X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Ftest%2Fmaasha%2Ftest_seq.rb;h=171e6b1ae9157205527a0613ef68fe65686bf4e7;hb=d4b9c1bec954d5ff3e6eb2f7dc6c1aaa1f7f810f;hp=927937ec3684097c9a42cfa773dc48e832f97b3b;hpb=73481219c95124438f7020da8af9b21498d4a269;p=biopieces.git diff --git a/code_ruby/test/maasha/test_seq.rb b/code_ruby/test/maasha/test_seq.rb index 927937e..171e6b1 100755 --- 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 @@ -538,10 +448,10 @@ class TestSeq < Test::Unit::TestCase end def test_Seq_mask_seq_hard_bang_returns_correctly - @entry.seq = "ATCG" - @entry.qual = "RSTU" + @entry.seq = "-ATCG" + @entry.qual = "RRSTU" - assert_equal("NNCG", @entry.mask_seq_hard!(20).seq) + assert_equal("-NNCG", @entry.mask_seq_hard!(20).seq) end def test_Seq_mask_seq_soft_bang_with_nil_seq_raises @@ -558,13 +468,6 @@ class TestSeq < Test::Unit::TestCase assert_raise(SeqError) { @entry.mask_seq_soft!(20) } end - def test_Seq_mask_seq_soft_bang_returns_correctly - @entry.seq = "ATCG" - @entry.qual = "RSTU" - - assert_equal("atCG", @entry.mask_seq_soft!(20).seq) - 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) } @@ -577,7 +480,207 @@ class TestSeq < Test::Unit::TestCase assert_nothing_raised { @entry.mask_seq_soft!(0) } assert_nothing_raised { @entry.mask_seq_soft!(40) } end -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, 40, 33], + ["454", 0, 40, 64], + ["solexa", -5, 40, 64], + ["illumina13", 0, 40, 64], + ["illumina15", 0, 40, 64], + ["illumina18", 0, 41, 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 __END__