+ def test_Seq_mask_seq_hard_bang_with_nil_seq_raises
+ @entry.seq = nil
+ @entry.qual = ""
+
+ assert_raise(SeqError) { @entry.mask_seq_hard!(20) }
+ end
+
+ def test_Seq_mask_seq_hard_bang_with_nil_qual_raises
+ @entry.seq = ""
+ @entry.qual = nil
+
+ assert_raise(SeqError) { @entry.mask_seq_hard!(20) }
+ end
+
+ def test_Seq_mask_seq_hard_bang_with_bad_cutoff_raises
+ assert_raise(SeqError) { @entry.mask_seq_hard!(-1) }
+ assert_raise(SeqError) { @entry.mask_seq_hard!(41) }
+ end
+
+ def test_Seq_mask_seq_hard_bang_with_OK_cutoff_dont_raise
+ @entry.seq = "ATCG"
+ @entry.qual = "RSTU"
+
+ assert_nothing_raised { @entry.mask_seq_hard!(0) }
+ assert_nothing_raised { @entry.mask_seq_hard!(40) }
+ end
+
+ def test_Seq_mask_seq_hard_bang_returns_correctly
+ @entry.seq = "-ATCG"
+ @entry.qual = "RRSTU"
+
+ assert_equal("-NNCG", @entry.mask_seq_hard!(20).seq)
+ end
+
+ def test_Seq_mask_seq_soft_bang_with_nil_seq_raises
+ @entry.seq = nil
+ @entry.qual = ""
+
+ assert_raise(SeqError) { @entry.mask_seq_soft!(20) }
+ end
+
+ def test_Seq_mask_seq_soft_bang_with_nil_qual_raises
+ @entry.seq = ""
+ @entry.qual = nil
+
+ assert_raise(SeqError) { @entry.mask_seq_soft!(20) }
+ end
+
+ def test_Seq_mask_seq_soft_bang_with_bad_cutoff_raises
+ assert_raise(SeqError) { @entry.mask_seq_soft!(-1) }
+ assert_raise(SeqError) { @entry.mask_seq_soft!(41) }
+ end
+
+ def test_Seq_mask_seq_soft_bang_with_OK_cutoff_dont_raise
+ @entry.seq = "ATCG"
+ @entry.qual = "RSTU"
+
+ assert_nothing_raised { @entry.mask_seq_soft!(0) }
+ assert_nothing_raised { @entry.mask_seq_soft!(40) }
+ end
+
+ def test_Seq_mask_seq_soft_bang_returns_correctly
+ @entry.seq = "-ATCG"
+ @entry.qual = "RRSTU"
+
+ assert_equal("-atCG", @entry.mask_seq_soft!(20).seq)
+ end
+
+ # qual score detection
+
+ def test_Seq_qual_base33_returns_correctly
+ # self.qual.match(/[!-:]/)
+ @entry.qual = '!"#$%&\'()*+,-./0123456789:'
+ assert_equal(true, @entry.qual_base33? )
+ @entry.qual = 32.chr
+ assert_equal(false, @entry.qual_base33? )
+ @entry.qual = 59.chr
+ assert_equal(false, @entry.qual_base33? )
+ end
+
+ def test_Seq_qual_base64_returns_correctly
+ # self.qual.match(/[K-h]/)
+ @entry.qual = 'KLMNOPQRSTUVWXYZ[\]^_`abcdefgh'
+ assert_equal(true, @entry.qual_base64? )
+ @entry.qual = 74.chr
+ assert_equal(false, @entry.qual_base64? )
+ @entry.qual = 105.chr
+ assert_equal(false, @entry.qual_base64? )
+ end
+
+ def test_Seq_qual_valid_with_nil_qual_raises
+ assert_raise(SeqError) { @entry.qual_valid?("illumina1.8") }
+ end
+
+ def test_Seq_qual_valid_with_bad_encoding_raises
+ @entry.qual = "abc"
+ assert_raise(SeqError) { @entry.qual_valid?("foobar") }
+ end
+
+ def test_Seq_qual_valid_returns_correctly
+ tests = [["sanger", 0, 93, 33],
+ ["454", 0, 62, 64],
+ ["solexa", -5, 62, 64],
+ ["illumina13", 0, 62, 64],
+ ["illumina15", 0, 62, 64],
+ ["illumina18", 0, 93, 33]]
+
+ tests.each do |test|
+ @entry.qual = (test[1] + test[-1]).chr + (test[2] + test[-1]).chr
+ assert_equal(true, @entry.qual_valid?(test[0]))
+ @entry.qual = (test[1] + test[-1] - 1).chr
+ assert_equal(false, @entry.qual_valid?(test[0]))
+ @entry.qual = (test[2] + test[-1] + 1).chr
+ assert_equal(false, @entry.qual_valid?(test[0]))
+ 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