test/data/test_collection_weak.yaml in macroape-4.0.2 vs test/data/test_collection_weak.yaml in macroape-4.1.0
- old
+ new
@@ -1,214 +1,231 @@
---- !ruby/object:Bioinform::Collection
-container:
-- !ruby/object:Bioinform::Motif
- parameters: !ruby/object:OpenStruct
- table:
- :original_data_model: :pwm
- :pwm: !ruby/object:Bioinform::PWM
- parameters: !ruby/object:OpenStruct
- table:
- :name: GABPA_f1
- :background: &19796448
- - 1
- - 1
- - 1
- - 1
- :max_hash_size: 1000000
- modifiable: true
- matrix:
- - - -0.1106670158341858
- - 0.013801606113892391
- - 0.6054596108973699
- - -1.3518085041421573
- - - 0.37030668921643345
- - 0.15761121480429963
- - 0.009069314183831202
- - -0.9888619717703562
- - - 0.47526546359546684
- - -0.3011678534572083
- - 0.4031522994412777
- - -1.8638752827041059
- - - -1.5544255540164373
- - 1.1082369687811506
- - -0.2814091552834454
- - -5.30708531823271
- - - -0.6362037835776368
- - 1.235338189985594
- - -3.5801322928552253
- - -5.717323067092849
- - - -5.852906870733575
- - -5.852906870733575
- - 1.3841383838057746
- - -5.852906870733575
- - - -5.852906870733575
- - -5.852906870733575
- - 1.3841383838057746
- - -5.852906870733575
- - - 1.3835219739184708
- - -5.2341956006430985
- - -5.852906870733575
- - -5.852906870733575
- - - 1.3756340514956562
- - -5.394962755562375
- - -5.394962755562375
- - -3.401117964959733
- - - -1.2176198315414444
- - -3.109079898175411
- - 1.2964067931472216
- - -5.717323067092849
- - - -1.3716559438167257
- - -0.2761401935045069
- - -1.8504445165866068
- - 1.0404320473626856
- - - -0.5440863133031895
- - -0.48103682561971345
- - 0.907381908447086
- - -1.1280642594012078
- - - 0.10557340209290218
- - -0.01814819455289191
- - 0.4381106695354074
- - -1.0304105539540915
- :rough:
- 5.0e-05: 16.0
- 0.0001: 15.0
- 0.0005: 12.0
- :precise:
- 5.0e-05: 8.6
- 0.0001: 7.6
- 0.0005: 4.5
- modifiable: true
-- !ruby/object:Bioinform::Motif
- parameters: !ruby/object:OpenStruct
- table:
- :original_data_model: :pwm
- :pwm: !ruby/object:Bioinform::PWM
- parameters: !ruby/object:OpenStruct
- table:
- :name: KLF4_f2
- :background: *19796448
- :max_hash_size: 1000000
- modifiable: true
- matrix:
- - - 0.30861857265872605
- - -2.254321000121579
- - 0.13505703522674192
- - 0.3285194224375633
- - - -1.227018967707036
- - -4.814127713368663
- - 1.3059890687390967
- - -4.908681463544344
- - - -2.443469374521196
- - -4.648238485031404
- - 1.3588686548279805
- - -4.441801801188402
- - - -2.7177827948276123
- - -3.8073538975356565
- - 1.356272809724262
- - -3.504104725510225
- - - -0.5563232977367343
- - 0.5340697765121405
- - -3.61417723090579
- - 0.5270259776377405
- - - -1.8687622060887386
- - -4.381483976582316
- - 1.337932245336098
- - -3.815629658877517
- - - -2.045671123823928
- - -2.384975142213679
- - 0.7198551207724355
- - 0.5449254135616948
- - - -1.373157530374372
- - -3.0063112097748217
- - 1.285188335493552
- - -2.5026044231773543
- - - -2.1030513122772208
- - -1.8941348100402244
- - 1.249265758393991
- - -1.4284210948906104
- - - -1.3277128628152939
- - 0.8982415633049462
- - -0.8080773665408135
- - -0.18161647647456935
- :rough:
- 5.0e-05: 14.0
- 0.0001: 13.0
- 0.0005: 11.0
- :precise:
- 5.0e-05: 8.5
- 0.0001: 7.9
- 0.0005: 5.8
- modifiable: true
-- !ruby/object:Bioinform::Motif
- parameters: !ruby/object:OpenStruct
- table:
- :original_data_model: :pwm
- :pwm: !ruby/object:Bioinform::PWM
- parameters: !ruby/object:OpenStruct
- table:
- :name: SP1_f1
- :background: *19796448
- :max_hash_size: 1000000
- modifiable: true
- matrix:
- - - -0.24435707885585292
- - -0.674823404693731
- - 0.8657012535789866
- - -1.1060188862599287
- - - -1.0631255752097797
- - -2.111925969423868
- - 1.0960627561110403
- - -0.6138563775211977
- - - -0.3872276234760535
- - -2.9739851913218045
- - 1.1807800242010378
- - -4.338927525031566
- - - -4.563896055436894
- - -2.9161633002532277
- - 1.3684371349982638
- - -5.077972423609655
- - - -2.2369752892820083
- - -3.7196436313301846
- - 1.3510439136452734
- - -4.889930670508233
- - - -0.07473964149330865
- - 0.944919654762011
- - -2.6246857648086044
- - -0.8510983487822436
- - - -1.9643526491643322
- - -2.978402770880115
- - 1.3113096718240573
- - -2.324334259499025
- - - -4.0155484139655835
- - -3.1384268078096667
- - 1.3387488589788057
- - -2.084673903537648
- - - -0.44509385828355363
- - -2.2510053061629702
- - 1.1265431574368685
- - -1.7780413702431372
- - - -1.1896356092245048
- - -1.2251832285630027
- - 1.1636760063747527
- - -1.6080243648157353
- - - -0.5166047365590571
- - 0.7641033353626657
- - -0.2862677570028208
- - -0.68254820978656
- :rough:
- 5.0e-05: 14.0
- 0.0001: 14.0
- 0.0005: 11.0
- :precise:
- 5.0e-05: 8.5
- 0.0001: 7.7
- 0.0005: 5.6
- modifiable: true
-parameters: !ruby/object:OpenStruct
- table:
- :rough_discretization: 1
- :precise_discretization: 10
- :background: *19796448
- :pvalues:
- - 0.0005
- - 0.0001
- - 5.0e-05
+--- !ruby/object:Macroape::Collection
+motifs:
+- !ruby/object:Macroape::MotifWithThresholds
+ model: !ruby/object:Bioinform::MotifModel::NamedModel
+ model: !ruby/object:Bioinform::MotifModel::PWM
+ matrix:
+ - - -0.1106670158341858
+ - 0.013801606113892391
+ - 0.6054596108973699
+ - -1.3518085041421573
+ - - 0.3703066892164342
+ - 0.15761121480430038
+ - 0.009069314183831861
+ - -0.9888619717703555
+ - - 0.47526546359546656
+ - -0.30116785345720876
+ - 0.40315229944127723
+ - -1.8638752827041063
+ - - -1.5544255540164387
+ - 1.1082369687811493
+ - -0.28140915528344673
+ - -5.307085318232711
+ - - -0.6362037835776333
+ - 1.2353381899855975
+ - -3.5801322928552217
+ - -5.717323067092845
+ - - -5.852906870733565
+ - -5.852906870733565
+ - 1.3841383838057844
+ - -5.852906870733565
+ - - -5.852906870733565
+ - -5.852906870733565
+ - 1.3841383838057844
+ - -5.852906870733565
+ - - 1.3835219739184805
+ - -5.234195600643089
+ - -5.852906870733565
+ - -5.852906870733565
+ - - 1.375634051495666
+ - -5.394962755562365
+ - -5.394962755562365
+ - -3.4011179649597234
+ - - -1.2176198315414393
+ - -3.109079898175406
+ - 1.2964067931472267
+ - -5.717323067092844
+ - - -1.3716559438167275
+ - -0.2761401935045087
+ - -1.8504445165866086
+ - 1.0404320473626838
+ - - -0.5440863133031892
+ - -0.4810368256197133
+ - 0.9073819084470863
+ - -1.1280642594012076
+ - - 0.10557340209290259
+ - -0.018148194552891343
+ - 0.43811066953540795
+ - -1.0304105539540909
+ alphabet: &1 !ruby/object:Bioinform::ComplementableAlphabet
+ alphabet:
+ - :A
+ - :C
+ - :G
+ - :T
+ complement_alphabet:
+ - :T
+ - :G
+ - :C
+ - :A
+ complements_by_letters:
+ A: T
+ :A: :T
+ a: t
+ :a: :t
+ C: G
+ :C: :G
+ c: g
+ :c: :g
+ G: C
+ :G: :C
+ g: c
+ :g: :c
+ T: A
+ :T: :A
+ t: a
+ :t: :a
+ index_by_letter:
+ a: 0
+ :a: 0
+ A: 0
+ :A: 0
+ c: 1
+ :c: 1
+ C: 1
+ :C: 1
+ g: 2
+ :g: 2
+ G: 2
+ :G: 2
+ t: 3
+ :t: 3
+ T: 3
+ :T: 3
+ name: GABPA_f1
+ rough:
+ 5.0e-05: 16.0
+ 0.0001: 15.0
+ 0.0005: 12.0
+ precise:
+ 5.0e-05: 8.6
+ 0.0001: 7.6
+ 0.0005: 4.5
+- !ruby/object:Macroape::MotifWithThresholds
+ model: !ruby/object:Bioinform::MotifModel::NamedModel
+ model: !ruby/object:Bioinform::MotifModel::PWM
+ matrix:
+ - - 0.30861857265872605
+ - -2.254321000121579
+ - 0.13505703522674192
+ - 0.3285194224375633
+ - - -1.2270189677070362
+ - -4.814127713368663
+ - 1.3059890687390965
+ - -4.908681463544344
+ - - -2.4434693745211966
+ - -4.648238485031404
+ - 1.3588686548279802
+ - -4.441801801188402
+ - - -2.7177827948276128
+ - -3.807353897535657
+ - 1.3562728097242616
+ - -3.504104725510225
+ - - -0.5563232977367345
+ - 0.5340697765121402
+ - -3.61417723090579
+ - 0.5270259776377402
+ - - -1.8687622060887386
+ - -4.381483976582316
+ - 1.337932245336098
+ - -3.815629658877517
+ - - -2.0456711238239285
+ - -2.3849751422136793
+ - 0.7198551207724353
+ - 0.5449254135616943
+ - - -1.3731575303743726
+ - -3.006311209774822
+ - 1.2851883354935514
+ - -2.5026044231773548
+ - - -2.103051312277221
+ - -1.8941348100402247
+ - 1.249265758393991
+ - -1.4284210948906106
+ - - -1.327712862815294
+ - 0.898241563304946
+ - -0.8080773665408136
+ - -0.1816164764745695
+ alphabet: *1
+ name: KLF4_f2
+ rough:
+ 5.0e-05: 14.0
+ 0.0001: 13.0
+ 0.0005: 11.0
+ precise:
+ 5.0e-05: 8.5
+ 0.0001: 7.9
+ 0.0005: 5.8
+- !ruby/object:Macroape::MotifWithThresholds
+ model: !ruby/object:Bioinform::MotifModel::NamedModel
+ model: !ruby/object:Bioinform::MotifModel::PWM
+ matrix:
+ - - -0.24435707885585292
+ - -0.674823404693731
+ - 0.8657012535789866
+ - -1.1060188862599287
+ - - -1.063125575209786
+ - -2.111925969423874
+ - 1.096062756111034
+ - -0.6138563775212038
+ - - -0.38722762347606526
+ - -2.9739851913218165
+ - 1.180780024201026
+ - -4.338927525031577
+ - - -4.563896055436912
+ - -2.916163300253245
+ - 1.3684371349982463
+ - -5.077972423609672
+ - - -2.2369752892820247
+ - -3.7196436313302015
+ - 1.3510439136452568
+ - -4.8899306705082495
+ - - -0.07473964149331284
+ - 0.9449196547620068
+ - -2.6246857648086084
+ - -0.8510983487822477
+ - - -1.9643526491643477
+ - -2.9784027708801304
+ - 1.3113096718240418
+ - -2.3243342594990404
+ - - -4.015548413965599
+ - -3.138426807809682
+ - 1.3387488589787901
+ - -2.0846739035376634
+ - - -0.44509385828356285
+ - -2.2510053061629796
+ - 1.1265431574368594
+ - -1.7780413702431463
+ - - -1.1896356092245128
+ - -1.2251832285630104
+ - 1.1636760063747449
+ - -1.608024364815743
+ - - -0.5166047365590577
+ - 0.7641033353626651
+ - -0.28626775700282125
+ - -0.6825482097865606
+ alphabet: *1
+ name: SP1_f1
+ rough:
+ 5.0e-05: 14.0
+ 0.0001: 14.0
+ 0.0005: 11.0
+ precise:
+ 5.0e-05: 8.5
+ 0.0001: 7.7
+ 0.0005: 5.6
+rough_discretization: 1
+precise_discretization: 10
+background: !ruby/object:Bioinform::WordwiseBackground {}
+pvalues:
+- 0.0005
+- 0.0001
+- 5.0e-05