changed upper/lower case output in assemble_pairs

[biopieces.git] / code_ruby / test / maasha / seq / test_assemble.rb

diff --git a/code_ruby/test/maasha/seq/test_assemble.rb b/code_ruby/test/maasha/seq/test_assemble.rb
index bdc759c3297a269493509a21419a27a249a29d32..b5ddb7d706c03b3b4ea633149b8e55f7741785e6 100755 (executable)
--- a/code_ruby/test/maasha/seq/test_assemble.rb
+++ b/code_ruby/test/maasha/seq/test_assemble.rb
@@ -12,19 +12,19 @@ class TestAssemble < Test::Unit::TestCase
   end
 
   test "Assemble.pair with overlap returns the correctly" do
-    assert_equal("atcgatc", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc")).seq)
-    assert_equal("atcgat",  Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat")).seq)
-    assert_equal("atcga",   Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga")).seq)
-    assert_equal("atcg",    Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg")).seq)
+    assert_equal("atcGatc", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc")).seq)
+    assert_equal("atCGat",  Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat")).seq)
+    assert_equal("aTCGa",   Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga")).seq)
+    assert_equal("ATCG",    Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg")).seq)
   end
 
   test "Assemble.pair with overlap and overlap_min returns correctly" do
     assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc"), :overlap_min => 2))
-    assert_equal("atcgat", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat"), :overlap_min => 2).seq)
+    assert_equal("atCGat", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat"), :overlap_min => 2).seq)
   end
 
   test "Assemble.pair with overlap and overlap_max returns correctly" do
-    assert_equal("atcga", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga"), :overlap_max => 3).seq)
+    assert_equal("aTCGa", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga"), :overlap_max => 3).seq)
     assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg"), :overlap_max => 3))
   end
 
@@ -33,4 +33,9 @@ class TestAssemble < Test::Unit::TestCase
     assert_equal("GH??43", Assemble.pair(Seq.new("test1", "atcg", :dna, "GHII"), Seq.new("test2", "cgat", :dna, "5543")).qual)
     assert_equal("I???5", Assemble.pair(Seq.new("test1", "atcg", :dna, "IIII"), Seq.new("test2", "tcga", :dna, "5555")).qual)
   end
+
+  test "Assemble.pair with mismatch returns the highest scoring" do
+    assert_equal("ATCGA", Assemble.pair(Seq.new("t1", "atcga", :dna, "IIIII"), Seq.new("t2", "attga", :dna, "55555"), :mismatches_max => 20).seq)
+    assert_equal("ATTGA", Assemble.pair(Seq.new("t1", "atcga", :dna, "55555"), Seq.new("t2", "attga", :dna, "IIIII"), :mismatches_max => 20).seq)
+  end
 end