macroape 3.3.3 → 3.3.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (54) hide show
  1. data/.gitignore +1 -0
  2. data/Rakefile.rb +7 -22
  3. data/TODO.txt +7 -6
  4. data/bin/align_motifs +4 -0
  5. data/bin/eval_alignment +2 -1
  6. data/bin/eval_similarity +2 -1
  7. data/bin/find_pvalue +2 -1
  8. data/bin/find_threshold +2 -1
  9. data/bin/preprocess_collection +2 -1
  10. data/bin/scan_collection +2 -1
  11. data/lib/macroape/aligned_pair_intersection.rb +2 -3
  12. data/lib/macroape/cli/align_motifs.rb +49 -0
  13. data/lib/macroape/cli/eval_alignment.rb +124 -0
  14. data/lib/macroape/cli/eval_similarity.rb +107 -0
  15. data/lib/macroape/cli/find_pvalue.rb +89 -0
  16. data/lib/macroape/cli/find_threshold.rb +84 -0
  17. data/lib/macroape/cli/preprocess_collection.rb +123 -0
  18. data/lib/macroape/cli/scan_collection.rb +141 -0
  19. data/lib/macroape/cli.rb +5 -0
  20. data/lib/macroape/counting.rb +15 -1
  21. data/lib/macroape/pwm_compare.rb +21 -1
  22. data/lib/macroape/pwm_compare_aligned.rb +21 -0
  23. data/lib/macroape/version.rb +1 -1
  24. data/macroape.gemspec +1 -1
  25. data/test/align_motifs_test.rb +12 -0
  26. data/test/data/KLF3_f1.pat +16 -0
  27. data/test/data/KLF3_f1.pcm +16 -0
  28. data/test/data/KLF4_f2.pcm +11 -0
  29. data/test/data/SP1_f1.pat +11 -11
  30. data/test/data/SP1_f1.pcm +12 -0
  31. data/test/data/SP1_f1_revcomp.pat +11 -11
  32. data/test/data/SP1_f1_revcomp.pcm +12 -0
  33. data/test/data/test_collection/SP1_f1.pat +11 -11
  34. data/test/data/test_collection.yaml +49 -109
  35. data/test/data/test_collection_pcm/GABPA_f1.pcm +14 -0
  36. data/test/data/test_collection_pcm/KLF4_f2.pcm +11 -0
  37. data/test/data/test_collection_pcm/SP1_f1.pcm +12 -0
  38. data/test/data/test_collection_single_file.txt +38 -0
  39. data/test/data/test_collection_single_file_pcm.txt +38 -0
  40. data/test/eval_alignment_test.rb +31 -0
  41. data/test/eval_similarity_test.rb +28 -13
  42. data/test/find_pvalue_test.rb +10 -13
  43. data/test/find_threshold_test.rb +10 -5
  44. data/test/preprocess_collection_test.rb +36 -2
  45. data/test/scan_collection_test.rb +9 -4
  46. data/test/test_helper.rb +61 -2
  47. metadata +38 -12
  48. data/lib/macroape/exec/eval_alignment.rb +0 -125
  49. data/lib/macroape/exec/eval_similarity.rb +0 -108
  50. data/lib/macroape/exec/find_pvalue.rb +0 -81
  51. data/lib/macroape/exec/find_threshold.rb +0 -77
  52. data/lib/macroape/exec/preprocess_collection.rb +0 -101
  53. data/lib/macroape/exec/scan_collection.rb +0 -124
  54. data/test/eval_alignment_similarity_test.rb +0 -20
data/test/data/test_collection.yaml CHANGED
@@ -3,7 +3,7 @@ pvalues:
3
3
  - 0.0005
4
4
  - 0.0001
5
5
  - 5.0e-05
6
- background:
6
+ background: &17959680
7
7
  - 1
8
8
  - 1
9
9
  - 1
@@ -12,26 +12,6 @@ precise_discretization: 10
12
12
  rough_discretization: 1
13
13
  pwms:
14
14
  GABPA_f1: !ruby/object:Bioinform::PWM
15
- background:
16
- - 1
17
- - 1
18
- - 1
19
- - 1
20
- input: ! "GABPA_f1\n-0.1106670158341858 0.013801606113892391 0.6054596108973699
21
- -1.3518085041421573 \n0.37030668921643345 0.15761121480429963 0.009069314183831202
22
- -0.9888619717703562 \n0.47526546359546684 -0.3011678534572083 0.4031522994412777
23
- -1.8638752827041059 \n-1.5544255540164373 1.1082369687811506 -0.2814091552834454
24
- -5.30708531823271 \n-0.6362037835776368 1.235338189985594 -3.5801322928552253
25
- -5.717323067092849 \n-5.852906870733575 -5.852906870733575 1.3841383838057746
26
- -5.852906870733575 \n-5.852906870733575 -5.852906870733575 1.3841383838057746
27
- -5.852906870733575 \n1.3835219739184708 -5.2341956006430985 -5.852906870733575
28
- -5.852906870733575 \n1.3756340514956562 -5.394962755562375 -5.394962755562375
29
- -3.401117964959733 \n-1.2176198315414444 -3.109079898175411 1.2964067931472216
30
- -5.717323067092849 \n-1.3716559438167257 -0.2761401935045069 -1.8504445165866068
31
- 1.0404320473626856 \n-0.5440863133031895 -0.48103682561971345 0.907381908447086
32
- -1.1280642594012078 \n0.10557340209290218 -0.01814819455289191 0.4381106695354074
33
- -1.0304105539540915 \n"
34
- parser: !ruby/class 'Bioinform::StringParser'
35
15
  matrix:
36
16
  - - -0.1106670158341858
37
17
  - 0.013801606113892391
@@ -86,24 +66,9 @@ pwms:
86
66
  - 0.4381106695354074
87
67
  - -1.0304105539540915
88
68
  name: GABPA_f1
69
+ background: *17959680
70
+ max_hash_size: 1000000
89
71
  KLF4_f2: !ruby/object:Bioinform::PWM
90
- background:
91
- - 1
92
- - 1
93
- - 1
94
- - 1
95
- input: ! "KLF4_f2\n0.30861857265872605 -2.254321000121579 0.13505703522674192
96
- 0.3285194224375633 \n-1.227018967707036 -4.814127713368663 1.3059890687390967
97
- -4.908681463544344 \n-2.443469374521196 -4.648238485031404 1.3588686548279805
98
- -4.441801801188402 \n-2.7177827948276123 -3.8073538975356565 1.356272809724262
99
- -3.504104725510225 \n-0.5563232977367343 0.5340697765121405 -3.61417723090579
100
- 0.5270259776377405 \n-1.8687622060887386 -4.381483976582316 1.337932245336098
101
- -3.815629658877517 \n-2.045671123823928 -2.384975142213679 0.7198551207724355
102
- 0.5449254135616948 \n-1.373157530374372 -3.0063112097748217 1.285188335493552
103
- -2.5026044231773543 \n-2.1030513122772208 -1.8941348100402244 1.249265758393991
104
- -1.4284210948906104 \n-1.3277128628152939 0.8982415633049462 -0.8080773665408135
105
- -0.18161647647456935 \n"
106
- parser: !ruby/class 'Bioinform::StringParser'
107
72
  matrix:
108
73
  - - 0.30861857265872605
109
74
  - -2.254321000121579
@@ -146,82 +111,57 @@ pwms:
146
111
  - -0.8080773665408135
147
112
  - -0.18161647647456935
148
113
  name: KLF4_f2
114
+ background: *17959680
115
+ max_hash_size: 1000000
149
116
  SP1_f1: !ruby/object:Bioinform::PWM
150
- background:
151
- - 1
152
- - 1
153
- - 1
154
- - 1
155
- input: ! '> SP1_f1
156
-
157
- -0.24435707885585334 -0.6748234046937317 0.8657012535789861 -1.1060188862599292
158
-
159
- -1.0631255752097801 -2.1119259694238686 1.0960627561110399 -0.6138563775211981
160
-
161
- -0.387227623476054 -2.973985191321805 1.1807800242010371 -4.338927525031567
162
-
163
- -4.563896055436894 -2.916163300253228 1.3684371349982631 -5.077972423609655
164
-
165
- -2.2369752892820087 -3.719643631330185 1.3510439136452728 -4.8899306705082335
166
-
167
- -0.07473964149330914 0.9449196547620103 -2.624685764808605 -0.851098348782244
168
-
169
- -1.9643526491643326 -2.9784027708801153 1.3113096718240569 -2.3243342594990253
170
-
171
- -4.015548413965584 -3.138426807809667 1.338748858978805 -2.0846739035376483
172
-
173
- -0.4450938582835542 -2.2510053061629707 1.126543157436868 -1.7780413702431377
174
-
175
- -1.1896356092245055 -1.2251832285630033 1.163676006374752 -1.6080243648157357
176
-
177
- -0.5166047365590577 0.7641033353626651 -0.28626775700282125 -0.6825482097865606'
178
- parser: !ruby/class 'Bioinform::StringParser'
179
117
  matrix:
180
- - - -0.24435707885585334
181
- - -0.6748234046937317
182
- - 0.8657012535789861
183
- - -1.1060188862599292
184
- - - -1.0631255752097801
185
- - -2.1119259694238686
186
- - 1.0960627561110399
187
- - -0.6138563775211981
188
- - - -0.387227623476054
189
- - -2.973985191321805
190
- - 1.1807800242010371
191
- - -4.338927525031567
118
+ - - -0.24435707885585292
119
+ - -0.674823404693731
120
+ - 0.8657012535789866
121
+ - -1.1060188862599287
122
+ - - -1.0631255752097797
123
+ - -2.111925969423868
124
+ - 1.0960627561110403
125
+ - -0.6138563775211977
126
+ - - -0.3872276234760535
127
+ - -2.9739851913218045
128
+ - 1.1807800242010378
129
+ - -4.338927525031566
192
130
  - - -4.563896055436894
193
- - -2.916163300253228
194
- - 1.3684371349982631
131
+ - -2.9161633002532277
132
+ - 1.3684371349982638
195
133
  - -5.077972423609655
196
- - - -2.2369752892820087
197
- - -3.719643631330185
198
- - 1.3510439136452728
199
- - -4.8899306705082335
200
- - - -0.07473964149330914
201
- - 0.9449196547620103
202
- - -2.624685764808605
203
- - -0.851098348782244
204
- - - -1.9643526491643326
205
- - -2.9784027708801153
206
- - 1.3113096718240569
207
- - -2.3243342594990253
208
- - - -4.015548413965584
209
- - -3.138426807809667
210
- - 1.338748858978805
211
- - -2.0846739035376483
212
- - - -0.4450938582835542
213
- - -2.2510053061629707
214
- - 1.126543157436868
215
- - -1.7780413702431377
216
- - - -1.1896356092245055
217
- - -1.2251832285630033
218
- - 1.163676006374752
219
- - -1.6080243648157357
220
- - - -0.5166047365590577
221
- - 0.7641033353626651
222
- - -0.28626775700282125
223
- - -0.6825482097865606
134
+ - - -2.2369752892820083
135
+ - -3.7196436313301846
136
+ - 1.3510439136452734
137
+ - -4.889930670508233
138
+ - - -0.07473964149330865
139
+ - 0.944919654762011
140
+ - -2.6246857648086044
141
+ - -0.8510983487822436
142
+ - - -1.9643526491643322
143
+ - -2.978402770880115
144
+ - 1.3113096718240573
145
+ - -2.324334259499025
146
+ - - -4.0155484139655835
147
+ - -3.1384268078096667
148
+ - 1.3387488589788057
149
+ - -2.084673903537648
150
+ - - -0.44509385828355363
151
+ - -2.2510053061629702
152
+ - 1.1265431574368685
153
+ - -1.7780413702431372
154
+ - - -1.1896356092245048
155
+ - -1.2251832285630027
156
+ - 1.1636760063747527
157
+ - -1.6080243648157353
158
+ - - -0.5166047365590571
159
+ - 0.7641033353626657
160
+ - -0.2862677570028208
161
+ - -0.68254820978656
224
162
  name: SP1_f1
163
+ background: *17959680
164
+ max_hash_size: 1000000
225
165
  infos:
226
166
  GABPA_f1:
227
167
  :rough:
data/test/data/test_collection_pcm/GABPA_f1.pcm ADDED
@@ -0,0 +1,14 @@
1
+ GABPA_f1
2
+ 615.2572649050138 697.0698715160123 1261.1903440712872 176.43506582414153
3
+ 996.4929869323321 805.1878697364007 693.7695793644275 254.5021102832924
4
+ 1106.9888035794224 508.19444415177276 1029.8329748714536 104.93632371380718
5
+ 143.7121486195701 2086.4279160661263 518.37507049306 1.4374111377025893
6
+ 362.9541452731307 2369.473894845734 17.23702397004065 0.2874822275405179
7
+ 0.0 0.0 2749.952546316428 0.0
8
+ 0.0 0.0 2749.952546316428 0.0
9
+ 2748.2567506938462 1.695795622582083 0.0 0.0
10
+ 2726.6484322711017 1.1499289101620715 1.1499289101620715 21.00425622500253
11
+ 202.05697400573305 28.799402471063658 2518.808687612104 0.2874822275405179
12
+ 172.92889618879767 521.1240363384483 106.38197600987633 1949.517637779338
13
+ 398.1679460365911 424.20938204069563 1706.4024212088275 221.17279703034018
14
+ 764.2587933951809 675.0883944902433 1066.5413633225007 244.06399510852864
data/test/data/test_collection_pcm/KLF4_f2.pcm ADDED
@@ -0,0 +1,11 @@
1
+ KLF4_f2
2
+ 1233.46088405354 93.18173277811673 1036.6014857092885 1258.2948629970272
3
+ 263.979242343185 5.314520555872139 3347.5949971525274 4.650205486388122
4
+ 76.7700780003465 6.643150694840173 3529.4896409394937 8.636095903292224
5
+ 57.86097393406657 18.102585643439472 3520.3342027139347 25.24120324653207
6
+ 518.1947904009378 1545.9062946905135 22.396758181071043 1535.0411222654507
7
+ 137.98151691820345 9.300410972776241 3456.320530770924 17.936506876068467
8
+ 115.27647661640499 81.51802997128804 1861.9425868567278 1562.801872093553
9
+ 227.8095486111286 42.84555258785854 3278.6396005325996 72.244263806387
10
+ 108.73384179997886 134.47328134862394 3162.880454846513 215.45138754285665
11
+ 238.49636899561344 2225.9561104691043 402.40727964384774 754.6792064294074
data/test/data/test_collection_pcm/SP1_f1.pcm ADDED
@@ -0,0 +1,12 @@
1
+ SP1_f1
2
+ 682.6436366358055 443.1455214015781 2075.655346294993 287.211468117951
3
+ 299.8883246804867 103.74338315843572 2613.8927022405364 471.1315623708902
4
+ 591.4892493324709 42.631827541794564 2845.1654083148564 9.36948726124641
5
+ 7.071084742361592 45.29093411231232 3432.8847704374107 3.409183158303573
6
+ 91.308984085713 19.1536481364332 3373.656949880137 4.5363903481026
7
+ 809.2082973387932 2246.941954176211 61.30766021687515 371.19806071846244
8
+ 120.56476435866055 42.4349244403591 3242.1560628684038 83.50022078295852
9
+ 13.72524477409959 35.858220519297525 3332.4066864946167 106.66582066236779
10
+ 558.1188080161639 90.0084504200356 2694.854973210736 145.67374080342415
11
+ 264.0088462230318 254.7175868081866 2796.88087480315 173.0486646159857
12
+ 519.46013914282 1874.9349086474765 654.5411208373813 439.7198038226514
data/test/data/test_collection_single_file.txt ADDED
@@ -0,0 +1,38 @@
1
+ > SP1_f1
2
+ -0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
3
+ -1.0631255752097797 -2.111925969423868 1.0960627561110403 -0.6138563775211977
4
+ -0.3872276234760535 -2.9739851913218045 1.1807800242010378 -4.338927525031566
5
+ -4.563896055436894 -2.9161633002532277 1.3684371349982638 -5.077972423609655
6
+ -2.2369752892820083 -3.7196436313301846 1.3510439136452734 -4.889930670508233
7
+ -0.07473964149330865 0.944919654762011 -2.6246857648086044 -0.8510983487822436
8
+ -1.9643526491643322 -2.978402770880115 1.3113096718240573 -2.324334259499025
9
+ -4.0155484139655835 -3.1384268078096667 1.3387488589788057 -2.084673903537648
10
+ -0.44509385828355363 -2.2510053061629702 1.1265431574368685 -1.7780413702431372
11
+ -1.1896356092245048 -1.2251832285630027 1.1636760063747527 -1.6080243648157353
12
+ -0.5166047365590571 0.7641033353626657 -0.2862677570028208 -0.68254820978656
13
+ KLF4_f2
14
+ 0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
15
+ -1.227018967707036 -4.814127713368663 1.3059890687390967 -4.908681463544344
16
+ -2.443469374521196 -4.648238485031404 1.3588686548279805 -4.441801801188402
17
+ -2.7177827948276123 -3.8073538975356565 1.356272809724262 -3.504104725510225
18
+ -0.5563232977367343 0.5340697765121405 -3.61417723090579 0.5270259776377405
19
+ -1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
20
+ -2.045671123823928 -2.384975142213679 0.7198551207724355 0.5449254135616948
21
+ -1.373157530374372 -3.0063112097748217 1.285188335493552 -2.5026044231773543
22
+ -2.1030513122772208 -1.8941348100402244 1.249265758393991 -1.4284210948906104
23
+ -1.3277128628152939 0.8982415633049462 -0.8080773665408135 -0.18161647647456935
24
+
25
+ GABPA_f1
26
+ -0.1106670158341858 0.013801606113892391 0.6054596108973699 -1.3518085041421573
27
+ 0.37030668921643345 0.15761121480429963 0.009069314183831202 -0.9888619717703562
28
+ 0.47526546359546684 -0.3011678534572083 0.4031522994412777 -1.8638752827041059
29
+ -1.5544255540164373 1.1082369687811506 -0.2814091552834454 -5.30708531823271
30
+ -0.6362037835776368 1.235338189985594 -3.5801322928552253 -5.717323067092849
31
+ -5.852906870733575 -5.852906870733575 1.3841383838057746 -5.852906870733575
32
+ -5.852906870733575 -5.852906870733575 1.3841383838057746 -5.852906870733575
33
+ 1.3835219739184708 -5.2341956006430985 -5.852906870733575 -5.852906870733575
34
+ 1.3756340514956562 -5.394962755562375 -5.394962755562375 -3.401117964959733
35
+ -1.2176198315414444 -3.109079898175411 1.2964067931472216 -5.717323067092849
36
+ -1.3716559438167257 -0.2761401935045069 -1.8504445165866068 1.0404320473626856
37
+ -0.5440863133031895 -0.48103682561971345 0.907381908447086 -1.1280642594012078
38
+ 0.10557340209290218 -0.01814819455289191 0.4381106695354074 -1.0304105539540915
data/test/data/test_collection_single_file_pcm.txt ADDED
@@ -0,0 +1,38 @@
1
+ > SP1_f1
2
+ 682.6436366358055 443.1455214015781 2075.655346294993 287.211468117951
3
+ 299.8883246804867 103.74338315843572 2613.8927022405364 471.1315623708902
4
+ 591.4892493324709 42.631827541794564 2845.1654083148564 9.36948726124641
5
+ 7.071084742361592 45.29093411231232 3432.8847704374107 3.409183158303573
6
+ 91.308984085713 19.1536481364332 3373.656949880137 4.5363903481026
7
+ 809.2082973387932 2246.941954176211 61.30766021687515 371.19806071846244
8
+ 120.56476435866055 42.4349244403591 3242.1560628684038 83.50022078295852
9
+ 13.72524477409959 35.858220519297525 3332.4066864946167 106.66582066236779
10
+ 558.1188080161639 90.0084504200356 2694.854973210736 145.67374080342415
11
+ 264.0088462230318 254.7175868081866 2796.88087480315 173.0486646159857
12
+ 519.46013914282 1874.9349086474765 654.5411208373813 439.7198038226514
13
+ KLF4_f2
14
+ 1233.46088405354 93.18173277811673 1036.6014857092885 1258.2948629970272
15
+ 263.979242343185 5.314520555872139 3347.5949971525274 4.650205486388122
16
+ 76.7700780003465 6.643150694840173 3529.4896409394937 8.636095903292224
17
+ 57.86097393406657 18.102585643439472 3520.3342027139347 25.24120324653207
18
+ 518.1947904009378 1545.9062946905135 22.396758181071043 1535.0411222654507
19
+ 137.98151691820345 9.300410972776241 3456.320530770924 17.936506876068467
20
+ 115.27647661640499 81.51802997128804 1861.9425868567278 1562.801872093553
21
+ 227.8095486111286 42.84555258785854 3278.6396005325996 72.244263806387
22
+ 108.73384179997886 134.47328134862394 3162.880454846513 215.45138754285665
23
+ 238.49636899561344 2225.9561104691043 402.40727964384774 754.6792064294074
24
+
25
+ GABPA_f1
26
+ 615.2572649050138 697.0698715160123 1261.1903440712872 176.43506582414153
27
+ 996.4929869323321 805.1878697364007 693.7695793644275 254.5021102832924
28
+ 1106.9888035794224 508.19444415177276 1029.8329748714536 104.93632371380718
29
+ 143.7121486195701 2086.4279160661263 518.37507049306 1.4374111377025893
30
+ 362.9541452731307 2369.473894845734 17.23702397004065 0.2874822275405179
31
+ 0.0 0.0 2749.952546316428 0.0
32
+ 0.0 0.0 2749.952546316428 0.0
33
+ 2748.2567506938462 1.695795622582083 0.0 0.0
34
+ 2726.6484322711017 1.1499289101620715 1.1499289101620715 21.00425622500253
35
+ 202.05697400573305 28.799402471063658 2518.808687612104 0.2874822275405179
36
+ 172.92889618879767 521.1240363384483 106.38197600987633 1949.517637779338
37
+ 398.1679460365911 424.20938204069563 1706.4024212088275 221.17279703034018
38
+ 764.2587933951809 675.0883944902433 1066.5413633225007 244.06399510852864
data/test/eval_alignment_test.rb ADDED
@@ -0,0 +1,31 @@
1
+ require 'test_helper'
2
+
3
+ class TestEvalAlignment < Test::Unit::TestCase
4
+ def test_process_at_optimal_alignment
5
+ assert_equal "0.2420758234928527\n779.0\t11\n.>>>>>>>>>>\n>>>>>>>>>>>\n-1\tdirect\n", Helpers.eval_alignment_output('test/data/KLF4_f2.pat test/data/SP1_f1.pat -1 direct')
6
+ end
7
+ def test_process_not_optimal_alignment
8
+ assert_equal "0.0017543859649122807\n7.0\t11\n>>>>>>>>>>.\n>>>>>>>>>>>\n0\tdirect\n", Helpers.eval_alignment_output('test/data/KLF4_f2.pat test/data/SP1_f1.pat 0 direct')
9
+ end
10
+ def test_process_alignment_first_motif_from_stdin
11
+ assert_equal "0.0017543859649122807\n7.0\t11\n>>>>>>>>>>.\n>>>>>>>>>>>\n0\tdirect\n",
12
+ Helpers.provide_stdin(File.read('test/data/KLF4_f2.pat')) {
13
+ Helpers.eval_alignment_output('.stdin test/data/SP1_f1.pat 0 direct')
14
+ }
15
+ end
16
+ def test_process_alignment_second_motif_from_stdin
17
+ assert_equal "0.0017543859649122807\n7.0\t11\n>>>>>>>>>>.\n>>>>>>>>>>>\n0\tdirect\n",
18
+ Helpers.provide_stdin(File.read('test/data/SP1_f1.pat')) {
19
+ Helpers.eval_alignment_output('test/data/KLF4_f2.pat .stdin 0 direct')
20
+ }
21
+ end
22
+ def test_process_alignment_both_motifs_from_stdin
23
+ assert_equal "0.0017543859649122807\n7.0\t11\n>>>>>>>>>>.\n>>>>>>>>>>>\n0\tdirect\n",
24
+ Helpers.provide_stdin(File.read('test/data/KLF4_f2.pat') + File.read('test/data/SP1_f1.pat')) {
25
+ Helpers.eval_alignment_output('.stdin .stdin 0 direct')
26
+ }
27
+ end
28
+ def test_process_at_optimal_alignment_reversed
29
+ assert_equal "0.0\n0.0\t11\n.>>>>>>>>>>\n<<<<<<<<<<<\n-1\trevcomp\n", Helpers.eval_alignment_output('test/data/KLF4_f2.pat test/data/SP1_f1.pat -1 revcomp')
30
+ end
31
+ end
data/test/eval_similarity_test.rb CHANGED
@@ -1,27 +1,42 @@
1
1
  require 'test_helper'
2
2
 
3
- puts "\n\neval_similarity test:"
4
3
  class TestEvalSimilarity < Test::Unit::TestCase
5
4
  def test_process_pair_of_pwms
6
- IO.popen(Helpers.exec_cmd('eval_similarity','test/data/KLF4_f2.pat test/data/SP1_f1.pat')){|f|
7
- assert_equal "0.2420758234928527\n779.0\t11\n.>>>>>>>>>>\n>>>>>>>>>>>\n-1\tdirect\n", f.read
8
- }
5
+ assert_equal "0.2420758234928527\n779.0\t11\n.>>>>>>>>>>\n>>>>>>>>>>>\n-1\tdirect\n", Helpers.eval_similarity_output('test/data/KLF4_f2.pat test/data/SP1_f1.pat')
9
6
  end
10
7
  def test_process_another_pair_of_pwms
11
- IO.popen(Helpers.exec_cmd('eval_similarity','test/data/SP1_f1.pat test/data/AHR_si.pat')){|f|
12
- assert_equal "0.0037332005973120955\n15.0\t11\n>>>>>>>>>>>\n.>>>>>>>>>.\n1\tdirect\n", f.read
13
- }
8
+ assert_equal "0.0037332005973120955\n15.0\t11\n>>>>>>>>>>>\n.>>>>>>>>>.\n1\tdirect\n", Helpers.eval_similarity_output('test/data/SP1_f1.pat test/data/AHR_si.pat')
14
9
  end
15
10
 
16
11
  def test_recognize_orientation_of_alignment
17
- IO.popen(Helpers.exec_cmd('eval_similarity','test/data/SP1_f1_revcomp.pat test/data/SP1_f1.pat')){|f|
18
- assert_equal "1.0\n2033.0\t11\n>>>>>>>>>>>\n<<<<<<<<<<<\n0\trevcomp\n", f.read
19
- }
12
+ assert_equal "1.0\n2033.0\t11\n>>>>>>>>>>>\n<<<<<<<<<<<\n0\trevcomp\n", Helpers.eval_similarity_output('test/data/SP1_f1_revcomp.pat test/data/SP1_f1.pat')
20
13
  end
21
14
 
22
15
  def test_process_custom_discretization
23
- IO.popen(Helpers.exec_cmd('eval_similarity','test/data/SP1_f1.pat test/data/KLF4_f2.pat -d 1')){|f|
24
- assert_equal "0.22754919499105544\n636.0\t11\n>>>>>>>>>>>\n.>>>>>>>>>>\n1\tdirect\n", f.read
25
- }
16
+ assert_equal "0.22754919499105544\n636.0\t11\n>>>>>>>>>>>\n.>>>>>>>>>>\n1\tdirect\n", Helpers.eval_similarity_output('test/data/SP1_f1.pat test/data/KLF4_f2.pat -d 1')
26
17
  end
18
+
19
+ def test_process_first_motif_from_stdin
20
+ assert_equal "0.22754919499105544\n636.0\t11\n>>>>>>>>>>>\n.>>>>>>>>>>\n1\tdirect\n",
21
+ Helpers.provide_stdin(File.read('test/data/SP1_f1.pat')){
22
+ Helpers.eval_similarity_output('.stdin test/data/KLF4_f2.pat -d 1')
23
+ }
24
+ end
25
+
26
+ def test_process_second_motif_from_stdin
27
+ assert_equal "0.22754919499105544\n636.0\t11\n>>>>>>>>>>>\n.>>>>>>>>>>\n1\tdirect\n",
28
+ Helpers.provide_stdin(File.read('test/data/KLF4_f2.pat')){
29
+ Helpers.eval_similarity_output('test/data/SP1_f1.pat .stdin -d 1')
30
+ }
31
+ end
32
+
33
+ def test_process_both_motifs_from_stdin
34
+ assert_equal "0.22754919499105544\n636.0\t11\n>>>>>>>>>>>\n.>>>>>>>>>>\n1\tdirect\n",
35
+ Helpers.provide_stdin(File.read('test/data/SP1_f1.pat') + File.read('test/data/KLF4_f2.pat')){
36
+ Helpers.eval_similarity_output('.stdin .stdin -d 1')
37
+ }
38
+ end
39
+
40
+
41
+
27
42
  end
data/test/find_pvalue_test.rb CHANGED
@@ -1,26 +1,23 @@
1
1
  require 'test_helper'
2
2
 
3
- puts "\n\nfind_pvalue test:"
4
3
  class FindPvalueTest < Test::Unit::TestCase
5
4
  def test_process_one_threshold
6
- IO.popen(Helpers.exec_cmd('find_pvalue', 'test/data/KLF4_f2.pat 4.1719')){|f|
7
- assert_equal "4.1719\t1048.0\t0.00099945068359375\n", f.read
8
- }
5
+ assert_equal "4.1719\t1048.0\t0.00099945068359375\n", Helpers.find_pvalue_output('test/data/KLF4_f2.pat 4.1719')
9
6
  end
10
7
  def test_process_several_thresholds
11
- IO.popen(Helpers.exec_cmd('find_pvalue','test/data/KLF4_f2.pat 4.1719 5.2403')){|f|
12
- assert_equal "4.1719\t1048.0\t0.00099945068359375\n5.2403\t524.0\t0.000499725341796875\n", f.read
13
- }
8
+ assert_equal "4.1719\t1048.0\t0.00099945068359375\n5.2403\t524.0\t0.000499725341796875\n", Helpers.find_pvalue_output('test/data/KLF4_f2.pat 4.1719 5.2403')
14
9
  end
15
10
  def test_process_several_thresholds_result_is_ordered
16
- IO.popen(Helpers.exec_cmd('find_pvalue','test/data/KLF4_f2.pat 5.2403 4.1719')){|f|
17
- assert_equal "5.2403\t524.0\t0.000499725341796875\n4.1719\t1048.0\t0.00099945068359375\n", f.read
18
- }
11
+ assert_equal "5.2403\t524.0\t0.000499725341796875\n4.1719\t1048.0\t0.00099945068359375\n", Helpers.find_pvalue_output('test/data/KLF4_f2.pat 5.2403 4.1719')
19
12
  end
20
13
  def test_custom_discretization
21
- IO.popen(Helpers.exec_cmd('find_pvalue','test/data/KLF4_f2.pat 5.2403 -d 100')){|f|
22
- assert_equal "5.2403\t527.0\t0.0005025863647460938\n", f.read
23
- }
14
+ assert_equal "5.2403\t527.0\t0.0005025863647460938\n", Helpers.find_pvalue_output('test/data/KLF4_f2.pat 5.2403 -d 100')
15
+ end
16
+ def test_process_pwm_from_stdin
17
+ assert_equal Helpers.find_pvalue_output('test/data/KLF4_f2.pat 1'),
18
+ Helpers.provide_stdin(File.read('test/data/KLF4_f2.pat')) {
19
+ Helpers.find_pvalue_output('.stdin 1')
20
+ }
24
21
  end
25
22
  end
26
23
 
data/test/find_threshold_test.rb CHANGED
@@ -1,10 +1,9 @@
1
1
  require 'test_helper'
2
2
 
3
- puts "\n\nfind_threshold test:"
4
3
  class FindThresholdTest < Test::Unit::TestCase
5
4
  def test_process_several_pvalues
6
5
  pvalues = []
7
- IO.popen(Helpers.exec_cmd('find_threshold', 'test/data/KLF4_f2.pat -p 0.001 0.0005'), &:read).lines.each{|line|
6
+ Helpers.find_threshold_output('test/data/KLF4_f2.pat -p 0.001 0.0005').lines.each{|line|
8
7
  pvalue, threshold, real_pvalue = line.strip.split("\t")
9
8
  pvalues << pvalue
10
9
  assert_equal Helpers.obtain_pvalue_by_threshold("test/data/KLF4_f2.pat #{threshold}"), real_pvalue
@@ -12,19 +11,25 @@ class FindThresholdTest < Test::Unit::TestCase
12
11
  assert_equal pvalues, ['0.0005', '0.001']
13
12
  end
14
13
  def test_process_one_pvalue
15
- pvalue, threshold, real_pvalue = IO.popen(Helpers.exec_cmd('find_threshold', 'test/data/KLF4_f2.pat -p 0.001'), &:read).strip.split("\t")
14
+ pvalue, threshold, real_pvalue = Helpers.find_threshold_output('test/data/KLF4_f2.pat -p 0.001').strip.split("\t")
16
15
  assert_equal '0.001', pvalue
17
16
  assert_equal Helpers.obtain_pvalue_by_threshold("test/data/KLF4_f2.pat #{threshold}"), real_pvalue
18
17
  end
19
18
  def test_process_default_pvalue
20
- pvalue, threshold, real_pvalue = IO.popen(Helpers.exec_cmd('find_threshold','test/data/KLF4_f2.pat'), &:read).strip.split("\t")
19
+ pvalue, threshold, real_pvalue = Helpers.find_threshold_output('test/data/KLF4_f2.pat').strip.split("\t")
21
20
  assert_equal '0.0005', pvalue
22
21
  assert_equal Helpers.obtain_pvalue_by_threshold("test/data/KLF4_f2.pat #{threshold}"), real_pvalue
23
22
  end
24
23
  def test_custom_discretization
25
- pvalue, threshold, real_pvalue = IO.popen(Helpers.exec_cmd('find_threshold','test/data/KLF4_f2.pat -d 100'), &:read).strip.split("\t")
24
+ pvalue, threshold, real_pvalue = Helpers.find_threshold_output('test/data/KLF4_f2.pat -d 100').strip.split("\t")
26
25
  assert_equal '0.0005', pvalue
27
26
  assert_equal Helpers.obtain_pvalue_by_threshold("test/data/KLF4_f2.pat #{threshold} -d 100"), real_pvalue
28
27
  end
28
+ def test_process_pwm_from_stdin
29
+ assert_equal Helpers.find_threshold_output('test/data/KLF4_f2.pat'),
30
+ Helpers.provide_stdin(File.read('test/data/KLF4_f2.pat')) {
31
+ Helpers.find_threshold_output('.stdin')
32
+ }
33
+ end
29
34
  end
30
35
 
data/test/preprocess_collection_test.rb CHANGED
@@ -2,13 +2,47 @@ require 'test_helper'
2
2
  require 'yaml'
3
3
  require 'macroape'
4
4
 
5
- puts "\n\npreprocess_collection test:"
6
5
  class TestPreprocessCollection < Test::Unit::TestCase
7
6
  def test_multipvalue_preproceessing
8
- system(Helpers.exec_cmd('preprocess_collection','test/data/test_collection -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent'))
7
+ Helpers.run_preprocess_collection('test/data/test_collection -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
9
8
  # Don't use YAML.load_file() instead of YAML.load(File.read()) because in ruby before v1.93 p194
10
9
  # it doesn't immediately release file descriptor (if I understood error right way) so File.delete fails
11
10
  assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
12
11
  File.delete 'test/data/test_collection.yaml.tmp'
13
12
  end
13
+
14
+ def test_preproceessing_collection_from_a_single_file
15
+ Helpers.run_preprocess_collection('test/data/test_collection_single_file.txt -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
16
+ assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
17
+ File.delete 'test/data/test_collection.yaml.tmp'
18
+ end
19
+
20
+ def test_preproceessing_collection_from_stdin
21
+ Helpers.provide_stdin(File.read('test/data/test_collection_single_file.txt')){
22
+ Helpers.run_preprocess_collection('.stdin -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
23
+ }
24
+ assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
25
+ File.delete 'test/data/test_collection.yaml.tmp'
26
+ end
27
+
28
+ def test_preproceessing_folder_pcm
29
+ Helpers.run_preprocess_collection('test/data/test_collection_pcm -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
30
+ assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
31
+ File.delete 'test/data/test_collection.yaml.tmp'
32
+ end
33
+
34
+ def test_preproceessing_collection_from_a_single_file_pcm
35
+ Helpers.run_preprocess_collection('test/data/test_collection_single_file_pcm.txt -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
36
+ assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
37
+ File.delete 'test/data/test_collection.yaml.tmp'
38
+ end
39
+
40
+ def test_preproceessing_collection_from_stdin_pcm
41
+ Helpers.provide_stdin(File.read('test/data/test_collection_single_file_pcm.txt')){
42
+ Helpers.run_preprocess_collection('.stdin -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
43
+ }
44
+ assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
45
+ File.delete 'test/data/test_collection.yaml.tmp'
46
+ end
47
+
14
48
  end
data/test/scan_collection_test.rb CHANGED
@@ -1,18 +1,23 @@
1
1
  require 'test_helper'
2
2
 
3
- puts "\n\nscan_collection test:"
4
3
  class TestScanCollection < Test::Unit::TestCase
5
4
  def test_scan_default_cutoff
6
5
  assert_equal File.read('test/data/KLF4_f2_scan_results_default_cutoff.txt').gsub("\r\n", "\n"),
7
- IO.popen(Helpers.exec_cmd('scan_collection','test/data/KLF4_f2.pat test/data/test_collection.yaml --silent'), &:read).gsub("\r\n","\n")
6
+ Helpers.scan_collection_output('test/data/KLF4_f2.pat test/data/test_collection.yaml --silent').gsub("\r\n","\n")
8
7
  end
9
8
  def test_scan_and_output_all_results
10
9
  assert_equal File.read('test/data/KLF4_f2_scan_results_all.txt').gsub("\r\n", "\n"),
11
- IO.popen(Helpers.exec_cmd('scan_collection','test/data/KLF4_f2.pat test/data/test_collection.yaml --all --silent'), &:read).gsub("\r\n","\n")
10
+ Helpers.scan_collection_output('test/data/KLF4_f2.pat test/data/test_collection.yaml --all --silent').gsub("\r\n","\n")
12
11
 
13
12
  end
14
13
  def test_scan_precise_mode
15
14
  assert_equal File.read('test/data/KLF4_f2_scan_results_precise_mode.txt').gsub("\r\n","\n"),
16
- IO.popen(Helpers.exec_cmd('scan_collection','test/data/KLF4_f2.pat test/data/test_collection.yaml --precise --all --silent'), &:read).gsub("\r\n", "\n")
15
+ Helpers.scan_collection_output('test/data/KLF4_f2.pat test/data/test_collection.yaml --precise --all --silent').gsub("\r\n", "\n")
16
+ end
17
+ def test_process_query_pwm_from_stdin
18
+ assert_equal Helpers.scan_collection_output('test/data/KLF4_f2.pat test/data/test_collection.yaml --silent'),
19
+ Helpers.provide_stdin(File.read('test/data/KLF4_f2.pat')) {
20
+ Helpers.scan_collection_output('.stdin test/data/test_collection.yaml --silent')
21
+ }
17
22
  end
18
23
  end
data/test/test_helper.rb CHANGED
@@ -1,12 +1,71 @@
1
1
  $lib_folder = File.dirname(__FILE__) + '/../lib'
2
2
  $LOAD_PATH.unshift $lib_folder
3
3
  require 'test/unit'
4
+ require 'stringio'
5
+
6
+ require 'macroape/cli/find_threshold'
7
+ require 'macroape/cli/find_pvalue'
8
+ require 'macroape/cli/eval_similarity'
9
+ require 'macroape/cli/eval_alignment'
10
+ require 'macroape/cli/preprocess_collection'
11
+ require 'macroape/cli/scan_collection'
12
+ require 'macroape/cli/align_motifs'
4
13
 
5
14
  module Helpers
15
+ # from minitest
16
+ def self.capture_io(&block)
17
+ orig_stdout, orig_stderr = $stdout, $stderr
18
+ captured_stdout, captured_stderr = StringIO.new, StringIO.new
19
+ $stdout, $stderr = captured_stdout, captured_stderr
20
+ yield
21
+ return {stdout: captured_stdout.string, stderr: captured_stderr.string}
22
+ ensure
23
+ $stdout = orig_stdout
24
+ $stderr = orig_stderr
25
+ end
26
+
27
+ # Method stubs $stdin not STDIN !
28
+ def self.provide_stdin(input, &block)
29
+ orig_stdin = $stdin
30
+ $stdin = StringIO.new(input)
31
+ yield
32
+ ensure
33
+ $stdin = orig_stdin
34
+ end
35
+
36
+ def self.capture_output(&block)
37
+ capture_io(&block)[:stdout]
38
+ end
39
+ def self.capture_stderr(&block)
40
+ capture_io(&block)[:stderr]
41
+ end
42
+
6
43
  def self.obtain_pvalue_by_threshold(args)
7
- IO.popen("ruby -I #{$lib_folder} #{$lib_folder}/macroape/exec/find_pvalue.rb #{args}",&:read).strip.split.last
44
+ find_pvalue_output(args).strip.split.last
8
45
  end
9
46
  def self.exec_cmd(executable, param_list)
10
- "ruby -I #{$lib_folder} #{$lib_folder}/macroape/exec/#{executable}.rb #{param_list}"
47
+ "ruby -I #{$lib_folder} #{$lib_folder}/../bin/#{executable} #{param_list}"
48
+ end
49
+ def self.find_threshold_output(param_list)
50
+ capture_output{ Macroape::CLI::FindThreshold.main(param_list.split) }
51
+ end
52
+ def self.align_motifs_output(param_list)
53
+ capture_output{ Macroape::CLI::AlignMotifs.main(param_list.split) }
54
+ end
55
+ def self.find_pvalue_output(param_list)
56
+ capture_output{ Macroape::CLI::FindPValue.main(param_list.split) }
57
+ end
58
+ def self.eval_similarity_output(param_list)
59
+ capture_output{ Macroape::CLI::EvalSimilarity.main(param_list.split) }
60
+ end
61
+ def self.eval_alignment_output(param_list)
62
+ capture_output{ Macroape::CLI::EvalAlignment.main(param_list.split) }
63
+ end
64
+ def self.scan_collection_output(param_list)
65
+ capture_output{ Macroape::CLI::ScanCollection.main(param_list.split) }
66
+ end
67
+ def self.run_preprocess_collection(param_list)
68
+ Macroape::CLI::PreprocessCollection.main(param_list.split)
11
69
  end
70
+
12
71
  end