add #genotype

misshie · Sep 11, 2011 · b693bc0 · b693bc0
1 parent 8cacfa5
commit b693bc0
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Showing 4 changed files with 18 additions and 140 deletions.
diff --git a/lib/bio/NCBI/dbsnp/bitfield.rb b/lib/bio/NCBI/dbsnp/bitfield.rb
@@ -105,6 +105,16 @@ def allele_frequency
           res
         end
 
+        # field F5
+        def genotype
+          fld = field(5)
+          res = Array.new
+          res << :high_density          if bit? fld, 0b0100
+          res << :haplotype_tagging_set if bit? fld, 0b0010
+          res << :available             if bit? fld, 0b0001
+          res
+        end
+
         # field F8
         def variation_class
           case (field(8) & 0b0000_1111)

diff --git a/lib/bio/dbsnp.rb b/lib/bio/dbsnp.rb
diff --git a/lib/bio/dbsnp/bitfield.rb b/lib/bio/dbsnp/bitfield.rb
diff --git a/spec/bio-dbsnp_spec.rb b/spec/bio-dbsnp_spec.rb
@@ -115,16 +115,14 @@
       end
     end
 
-    # describe "#genotype [F5]" do
-    #   context "given a string '05_0300_0003_01_04_04_00_00_01_00' of rs55874132 for .parse" do
-    #     it "returns an array containing :reference, :synonymous" do
-    #       obj = Bio::NCBI::Dbsnp::Bitfield.parse('05_0300_0003_01_04_04_00_00_01_00')
-    #       obj.genotype.should include(:high_density)
-    #     end
-    #   end
-    # end
-
-
+    describe "#genotype [F5]" do
+      context "given a string '05_0300_0003_01_04_04_00_00_01_00' of rs55874132 for .parse" do
+        it "returns an array containing :reference, :synonymous" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('05_0300_0003_01_04_04_00_00_01_00')
+          obj.genotype.should include(:high_density)
+        end
+      end
+    end
 
   end
 end