test_insert.rb in scaffolder-0.4.0

- old
+ new
@@ -1,59 +1,51 @@
 require 'helper'
 
 class TestInsert < Test::Unit::TestCase
-  context Scaffolder::Insert do
+  context Scaffolder::Region::Insert do
 
-    setup do
-      @options = {
-        :start    => 5,
-        :stop     => 10,
-        :sequence => "ATGCGGGC"
-      }
-    end
+    context "attributes" do
 
-    should "correctly store the passed options" do
-      i = Scaffolder::Insert.new @options
-      assert_equal(i.start, @options[:start])
-      assert_equal(i.stop, @options[:stop])
-      assert_equal(i.sequence, @options[:sequence])
-    end
+      should_have_attribute Scaffolder::Region::Insert, :source, :open, :close
 
-    should "reverse the sequence when passed the reverse tag" do
-      i = Scaffolder::Insert.new @options.merge(:reverse => true)
-      rev = Bio::Sequence::NA.new(@options[:sequence]).reverse_complement
-      assert_equal(i.sequence, rev.upcase)
-    end
+      setup do
+        @length = 15
+        @insert = Scaffolder::Region::Insert.new
+        @insert.raw_sequence('N' * @length)
+      end
 
-    should "correctly generate the position" do
-      i = Scaffolder::Insert.new @options
-      assert_equal(i.position, (@options[:start]-1)..(@options[:stop]-1))
-    end
+      should "return open plus sequence length as default close" do
+        @insert.open  5
+        assert_equal(@insert.close,@insert.open + @length - 1)
+      end
 
-    should "estimate the sequence end position" do
-      @options.delete(:stop)
-      i = Scaffolder::Insert.new @options
-      assert_equal(i.stop, @options[:start] + @options[:sequence].length - 1)
-    end
+      should "return close minus sequence length as default open" do
+        @insert.close 20
+        assert_equal(@insert.open,@insert.close - @length - 1)
+      end
 
-    should "estimate the sequence start position" do
-      @options.delete(:start)
-      i = Scaffolder::Insert.new @options
-      assert_equal(i.start, @options[:stop] - @options[:sequence].length - 1)
-    end
+      should "include the insert position" do
+        @insert.open  5
+        @insert.close 10
+        assert_equal(@insert.position,4..9)
+      end
 
-    should "throw error when neither start or stop are provided" do
-      @options.delete(:start)
-      @options.delete(:stop)
-      assert_raise ArgumentError do
-        Scaffolder::Insert.new @options
+      should "throw an error when neither open or close are provided" do
+        assert_raise(Scaffolder::Errors::CoordinateError){ @insert.position }
       end
+
     end
 
-    should "be comparable by end position" do
-      a = Scaffolder::Insert.new @options
-      b = Scaffolder::Insert.new @options.merge(:stop => @options[:stop] + 1)
-      c = Scaffolder::Insert.new @options.merge(:stop => @options[:stop] + 2)
+    should "be comparable by close position" do
+      a = Scaffolder::Region::Insert.new
+      a.close 1
+
+      b = a.clone
+      b.close 2
+
+      c = b.clone
+      c.close 3
+
       assert_equal([c,a,b].sort, [a,b,c])
     end
 
   end
 end