macroape 4.0.2 → 4.1.0

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 (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
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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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114
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168
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