added test for align dir

[biopieces.git] / code_ruby / test / maasha / test_seq.rb

diff --git a/code_ruby/test/maasha/test_seq.rb b/code_ruby/test/maasha/test_seq.rb
index 9a8deef34c8a443cad8c9f5817e744cda8cd0d05..d177d311467901296a0d2d0aa90f01dce29ffd86 100755 (executable)
--- a/code_ruby/test/maasha/test_seq.rb
+++ b/code_ruby/test/maasha/test_seq.rb
@@ -282,11 +282,6 @@ class TestSeq < Test::Unit::TestCase
     assert_raise(SeqError) { @entry.subseq(-1, 1) }
   end
 
-  def test_Seq_subseq_with_length_lt_1_raises
-    @entry.seq = "ATCG"
-    assert_raise(SeqError) { @entry.subseq(0, 0) }
-  end
-
   def test_Seq_subseq_with_start_plus_length_gt_seq_raises
     @entry.seq = "ATCG"
     assert_raise(SeqError) { @entry.subseq(0, 5) }
@@ -323,11 +318,6 @@ class TestSeq < Test::Unit::TestCase
     assert_raise(SeqError) { @entry.subseq!(-1, 1) }
   end
 
-  def test_Seq_subseq_bang_with_length_lt_1_raises
-    @entry.seq = "ATCG"
-    assert_raise(SeqError) { @entry.subseq!(0, 0) }
-  end
-
   def test_Seq_subseq_bang_with_start_plus_length_gt_seq_raises
     @entry.seq = "ATCG"
     assert_raise(SeqError) { @entry.subseq!(0, 5) }
@@ -378,86 +368,6 @@ class TestSeq < Test::Unit::TestCase
     assert_equal("ATCG", @entry.subseq_rand(4).seq)
   end
 
-  def test_Seq_quality_trim_right_with_missing_seq_raises
-    @entry.qual = "hhhh"
-    assert_raise(SeqError) { @entry.quality_trim_right(20) }
-  end
-
-  def test_Seq_quality_trim_right_with_missing_qual_raises
-    @entry.seq = "ATCG"
-    assert_raise(SeqError) { @entry.quality_trim_right(20) }
-  end
-
-  def test_Seq_quality_trim_right_with_bad_min_raises
-    @entry.seq  = "ATCG"
-    @entry.qual = "hhhh"
-
-    [-1, 41].each do |min|
-      assert_raise(SeqError) { @entry.quality_trim_right(min) }
-    end
-  end
-
-  def test_Seq_quality_trim_right_with_ok_min_dont_raise
-    @entry.seq  = "ATCG"
-    @entry.qual = "hhhh"
-
-    [0, 40].each do |min|
-      assert_nothing_raised { @entry.quality_trim_right(min) }
-    end
-  end
-
-  def test_Seq_quality_trim_right_returns_correctly
-    @entry.seq  = "AAAAATCG"
-    @entry.qual = "hhhhhgfe"
-    @entry.quality_trim_right(38)
-    assert_equal("AAAAAT", @entry.seq) 
-    assert_equal("hhhhhg", @entry.qual) 
-  end
-
-  def test_Seq_quality_trim_left_with_missing_seq_raises
-    @entry.qual = "hhhh"
-    assert_raise(SeqError) { @entry.quality_trim_left(20) }
-  end
-
-  def test_Seq_quality_trim_left_with_missing_qual_raises
-    @entry.seq = "ATCG"
-    assert_raise(SeqError) { @entry.quality_trim_left(20) }
-  end
-
-  def test_Seq_quality_trim_left_with_bad_min_raises
-    @entry.seq  = "ATCG"
-    @entry.qual = "hhhh"
-
-    [-1, 41].each do |min|
-      assert_raise(SeqError) { @entry.quality_trim_left(min) }
-    end
-  end
-
-  def test_Seq_quality_trim_left_with_ok_min_dont_raise
-    @entry.seq  = "ATCG"
-    @entry.qual = "hhhh"
-
-    [0, 40].each do |min|
-      assert_nothing_raised { @entry.quality_trim_left(min) }
-    end
-  end
-
-  def test_Seq_quality_trim_left_returns_correctly
-    @entry.seq  = "GCTAAAAA"
-    @entry.qual = "efghhhhh"
-    @entry.quality_trim_left(38)
-    assert_equal("TAAAAA", @entry.seq) 
-    assert_equal("ghhhhh", @entry.qual) 
-  end
-
-  def test_Seq_quality_trim_returns_correctly
-    @entry.seq  = "GCTAAAAAGTG"
-    @entry.qual = "efghhhhhgfe"
-    @entry.quality_trim(38)
-    assert_equal("TAAAAAG", @entry.seq) 
-    assert_equal("ghhhhhg", @entry.qual) 
-  end
-
   def test_Seq_indels_remove_without_qual_returns_correctly
     @entry.seq  = "A-T.CG~CG"
     @entry.qual = nil
@@ -577,7 +487,151 @@ class TestSeq < Test::Unit::TestCase
 
     assert_equal("-atCG", @entry.mask_seq_soft!(20).seq)
   end
-end
 
+  # convert sanger to ...
+
+  def test_Seq_convert_scores_bang_from_sanger_to_sanger_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('sanger', 'sanger').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_sanger_to_solexa_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('abcdefgh', @entry.convert_scores!('sanger', 'solexa').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_sanger_to_illumina13_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('abcdefgh', @entry.convert_scores!('sanger', 'illumina13').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_sanger_to_illumina15_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('abcdefgh', @entry.convert_scores!('sanger', 'illumina15').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_sanger_to_illumina18_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('sanger', 'illumina18').qual)
+  end
+
+  # convert solexa to ...
+
+  def test_Seq_convert_scores_bang_from_solexa_to_sanger_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal(%q[#$%&'()*], @entry.convert_scores!('solexa', 'sanger').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_solexa_to_solexa_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('solexa', 'solexa').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_solexa_to_illumina13_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('solexa', 'illumina13').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_solexa_to_illumina15_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('solexa', 'illumina15').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_solexa_to_illumina18_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal(%q[#$%&'()*], @entry.convert_scores!('solexa', 'illumina18').qual)
+  end
+
+  # convert illumina13 to ...
+
+  def test_Seq_convert_scores_bang_from_illumina13_to_sanger_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal(%q[#$%&'()*], @entry.convert_scores!('illumina13', 'sanger').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina13_to_solexa_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('illumina13', 'solexa').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina13_to_illumina13_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('illumina13', 'illumina13').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina13_to_illumina15_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('illumina13', 'illumina15').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina13_to_illumina18_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal(%q[#$%&'()*], @entry.convert_scores!('illumina13', 'illumina18').qual)
+  end
+
+  # convert illumina15 to ...
+
+  def test_Seq_convert_scores_bang_from_illumina15_to_sanger_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal(%q[#$%&'()*], @entry.convert_scores!('illumina15', 'sanger').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina15_to_solexa_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('illumina15', 'solexa').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina15_to_illumina13_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('illumina15', 'illumina13').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina15_to_illumina15_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('illumina15', 'illumina15').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina15_to_illumina18_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal(%q[#$%&'()*], @entry.convert_scores!('illumina15', 'illumina18').qual)
+  end
+
+  # convert illumina18 to ...
+
+  def test_Seq_convert_scores_bang_from_illumina18_to_sanger_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('illumina18', 'sanger').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina18_to_solexa_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('abcdefgh', @entry.convert_scores!('illumina18', 'solexa').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina18_to_illumina13_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('abcdefgh', @entry.convert_scores!('illumina18', 'illumina13').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina18_to_illumina15_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('abcdefgh', @entry.convert_scores!('illumina18', 'illumina15').qual)
+  end
+
+  def test_Seq_convert_scores_bang_from_illumina18_to_illumina18_returns_OK
+    @entry.qual = 'BCDEFGHI'
+    assert_equal('BCDEFGHI', @entry.convert_scores!('illumina18', 'illumina18').qual)
+  end
+
+  def test_Seq_scores_mean_without_qual_raises
+    @entry.qual = nil
+    assert_raise(SeqError) { @entry.scores_mean }
+  end
+
+  def test_Seq_scores_mean_returns_correctly
+    @entry.qual = '@@hh'
+    assert_equal(20.0, @entry.scores_mean)
+  end
+end
 
 __END__