macroape 4.0.2 → 4.1.0

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Files changed (74) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +17 -17
  3. data/Gemfile +4 -4
  4. data/LICENSE +22 -22
  5. data/README.md +70 -70
  6. data/Rakefile.rb +49 -49
  7. data/TODO.txt +46 -46
  8. data/benchmark/benchmark_helper.rb +4 -4
  9. data/benchmark/similarity_benchmark.rb +52 -52
  10. data/bin/align_motifs +4 -4
  11. data/bin/eval_alignment +4 -4
  12. data/bin/eval_similarity +4 -4
  13. data/bin/find_pvalue +4 -4
  14. data/bin/find_threshold +4 -4
  15. data/bin/preprocess_collection +4 -4
  16. data/bin/scan_collection +4 -4
  17. data/lib/macroape.rb +14 -11
  18. data/lib/macroape/aligned_pair_intersection.rb +61 -62
  19. data/lib/macroape/cli.rb +191 -188
  20. data/lib/macroape/cli/align_motifs.rb +120 -100
  21. data/lib/macroape/cli/eval_alignment.rb +157 -156
  22. data/lib/macroape/cli/eval_similarity.rb +138 -137
  23. data/lib/macroape/cli/find_pvalue.rb +93 -87
  24. data/lib/macroape/cli/find_threshold.rb +103 -96
  25. data/lib/macroape/cli/preprocess_collection.rb +169 -161
  26. data/lib/macroape/cli/scan_collection.rb +171 -163
  27. data/lib/macroape/collection.rb +29 -0
  28. data/lib/macroape/motif_with_thresholds.rb +18 -0
  29. data/lib/macroape/pwm_compare.rb +39 -44
  30. data/lib/macroape/pwm_compare_aligned.rb +139 -130
  31. data/lib/macroape/{counting.rb → pwm_counting.rb} +175 -121
  32. data/lib/macroape/support/inverf.rb +13 -0
  33. data/lib/macroape/support/partial_sums.rb +17 -0
  34. data/lib/macroape/version.rb +4 -4
  35. data/macroape.gemspec +19 -19
  36. data/spec/count_distribution_spec.rb +112 -109
  37. data/spec/inverf_spec.rb +23 -0
  38. data/spec/partial_sums_spec.rb +28 -0
  39. data/spec/spec_helper.rb +11 -11
  40. data/test/align_motifs_test.rb +42 -43
  41. data/test/data/AHR_si.pwm +10 -10
  42. data/test/data/KLF3_f1.pcm +16 -16
  43. data/test/data/KLF3_f1.pwm +16 -16
  44. data/test/data/KLF4_f2.pcm +11 -11
  45. data/test/data/KLF4_f2.pwm +11 -11
  46. data/test/data/KLF4_f2_scan_results_all.txt +2 -2
  47. data/test/data/KLF4_f2_scan_results_default_cutoff.txt +1 -1
  48. data/test/data/KLF4_f2_scan_results_precise_mode.txt +2 -2
  49. data/test/data/SP1_f1.pcm +12 -12
  50. data/test/data/SP1_f1.pwm +12 -12
  51. data/test/data/SP1_f1_revcomp.pcm +12 -12
  52. data/test/data/SP1_f1_revcomp.pwm +12 -12
  53. data/test/data/medium_motif.pwm +8 -8
  54. data/test/data/short_motif.pwm +7 -7
  55. data/test/data/test_collection.yaml +231 -214
  56. data/test/data/test_collection/GABPA_f1.pwm +14 -14
  57. data/test/data/test_collection/KLF4_f2.pwm +10 -10
  58. data/test/data/test_collection/SP1_f1.pwm +12 -12
  59. data/test/data/test_collection_pcm/GABPA_f1.pcm +14 -14
  60. data/test/data/test_collection_pcm/KLF4_f2.pcm +11 -11
  61. data/test/data/test_collection_pcm/SP1_f1.pcm +12 -12
  62. data/test/data/test_collection_single_file.txt +38 -38
  63. data/test/data/test_collection_single_file_pcm.txt +37 -37
  64. data/test/data/test_collection_weak.yaml +231 -214
  65. data/test/eval_alignment_test.rb +90 -111
  66. data/test/eval_similarity_test.rb +105 -123
  67. data/test/find_pvalue_test.rb +34 -39
  68. data/test/find_threshold_test.rb +87 -91
  69. data/test/preprocess_collection_test.rb +56 -65
  70. data/test/scan_collection_test.rb +42 -48
  71. data/test/test_helper.rb +159 -160
  72. metadata +14 -10
  73. data/test/data/collection_pcm_without_thresholds.yaml +0 -188
  74. data/test/data/collection_without_thresholds.yaml +0 -188
data/test/eval_alignment_test.rb CHANGED
@@ -1,111 +1,90 @@
1
- require_relative 'test_helper'
2
-
3
- class TestEvalAlignment < Test::Unit::TestCase
4
- include Helpers
5
- def setup
6
- @start_dir = Dir.pwd
7
- Dir.chdir File.join(File.dirname(__FILE__), 'data')
8
- end
9
- def teardown
10
- Dir.chdir(@start_dir)
11
- end
12
-
13
- def test_process_weak_threshold
14
- assert_similarity_info_output({similarity: 0.24382446963092125,
15
- distance: 0.7561755303690787,
16
- length: 11,
17
- shift: -1,
18
- orientation: 'direct',
19
- words_recognized_by_both: 839.0,
20
- threshold_first: 5.8,
21
- words_recognized_by_first: 2104.0,
22
- pvalue_recognized_by_first: 0.0005016326904296875,
23
- threshold_second: 5.6,
24
- words_recognized_by_second: 2176.0,
25
- pvalue_recognized_by_second: 0.000518798828125,
26
- matrix_first_alignment: '.>>>>>>>>>>',
27
- matrix_second_alignment: '>>>>>>>>>>>' #, discretization: 10.0
28
- },
29
- Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm -1 direct'))
30
- end
31
-
32
-
33
- def test_process_strong_threshold
34
- assert_similarity_info_output({similarity: 0.2420758234928527,
35
- distance: 0.7579241765071473,
36
- length: 11,
37
- shift: -1,
38
- orientation: 'direct',
39
- words_recognized_by_both: 779.0,
40
- threshold_first: 5.8100000000000005,
41
- words_recognized_by_first: 1964.0,
42
- pvalue_recognized_by_first: 0.00046825408935546875,
43
- threshold_second: 5.61,
44
- words_recognized_by_second: 2033.0,
45
- pvalue_recognized_by_second: 0.00048470497131347656,
46
- matrix_first_alignment: '.>>>>>>>>>>',
47
- matrix_second_alignment: '>>>>>>>>>>>' #, discretization: 10.0
48
- },
49
- Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm -1 direct --boundary lower'))
50
- end
51
-
52
- def test_process_custom_thresholds
53
- assert_similarity_info_output({similarity: 0.28505023241865346,
54
- words_recognized_by_both: 1901.0,
55
- words_recognized_by_first: 4348.0,
56
- words_recognized_by_second: 4222.0,
57
- # threshold_first: 4.7,
58
- # threshold_second: 4.6
59
- },
60
- Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm -1 direct --first-threshold 4.7 --second-threshold 4.6'))
61
- end
62
- def test_process_not_optimal_alignment
63
- assert_similarity_info_output({similarity: 0.004517983923018248,
64
- length: 12,
65
- words_recognized_by_both: 77.0,
66
- words_recognized_by_first: 8416.0,
67
- words_recognized_by_second: 8704.0,
68
- matrix_first_alignment: '>>>>>>>>>>..',
69
- matrix_second_alignment: '.>>>>>>>>>>>',
70
- shift: 1,
71
- orientation: 'direct'},
72
- Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm 1 direct'))
73
- end
74
-
75
- def test_process_at_optimal_alignment_reversed
76
- assert_similarity_info_output({similarity: 0.0,
77
- words_recognized_by_both: 0.0,
78
- length: 11,
79
- matrix_first_alignment: '.>>>>>>>>>>',
80
- matrix_second_alignment:'<<<<<<<<<<<',
81
- shift: -1,
82
- orientation: 'revcomp'},
83
- Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm -1 revcomp'))
84
- end
85
-
86
- def test_process_pcm_files
87
- assert_equal( Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm -1 direct'),
88
- Helpers.eval_alignment_output('KLF4_f2.pcm SP1_f1.pcm -1 direct --pcm'))
89
- end
90
-
91
- def test_process_alignment_first_motif_from_stdin
92
- result = Helpers.provide_stdin(File.read('KLF4_f2.pwm')) {
93
- Helpers.eval_alignment_output('.stdin SP1_f1.pwm 0 direct') }
94
- assert_equal( Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm 0 direct'),
95
- result )
96
- end
97
-
98
- def test_process_alignment_second_motif_from_stdin
99
- result = Helpers.provide_stdin(File.read('SP1_f1.pwm')) {
100
- Helpers.eval_alignment_output('KLF4_f2.pwm .stdin 0 direct') }
101
- assert_equal( Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm 0 direct'),
102
- result )
103
- end
104
-
105
- def test_process_alignment_both_motifs_from_stdin
106
- result = Helpers.provide_stdin(File.read('KLF4_f2.pwm') + File.read('SP1_f1.pwm')) {
107
- Helpers.eval_alignment_output('.stdin .stdin 0 direct') }
108
- assert_equal( Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm 0 direct'),
109
- result )
110
- end
111
- end
1
+ require_relative 'test_helper'
2
+
3
+ class TestEvalAlignment < Test::Unit::TestCase
4
+ include Helpers
5
+ def setup
6
+ @start_dir = Dir.pwd
7
+ Dir.chdir File.join(File.dirname(__FILE__), 'data')
8
+ end
9
+ def teardown
10
+ Dir.chdir(@start_dir)
11
+ end
12
+
13
+ def test_process_weak_threshold
14
+ assert_similarity_info_output({similarity: 0.24382446963092125,
15
+ distance: 0.7561755303690787,
16
+ length: 11,
17
+ shift: -1,
18
+ orientation: 'direct',
19
+ words_recognized_by_both: 839.0,
20
+ threshold_first: 5.8,
21
+ words_recognized_by_first: 2104.0,
22
+ pvalue_recognized_by_first: 0.0005016326904296875,
23
+ threshold_second: 5.6,
24
+ words_recognized_by_second: 2176.0,
25
+ pvalue_recognized_by_second: 0.000518798828125,
26
+ matrix_first_alignment: '.>>>>>>>>>>',
27
+ matrix_second_alignment: '>>>>>>>>>>>' #, discretization: 10.0
28
+ },
29
+ Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm -1 direct'))
30
+ end
31
+
32
+
33
+ def test_process_strong_threshold
34
+ assert_similarity_info_output({similarity: 0.2420758234928527,
35
+ distance: 0.7579241765071473,
36
+ length: 11,
37
+ shift: -1,
38
+ orientation: 'direct',
39
+ words_recognized_by_both: 779.0,
40
+ threshold_first: 5.8100000000000005,
41
+ words_recognized_by_first: 1964.0,
42
+ pvalue_recognized_by_first: 0.00046825408935546875,
43
+ threshold_second: 5.61,
44
+ words_recognized_by_second: 2033.0,
45
+ pvalue_recognized_by_second: 0.00048470497131347656,
46
+ matrix_first_alignment: '.>>>>>>>>>>',
47
+ matrix_second_alignment: '>>>>>>>>>>>' #, discretization: 10.0
48
+ },
49
+ Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm -1 direct --boundary lower'))
50
+ end
51
+
52
+ def test_process_custom_thresholds
53
+ assert_similarity_info_output({similarity: 0.28505023241865346,
54
+ words_recognized_by_both: 1901.0,
55
+ words_recognized_by_first: 4348.0,
56
+ words_recognized_by_second: 4222.0,
57
+ # threshold_first: 4.7,
58
+ # threshold_second: 4.6
59
+ },
60
+ Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm -1 direct --first-threshold 4.7 --second-threshold 4.6'))
61
+ end
62
+ def test_process_not_optimal_alignment
63
+ assert_similarity_info_output({similarity: 0.004517983923018248,
64
+ length: 12,
65
+ words_recognized_by_both: 77.0,
66
+ words_recognized_by_first: 8416.0,
67
+ words_recognized_by_second: 8704.0,
68
+ matrix_first_alignment: '>>>>>>>>>>..',
69
+ matrix_second_alignment: '.>>>>>>>>>>>',
70
+ shift: 1,
71
+ orientation: 'direct'},
72
+ Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm 1 direct'))
73
+ end
74
+
75
+ def test_process_at_optimal_alignment_reversed
76
+ assert_similarity_info_output({similarity: 0.0,
77
+ words_recognized_by_both: 0.0,
78
+ length: 11,
79
+ matrix_first_alignment: '.>>>>>>>>>>',
80
+ matrix_second_alignment:'<<<<<<<<<<<',
81
+ shift: -1,
82
+ orientation: 'revcomp'},
83
+ Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm -1 revcomp'))
84
+ end
85
+
86
+ def test_process_pcm_files
87
+ assert_equal( Helpers.eval_alignment_output('KLF4_f2.pwm SP1_f1.pwm -1 direct'),
88
+ Helpers.eval_alignment_output('KLF4_f2.pcm SP1_f1.pcm -1 direct --pcm'))
89
+ end
90
+ end
data/test/eval_similarity_test.rb CHANGED
@@ -1,123 +1,105 @@
1
- require_relative 'test_helper'
2
-
3
- class TestEvalSimilarity < Test::Unit::TestCase
4
- include Helpers
5
- def setup
6
- @start_dir = Dir.pwd
7
- Dir.chdir File.join(File.dirname(__FILE__), 'data')
8
- end
9
- def teardown
10
- Dir.chdir(@start_dir)
11
- end
12
-
13
- def test_process_strong_thresholds
14
- assert_similarity_info_output({similarity: 0.2420758234928527,
15
- distance: 0.7579241765071473,
16
- length: 11,
17
- shift: -1,
18
- orientation: 'direct',
19
- words_recognized_by_both: 779.0,
20
- threshold_first: 5.8100000000000005,
21
- words_recognized_by_first: 1964.0,
22
- pvalue_recognized_by_first: 0.00046825408935546875,
23
- threshold_second: 5.61,
24
- words_recognized_by_second: 2033.0,
25
- pvalue_recognized_by_second: 0.00048470497131347656,
26
- matrix_first_alignment: '.>>>>>>>>>>',
27
- matrix_second_alignment: '>>>>>>>>>>>' #, discretization: 10.0
28
- },
29
- Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm --boundary lower'))
30
- end
31
-
32
- def test_process_weak_thresholds
33
- assert_similarity_info_output({similarity: 0.24382446963092125,
34
- distance: 0.7561755303690787,
35
- length: 11,
36
- shift: -1,
37
- orientation: 'direct',
38
- words_recognized_by_both: 839.0,
39
- threshold_first: 5.8,
40
- words_recognized_by_first: 2104.0,
41
- pvalue_recognized_by_first: 0.0005016326904296875,
42
- threshold_second: 5.6,
43
- words_recognized_by_second: 2176.0,
44
- pvalue_recognized_by_second: 0.000518798828125,
45
- matrix_first_alignment: '.>>>>>>>>>>',
46
- matrix_second_alignment: '>>>>>>>>>>>' #, discretization: 10.0
47
- },
48
- Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm'))
49
- end
50
- def test_process_custom_threshold
51
- assert_similarity_info_output({similarity: 0.28505023241865346,
52
- words_recognized_by_both: 1901.0,
53
- words_recognized_by_first: 4348.0,
54
- words_recognized_by_second: 4222.0,
55
- # threshold_first: 4.7,
56
- # threshold_second: 4.6
57
- },
58
- Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm --first-threshold 4.7 --second-threshold 4.6'))
59
- end
60
-
61
- def test_process_dissimilar_pair_of_pwms
62
- assert_similarity_info_output({similarity: 0.0037332005973120955,
63
- words_recognized_by_both: 15.0,
64
- words_recognized_by_first: 2033.0,
65
- words_recognized_by_second: 2000.0,
66
- length: 11,
67
- matrix_first_alignment: '>>>>>>>>>>>',
68
- matrix_second_alignment: '.>>>>>>>>>.',
69
- shift: 1,
70
- orientation: 'direct'},
71
- Helpers.eval_similarity_output('SP1_f1.pwm AHR_si.pwm --boundary lower'))
72
- end
73
-
74
- def test_recognize_orientation_of_alignment
75
- assert_similarity_info_output({similarity: 1.0,
76
- words_recognized_by_both: 2176.0,
77
- words_recognized_by_first: 2176.0,
78
- words_recognized_by_second: 2176.0,
79
- length: 11,
80
- matrix_first_alignment: '>>>>>>>>>>>',
81
- matrix_second_alignment: '<<<<<<<<<<<',
82
- shift: 0,
83
- orientation: 'revcomp'},
84
- Helpers.eval_similarity_output('SP1_f1_revcomp.pwm SP1_f1.pwm'))
85
- end
86
-
87
- def test_process_custom_discretization
88
- assert_similarity_info_output({similarity: 0.2580456407255705,
89
- words_recognized_by_both: 1323.0,
90
- words_recognized_by_first: 3554.0,
91
- words_recognized_by_second: 2896.0,
92
- length: 11,
93
- matrix_first_alignment: '>>>>>>>>>>>',
94
- matrix_second_alignment: '.>>>>>>>>>>',
95
- shift: 1,
96
- orientation: 'direct' #, discretization: 1.0
97
- },
98
- Helpers.eval_similarity_output('SP1_f1.pwm KLF4_f2.pwm -d 1'))
99
- end
100
-
101
- def test_process_pcm_files
102
- assert_equal( Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm'),
103
- Helpers.eval_similarity_output('KLF4_f2.pcm SP1_f1.pcm --pcm'))
104
- end
105
-
106
- def test_process_first_motif_from_stdin
107
- result = Helpers.provide_stdin(File.read('KLF4_f2.pwm')){
108
- Helpers.eval_similarity_output('.stdin SP1_f1.pwm') }
109
- assert_equal(Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm'), result)
110
- end
111
-
112
- def test_process_second_motif_from_stdin
113
- result = Helpers.provide_stdin(File.read('SP1_f1.pwm')){
114
- Helpers.eval_similarity_output('KLF4_f2.pwm .stdin') }
115
- assert_equal(Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm'), result)
116
- end
117
-
118
- def test_process_both_motifs_from_stdin
119
- result = Helpers.provide_stdin(File.read('KLF4_f2.pwm') + File.read('SP1_f1.pwm')){
120
- Helpers.eval_similarity_output('.stdin .stdin') }
121
- assert_equal(Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm'), result)
122
- end
123
- end
1
+ require_relative 'test_helper'
2
+
3
+ class TestEvalSimilarity < Test::Unit::TestCase
4
+ include Helpers
5
+ def setup
6
+ @start_dir = Dir.pwd
7
+ Dir.chdir File.join(File.dirname(__FILE__), 'data')
8
+ end
9
+ def teardown
10
+ Dir.chdir(@start_dir)
11
+ end
12
+
13
+ def test_process_strong_thresholds
14
+ assert_similarity_info_output({similarity: 0.2420758234928527,
15
+ distance: 0.7579241765071473,
16
+ length: 11,
17
+ shift: -1,
18
+ orientation: 'direct',
19
+ words_recognized_by_both: 779.0,
20
+ threshold_first: 5.8100000000000005,
21
+ words_recognized_by_first: 1964.0,
22
+ pvalue_recognized_by_first: 0.00046825408935546875,
23
+ threshold_second: 5.61,
24
+ words_recognized_by_second: 2033.0,
25
+ pvalue_recognized_by_second: 0.00048470497131347656,
26
+ matrix_first_alignment: '.>>>>>>>>>>',
27
+ matrix_second_alignment: '>>>>>>>>>>>' #, discretization: 10.0
28
+ },
29
+ Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm --boundary lower'))
30
+ end
31
+
32
+ def test_process_weak_thresholds
33
+ assert_similarity_info_output({similarity: 0.24382446963092125,
34
+ distance: 0.7561755303690787,
35
+ length: 11,
36
+ shift: -1,
37
+ orientation: 'direct',
38
+ words_recognized_by_both: 839.0,
39
+ threshold_first: 5.8,
40
+ words_recognized_by_first: 2104.0,
41
+ pvalue_recognized_by_first: 0.0005016326904296875,
42
+ threshold_second: 5.6,
43
+ words_recognized_by_second: 2176.0,
44
+ pvalue_recognized_by_second: 0.000518798828125,
45
+ matrix_first_alignment: '.>>>>>>>>>>',
46
+ matrix_second_alignment: '>>>>>>>>>>>' #, discretization: 10.0
47
+ },
48
+ Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm'))
49
+ end
50
+ def test_process_custom_threshold
51
+ assert_similarity_info_output({similarity: 0.28505023241865346,
52
+ words_recognized_by_both: 1901.0,
53
+ words_recognized_by_first: 4348.0,
54
+ words_recognized_by_second: 4222.0,
55
+ # threshold_first: 4.7,
56
+ # threshold_second: 4.6
57
+ },
58
+ Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm --first-threshold 4.7 --second-threshold 4.6'))
59
+ end
60
+
61
+ def test_process_dissimilar_pair_of_pwms
62
+ assert_similarity_info_output({similarity: 0.0037332005973120955,
63
+ words_recognized_by_both: 15.0,
64
+ words_recognized_by_first: 2033.0,
65
+ words_recognized_by_second: 2000.0,
66
+ length: 11,
67
+ matrix_first_alignment: '>>>>>>>>>>>',
68
+ matrix_second_alignment: '.>>>>>>>>>.',
69
+ shift: 1,
70
+ orientation: 'direct'},
71
+ Helpers.eval_similarity_output('SP1_f1.pwm AHR_si.pwm --boundary lower'))
72
+ end
73
+
74
+ def test_recognize_orientation_of_alignment
75
+ assert_similarity_info_output({similarity: 1.0,
76
+ words_recognized_by_both: 2176.0,
77
+ words_recognized_by_first: 2176.0,
78
+ words_recognized_by_second: 2176.0,
79
+ length: 11,
80
+ matrix_first_alignment: '>>>>>>>>>>>',
81
+ matrix_second_alignment: '<<<<<<<<<<<',
82
+ shift: 0,
83
+ orientation: 'revcomp'},
84
+ Helpers.eval_similarity_output('SP1_f1_revcomp.pwm SP1_f1.pwm'))
85
+ end
86
+
87
+ def test_process_custom_discretization
88
+ assert_similarity_info_output({similarity: 0.2580456407255705,
89
+ words_recognized_by_both: 1323.0,
90
+ words_recognized_by_first: 3554.0,
91
+ words_recognized_by_second: 2896.0,
92
+ length: 11,
93
+ matrix_first_alignment: '>>>>>>>>>>>',
94
+ matrix_second_alignment: '.>>>>>>>>>>',
95
+ shift: 1,
96
+ orientation: 'direct' #, discretization: 1.0
97
+ },
98
+ Helpers.eval_similarity_output('SP1_f1.pwm KLF4_f2.pwm -d 1'))
99
+ end
100
+
101
+ def test_process_pcm_files
102
+ assert_equal( Helpers.eval_similarity_output('KLF4_f2.pwm SP1_f1.pwm'),
103
+ Helpers.eval_similarity_output('KLF4_f2.pcm SP1_f1.pcm --pcm'))
104
+ end
105
+ end
data/test/find_pvalue_test.rb CHANGED
@@ -1,39 +1,34 @@
1
- require_relative 'test_helper'
2
-
3
- class FindPvalueTest < Test::Unit::TestCase
4
- def setup
5
- @start_dir = Dir.pwd
6
- Dir.chdir File.join(File.dirname(__FILE__), 'data')
7
- end
8
- def teardown
9
- Dir.chdir(@start_dir)
10
- end
11
- def test_process_pcm
12
- assert_equal [%w[4.1719 1048.0 0.00099945068359375]], Helpers.find_pvalue_output('KLF4_f2.pcm 4.1719 --pcm')
13
- end
14
- def test_process_one_threshold
15
- assert_equal [%w[4.1719 1048.0 0.00099945068359375]], Helpers.find_pvalue_output('KLF4_f2.pwm 4.1719')
16
- end
17
- def test_process_several_thresholds
18
- assert_equal [%w[4.1719 1048.0 0.00099945068359375],
19
- %w[5.2403 524.0 0.000499725341796875]], Helpers.find_pvalue_output('KLF4_f2.pwm 4.1719 5.2403')
20
- end
21
- def test_process_several_thresholds_result_is_ordered
22
- assert_equal [%w[5.2403 524.0 0.000499725341796875],
23
- %w[4.1719 1048.0 0.00099945068359375]], Helpers.find_pvalue_output('KLF4_f2.pwm 5.2403 4.1719')
24
- end
25
- def test_custom_discretization
26
- assert_equal [%w[5.2403 527.0 0.0005025863647460938]], Helpers.find_pvalue_output('KLF4_f2.pwm 5.2403 -d 100')
27
- end
28
- def test_probability_wise_backgrond
29
- assert_equal [%w[5.2403 0.0005025863647460938]], Helpers.find_pvalue_output('KLF4_f2.pwm 5.2403 -d 100 -b 0.25,0.25,0.25,0.25')
30
- end
31
- def test_custom_background
32
- assert_equal [%w[5.2403 6.815000000000001e-06]], Helpers.find_pvalue_output('KLF4_f2.pwm 5.2403 -b 0.4,0.1,0.1,0.4')
33
- end
34
- def test_process_pwm_from_stdin
35
- assert_equal Helpers.find_pvalue_output('KLF4_f2.pwm 1'),
36
- Helpers.provide_stdin(File.read 'KLF4_f2.pwm'){ Helpers.find_pvalue_output('.stdin 1') }
37
- end
38
- end
39
-
1
+ require_relative 'test_helper'
2
+
3
+ class FindPvalueTest < Test::Unit::TestCase
4
+ def setup
5
+ @start_dir = Dir.pwd
6
+ Dir.chdir File.join(File.dirname(__FILE__), 'data')
7
+ end
8
+ def teardown
9
+ Dir.chdir(@start_dir)
10
+ end
11
+ def test_process_pcm
12
+ assert_equal [%w[4.1719 1048.0 0.00099945068359375]], Helpers.find_pvalue_output('KLF4_f2.pcm 4.1719 --pcm')
13
+ end
14
+ def test_process_one_threshold
15
+ assert_equal [%w[4.1719 1048.0 0.00099945068359375]], Helpers.find_pvalue_output('KLF4_f2.pwm 4.1719')
16
+ end
17
+ def test_process_several_thresholds
18
+ assert_equal [%w[4.1719 1048.0 0.00099945068359375],
19
+ %w[5.2403 524.0 0.000499725341796875]], Helpers.find_pvalue_output('KLF4_f2.pwm 4.1719 5.2403')
20
+ end
21
+ def test_process_several_thresholds_result_is_ordered
22
+ assert_equal [%w[5.2403 524.0 0.000499725341796875],
23
+ %w[4.1719 1048.0 0.00099945068359375]], Helpers.find_pvalue_output('KLF4_f2.pwm 5.2403 4.1719')
24
+ end
25
+ def test_custom_discretization
26
+ assert_equal [%w[5.2403 527.0 0.0005025863647460938]], Helpers.find_pvalue_output('KLF4_f2.pwm 5.2403 -d 100')
27
+ end
28
+ def test_probability_wise_backgrond
29
+ assert_equal [%w[5.2403 0.0005025863647460938]], Helpers.find_pvalue_output('KLF4_f2.pwm 5.2403 -d 100 -b 0.25,0.25,0.25,0.25')
30
+ end
31
+ def test_custom_background
32
+ assert_equal [%w[5.2403 6.815000000000001e-06]], Helpers.find_pvalue_output('KLF4_f2.pwm 5.2403 -b 0.4,0.1,0.1,0.4')
33
+ end
34
+ end