7 class TestSeq < Test::Unit::TestCase
12 # def test_Seq# autoremoves whitespace, newlines, and carriage returns
14 # dna.seq = "A\tT\r\tC\nG "
15 # assert_equal(dna.seq, "ATCG")
18 def test_Seq_new_bp_returns_correctly
19 record = {:SEQ_NAME => "test", :SEQ => "ATCG", :SEQ_TYPE => "dna", :SCORES => "hhhh"}
20 seq = Seq.new_bp(record)
21 assert_equal("test", seq.seq_name)
22 assert_equal("ATCG", seq.seq)
23 assert_equal("dna", seq.type)
24 assert_equal("hhhh", seq.qual)
27 def test_Seq_is_dna_with_no_sequence_type_returns_false
28 assert(@entry.is_dna? == false)
31 def test_Seq_is_dna_with_dna_sequence_type_returns_true
33 assert(@entry.is_dna? == true)
36 def test_Seq_is_rna_with_no_sequence_type_returns_false
37 assert(@entry.is_rna? == false)
40 def test_Seq_is_rna_with_rna_sequence_type_returns_true
42 assert(@entry.is_rna? == true)
45 def test_Seq_is_protein_with_no_sequence_type_returns_false
46 assert(@entry.is_protein? == false)
49 def test_Seq_is_protein_with_protein_sequence_type_returns_true
50 @entry.type = 'protein'
51 assert_equal(true, @entry.is_protein?)
54 def test_Seq_type_guess_without_sequence_raises
55 assert_raise(SeqError) { @entry.type_guess }
58 def test_Seq_type_guess_with_protein_returns_protein
59 @entry.seq = 'atcatcrFgatcg'
60 assert_equal('protein', @entry.type_guess)
63 def test_Seq_type_guess_with_rna_returns_rna
64 @entry.seq = 'atcatcrUgatcg'
65 assert_equal('rna', @entry.type_guess)
68 def test_Seq_type_guess_with_dna_returns_dna
69 @entry.seq = 'atcatcgatcg'
70 assert_equal('dna', @entry.type_guess)
73 def test_Seq_type_guess_EM_without_sequence_raises
74 assert_raise(SeqError) { @entry.type_guess! }
77 def test_Seq_type_guess_EM_with_protein_returns_protein
78 @entry.seq = 'atcatcrFgatcg'
80 assert_equal('protein', @entry.type)
83 def test_Seq_type_guess_EM_with_rna_returns_rna
84 @entry.seq = 'atcatcrUgatcg'
86 assert_equal('rna', @entry.type)
89 def test_Seq_type_guess_EM_with_dna_returns_dna
90 @entry.seq = 'atcatcgatcg'
92 assert_equal('dna', @entry.type)
95 def test_Seq_length_is_correct
97 assert_equal(4, @entry.length)
100 def test_Seq_indels_is_correct
101 @entry.seq = 'ATCG.-~_'
102 assert_equal(4, @entry.indels)
105 def test_Seq_to_rna_raises_if_no_sequence
107 assert_raise(SeqError) { @entry.to_rna }
110 def test_Seq_to_rna_raises_on_bad_type
113 assert_raise(SeqError) { @entry.to_rna }
116 def test_Seq_to_rna_transcribes_correctly
117 @entry.seq = 'ATCGatcg'
119 assert_equal("AUCGaucg", @entry.to_rna)
122 def test_Seq_to_rna_changes_entry_type_to_rna
123 @entry.seq = 'ATCGatcg'
126 assert_equal("rna", @entry.type)
129 def test_Seq_to_dna_raises_if_no_sequence
131 assert_raise(SeqError) { @entry.to_dna }
134 def test_Seq_to_dna_raises_on_bad_type
137 assert_raise(SeqError) { @entry.to_dna }
140 def test_Seq_to_dna_transcribes_correctly
141 @entry.seq = 'AUCGaucg'
143 assert_equal("ATCGatcg", @entry.to_dna)
146 def test_Seq_to_dna_changes_entry_type_to_dna
147 @entry.seq = 'AUCGaucg'
150 assert_equal("dna", @entry.type)
153 def test_Seq_to_bp_returns_correct_record
154 @entry.seq_name = 'test'
156 assert_equal({:SEQ_NAME=>"test", :SEQ=>"ATCG", :SEQ_LEN=>4}, @entry.to_bp)
159 def test_Seq_to_bp_raises_on_missing_seq_name
161 assert_raise(SeqError) { @entry.to_bp }
164 def test_Seq_to_bp_raises_on_missing_sequence
165 @entry.seq_name = 'test'
166 assert_raise(SeqError) { @entry.to_bp }
169 def test_Seq_to_fasta_raises_on_missing_seq_name
171 assert_raise(SeqError) { @entry.to_fasta }
174 def test_Seq_to_fasta_raises_on_empty_seq_name
177 assert_raise(SeqError) { @entry.to_fasta }
180 def test_Seq_to_fasta_raises_on_missing_seq
181 @entry.seq_name = 'test'
182 assert_raise(SeqError) { @entry.to_fasta }
185 def test_Seq_to_fasta_raises_on_empty_seq
186 @entry.seq_name = 'test'
188 assert_raise(SeqError) { @entry.to_fasta }
191 def test_Seq_to_fasta_returns_correct_entry
192 @entry.seq_name = 'test'
194 assert_equal(">test\nATCG\n", @entry.to_fasta)
197 def test_Seq_to_fasta_wraps_correctly
198 entry = Seq.new("test", "ATCG")
199 assert_equal(">test\nAT\nCG\n", entry.to_fasta(2))
202 def test_Seq_to_fastq_returns_correct_entry
203 @entry.seq_name = 'test'
206 assert_equal("@test\nATCG\n+\nhhhh\n", @entry.to_fastq)
209 def test_Seq_to_key_with_bad_residue_raises
210 entry = Seq.new("test", "AUCG")
211 assert_raise(SeqError) { entry.to_key }
214 def test_Seq_to_key_returns_correctly
215 entry = Seq.new("test", "ATCG")
216 assert_equal(54, entry.to_key)
219 def test_Seq_reverse_returns_correctly
221 assert_equal("GCTA", @entry.reverse.seq)
224 def test_Seq_complement_raises_if_no_sequence
226 assert_raise(SeqError) { @entry.complement }
229 def test_Seq_complement_raises_on_bad_type
231 @entry.type = 'protein'
232 assert_raise(SeqError) { @entry.complement }
235 def test_Seq_complement_for_DNA_is_correct
236 @entry.seq = 'ATCGatcg'
238 assert_equal("TAGCtagc", @entry.complement)
241 def test_Seq_complement_for_RNA_is_correct
242 @entry.seq = 'AUCGaucg'
244 assert_equal("UAGCuagc", @entry.complement)
247 def test_Seq_reverse_complement_for_DNA_is_correct
248 @entry.seq = 'ATCGatcg'
250 assert_equal("cgatCGAT", @entry.reverse_complement.seq)
253 def test_Seq_reverse_complement_for_RNA_is_correct
254 @entry.seq = 'AUCGaucg'
256 assert_equal("cgauCGAU", @entry.reverse_complement.seq)
259 def test_Seq_hamming_distance_returns_correctly
260 seq1 = Seq.new("test1", "ATCG")
261 seq2 = Seq.new("test2", "atgg")
262 assert_equal(1, seq1.hamming_distance(seq2))
265 def test_Seq_generate_with_length_lt_1_raises
266 assert_raise(SeqError) { @entry.generate(-10, "dna") }
267 assert_raise(SeqError) { @entry.generate(0, "dna") }
270 def test_Seq_generate_with_bad_type_raises
271 assert_raise(SeqError) { @entry.generate(10, "foo") }
274 def test_Seq_generate_with_ok_type_dont_raise
275 %w[dna DNA rna RNA protein Protein].each do |type|
276 assert_nothing_raised { @entry.generate(10, type) }
280 def test_Seq_subseq_with_start_lt_0_raises
282 assert_raise(SeqError) { @entry.subseq(-1, 1) }
285 def test_Seq_subseq_with_length_lt_1_raises
287 assert_raise(SeqError) { @entry.subseq(0, 0) }
290 def test_Seq_subseq_with_start_plus_length_gt_seq_raises
292 assert_raise(SeqError) { @entry.subseq(0, 5) }
295 def test_Seq_subseq_returns_correct_sequence
297 assert_equal("AT", @entry.subseq(0, 2).seq)
298 assert_equal("CG", @entry.subseq(2, 2).seq)
301 def test_Seq_subseq_without_len_returns_correct_sequence
303 assert_equal("ATCG", @entry.subseq(0).seq)
304 assert_equal("CG", @entry.subseq(2).seq)
307 def test_Seq_subseq_returns_correct_qual
310 assert_equal("ab", @entry.subseq(0, 2).qual)
311 assert_equal("cd", @entry.subseq(2, 2).qual)
314 def test_Seq_subseq_without_len_returns_correct_qual
317 assert_equal("abcd", @entry.subseq(0).qual)
318 assert_equal("cd", @entry.subseq(2).qual)
321 def test_Seq_subseq_bang_with_start_lt_0_raises
323 assert_raise(SeqError) { @entry.subseq!(-1, 1) }
326 def test_Seq_subseq_bang_with_length_lt_1_raises
328 assert_raise(SeqError) { @entry.subseq!(0, 0) }
331 def test_Seq_subseq_bang_with_start_plus_length_gt_seq_raises
333 assert_raise(SeqError) { @entry.subseq!(0, 5) }
336 def test_Seq_subseq_bang_returns_correct_sequence
339 assert_equal("AT", @entry.seq)
342 assert_equal("CG", @entry.seq)
345 def test_Seq_subseq_bang_without_len_returns_correct_sequence
348 assert_equal("ATCG", @entry.seq)
351 assert_equal("CG", @entry.seq)
354 def test_Seq_subseq_bang_with_pos_and_len_returns_correct_qual
358 assert_equal("ab", @entry.qual)
362 assert_equal("cd", @entry.qual)
365 def test_Seq_subseq_bang_with_pos_returns_correct_qual
369 assert_equal("abcd", @entry.qual)
373 assert_equal("cd", @entry.qual)
376 def test_Seq_subseq_rand_returns_correct_sequence
378 assert_equal("ATCG", @entry.subseq_rand(4).seq)
381 def test_Seq_quality_trim_right_with_missing_seq_raises
383 assert_raise(SeqError) { @entry.quality_trim_right(20) }
386 def test_Seq_quality_trim_right_with_missing_qual_raises
388 assert_raise(SeqError) { @entry.quality_trim_right(20) }
391 def test_Seq_quality_trim_right_with_bad_min_raises
395 [-1, 41].each do |min|
396 assert_raise(SeqError) { @entry.quality_trim_right(min) }
400 def test_Seq_quality_trim_right_with_ok_min_dont_raise
404 [0, 40].each do |min|
405 assert_nothing_raised { @entry.quality_trim_right(min) }
409 def test_Seq_quality_trim_right_returns_correctly
410 @entry.seq = "AAAAATCG"
411 @entry.qual = "hhhhhgfe"
412 @entry.quality_trim_right(38)
413 assert_equal("AAAAAT", @entry.seq)
414 assert_equal("hhhhhg", @entry.qual)
417 def test_Seq_quality_trim_left_with_missing_seq_raises
419 assert_raise(SeqError) { @entry.quality_trim_left(20) }
422 def test_Seq_quality_trim_left_with_missing_qual_raises
424 assert_raise(SeqError) { @entry.quality_trim_left(20) }
427 def test_Seq_quality_trim_left_with_bad_min_raises
431 [-1, 41].each do |min|
432 assert_raise(SeqError) { @entry.quality_trim_left(min) }
436 def test_Seq_quality_trim_left_with_ok_min_dont_raise
440 [0, 40].each do |min|
441 assert_nothing_raised { @entry.quality_trim_left(min) }
445 def test_Seq_quality_trim_left_returns_correctly
446 @entry.seq = "GCTAAAAA"
447 @entry.qual = "efghhhhh"
448 @entry.quality_trim_left(38)
449 assert_equal("TAAAAA", @entry.seq)
450 assert_equal("ghhhhh", @entry.qual)
453 def test_Seq_quality_trim_returns_correctly
454 @entry.seq = "GCTAAAAAGTG"
455 @entry.qual = "efghhhhhgfe"
456 @entry.quality_trim(38)
457 assert_equal("TAAAAAG", @entry.seq)
458 assert_equal("ghhhhhg", @entry.qual)
461 def test_Seq_indels_remove_without_qual_returns_correctly
462 @entry.seq = "A-T.CG~CG"
464 assert_equal("ATCGCG", @entry.indels_remove.seq)
467 def test_Seq_indels_remove_with_qual_returns_correctly
468 @entry.seq = "A-T.CG~CG"
469 @entry.qual = "a@b@cd@fg"
470 assert_equal("ATCGCG", @entry.indels_remove.seq)
471 assert_equal("abcdfg", @entry.indels_remove.qual)
474 def test_Seq_composition_returns_correctly
475 @entry.seq = "AAAATTTCCG"
476 assert_equal(4, @entry.composition["A"])
477 assert_equal(3, @entry.composition["T"])
478 assert_equal(2, @entry.composition["C"])
479 assert_equal(1, @entry.composition["G"])
480 assert_equal(0, @entry.composition["X"])
483 def test_Seq_homopol_max_returns_0_with_empty_sequence
485 assert_equal(0, @entry.homopol_max)
488 def test_Seq_homopol_max_returns_0_with_nil_sequence
490 assert_equal(0, @entry.homopol_max)
493 def test_Seq_homopol_max_returns_0_when_not_found
494 @entry.seq = "AtTcCcGggGnnNnn"
495 assert_equal(0, @entry.homopol_max(6))
498 def test_Seq_homopol_max_returns_correctly
499 @entry.seq = "AtTcCcGggGnnNnn"
500 assert_equal(5, @entry.homopol_max(3))
503 def test_Seq_hard_mask_returns_correctly
504 @entry.seq = "--AAAANn"
505 assert_equal(33.33, @entry.hard_mask)
508 def test_Seq_soft_mask_returns_correctly
509 @entry.seq = "--AAAa"
510 assert_equal(25.00, @entry.soft_mask)