Implement duplicate features

Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>

lib/genomer-plugin-view/gff_record_helper.rb

@@ -2,7 +2,6 @@
 
 module GenomerPluginView::GffRecordHelper
 
-
   DEFAULT_GFF_MAPPING = {'product' => 'product', 'Note' => 'note' }
 
   GFF_TO_TABLE = {

lib/genomer-plugin-view/table.rb

@@ -21,33 +21,37 @@ def run
   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

spec/genomer-view-plugin/gff_record_helper_spec.rb

@@ -68,7 +68,7 @@
     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 @@
     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 +199,34 @@
     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 => [
+       ['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' ]]}
 
     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 +238,6 @@
       end
     end
 
-
   end
 
 end

spec/genomer-view-plugin/table_spec.rb

@@ -73,7 +73,7 @@
 
       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 @@
 
       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 "#create_encoded_features" do
 
     let(:prefix) do
-      nil
+      true
     end
 
     subject do
@@ -143,10 +143,26 @@
 
     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 "passed a gene with an unknown feature_type attribute" do
 
       let(:attributes) do
-        {'feature_type' => 'unknown'}
+        [['feature_type', 'unknown']]
       end
 
       let(:annotations) do
@@ -176,26 +192,42 @@
 
     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
         [gene({:attributes => attributes})]
       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
 
     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 "passed a gene with a function attribute" do
 
       let(:attributes) do
-        {'function' => 'abcd'}
+        [['function', 'abcd']]
       end
 
       let(:annotations) do
@@ -227,7 +259,7 @@
     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 "passed a gene with Name and product attributes" do
 
       let(:attributes) do
-        {'Name' => 'abcD','product' => 'efgh'}
+        [['Name', 'abcD'], ['product', 'efgh']]
       end
 
       let(:annotations) do
@@ -252,15 +284,15 @@
 
       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 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
@@ -269,7 +301,7 @@
 
       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

spec/spec_helper.rb

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