rewrite of seq.rb and addition of seq/trim.rb

[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 a90c565072503641160ea2c7c2e24fded0e0563b..a8f58ce565d7b0598ee919fa372cfa1991119434 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