X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Ftest%2Fmaasha%2Ftest_seq.rb;h=e50271d647e1b253798f06a1aa8864d4cc0dcbe5;hb=a30677c14f1738f6a76e8c12f2e732cdef9958d6;hp=b3bdd790baa16546e74d655e79dd1ec06f3d57eb;hpb=128ec42589b930642cf8863baa8a844dc5fd2c3f;p=biopieces.git

diff --git a/code_ruby/test/maasha/test_seq.rb b/code_ruby/test/maasha/test_seq.rb
index b3bdd79..e50271d 100755
--- a/code_ruby/test/maasha/test_seq.rb
+++ b/code_ruby/test/maasha/test_seq.rb
@@ -34,6 +34,10 @@ class TestSeq < Test::Unit::TestCase
     @entry = Seq.new
   end
 
+  test "Seq.new with differnet length SEQ and SCORES raises" do
+    assert_raise(SeqError) { Seq.new(seq_name: "test", seq: "ATCG", type: :dna, qual: "hhh") }
+  end
+
   test "Seq.new_bp returns correctly" do
     record = {:SEQ_NAME => "test", :SEQ => "ATCG", :SEQ_TYPE => :dna, :SCORES => "hhhh"}
     seq    = Seq.new_bp(record)
@@ -214,7 +218,7 @@ class TestSeq < Test::Unit::TestCase
   end
 
   test "#to_fasta wraps correctly" do
-    entry = Seq.new("test", "ATCG")
+    entry = Seq.new(seq_name: "test", seq: "ATCG")
     assert_equal(">test\nAT\nCG\n", entry.to_fasta(2))
   end
 
@@ -226,12 +230,12 @@ class TestSeq < Test::Unit::TestCase
   end
 
   test "#to_key with bad residue raises" do
-    entry = Seq.new("test", "AUCG")
+    entry = Seq.new(seq_name: "test", seq: "AUCG")
     assert_raise(SeqError) { entry.to_key }
   end
 
   test "#to_key returns correctly" do
-    entry = Seq.new("test", "ATCG")
+    entry = Seq.new(seq_name: "test", seq: "ATCG")
     assert_equal(54, entry.to_key)
   end
 
@@ -298,11 +302,24 @@ class TestSeq < Test::Unit::TestCase
     assert_equal("UAGCuagc", @entry.complement!.seq)
   end
 
+  test "#hamming_distance returns correctly" do
+    seq1 = Seq.new(seq: "ATCG")
+    seq2 = Seq.new(seq: "atgg")
+    assert_equal(1, seq1.hamming_distance(seq2))
+  end
+
+  test "#hamming_distance with ambiguity codes return correctly" do
+    seq1 = Seq.new(seq: "ATCG")
+    seq2 = Seq.new(seq: "atng")
 
-  test "#hamming distance returns correctly" do
-    seq1 = Seq.new("test1", "ATCG")
-    seq2 = Seq.new("test2", "atgg")
     assert_equal(1, seq1.hamming_distance(seq2))
+    assert_equal(0, seq1.hamming_distance(seq2, ambiguity: true))
+  end
+
+  test "#edit_distance returns correctly" do
+    seq1 = Seq.new(seq: "ATCG")
+    seq2 = Seq.new(seq: "tgncg")
+    assert_equal(2, seq1.edit_distance(seq2))
   end
 
   test "#generate with length < 1 raises" do
@@ -333,34 +350,50 @@ class TestSeq < Test::Unit::TestCase
     assert_not_equal(@entry.seq, @entry.shuffle!.seq)
   end
 
+  test "#+ without qual returns correctly" do
+    entry = Seq.new(seq_name: "test1", seq: "at") + Seq.new(seq_name: "test2", seq: "cg")
+    assert_nil(entry.seq_name)
+    assert_equal("atcg", entry.seq)
+    assert_nil(entry.type)
+    assert_nil(entry.qual)
+  end
+
+  test "#+ with qual returns correctly" do
+    entry = Seq.new(seq_name: "test1", seq: "at", type: :dna, qual: "II") + Seq.new(seq_name: "test2", seq: "cg", type: :dna, qual: "JJ")
+    assert_nil(entry.seq_name)
+    assert_equal("atcg", entry.seq)
+    assert_equal(:dna,   entry.type)
+    assert_equal("IIJJ", entry.qual)
+  end
+
   test "#<< with different types raises" do
     @entry.seq = "atcg"
-    assert_raise(SeqError) { @entry << Seq.new("test", "atcg", :dna) }
+    assert_raise(SeqError) { @entry << Seq.new(seq_name: "test", seq: "atcg", type: :dna) }
   end
 
   test "#<< with missing qual in one entry raises" do
     @entry.seq  = "atcg"
     @entry.type = :dna
-    assert_raise(SeqError) { @entry << Seq.new("test", "atcg", :dna, "IIII") }
+    assert_raise(SeqError) { @entry << Seq.new(seq_name: "test", seq: "atcg", type: :dna, qual: "IIII") }
     @entry.qual = "IIII"
-    assert_raise(SeqError) { @entry << Seq.new("test", "atcg", :dna) }
+    assert_raise(SeqError) { @entry << Seq.new(seq_name: "test", seq: "atcg", type: :dna) }
   end
 
   test "#<< with nil qual in both entries dont raise" do
     @entry.seq = "atcg"
-    assert_nothing_raised { @entry << Seq.new("test", "atcg") }
+    assert_nothing_raised { @entry << Seq.new(seq_name: "test", seq: "atcg") }
   end
 
   test "#<< with qual in both entries dont raise" do
     @entry.seq  = "atcg"
     @entry.type = :dna
     @entry.qual = "IIII"
-    assert_nothing_raised { @entry << Seq.new("test", "atcg", :dna, "IIII") }
+    assert_nothing_raised { @entry << Seq.new(seq_name: "test", seq: "atcg", type: :dna, qual: "IIII") }
   end
 
   test "#<< without qual returns correctly" do
     @entry.seq  = "atcg"
-    @entry <<  Seq.new("test", "ATCG")
+    @entry <<  Seq.new(seq_name: "test", seq: "ATCG")
     assert_equal("atcgATCG", @entry.seq)
   end
 
@@ -368,21 +401,53 @@ class TestSeq < Test::Unit::TestCase
     @entry.seq  = "atcg"
     @entry.type = :dna
     @entry.qual = "HHHH"
-    @entry <<  Seq.new("test", "ATCG", :dna, "IIII")
+    @entry <<  Seq.new(seq_name: "test", seq: "ATCG", type: :dna, qual: "IIII")
     assert_equal("atcgATCG", @entry.seq)
     assert_equal("HHHHIIII", @entry.qual)
   end
 
-  test "#[] returns correctly" do
-    @entry.seq  = "atcg"
-    @entry.type = :dna
-    @entry.qual = "FGHI"
+  test "#[] with qual returns correctly" do
+    entry = Seq.new(seq_name: "test", seq: "atcg", type: :dna, qual: "FGHI")
+
+    e = entry[2]
+
+    assert_equal("test", e.seq_name)
+    assert_equal("c",    e.seq)
+    assert_equal(:dna,   e.type)
+    assert_equal("H",    e.qual)
+    assert_equal("atcg", entry.seq)
+    assert_equal("FGHI", entry.qual)
+  end
 
-    fail
+  test "#[] without qual returns correctly" do
+    entry = Seq.new(seq_name: "test", seq: "atcg")
+
+    e = entry[2]
+
+    assert_equal("test", e.seq_name)
+    assert_equal("c",    e.seq)
+    assert_nil(e.qual)
+    assert_equal("atcg", entry.seq)
+  end
+
+  test "[]= with qual returns correctly" do
+    entry = Seq.new(seq_name: "test", seq: "atcg", type: :dna, qual: "FGHI")
+
+    entry[0] = Seq.new(seq_name: "foo", seq: "T", type: :dna, qual: "I")
+
+    assert_equal("test", entry.seq_name)
+    assert_equal("Ttcg", entry.seq)
+    assert_equal(:dna,   entry.type)
+    assert_equal("IGHI", entry.qual)
   end
 
-  test "[]= returns correctly" do
-    fail
+  test "[]= without qual returns correctly" do
+    entry = Seq.new(seq_name: "test", seq: "atcg")
+
+    entry[0] = Seq.new(seq_name: "foo", seq: "T")
+
+    assert_equal("test", entry.seq_name)
+    assert_equal("Ttcg", entry.seq)
   end
 
   test "#subseq with start < 0 raises" do
@@ -498,26 +563,6 @@ class TestSeq < Test::Unit::TestCase
     assert_equal(0, @entry.composition["X"])
   end
 
-  test "#homopol_max returns 0 with empty sequence" do
-    @entry.seq = ""
-    assert_equal(0, @entry.homopol_max)
-  end
-
-  test "#homopol_max returns 0 with nil sequence" do
-    @entry.seq = nil
-    assert_equal(0, @entry.homopol_max)
-  end
-
-  test "#homopol_max returns 0 when not found" do
-    @entry.seq = "AtTcCcGggGnnNnn"
-    assert_equal(0, @entry.homopol_max(6))
-  end
-
-  test "#homopol_max returns correctly" do
-    @entry.seq = "AtTcCcGggGnnNnn"
-    assert_equal(5, @entry.homopol_max(3))
-  end
-
   test "#hard_mask returns correctly" do
     @entry.seq = "--AAAANn"
     assert_equal(33.33, @entry.hard_mask)