genomer-plugin-view 0.0.5 → 0.0.6

data/features/core.feature

@@ -10,3 +10,19 @@ Feature: Producing different views of a genomes scaffold
      Then the exit status should be 0
       And the output should contain a valid man page
       And the output should contain "GENOMER-VIEW(1)"
+
+  @disable-bundler
+  Scenario: Running `genomer view` without a subcommand
+    Given I create a new genomer project
+     When I run `genomer view`
+     Then the exit status should be 0
+      And the output should contain:
+      """
+      Run `genomer man view COMMAND` to review available formats
+      Where COMMAND is one of the following:
+        agp
+        fasta
+        gff
+        mapping
+        table
+      """

data/features/table/cds_entries.feature

@@ -302,3 +302,76 @@ Feature: Producing cds annotation view from a scaffold
 
         """
 
+  @disable-bundler
+  Scenario: A CDS entry with a single DBxref attribute
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+        """
+        ---
+          - sequence:
+              source: contig1
+        """
+      And I write to "assembly/sequence.fna" with:
+        """
+        >contig1
+        AAAAATTTTTGGGGGCCCCC
+        """
+      And I write to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+	contig1	.	gene	1	3	.	-	1	ID=gene1;DBxref=GO:000001
+        """
+      And I append to "Gemfile" with:
+        """
+        gem 'genomer-plugin-view', :path => '../../../'
+        """
+     When I run `genomer view table --identifier=genome --generate_encoded_features`
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        >Feature	genome	annotation_table
+        3	1	gene
+        			locus_tag	gene1
+        3	1	CDS
+        			protein_id	gene1
+        			db_xref	GO:000001
+
+        """
+
+  @disable-bundler
+  Scenario: A CDS entry with multiple DBxref attributes
+    Given I successfully run `genomer init project`
+      And I cd to "project"
+      And I write to "assembly/scaffold.yml" with:
+        """
+        ---
+          - sequence:
+              source: contig1
+        """
+      And I write to "assembly/sequence.fna" with:
+        """
+        >contig1
+        AAAAATTTTTGGGGGCCCCC
+        """
+      And I write to "assembly/annotations.gff" with:
+        """
+        ##gff-version 3
+	contig1	.	gene	1	3	.	-	1	ID=gene1;DBxref=GO:000001;DBxref=InterPro:IPR000111
+        """
+      And I append to "Gemfile" with:
+        """
+        gem 'genomer-plugin-view', :path => '../../../'
+        """
+     When I run `genomer view table --identifier=genome --generate_encoded_features`
+     Then the exit status should be 0
+      And the output should contain:
+        """
+        >Feature	genome	annotation_table
+        3	1	gene
+        			locus_tag	gene1
+        3	1	CDS
+        			protein_id	gene1
+        			db_xref	GO:000001
+        			db_xref	InterPro:IPR000111
+        """

data/genomer-plugin-view.gemspec

@@ -6,7 +6,7 @@ Gem::Specification.new do |s|
   s.name        = "genomer-plugin-view"
   s.version     = GenomerViewPlugin::VERSION
   s.platform    = Gem::Platform::RUBY
-  s.homepage    = "http://github.com/michaelbarton/genomer-plugin-view"
+  s.homepage    = "http://next.gs"
   s.license     = "MIT"
   s.authors     = ["Michael Barton"]
   s.email       = ["mail@michaelbarton.me.uk"]
@@ -16,7 +16,7 @@ Gem::Specification.new do |s|
   s.required_rubygems_version = "~> 1.8.0"
   s.rubyforge_project         = "genomer-view-plugin"
 
-  s.add_dependency "genomer", ">= 0.0.6"
+  s.add_dependency "genomer", ">= 0.0.10"
 
   # Specs
   s.add_development_dependency "rspec",                   "~> 2.9.0"

data/lib/genomer-plugin-view/gff_record_helper.rb

@@ -2,8 +2,7 @@ require 'bio'
 
 module GenomerPluginView::GffRecordHelper
 
-
-  DEFAULT_GFF_MAPPING = {'product' => 'product', 'Note' => 'note' }
+  DEFAULT_GFF_MAPPING = {'product' => 'product', 'Note' => 'note', 'DBxref' => 'db_xref'}
 
   GFF_TO_TABLE = {
     'gene' => {

data/lib/genomer-plugin-view/table.rb

@@ -21,33 +21,37 @@ class GenomerPluginView::Table < Genomer::Plugin
   def create_encoded_features(genes,prefix)
     features = genes.map do |gene|
       feature = gene.clone
-      attrs   = Hash[feature.attributes]
+      attrs   = feature.attributes.clone
 
-      if id = attrs['ID']
-        attrs['ID'] = (prefix.is_a?(String) ? prefix + id : id)
-      end
-
-      feature.feature = attrs['feature_type'] || 'CDS'
+      feature_type    = attrs.detect{|k,v| k == 'feature_type'}
+      feature.feature = (feature_type ? feature_type.last : 'CDS')
 
       unless SUPPORTED_FEATURE_TYPES.include?(feature.feature)
         raise Genomer::Error, "Unknown feature_type '#{feature.feature}'"
       end
 
+      attrs.map! do |(k,v)|
+        v = (k == 'ID' && prefix.instance_of?(String) ? prefix + v : v)
+        [k,v]
+      end
+
       if feature.feature == "CDS"
-        name, prdt, ftn = attrs['Name'], attrs['product'], attrs['function']
 
-        if name
-          name = name.clone
-          name[0,1] = name[0,1].upcase
-          prdt, ftn = name,prdt
-        end
+        if attrs.detect{|(k,v)| k == 'Name' }
+          attrs.map! do |(k,v)|
+            v      = v.clone
+            v[0,1] = v[0,1].upcase if k == 'Name'
 
-        attrs.delete('Name')
-        attrs['product']  = prdt
-        attrs['function'] = ftn
+            v = nil                if k == 'function'
+            k = 'function'         if k == 'product'
+            k = 'product'          if k == 'Name'
+            [k,v]
+          end
+        end
+        #attrs.delete('Name')
       end
 
-      feature.attributes = attrs.to_a.reject{|(_,value)| value.nil? }
+      feature.attributes = attrs.reject{|(_,value)| value.nil? }
       feature
     end
     genes.zip(features).flatten

data/lib/genomer-plugin-view/version.rb

@@ -1,3 +1,3 @@
 class GenomerViewPlugin
-  VERSION = "0.0.5"
+  VERSION = "0.0.6"
 end

data/lib/genomer-plugin-view.rb

@@ -3,6 +3,7 @@ require 'genomer'
 class GenomerPluginView < Genomer::Plugin
 
   def run
+    return help if arguments.empty?
     self.class.fetch_view(arguments.shift).new(arguments,flags).run
   end
 
@@ -26,4 +27,19 @@ class GenomerPluginView < Genomer::Plugin
     end
   end
 
+  def help
+    message = <<-STRING.unindent
+      Run `genomer man view COMMAND` to review available formats
+      Where COMMAND is one of the following:
+    STRING
+
+    message + Dir[File.dirname(__FILE__) + '/genomer-plugin-view/*.rb'].
+      map{|f| File.basename(f).gsub('.rb','')}.
+      delete_if{|i| i == 'version'}.
+      delete_if{|i| i == 'gff_record_helper'}.
+      sort.
+      map{|i| " " * 2 + i}.
+      join("\n") + "\n"
+  end
+
 end

data/man/genomer-view.ronn

@@ -68,6 +68,10 @@ begin with an upper case letter.
     Used to populate the **Note** field for entries when the 
     `--generate_encoded_features` option is passed.
 
+  * `DBxref`: Used to link the annotation to other database references. This
+    field is added verbatim to generated output. Multiple entires of this
+    field may be used.
+
 ### GENOMER ATTRIBUTES
 
 These attributes are specific to genomer and should begin with a lower case 

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

@@ -68,7 +68,7 @@ describe GenomerPluginView::GffRecordHelper do
     context "gene feature with attributes" do
 
       let(:annotation) do
-        @attn.feature('gene').attributes('ID' => 'id')
+        @attn.feature('gene').attributes([['ID', 'id']])
       end
 
       it "should return a table entry" do
@@ -189,7 +189,7 @@ describe GenomerPluginView::GffRecordHelper do
     context "for a feature with an unknown attribute" do
 
       let(:annotation) do
-        @attn.attributes('something' => 'else')
+        @attn.attributes([['something','else']])
       end
 
       it "should return an empty array" do
@@ -199,34 +199,38 @@ describe GenomerPluginView::GffRecordHelper do
     end
 
     feature_keys = {
-      :gene => {
-        'Name' => 'gene',
-        'ID'   => 'locus_tag' },
-      :tRNA => {
-        'product' => 'product',
-        'Note'    => 'note'},
-      :rRNA => {
-        'product' => 'product',
-        'Note'    => 'note'},
-      :miscRNA => {
-        'product' => 'product',
-        'Note'    => 'note'},
-      :tmRNA => {
-        'product' => 'product',
-        'Note'    => 'note'},
-      :CDS  => {
-        'ec_number' => 'EC_number',
-        'function'  => 'function',
-        'product'   => 'product',
-        'Note'      => 'note',
-        'ID'        => 'protein_id' }}
+      :gene => [
+       ['Name',    'gene'],
+       ['ID',      'locus_tag']],
+      :tRNA => [
+       ['DBxref',    'db_xref'],
+       ['product', 'product'],
+       ['Note',    'note']],
+      :rRNA => [
+       ['product', 'product'],
+       ['Note',    'note']],
+      :miscRNA => [
+       ['DBxref',    'db_xref'],
+       ['product',   'product'],
+       ['Note',      'note']],
+      :tmRNA => [
+       ['DBxref',    'db_xref'],
+       ['product',   'product'],
+       ['Note',      'note']],
+      :CDS => [
+       ['ec_number', 'EC_number'],
+       ['DBxref',    'db_xref'],
+       ['function',  'function'],
+       ['product',   'product'],
+       ['Note',      'note'],
+       ['ID',        'protein_id' ]]}
 
     feature_keys.each do |type,mappings|
       mappings.each do |a,b|
         context "#{type.to_s} feature" do
 
           let(:annotation) do
-            @attn.feature(type.to_s).attributes(a => :value)
+            @attn.feature(type.to_s).attributes([[a, :value]])
           end
 
           it "should return #{b} for the attribute #{a}" do
@@ -238,7 +242,6 @@ describe GenomerPluginView::GffRecordHelper do
       end
     end
 
-
   end
 
 end

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

@@ -73,7 +73,7 @@ describe GenomerPluginView::Table do
 
       let(:flags){ {:generate_encoded_features => 'pre_'} }
 
-      let(:annotations){ [gene({:attributes => {'ID' => '1'}})] }
+      let(:annotations){ [gene({:attributes => [['ID', '1']]})] }
 
       it "should call the to_genbank_features method " do
         subject.run.should == <<-EOS.unindent
@@ -91,9 +91,9 @@ describe GenomerPluginView::Table do
 
       let(:flags){ {:generate_encoded_features => 'pre_'} }
 
-      let(:annotations){ [gene({:attributes => {'ID'           => '1',
-                                                'feature_type' => 'tRNA',
-                                                'product'      => 'tRNA-Gly'}})] }
+      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
@@ -112,7 +112,7 @@ describe GenomerPluginView::Table do
   describe "#create_encoded_features" do
 
     let(:prefix) do
-      nil
+      true
     end
 
     subject do
@@ -143,10 +143,26 @@ describe GenomerPluginView::Table do
 
     end
 
+    describe "passed a gene with an ID attributes" do
+
+      let(:attributes) do
+        [['ID', 'something']]
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should not change the attributes" do
+        subject.attributes.should == attributes
+      end
+
+    end
+
     describe "passed a gene with a known feature_type attribute" do
 
       let(:attributes) do
-        {'feature_type' => 'tRNA'}
+        [['feature_type', 'tRNA']]
       end
 
       let(:annotations) do
@@ -162,7 +178,7 @@ describe GenomerPluginView::Table do
     describe "passed a gene with an unknown feature_type attribute" do
 
       let(:attributes) do
-        {'feature_type' => 'unknown'}
+        [['feature_type', 'unknown']]
       end
 
       let(:annotations) do
@@ -176,10 +192,26 @@ describe GenomerPluginView::Table do
 
     end
 
+    describe "passed a gene with a duplicate attribute" do
+
+      let(:attributes) do
+        [['product', 'abcd'],['product', 'efgh']]
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should not change attributes" do
+        subject.should have_identical_attributes cds({:attributes => attributes})
+      end
+
+    end
+
     describe "passed a gene with a Name attribute" do
 
       let(:attributes) do
-        {'Name' => 'abcD'}
+        [['Name', 'abcD']]
       end
 
       let(:annotations) do
@@ -187,7 +219,7 @@ describe GenomerPluginView::Table do
       end
 
       it "should set the capitalise value to the product key" do
-        subject.should have_identical_attributes cds({:attributes => {'product' => 'AbcD'}})
+        subject.should have_identical_attributes cds({:attributes => [['product', 'AbcD']]})
       end
 
     end
@@ -195,7 +227,7 @@ describe GenomerPluginView::Table do
     describe "passed a gene with a product attribute" do
 
       let(:attributes) do
-        {'product' => 'abcd'}
+        [['product', 'abcd']]
       end
 
       let(:annotations) do
@@ -211,7 +243,7 @@ describe GenomerPluginView::Table do
     describe "passed a gene with a function attribute" do
 
       let(:attributes) do
-        {'function' => 'abcd'}
+        [['function', 'abcd']]
       end
 
       let(:annotations) do
@@ -227,7 +259,7 @@ describe GenomerPluginView::Table do
     describe "passed a gene with product and function attributes" do
 
       let(:attributes) do
-        {'product' => 'abcd', 'function' => 'efgh'}
+        [['product', 'abcd'], ['function', 'efgh']]
       end
 
       let(:annotations) do
@@ -243,7 +275,7 @@ describe GenomerPluginView::Table do
     describe "passed a gene with Name and product attributes" do
 
       let(:attributes) do
-        {'Name' => 'abcD','product' => 'efgh'}
+        [['Name', 'abcD'], ['product', 'efgh']]
       end
 
       let(:annotations) do
@@ -252,7 +284,7 @@ describe GenomerPluginView::Table do
 
       it "should map Name to product and product to function" do
         subject.should have_identical_attributes cds({:attributes =>
-          {'product' => 'AbcD','function' => 'efgh'}})
+          [['product', 'AbcD'], ['function', 'efgh']]})
       end
 
     end
@@ -260,7 +292,7 @@ describe GenomerPluginView::Table do
     describe "passed a gene with Name, product and function attributes" do
 
       let(:attributes) do
-        {'Name' => 'abcD','product' => 'efgh', 'function' => 'ijkl'}
+        [['Name', 'abcD'], ['product', 'efgh'], ['function', 'ijkl']]
       end
 
       let(:annotations) do
@@ -269,11 +301,42 @@ describe GenomerPluginView::Table do
 
       it "should map Name to product and product to function" do
         subject.should have_identical_attributes cds({:attributes =>
-          {'product' => 'AbcD','function' => 'efgh'}})
+          [['product', 'AbcD'], ['function', 'efgh']]})
       end
 
     end
 
+    describe "passed a gene with a single db_xref attribute" do
+
+      let(:attributes) do
+        {'db_xref' => 'InterPro:IPR000111'}
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should not change attributes" do
+        subject.should have_identical_attributes cds({:attributes => attributes})
+      end
+
+    end
+
+    describe "passed a gene with multiple db_xref attribute" do
+
+      let(:attributes) do
+        {'db_xref' => 'InterPro:IPR000111','db_xref' => 'GO:000001'}
+      end
+
+      let(:annotations) do
+        [gene({:attributes => attributes})]
+      end
+
+      it "should not change attributes" do
+        subject.should have_identical_attributes cds({:attributes => attributes})
+      end
+
+    end
   end
 
 end

data/spec/genomer-view-plugin_spec.rb

@@ -16,18 +16,38 @@ describe GenomerPluginView do
       GenomerPluginView::Example = Class.new(GenomerPluginView)
     end
 
-    before do
-      mock(described_class).fetch_view('example') do
-        example
+    context "with a view argument passed" do
+
+      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
 
-    it "should initialize and run the required view plugin" do
-      mock.proxy(example).new([:arg],:flags) do |instance|
-        mock(instance).run
+    context "with no argument passed" do
+
+      it "should return help information" do
+        described_class.new([],[]).run.should ==<<-STRING.unindent
+      Run `genomer man view COMMAND` to review available formats
+      Where COMMAND is one of the following:
+        agp
+        fasta
+        gff
+        mapping
+        table
+        STRING
       end
 
-      described_class.new(['example',:arg],:flags).run
     end
 
   end

data/spec/spec_helper.rb

@@ -22,7 +22,7 @@ RSpec.configure do |config|
       :start      => 1,
       :end        => 3,
       :feature    => 'gene',
-      :attributes => Hash.new}
+      :attributes => Array.new}
     Annotation.new(default.merge(opts)).to_gff3_record
   end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genomer-plugin-view
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-25 00:00:00.000000000 Z
+date: 2013-03-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: genomer
@@ -18,7 +18,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.0.6
+        version: 0.0.10
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -26,7 +26,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.0.6
+        version: 0.0.10
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -172,7 +172,7 @@ files:
 - 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
+homepage: http://next.gs
 licenses:
 - MIT
 post_install_message: 
@@ -187,7 +187,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -207727351507926591
+      hash: 390518256786568765
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -196,7 +196,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: 1.8.0
 requirements: []
 rubyforge_project: genomer-view-plugin
-rubygems_version: 1.8.23
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: Provide different views of scaffold.