Bio::EMBL: add #co / #contig (CO line)

CON-division entries (e.g. chromosome-level assemblies built by
joining other entries, such as WGS scaffolds -- human GRCh38
chromosome 1, accession CM000663, is a real example) do not embed
their sequence in an SQ/sequence record; instead they describe it as
a join of other entries in a CO record. This line was previously
unhandled, so such entries silently looked like empty (0 bp)
sequences via sq/seq, with no way to retrieve the assembly
instruction.

Add #co (aliased as #contig, mirroring the recently added
Bio::GenBank#contig), returning the CO content as a String. As with
GenBank's #contig, sq/seq behavior for CO-only entries is left
unchanged (they keep returning an empty sequence); #co/#contig is a
complementary accessor, not a replacement.

Author: ngoto

lib/bio/db/embl/embl.rb

@@ -462,6 +462,22 @@ def seq
   alias naseq seq
   alias ntseq seq
 
+  # CO -- Returns contents of the CO (contig/construction) line as a
+  # String. Note that CON-division entries (e.g. chromosome-level
+  # assemblies constructed by joining other entries, such as WGS
+  # scaffolds) do not embed the sequence itself in an SQ/sequence
+  # record, and instead describe it as a join of other entries in a
+  # CO record; in this case, sq/seq return an empty sequence while co
+  # returns the assembly instruction string (e.g.
+  # "join(BX000000.1:1..1000,gap(100),BX000001.1:1..2000)"). Entries
+  # without a CO line return an empty String.
+  #
+  # CO Line; contig/construction information (>=0 per entry)
+  def co
+    field_fetch('CO')
+  end
+  alias contig co
+
   #--
   # // Line; termination line (end; 1/entry)
   #++

test/unit/bio/db/embl/test_embl_new_part.rb

@@ -64,4 +64,58 @@ def test_pr_absent
       assert_equal([], @obj.pr)
     end
   end # class TestEMBL_PR_line_absent
+
+  class TestEMBL_CO_line < Test::Unit::TestCase
+    def setup
+      # CON-division entries (e.g. chromosome-level assemblies built
+      # by joining WGS scaffolds, such as human GRCh38 chromosome 1,
+      # accession CM000663) do not embed the sequence itself in an
+      # SQ/sequence record; a CO line describes it as a join of other
+      # entries instead.
+      text = <<~THE_END_OF_THE_TEXT
+        ID   AB123456; SV 1; linear; genomic DNA; CON; PRO; 3100 BP.
+        XX
+        AC   AB123456;
+        XX
+        CO   join(BX000000.1:1..1000,gap(100),BX000001.1:1..2000)
+        //
+      THE_END_OF_THE_TEXT
+
+      @obj = Bio::EMBL.new(text)
+    end
+
+    def test_co
+      assert_equal('join(BX000000.1:1..1000,gap(100),BX000001.1:1..2000)',
+                   @obj.co)
+    end
+
+    def test_contig
+      assert_equal('join(BX000000.1:1..1000,gap(100),BX000001.1:1..2000)',
+                   @obj.contig)
+    end
+
+    def test_seq_is_empty_when_only_co_line_present
+      assert_equal('', @obj.seq.to_s)
+    end
+  end # class TestEMBL_CO_line
+
+  class TestEMBL_CO_line_absent < Test::Unit::TestCase
+    def setup
+      text = <<~THE_END_OF_THE_TEXT
+        ID   AB123456; SV 1; linear; genomic DNA; STD; PRO; 4 BP.
+        XX
+        AC   AB123456;
+        XX
+        SQ   Sequence 4 BP; 1 A; 1 C; 1 G; 1 T; 0 other;
+             acgt                                                               4
+        //
+      THE_END_OF_THE_TEXT
+
+      @obj = Bio::EMBL.new(text)
+    end
+
+    def test_co_absent
+      assert_equal('', @obj.co)
+    end
+  end # class TestEMBL_CO_line_absent
 end # module Bio