+
+      let(:flags){ {:generate_encoded_features => true} }
+
+      let(:annotations){ [gene] }
+
+      it "should call the to_genbank_features method " do
+        subject.run.should == <<-EOS.unindent
+        >Feature\t\tannotation_table
+        1\t3\tgene
+        1\t3\tCDS
+        EOS
+      end
+
+    end
+
+    describe "with one gene annotation and the CDS prefix flag" do
+
+      let(:flags){ {:generate_encoded_features => 'pre_'} }
+
+      let(:annotations){ [gene({:attributes => {'ID' => '1'}})] }
+
+      it "should call the to_genbank_features method " do
+        subject.run.should == <<-EOS.unindent
+        >Feature\t\tannotation_table
+        1\t3\tgene
+        \t\t\tlocus_tag\t1
+        1\t3\tCDS
+        \t\t\tprotein_id\tpre_1
+        EOS
+      end
+
+    end
+
+    describe "with one tRNA gene annotation and the CDS prefix flag" do
+
+      let(:flags){ {:generate_encoded_features => 'pre_'} }
+
+      let(:annotations){ [gene({:attributes => {'ID'           => '1',
+                                                'feature_type' => 'tRNA',
+                                                'product'      => 'tRNA-Gly'}})] }
+
+      it "should call the to_genbank_features method " do
+        subject.run.should == <<-EOS.unindent
+        >Feature\t\tannotation_table
+        1\t3\tgene
+        \t\t\tlocus_tag\t1
+        1\t3\ttRNA
+        \t\t\tproduct\ttRNA-Gly
+        EOS
+      end
+
+    end
+
+  end
+
+  describe "#create_encoded_features" do
+
+    let(:prefix) do
+      nil
+    end
+
+    subject do
+      described_class.new([],{}).create_encoded_features(annotations,prefix).last
+    end
+
+    describe "passed an empty array" do
+
+      let(:annotations) do
+        []
+      end
+
+      it "should return an empty array" do
+        subject.should be_nil
+      end
+
+    end
+
+    describe "passed a gene with no attributes" do
+
+      let(:annotations) do
+        [gene]
+      end
+
+      it "should return a CDS feature" do
+        subject.should == cds
+      end
+
+    end
+
+    describe "passed a gene with a known feature_type attribute" do
+
+      let(:attributes) do
+        {'feature_type' => 'tRNA'}
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should return a tRNA feature" do
+        subject.should == gene({:feature => 'tRNA',:attributes => attributes})
+      end
+
+    end
+
+    describe "passed a gene with an unknown feature_type attribute" do
+
+      let(:attributes) do
+        {'feature_type' => 'unknown'}
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should raise a Genomer::Error" do
+        lambda{ subject.call }.should raise_error Genomer::Error,
+          "Unknown feature_type 'unknown'"
+      end
+
+    end
+
+    describe "passed a gene with a Name attribute" do
+
+      let(:attributes) do
+        {'Name' => 'abcD'}
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should set the capitalise value to the product key" do
+        subject.should == cds({:attributes => {'product' => 'AbcD'}})
+      end
+
+    end
+
+    describe "passed a gene with a product attribute" do
+
+      let(:attributes) do
+        {'product' => 'abcd'}
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should not change attributes" do
+        subject.should == cds({:attributes => attributes})
+      end
+
+    end
+
+    describe "passed a gene with a function attribute" do
+
+      let(:attributes) do
+        {'function' => 'abcd'}
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should not change attributes" do
+        subject.should == cds({:attributes => attributes})
+      end
+
+    end
+
+    describe "passed a gene with product and function attributes" do
+
+      let(:attributes) do
+        {'product' => 'abcd','function' => 'efgh'}
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should not change attributes" do
+        subject.should == cds({:attributes => attributes})
+      end
+
+    end
+
+    describe "passed a gene with Name and product attributes" do
+
+      let(:attributes) do
+        {'Name' => 'abcD','product' => 'efgh'}
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should map Name to product and product to function" do
+        subject.should == cds({:attributes =>
+          {'product' => 'AbcD','function' => 'efgh'}})
+      end
+
+    end
+
+    describe "passed a gene with Name, product and function attributes" do
+
+      let(:attributes) do
+        {'Name' => 'abcD','product' => 'efgh', 'function' => 'ijkl'}
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should map Name to product and product to function" do
+        subject.should == cds({:attributes =>
+          {'product' => 'AbcD','function' => 'efgh'}})
+      end
+
+    end
+
+  end
+
+end

data/spec/genomer-view-plugin_spec.rb

@@ -0,0 +1,103 @@
+require 'spec_helper'
+
+describe GenomerPluginView do
+
+  describe "#fetch_view" do
+
+    it "should return the required view plugin class" do
+      GenomerPluginView.fetch_view('fasta').should == GenomerPluginView::Fasta
+    end
+
+  end
+
+  describe "#run" do
+
+    let(:example) do
+      GenomerPluginView::Example = Class.new(GenomerPluginView)
+    end
+
+    before do
+      mock(described_class).fetch_view('example') do
+        example
+      end
+    end
+
+    it "should initialize and run the required view plugin" do
+      mock.proxy(example).new([:arg],:flags) do |instance|
+        mock(instance).run
+      end
+
+      described_class.new(['example',:arg],:flags).run
+    end
+
+  end
+
+  describe '#convert_command_line_flags' do
+
+    subject do
+      described_class.convert_command_line_flags(flags)
+    end
+
+    describe "with no command line arguments" do
+
+      let(:flags) do
+        {}
+      end
+
+      it "should return an empty hash" do
+        subject.should == {}
+      end
+
+    end
+
+    describe "with an unrelated command line argument" do
+
+      let(:flags) do
+        {:something => :unknown}
+      end
+
+      it "should return an empty hash" do
+        subject.should == {}
+      end
+
+    end
+
+    describe "with the prefix command line argument" do
+
+      let(:flags) do
+        {:prefix => 'pre_'}
+      end
+
+      it "should return the prefix argument" do
+        subject.should == {:prefix => 'pre_'}
+      end
+
+    end
+
+    describe "with the generate_encoded_features command line argument" do
+
+      let(:flags) do
+        {:'generate_encoded_features' => true}
+      end
+
+      it "should return the prefix argument" do
+        subject.should == {:encoded => true}
+      end
+
+    end
+
+    describe "with the reset_locus_numbering command line argument" do
+
+      let(:flags) do
+        {:reset_locus_numbering => true}
+      end
+
+      it "should map this to the the reset argument" do
+        subject.should == {:reset => true}
+      end
+
+    end
+
+  end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,32 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'heredoc_unindent'
+require 'scaffolder/test/helpers'
+require 'genomer-plugin-view'
+require 'genomer-plugin-view/gff_record_helper'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  config.mock_with :rr
+
+  include Scaffolder::Test
+  Scaffolder::Test::Annotation.send(:include, GenomerPluginView::GffRecordHelper)
+
+  def gene(opts = Hash.new)
+    default = {
+      :seqname    => 'seq1',
+      :start      => 1,
+      :end        => 3,
+      :feature    => 'gene',
+      :attributes => Hash.new}
+    Annotation.new(default.merge(opts)).to_gff3_record
+  end
+
+  def cds(opts = Hash.new)
+    gene({:feature => 'CDS'}.merge(opts))
+  end
+end

metadata

@@ -0,0 +1,192 @@
+--- !ruby/object:Gem::Specification
+name: genomer-plugin-view
+version: !ruby/object:Gem::Version
+  version: 0.0.2
+  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: 0.0.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.5
+- !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: 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: scaffolder-test-helpers
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.1
+- !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: 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: Convert genome scaffold into different sequence format views
+email:
+- mail@michaelbarton.me.uk
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .document
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- features/agp/generation.feature
+- features/fasta/contigs.feature
+- features/fasta/single_sequence.feature
+- features/mappings/core.feature
+- features/support/env.rb
+- features/table/cds_entries.feature
+- features/table/core.feature
+- features/table/feature_type.feature
+- genomer-plugin-view.gemspec
+- lib/genomer-plugin-view.rb
+- lib/genomer-plugin-view/agp.rb
+- lib/genomer-plugin-view/fasta.rb
+- lib/genomer-plugin-view/gff_record_helper.rb
+- lib/genomer-plugin-view/mapping.rb
+- lib/genomer-plugin-view/table.rb
+- lib/genomer-plugin-view/version.rb
+- man/genomer-view-agp.ronn
+- man/genomer-view.ronn
+- spec/genomer-view-plugin/agp_spec.rb
+- spec/genomer-view-plugin/fasta_spec.rb
+- spec/genomer-view-plugin/gff_record_helper_spec.rb
+- spec/genomer-view-plugin/mapping_spec.rb
+- spec/genomer-view-plugin/table_spec.rb
+- spec/genomer-view-plugin_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/michaelbarton/genomer-plugin-view
+licenses:
+- MIT
+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: 3613905158544904544
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ~>
+    - !ruby/object:Gem::Version
+      version: 1.8.0
+requirements: []
+rubyforge_project: genomer-view-plugin
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Provide different views of scaffold.
+test_files: []