Reverse seq

lib/bigbio/db/emitters/orf_emitter.rb

@@ -34,6 +34,21 @@ def CreateShortFrame.create_right fr,orfs,rseq
           nseq = seq[remove..-1] + rseq
           ShortFrameState.new nseq,ntseq_pos,fr.min_size_codons*3
         end
+
+        def CreateShortFrame.create_left fr,orfs,lseq
+          seq = fr.seq  # original sequence
+          ntseq_pos = fr.ntseq_pos # right side of seq
+          bridge = seq.size % 3    # chomp left side
+          remove = if orfs.size > 0
+            # remove the tail of the sequence
+            seq.size - bridge - (orfs.first.pos)*3 +1
+          else 
+            0
+          end
+          ntseq_pos += remove
+          nseq = lseq + seq[0..(seq.size-remove)]
+          ShortFrameState.new nseq,ntseq_pos,fr.min_size_codons*3
+        end
       end
 
       class FrameCodonSequence 
@@ -150,13 +165,16 @@ def split codons, is_splitter_func
 
     end
 
+    # This is the reversed version, which is rather the same as the forward,
+    # though the tracked ntseq_pos should be seen from the end of the sequence,
+    # as we are emmiting sequences from the end(!) Also we need to make sure
+    # the sequence is always in frame (from the left).
     class ShortReversedFrameState < ShortFrameState
 
       def initialize seq, ntseq_pos, ntmin_size
-        chop = seq.size % 3
-        @chopped_seq = seq[0..chop-1] if chop
-        seq = seq[chop..-1]
-        super seq,ntseq_pos,ntmin_size
+        chop = seq.size % 3 # align on codons
+        super seq[chop..-1],ntseq_pos,ntmin_size
+        @seq = seq # but record full seq
       end
 
     end

spec/emitter_spec.rb

@@ -183,22 +183,26 @@
   end
 
   it "should combine a reverse frame" do
-    s1 = "atggattaaatgta"
     s2 = "tatttaaatggatttaatgtaaatt"
+    #     ~===xxx============---...                               
+    s1 = "atggattaaatgta"
+    #     ......xxx=====
     # now move the other way, as sequences get emitted on the left
     fr = ShortReversedFrameState.new s2,0,0
     # p fr
+    fr.codons.to_seq.should == "ATTTAAATGGATTTAATGTAAATT"
     fr.ntseq_pos.should == 0
     orfs = fr.get_stopstop_orfs
-    # p orfs
+    orfs.map{ | orf | orf.to_seq }.should == ["ATGGATTTAATGTAA"]
     orfs.first.pos.should == 2 # in codons
-    fr3 = FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
-    fr3.ntseq_pos.should == 9
-    fr3.codons.to_seq.should == "ATGTAATGGATTTAATGTAAA"
+    fr3 = FrameCodonHelpers::CreateShortFrame.create_left(fr,orfs,s1)
+    fr3.ntseq_pos.should == 19
+    fr3.codons.to_seq.should == "ATGGATTAAATGTATATTTAA"
     norfs = fr3.get_stopstop_orfs
     orfs += norfs
-    orfs.map{ | orf | orf.to_seq }.should == ["ATGGATTAA", "TGGATTTAA"]
-    orfs.map{ | orf | orf.track_sequence_pos }.should == [0,11]
+    p orfs
+    orfs.map{ | orf | orf.to_seq }.should == ["ATGGATTTAATGTAA", "ATGTATATTTAA"]
+    orfs.map{ | orf | orf.track_ntseq_pos }.should == [18,18+12]
   end
 
 end