macroape 4.0.2 → 4.1.0
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- checksums.yaml +4 -4
- data/.gitignore +17 -17
- data/Gemfile +4 -4
- data/LICENSE +22 -22
- data/README.md +70 -70
- data/Rakefile.rb +49 -49
- data/TODO.txt +46 -46
- data/benchmark/benchmark_helper.rb +4 -4
- data/benchmark/similarity_benchmark.rb +52 -52
- data/bin/align_motifs +4 -4
- data/bin/eval_alignment +4 -4
- data/bin/eval_similarity +4 -4
- data/bin/find_pvalue +4 -4
- data/bin/find_threshold +4 -4
- data/bin/preprocess_collection +4 -4
- data/bin/scan_collection +4 -4
- data/lib/macroape.rb +14 -11
- data/lib/macroape/aligned_pair_intersection.rb +61 -62
- data/lib/macroape/cli.rb +191 -188
- data/lib/macroape/cli/align_motifs.rb +120 -100
- data/lib/macroape/cli/eval_alignment.rb +157 -156
- data/lib/macroape/cli/eval_similarity.rb +138 -137
- data/lib/macroape/cli/find_pvalue.rb +93 -87
- data/lib/macroape/cli/find_threshold.rb +103 -96
- data/lib/macroape/cli/preprocess_collection.rb +169 -161
- data/lib/macroape/cli/scan_collection.rb +171 -163
- data/lib/macroape/collection.rb +29 -0
- data/lib/macroape/motif_with_thresholds.rb +18 -0
- data/lib/macroape/pwm_compare.rb +39 -44
- data/lib/macroape/pwm_compare_aligned.rb +139 -130
- data/lib/macroape/{counting.rb → pwm_counting.rb} +175 -121
- data/lib/macroape/support/inverf.rb +13 -0
- data/lib/macroape/support/partial_sums.rb +17 -0
- data/lib/macroape/version.rb +4 -4
- data/macroape.gemspec +19 -19
- data/spec/count_distribution_spec.rb +112 -109
- data/spec/inverf_spec.rb +23 -0
- data/spec/partial_sums_spec.rb +28 -0
- data/spec/spec_helper.rb +11 -11
- data/test/align_motifs_test.rb +42 -43
- data/test/data/AHR_si.pwm +10 -10
- data/test/data/KLF3_f1.pcm +16 -16
- data/test/data/KLF3_f1.pwm +16 -16
- data/test/data/KLF4_f2.pcm +11 -11
- data/test/data/KLF4_f2.pwm +11 -11
- data/test/data/KLF4_f2_scan_results_all.txt +2 -2
- data/test/data/KLF4_f2_scan_results_default_cutoff.txt +1 -1
- data/test/data/KLF4_f2_scan_results_precise_mode.txt +2 -2
- data/test/data/SP1_f1.pcm +12 -12
- data/test/data/SP1_f1.pwm +12 -12
- data/test/data/SP1_f1_revcomp.pcm +12 -12
- data/test/data/SP1_f1_revcomp.pwm +12 -12
- data/test/data/medium_motif.pwm +8 -8
- data/test/data/short_motif.pwm +7 -7
- data/test/data/test_collection.yaml +231 -214
- data/test/data/test_collection/GABPA_f1.pwm +14 -14
- data/test/data/test_collection/KLF4_f2.pwm +10 -10
- data/test/data/test_collection/SP1_f1.pwm +12 -12
- data/test/data/test_collection_pcm/GABPA_f1.pcm +14 -14
- data/test/data/test_collection_pcm/KLF4_f2.pcm +11 -11
- data/test/data/test_collection_pcm/SP1_f1.pcm +12 -12
- data/test/data/test_collection_single_file.txt +38 -38
- data/test/data/test_collection_single_file_pcm.txt +37 -37
- data/test/data/test_collection_weak.yaml +231 -214
- data/test/eval_alignment_test.rb +90 -111
- data/test/eval_similarity_test.rb +105 -123
- data/test/find_pvalue_test.rb +34 -39
- data/test/find_threshold_test.rb +87 -91
- data/test/preprocess_collection_test.rb +56 -65
- data/test/scan_collection_test.rb +42 -48
- data/test/test_helper.rb +159 -160
- metadata +14 -10
- data/test/data/collection_pcm_without_thresholds.yaml +0 -188
- data/test/data/collection_without_thresholds.yaml +0 -188
@@ -1,14 +1,14 @@
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GABPA_f1
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-0.1106670158341858 0.013801606113892391 0.6054596108973699 -1.3518085041421573
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GABPA_f1
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-0.1106670158341858 0.013801606113892391 0.6054596108973699 -1.3518085041421573
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0.3703066892164342 0.15761121480430038 0.009069314183831861 -0.9888619717703555
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0.47526546359546656 -0.30116785345720876 0.40315229944127723 -1.8638752827041063
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-0.6362037835776333 1.2353381899855975 -3.5801322928552217 -5.717323067092845
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-5.852906870733565 -5.852906870733565 1.3841383838057844 -5.852906870733565
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-5.852906870733565 -5.852906870733565 1.3841383838057844 -5.852906870733565
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1.3835219739184805 -5.234195600643089 -5.852906870733565 -5.852906870733565
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1.375634051495666 -5.394962755562365 -5.394962755562365 -3.4011179649597234
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-1.2176198315414393 -3.109079898175406 1.2964067931472267 -5.717323067092844
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-1.3716559438167275 -0.2761401935045087 -1.8504445165866086 1.0404320473626838
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0.10557340209290259 -0.018148194552891343 0.43811066953540795 -1.0304105539540909
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@@ -1,10 +1,10 @@
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0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
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-1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
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0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
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-1.2270189677070362 -4.814127713368663 1.3059890687390965 -4.908681463544344
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-2.4434693745211966 -4.648238485031404 1.3588686548279802 -4.441801801188402
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-2.7177827948276128 -3.807353897535657 1.3562728097242616 -3.504104725510225
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-0.5563232977367345 0.5340697765121402 -3.61417723090579 0.5270259776377402
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-1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
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-2.0456711238239285 -2.3849751422136793 0.7198551207724353 0.5449254135616943
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-1.3731575303743726 -3.006311209774822 1.2851883354935514 -2.5026044231773548
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-2.103051312277221 -1.8941348100402247 1.249265758393991 -1.4284210948906106
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-1.327712862815294 0.898241563304946 -0.8080773665408136 -0.1816164764745695
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@@ -1,12 +1,12 @@
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> SP1_f1
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-0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
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> SP1_f1
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-0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
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-1.063125575209786 -2.111925969423874 1.096062756111034 -0.6138563775212038
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-0.38722762347606526 -2.9739851913218165 1.180780024201026 -4.338927525031577
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-4.563896055436912 -2.916163300253245 1.3684371349982463 -5.077972423609672
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-2.2369752892820247 -3.7196436313302015 1.3510439136452568 -4.8899306705082495
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-0.07473964149331284 0.9449196547620068 -2.6246857648086084 -0.8510983487822477
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-1.9643526491643477 -2.9784027708801304 1.3113096718240418 -2.3243342594990404
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-4.015548413965599 -3.138426807809682 1.3387488589787901 -2.0846739035376634
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-0.44509385828356285 -2.2510053061629796 1.1265431574368594 -1.7780413702431463
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-1.1896356092245128 -1.2251832285630104 1.1636760063747449 -1.608024364815743
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-0.5166047365590577 0.7641033353626651 -0.28626775700282125 -0.6825482097865606
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@@ -1,14 +1,14 @@
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1
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GABPA_f1
|
2
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-
615.2572649050138 697.0698715160123 1261.1903440712872 176.43506582414153
|
3
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-
996.4929869323321 805.1878697364007 693.7695793644275 254.5021102832924
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1106.9888035794224 508.19444415177276 1029.8329748714536 104.93632371380718
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143.7121486195701 2086.4279160661263 518.37507049306 1.4374111377025893
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6
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362.9541452731307 2369.473894845734 17.23702397004065 0.2874822275405179
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0.0 0.0 2749.952546316428 0.0
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0.0 0.0 2749.952546316428 0.0
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2748.2567506938462 1.695795622582083 0.0 0.0
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2726.6484322711017 1.1499289101620715 1.1499289101620715 21.00425622500253
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202.05697400573305 28.799402471063658 2518.808687612104 0.2874822275405179
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172.92889618879767 521.1240363384483 106.38197600987633 1949.517637779338
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398.1679460365911 424.20938204069563 1706.4024212088275 221.17279703034018
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764.2587933951809 675.0883944902433 1066.5413633225007 244.06399510852864
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GABPA_f1
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615.2572649050138 697.0698715160123 1261.1903440712872 176.43506582414153
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996.4929869323321 805.1878697364007 693.7695793644275 254.5021102832924
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1106.9888035794224 508.19444415177276 1029.8329748714536 104.93632371380718
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143.7121486195701 2086.4279160661263 518.37507049306 1.4374111377025893
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362.9541452731307 2369.473894845734 17.23702397004065 0.2874822275405179
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0.0 0.0 2749.952546316428 0.0
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0.0 0.0 2749.952546316428 0.0
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2748.2567506938462 1.695795622582083 0.0 0.0
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2726.6484322711017 1.1499289101620715 1.1499289101620715 21.00425622500253
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202.05697400573305 28.799402471063658 2518.808687612104 0.2874822275405179
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172.92889618879767 521.1240363384483 106.38197600987633 1949.517637779338
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398.1679460365911 424.20938204069563 1706.4024212088275 221.17279703034018
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764.2587933951809 675.0883944902433 1066.5413633225007 244.06399510852864
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@@ -1,11 +1,11 @@
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1
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KLF4_f2
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2
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1233.46088405354 93.18173277811673 1036.6014857092885 1258.2948629970272
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3
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263.979242343185 5.314520555872139 3347.5949971525274 4.650205486388122
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76.7700780003465 6.643150694840173 3529.4896409394937 8.636095903292224
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57.86097393406657 18.102585643439472 3520.3342027139347 25.24120324653207
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518.1947904009378 1545.9062946905135 22.396758181071043 1535.0411222654507
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137.98151691820345 9.300410972776241 3456.320530770924 17.936506876068467
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115.27647661640499 81.51802997128804 1861.9425868567278 1562.801872093553
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227.8095486111286 42.84555258785854 3278.6396005325996 72.244263806387
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108.73384179997886 134.47328134862394 3162.880454846513 215.45138754285665
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11
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238.49636899561344 2225.9561104691043 402.40727964384774 754.6792064294074
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KLF4_f2
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2
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1233.46088405354 93.18173277811673 1036.6014857092885 1258.2948629970272
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3
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263.979242343185 5.314520555872139 3347.5949971525274 4.650205486388122
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76.7700780003465 6.643150694840173 3529.4896409394937 8.636095903292224
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57.86097393406657 18.102585643439472 3520.3342027139347 25.24120324653207
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518.1947904009378 1545.9062946905135 22.396758181071043 1535.0411222654507
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137.98151691820345 9.300410972776241 3456.320530770924 17.936506876068467
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115.27647661640499 81.51802997128804 1861.9425868567278 1562.801872093553
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227.8095486111286 42.84555258785854 3278.6396005325996 72.244263806387
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108.73384179997886 134.47328134862394 3162.880454846513 215.45138754285665
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238.49636899561344 2225.9561104691043 402.40727964384774 754.6792064294074
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@@ -1,12 +1,12 @@
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SP1_f1
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682.6436366358055 443.1455214015781 2075.655346294993 287.211468117951
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3
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299.8883246804867 103.74338315843572 2613.8927022405364 471.1315623708902
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591.4892493324709 42.631827541794564 2845.1654083148564 9.36948726124641
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7.071084742361592 45.29093411231232 3432.8847704374107 3.409183158303573
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91.308984085713 19.1536481364332 3373.656949880137 4.5363903481026
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809.2082973387932 2246.941954176211 61.30766021687515 371.19806071846244
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120.56476435866055 42.4349244403591 3242.1560628684038 83.50022078295852
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13.72524477409959 35.858220519297525 3332.4066864946167 106.66582066236779
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10
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558.1188080161639 90.0084504200356 2694.854973210736 145.67374080342415
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11
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264.0088462230318 254.7175868081866 2796.88087480315 173.0486646159857
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12
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519.46013914282 1874.9349086474765 654.5411208373813 439.7198038226514
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1
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SP1_f1
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2
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682.6436366358055 443.1455214015781 2075.655346294993 287.211468117951
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3
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299.8883246804867 103.74338315843572 2613.8927022405364 471.1315623708902
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591.4892493324709 42.631827541794564 2845.1654083148564 9.36948726124641
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7.071084742361592 45.29093411231232 3432.8847704374107 3.409183158303573
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91.308984085713 19.1536481364332 3373.656949880137 4.5363903481026
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809.2082973387932 2246.941954176211 61.30766021687515 371.19806071846244
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120.56476435866055 42.4349244403591 3242.1560628684038 83.50022078295852
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9
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13.72524477409959 35.858220519297525 3332.4066864946167 106.66582066236779
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10
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558.1188080161639 90.0084504200356 2694.854973210736 145.67374080342415
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264.0088462230318 254.7175868081866 2796.88087480315 173.0486646159857
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519.46013914282 1874.9349086474765 654.5411208373813 439.7198038226514
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@@ -1,38 +1,38 @@
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> GABPA_f1
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-0.1106670158341858 0.013801606113892391
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0.
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KLF4_f2
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0.30861857265872605 -2.254321000121579
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-1.
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-1.8687622060887386 -4.381483976582316
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-1.
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SP1_f1
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-0.24435707885585292
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> GABPA_f1
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-0.1106670158341858 0.013801606113892391 0.6054596108973699 -1.3518085041421573
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3
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0.3703066892164342 0.15761121480430038 0.009069314183831861 -0.9888619717703555
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|
+
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|
15
|
+
|
16
|
+
KLF4_f2
|
17
|
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|
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|
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|
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|
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SP1_f1
|
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|
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-0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
|
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|
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|
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|
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|
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+
-0.5166047365590577 0.7641033353626651 -0.28626775700282125 -0.6825482097865606
|
@@ -1,38 +1,38 @@
|
|
1
|
-
> GABPA_f1
|
2
|
-
615.2572649050138 697.0698715160123 1261.1903440712872 176.43506582414153
|
3
|
-
996.4929869323321 805.1878697364007 693.7695793644275 254.5021102832924
|
4
|
-
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|
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|
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|
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|
-
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|
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
|
15
|
-
KLF4_f2
|
16
|
-
1233.46088405354 93.18173277811673 1036.6014857092885 1258.2948629970272
|
17
|
-
263.979242343185 5.314520555872139 3347.5949971525274 4.650205486388122
|
18
|
-
76.7700780003465 6.643150694840173 3529.4896409394937 8.636095903292224
|
19
|
-
57.86097393406657 18.102585643439472 3520.3342027139347 25.24120324653207
|
20
|
-
518.1947904009378 1545.9062946905135 22.396758181071043 1535.0411222654507
|
21
|
-
137.98151691820345 9.300410972776241 3456.320530770924 17.936506876068467
|
22
|
-
115.27647661640499 81.51802997128804 1861.9425868567278 1562.801872093553
|
23
|
-
227.8095486111286 42.84555258785854 3278.6396005325996 72.244263806387
|
24
|
-
108.73384179997886 134.47328134862394 3162.880454846513 215.45138754285665
|
25
|
-
238.49636899561344 2225.9561104691043 402.40727964384774 754.6792064294074
|
26
|
-
|
27
|
-
SP1_f1
|
28
|
-
682.6436366358055 443.1455214015781 2075.655346294993 287.211468117951
|
29
|
-
299.8883246804867 103.74338315843572 2613.8927022405364 471.1315623708902
|
30
|
-
591.4892493324709 42.631827541794564 2845.1654083148564 9.36948726124641
|
31
|
-
7.071084742361592 45.29093411231232 3432.8847704374107 3.409183158303573
|
32
|
-
91.308984085713 19.1536481364332 3373.656949880137 4.5363903481026
|
33
|
-
809.2082973387932 2246.941954176211 61.30766021687515 371.19806071846244
|
34
|
-
120.56476435866055 42.4349244403591 3242.1560628684038 83.50022078295852
|
35
|
-
13.72524477409959 35.858220519297525 3332.4066864946167 106.66582066236779
|
36
|
-
558.1188080161639 90.0084504200356 2694.854973210736 145.67374080342415
|
37
|
-
264.0088462230318 254.7175868081866 2796.88087480315 173.0486646159857
|
1
|
+
> GABPA_f1
|
2
|
+
615.2572649050138 697.0698715160123 1261.1903440712872 176.43506582414153
|
3
|
+
996.4929869323321 805.1878697364007 693.7695793644275 254.5021102832924
|
4
|
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|
5
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|
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|
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362.9541452731307 2369.473894845734 17.23702397004065 0.2874822275405179
|
7
|
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0.0 0.0 2749.952546316428 0.0
|
8
|
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0.0 0.0 2749.952546316428 0.0
|
9
|
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2748.2567506938462 1.695795622582083 0.0 0.0
|
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|
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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
|
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398.1679460365911 424.20938204069563 1706.4024212088275 221.17279703034018
|
14
|
+
764.2587933951809 675.0883944902433 1066.5413633225007 244.06399510852864
|
15
|
+
KLF4_f2
|
16
|
+
1233.46088405354 93.18173277811673 1036.6014857092885 1258.2948629970272
|
17
|
+
263.979242343185 5.314520555872139 3347.5949971525274 4.650205486388122
|
18
|
+
76.7700780003465 6.643150694840173 3529.4896409394937 8.636095903292224
|
19
|
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57.86097393406657 18.102585643439472 3520.3342027139347 25.24120324653207
|
20
|
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518.1947904009378 1545.9062946905135 22.396758181071043 1535.0411222654507
|
21
|
+
137.98151691820345 9.300410972776241 3456.320530770924 17.936506876068467
|
22
|
+
115.27647661640499 81.51802997128804 1861.9425868567278 1562.801872093553
|
23
|
+
227.8095486111286 42.84555258785854 3278.6396005325996 72.244263806387
|
24
|
+
108.73384179997886 134.47328134862394 3162.880454846513 215.45138754285665
|
25
|
+
238.49636899561344 2225.9561104691043 402.40727964384774 754.6792064294074
|
26
|
+
|
27
|
+
SP1_f1
|
28
|
+
682.6436366358055 443.1455214015781 2075.655346294993 287.211468117951
|
29
|
+
299.8883246804867 103.74338315843572 2613.8927022405364 471.1315623708902
|
30
|
+
591.4892493324709 42.631827541794564 2845.1654083148564 9.36948726124641
|
31
|
+
7.071084742361592 45.29093411231232 3432.8847704374107 3.409183158303573
|
32
|
+
91.308984085713 19.1536481364332 3373.656949880137 4.5363903481026
|
33
|
+
809.2082973387932 2246.941954176211 61.30766021687515 371.19806071846244
|
34
|
+
120.56476435866055 42.4349244403591 3242.1560628684038 83.50022078295852
|
35
|
+
13.72524477409959 35.858220519297525 3332.4066864946167 106.66582066236779
|
36
|
+
558.1188080161639 90.0084504200356 2694.854973210736 145.67374080342415
|
37
|
+
264.0088462230318 254.7175868081866 2796.88087480315 173.0486646159857
|
38
38
|
519.46013914282 1874.9349086474765 654.5411208373813 439.7198038226514
|
@@ -1,214 +1,231 @@
|
|
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--- !ruby/object:
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- !ruby/object:
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0.
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1
|
+
--- !ruby/object:Macroape::Collection
|
2
|
+
motifs:
|
3
|
+
- !ruby/object:Macroape::MotifWithThresholds
|
4
|
+
model: !ruby/object:Bioinform::MotifModel::NamedModel
|
5
|
+
model: !ruby/object:Bioinform::MotifModel::PWM
|
6
|
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matrix:
|
7
|
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|
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- 0.013801606113892391
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|
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- - -5.852906870733565
|
28
|
+
- -5.852906870733565
|
29
|
+
- 1.3841383838057844
|
30
|
+
- -5.852906870733565
|
31
|
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- - -5.852906870733565
|
32
|
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- -5.852906870733565
|
33
|
+
- 1.3841383838057844
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34
|
+
- -5.852906870733565
|
35
|
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- - 1.3835219739184805
|
36
|
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- -5.234195600643089
|
37
|
+
- -5.852906870733565
|
38
|
+
- -5.852906870733565
|
39
|
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|
40
|
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41
|
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|
42
|
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- -3.4011179649597234
|
43
|
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44
|
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45
|
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46
|
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|
47
|
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|
48
|
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|
49
|
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|
50
|
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|
51
|
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|
52
|
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|
53
|
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- 0.9073819084470863
|
54
|
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|
55
|
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|
56
|
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- -0.018148194552891343
|
57
|
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- 0.43811066953540795
|
58
|
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- -1.0304105539540909
|
59
|
+
alphabet: &1 !ruby/object:Bioinform::ComplementableAlphabet
|
60
|
+
alphabet:
|
61
|
+
- :A
|
62
|
+
- :C
|
63
|
+
- :G
|
64
|
+
- :T
|
65
|
+
complement_alphabet:
|
66
|
+
- :T
|
67
|
+
- :G
|
68
|
+
- :C
|
69
|
+
- :A
|
70
|
+
complements_by_letters:
|
71
|
+
A: T
|
72
|
+
:A: :T
|
73
|
+
a: t
|
74
|
+
:a: :t
|
75
|
+
C: G
|
76
|
+
:C: :G
|
77
|
+
c: g
|
78
|
+
:c: :g
|
79
|
+
G: C
|
80
|
+
:G: :C
|
81
|
+
g: c
|
82
|
+
:g: :c
|
83
|
+
T: A
|
84
|
+
:T: :A
|
85
|
+
t: a
|
86
|
+
:t: :a
|
87
|
+
index_by_letter:
|
88
|
+
a: 0
|
89
|
+
:a: 0
|
90
|
+
A: 0
|
91
|
+
:A: 0
|
92
|
+
c: 1
|
93
|
+
:c: 1
|
94
|
+
C: 1
|
95
|
+
:C: 1
|
96
|
+
g: 2
|
97
|
+
:g: 2
|
98
|
+
G: 2
|
99
|
+
:G: 2
|
100
|
+
t: 3
|
101
|
+
:t: 3
|
102
|
+
T: 3
|
103
|
+
:T: 3
|
104
|
+
name: GABPA_f1
|
105
|
+
rough:
|
106
|
+
5.0e-05: 16.0
|
107
|
+
0.0001: 15.0
|
108
|
+
0.0005: 12.0
|
109
|
+
precise:
|
110
|
+
5.0e-05: 8.6
|
111
|
+
0.0001: 7.6
|
112
|
+
0.0005: 4.5
|
113
|
+
- !ruby/object:Macroape::MotifWithThresholds
|
114
|
+
model: !ruby/object:Bioinform::MotifModel::NamedModel
|
115
|
+
model: !ruby/object:Bioinform::MotifModel::PWM
|
116
|
+
matrix:
|
117
|
+
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|
118
|
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119
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120
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121
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122
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123
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124
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125
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126
|
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127
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128
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129
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130
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131
|
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132
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133
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134
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135
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136
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137
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138
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139
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140
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141
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142
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- -2.3849751422136793
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143
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- 0.7198551207724353
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144
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- 0.5449254135616943
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145
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146
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147
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- 1.2851883354935514
|
148
|
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- -2.5026044231773548
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149
|
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150
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151
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152
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153
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154
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155
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156
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157
|
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alphabet: *1
|
158
|
+
name: KLF4_f2
|
159
|
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rough:
|
160
|
+
5.0e-05: 14.0
|
161
|
+
0.0001: 13.0
|
162
|
+
0.0005: 11.0
|
163
|
+
precise:
|
164
|
+
5.0e-05: 8.5
|
165
|
+
0.0001: 7.9
|
166
|
+
0.0005: 5.8
|
167
|
+
- !ruby/object:Macroape::MotifWithThresholds
|
168
|
+
model: !ruby/object:Bioinform::MotifModel::NamedModel
|
169
|
+
model: !ruby/object:Bioinform::MotifModel::PWM
|
170
|
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matrix:
|
171
|
+
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172
|
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173
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174
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175
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177
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178
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179
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180
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181
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182
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183
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184
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185
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186
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187
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188
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189
|
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190
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191
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192
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193
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194
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195
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196
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197
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198
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199
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200
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201
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202
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203
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|
204
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- -2.2510053061629796
|
205
|
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|
206
|
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207
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208
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209
|
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- 1.1636760063747449
|
210
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|
211
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|
212
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213
|
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|
214
|
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- -0.6825482097865606
|
215
|
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alphabet: *1
|
216
|
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name: SP1_f1
|
217
|
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rough:
|
218
|
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5.0e-05: 14.0
|
219
|
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0.0001: 14.0
|
220
|
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0.0005: 11.0
|
221
|
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precise:
|
222
|
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5.0e-05: 8.5
|
223
|
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0.0001: 7.7
|
224
|
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0.0005: 5.6
|
225
|
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rough_discretization: 1
|
226
|
+
precise_discretization: 10
|
227
|
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background: !ruby/object:Bioinform::WordwiseBackground {}
|
228
|
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pvalues:
|
229
|
+
- 0.0005
|
230
|
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- 0.0001
|
231
|
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- 5.0e-05
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