Added convenience methods for synteny data from 'i' lines.

For #68.

lib/bio/maf/maf.rb

@@ -263,6 +263,43 @@ def gapped?
         size != text.size
       end
 
+      I_STATUS = {
+        'C' => :contiguous,
+        'I' => :intervening,
+        'N' => :first,
+        'n' => :first_bridged,
+        'M' => :missing_data,
+        'T' => :tandem
+      }
+
+      def decode_status_char(c)
+        I_STATUS[c] || raise("Unsupported status character #{c}!")
+      end
+
+      def left_status_char
+        i_data && i_data[0]
+      end
+
+      def left_status
+        i_data && decode_status_char(left_status_char())
+      end
+
+      def left_count
+        i_data && i_data[1].to_i
+      end
+
+      def right_status_char
+        i_data && i_data[2]
+      end
+
+      def right_status
+        i_data && decode_status_char(right_status_char())
+      end
+
+      def right_count
+        i_data && i_data[3].to_i
+      end
+
       def species
         parts = source.split('.', 2)
         parts.size == 2 ? parts[0] : nil

spec/bio/maf/maf_spec.rb

@@ -141,7 +141,30 @@ module MAF
             range = s.text_range(9076...(9077 + 9))
           }.to raise_error
         end
+      end
 
+      describe "synteny data" do
+        it "extracts basic data from i lines" do
+          p = Parser.new(TestData + 'chr22_ieq2.maf',
+                         :parse_extended => true)
+          b = p.parse_block
+          b.sequences[0].left_status_char.should be_nil
+          b.sequences[0].left_status.should be_nil
+          b.sequences[0].left_count.should be_nil
+          b.sequences[0].right_status_char.should be_nil
+          b.sequences[0].right_status.should be_nil
+          b.sequences[0].right_count.should be_nil
+          # works but let's not over-specify internal state
+          #b.sequences[1].i_data.should == %w(N 0 C 0)
+          b.sequences[1].left_status_char.should == 'N'
+          b.sequences[1].left_status.should == :first
+          b.sequences[1].right_status_char.should == 'C'
+          b.sequences[1].right_status.should == :contiguous
+          b.sequences[2].left_status.should == :contiguous
+          b.sequences[2].right_status_char.should == 'I'
+          b.sequences[2].right_status.should == :intervening
+          b.sequences[2].right_count.should == 146
+        end
       end
 
       describe "#to_bioalignment" do

test/data/chr22_ieq2.maf

@@ -0,0 +1,11 @@
+##maf version=1 scoring=autoMZ.v1
+a score=13668.000000
+s hg19.chr22              16054189 54 + 51304566 TCTGTGAAACCCACAGTAATGGGGCTGACATCCTCTGCCCTATGCAAGAGAGGT
+s ponAbe2.chrUn           13354616 54 + 72422247 TCTTTCAAACCCACAGTAATGGGGCTGACATCCTCTACCATATGCAAGAGAGGT
+q ponAbe2.chrUn                                  855489998999999899968899889893997969799999879999999989
+i ponAbe2.chrUn           N 0 C 0
+s panTro2.chrUn            7684562 54 + 58616431 TCTGTGAAACCCACAGTAATGGGGCTGACATCCTCTGCCCTATGCAAGAGAGAT
+q panTro2.chrUn                                  999999999999999999999999999999999999999999999999999999
+i panTro2.chrUn           C 0 I 146
+e turTru1.scaffold_109008    25049 1601 +    50103 I
+