ported write_fastq to ruby and allowed different encoding support

[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..a90c565072503641160ea2c7c2e24fded0e0563b 100755 (executable)
--- a/code_ruby/test/maasha/test_seq.rb
+++ b/code_ruby/test/maasha/test_seq.rb
@@ -577,7 +577,141 @@ 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
+end
 
 __END__