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/data/AHR_si.pwm CHANGED
@@ -1,10 +1,10 @@
1
- AHR_si
2
- 0.049659785047588834 -0.7112292711652757 0.3721858143748157 0.007118345755728267
3
- -1.1863517717347094 -1.107677589450009 -0.10122262270571995 0.9004092051347228
4
- -0.5481419620395529 0.12723771473208506 -0.5930888656288792 0.5502420250441413
5
- -2.3460850844035757 -2.7362137930742167 1.3086872088653387 -1.9795601218727432
6
- -3.45212725495741 1.3387809407527818 -2.67026944276278 -2.46866856874775
7
- -2.1349735467777395 -2.965000508388952 1.3322808172765488 -3.206089427067848
8
- -3.45212725495741 -2.1349735467777395 -3.0087911229263207 1.335191259740944
9
- -3.45212725495741 -3.45212725495741 1.3622489404156526 -3.45212725495741
10
- 0.10927007207680632 0.5389064901558549 -0.8250174241334556 -0.3117320885632525
1
+ AHR_si
2
+ 0.049659785047588834 -0.7112292711652757 0.3721858143748157 0.007118345755728267
3
+ -1.1863517717347094 -1.107677589450009 -0.10122262270571995 0.9004092051347228
4
+ -0.5481419620395529 0.12723771473208506 -0.5930888656288792 0.5502420250441413
5
+ -2.3460850844035757 -2.7362137930742167 1.3086872088653387 -1.9795601218727432
6
+ -3.45212725495741 1.3387809407527818 -2.67026944276278 -2.46866856874775
7
+ -2.1349735467777395 -2.965000508388952 1.3322808172765488 -3.206089427067848
8
+ -3.45212725495741 -2.1349735467777395 -3.0087911229263207 1.335191259740944
9
+ -3.45212725495741 -3.45212725495741 1.3622489404156526 -3.45212725495741
10
+ 0.10927007207680632 0.5389064901558549 -0.8250174241334556 -0.3117320885632525
data/test/data/KLF3_f1.pcm CHANGED
@@ -1,16 +1,16 @@
1
- KLF3_f1
2
- 2.625 2.125 0.0 3.25
3
- 3.125 1.125 3.75 0.0
4
- 0.0 6.375 1.0 0.625
5
- 1.125 3.125 1.0 2.75
6
- 2.75 0.0 1.0 4.25
7
- 1.125 0.0 6.875 0.0
8
- 0.0 0.0 6.875 1.125
9
- 0.0 0.0 8.0 0.0
10
- 0.0 0.0 0.0 8.0
11
- 1.125 0.0 6.875 0.0
12
- 0.0 0.0 3.125 4.875
13
- 1.125 2.125 4.75 0.0
14
- 0.0 1.0 5.875 1.125
15
- 1.625 4.125 1.125 1.125
16
- 1.90625 0.28125 0.28125 5.53125
1
+ KLF3_f1
2
+ 2.625 2.125 0.0 3.25
3
+ 3.125 1.125 3.75 0.0
4
+ 0.0 6.375 1.0 0.625
5
+ 1.125 3.125 1.0 2.75
6
+ 2.75 0.0 1.0 4.25
7
+ 1.125 0.0 6.875 0.0
8
+ 0.0 0.0 6.875 1.125
9
+ 0.0 0.0 8.0 0.0
10
+ 0.0 0.0 0.0 8.0
11
+ 1.125 0.0 6.875 0.0
12
+ 0.0 0.0 3.125 4.875
13
+ 1.125 2.125 4.75 0.0
14
+ 0.0 1.0 5.875 1.125
15
+ 1.625 4.125 1.125 1.125
16
+ 1.90625 0.28125 0.28125 5.53125
data/test/data/KLF3_f1.pwm CHANGED
@@ -1,16 +1,16 @@
1
- KLF3_f1
2
- 0.22156599923632986 0.0484147821994171 -1.5783984904108685 0.4028344703516524
3
- 0.3691145643098263 -0.42654798884705847 0.5273776327056031 -1.5783984904108685
4
- -1.5783984904108685 1.006572764992778 -0.5055850184352592 -0.7889208019368309
5
- -0.42654798884705847 0.3691145643098263 -0.5055850184352592 0.26054379103002956
6
- 0.26054379103002956 -1.5783984904108685 -0.5055850184352592 0.6381135377904803
7
- -0.42654798884705847 -1.5783984904108685 1.0765817190154965 -1.5783984904108685
8
- -1.5783984904108685 -1.5783984904108685 1.0765817190154965 -0.42654798884705847
9
- -1.5783984904108685 -1.5783984904108685 1.2181964566417396 -1.5783984904108685
10
- -1.5783984904108685 -1.5783984904108685 -1.5783984904108685 1.2181964566417396
11
- -0.42654798884705847 -1.5783984904108685 1.0765817190154965 -1.5783984904108685
12
- -1.5783984904108685 -1.5783984904108685 0.3691145643098263 0.7612432224843741
13
- -0.42654798884705847 0.0484147821994171 0.7378003724947412 -1.5783984904108685
14
- -1.5783984904108685 -0.5055850184352592 0.9312911055808129 -0.42654798884705847
15
- -0.1611290354980871 0.611557817476478 -0.42654798884705847 -0.42654798884705847
16
- -0.03791418689319392 -1.1459600292730023 -1.1459600292730023 0.8760382926050381
1
+ KLF3_f1
2
+ 0.22156599923632986 0.0484147821994171 -1.5783984904108685 0.4028344703516524
3
+ 0.3691145643098263 -0.42654798884705847 0.5273776327056031 -1.5783984904108685
4
+ -1.5783984904108685 1.006572764992778 -0.5055850184352592 -0.7889208019368309
5
+ -0.42654798884705847 0.3691145643098263 -0.5055850184352592 0.26054379103002956
6
+ 0.26054379103002956 -1.5783984904108685 -0.5055850184352592 0.6381135377904803
7
+ -0.42654798884705847 -1.5783984904108685 1.0765817190154965 -1.5783984904108685
8
+ -1.5783984904108685 -1.5783984904108685 1.0765817190154965 -0.42654798884705847
9
+ -1.5783984904108685 -1.5783984904108685 1.2181964566417396 -1.5783984904108685
10
+ -1.5783984904108685 -1.5783984904108685 -1.5783984904108685 1.2181964566417396
11
+ -0.42654798884705847 -1.5783984904108685 1.0765817190154965 -1.5783984904108685
12
+ -1.5783984904108685 -1.5783984904108685 0.3691145643098263 0.7612432224843741
13
+ -0.42654798884705847 0.0484147821994171 0.7378003724947412 -1.5783984904108685
14
+ -1.5783984904108685 -0.5055850184352592 0.9312911055808129 -0.42654798884705847
15
+ -0.1611290354980871 0.611557817476478 -0.42654798884705847 -0.42654798884705847
16
+ -0.03791418689319392 -1.1459600292730023 -1.1459600292730023 0.8760382926050381
data/test/data/KLF4_f2.pcm CHANGED
@@ -1,11 +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
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/KLF4_f2.pwm CHANGED
@@ -1,11 +1,11 @@
1
- KLF4_f2.xml
2
- 0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
3
- -1.227018967707036 -4.814127713368663 1.3059890687390967 -4.908681463544344
4
- -2.443469374521196 -4.648238485031404 1.3588686548279805 -4.441801801188402
5
- -2.7177827948276123 -3.8073538975356565 1.356272809724262 -3.504104725510225
6
- -0.5563232977367343 0.5340697765121405 -3.61417723090579 0.5270259776377405
7
- -1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
8
- -2.045671123823928 -2.384975142213679 0.7198551207724355 0.5449254135616948
9
- -1.373157530374372 -3.0063112097748217 1.285188335493552 -2.5026044231773543
10
- -2.1030513122772208 -1.8941348100402244 1.249265758393991 -1.4284210948906104
11
- -1.3277128628152939 0.8982415633049462 -0.8080773665408135 -0.18161647647456935
1
+ KLF4_f2.xml
2
+ 0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
3
+ -1.2270189677070362 -4.814127713368663 1.3059890687390965 -4.908681463544344
4
+ -2.4434693745211966 -4.648238485031404 1.3588686548279802 -4.441801801188402
5
+ -2.7177827948276128 -3.807353897535657 1.3562728097242616 -3.504104725510225
6
+ -0.5563232977367345 0.5340697765121402 -3.61417723090579 0.5270259776377402
7
+ -1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
8
+ -2.0456711238239285 -2.3849751422136793 0.7198551207724353 0.5449254135616943
9
+ -1.3731575303743726 -3.006311209774822 1.2851883354935514 -2.5026044231773548
10
+ -2.103051312277221 -1.8941348100402247 1.249265758393991 -1.4284210948906106
11
+ -1.327712862815294 0.898241563304946 -0.8080773665408136 -0.1816164764745695
data/test/data/KLF4_f2_scan_results_all.txt CHANGED
@@ -1,3 +1,3 @@
1
- KLF4_f2 1.0 0 10 direct
2
- SP1_f1 0.22754919499105544 -1 10 direct
1
+ KLF4_f2 1.0 0 10 direct
2
+ SP1_f1 0.22754919499105544 -1 10 direct
3
3
  GABPA_f1 0.00043527658136684877 -8 5 direct
data/test/data/KLF4_f2_scan_results_default_cutoff.txt CHANGED
@@ -1,2 +1,2 @@
1
- KLF4_f2 1.0 0 10 direct
1
+ KLF4_f2 1.0 0 10 direct
2
2
  SP1_f1 0.22754919499105544 -1 10 direct
data/test/data/KLF4_f2_scan_results_precise_mode.txt CHANGED
@@ -1,3 +1,3 @@
1
- KLF4_f2 1.0 0 10 direct *
2
- SP1_f1 0.2420758234928527 -1 10 direct *
1
+ KLF4_f2 1.0 0 10 direct *
2
+ SP1_f1 0.2420758234928527 -1 10 direct *
3
3
  GABPA_f1 0.00043527658136684877 -8 5 direct .
data/test/data/SP1_f1.pcm CHANGED
@@ -1,12 +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
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/SP1_f1.pwm CHANGED
@@ -1,12 +1,12 @@
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
1
+ > SP1_f1
2
+ -0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
3
+ -1.063125575209786 -2.111925969423874 1.096062756111034 -0.6138563775212038
4
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data/test/data/SP1_f1_revcomp.pcm CHANGED
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data/test/data/SP1_f1_revcomp.pwm CHANGED
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data/test/data/medium_motif.pwm CHANGED
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data/test/data/short_motif.pwm CHANGED
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168
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