RubyGems - macroape - Versions diffs - 3.3.7 → 3.3.8 - Mend

macroape 3.3.7 → 3.3.8

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 (46) hide show

data/README.md +2 -2
data/Rakefile.rb +6 -6
data/TODO.txt +23 -3
data/benchmark/similarity_benchmark.rb +18 -18
data/lib/macroape/aligned_pair_intersection.rb +4 -4
data/lib/macroape/cli/align_motifs.rb +34 -28
data/lib/macroape/cli/eval_alignment.rb +73 -47
data/lib/macroape/cli/eval_similarity.rb +65 -40
data/lib/macroape/cli/find_pvalue.rb +30 -34
data/lib/macroape/cli/find_threshold.rb +52 -41
data/lib/macroape/cli/preprocess_collection.rb +68 -58
data/lib/macroape/cli/scan_collection.rb +89 -73
data/lib/macroape/cli.rb +184 -1
data/lib/macroape/counting.rb +31 -5
data/lib/macroape/pwm_compare.rb +8 -2
data/lib/macroape/pwm_compare_aligned.rb +15 -10
data/lib/macroape/version.rb +2 -1
data/macroape.gemspec +2 -1
data/spec/count_distribution_spec.rb +11 -11
data/test/align_motifs_test.rb +16 -4
data/test/data/{AHR_si.pat → AHR_si.pwm} +0 -0
data/test/data/{KLF3_f1.pat → KLF3_f1.pwm} +0 -0
data/test/data/{KLF4_f2.pat → KLF4_f2.pwm} +0 -0
data/test/data/KLF4_f2_scan_results_all.txt +1 -2
data/test/data/KLF4_f2_scan_results_default_cutoff.txt +1 -2
data/test/data/KLF4_f2_scan_results_precise_mode.txt +1 -2
data/test/data/KLF4_f2_scan_results_weak_threshold.txt +2 -0
data/test/data/{SP1_f1.pat → SP1_f1.pwm} +0 -0
data/test/data/{SP1_f1_revcomp.pat → SP1_f1_revcomp.pwm} +0 -0
data/test/data/collection_pcm_without_thresholds.yaml +186 -183
data/test/data/collection_without_thresholds.yaml +186 -183
data/test/data/{medium_motif.pat → medium_motif.pwm} +0 -0
data/test/data/{short_motif.pat → short_motif.pwm} +0 -0
data/test/data/test_collection/{GABPA_f1.pat → GABPA_f1.pwm} +0 -0
data/test/data/test_collection/{KLF4_f2.pat → KLF4_f2.pwm} +0 -0
data/test/data/test_collection/{SP1_f1.pat → SP1_f1.pwm} +0 -0
data/test/data/test_collection.yaml +179 -176
data/test/data/test_collection_weak.yaml +214 -0
data/test/eval_alignment_test.rb +97 -21
data/test/eval_similarity_test.rb +104 -26
data/test/find_pvalue_test.rb +22 -9
data/test/find_threshold_test.rb +76 -25
data/test/preprocess_collection_test.rb +16 -21
data/test/scan_collection_test.rb +26 -14
data/test/test_helper.rb +96 -12
metadata +44 -24

data/test/data/test_collection.yaml CHANGED Viewed

@@ -1,73 +1,73 @@
---- &19230696 !ruby/object:Bioinform::Collection
-collection:
-- - !ruby/object:Bioinform::PWM
-    parameters: !ruby/object:OpenStruct
-      table:
-        :name: GABPA_f1
-        :tags:
-        - *19230696
-        :background: &19231104
-        - 1
-        - 1
-        - 1
-        - 1
-      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
-    max_hash_size: 1000000
-  - !ruby/object:OpenStruct
+--- !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: &15478152
+            - 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: 16.1
         0.0001: 15.1
@@ -76,58 +76,59 @@ collection:
         5.0e-05: 8.61
         0.0001: 7.609999999999999
         0.0005: 4.51
-- - !ruby/object:Bioinform::PWM
-    parameters: !ruby/object:OpenStruct
-      table:
-        :name: KLF4_f2
-        :tags:
-        - *19230696
-        :background: *19231104
-      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
-    max_hash_size: 1000000
-  - !ruby/object:OpenStruct
+    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: *15478152
+            :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: 14.1
         0.0001: 13.1
@@ -136,62 +137,63 @@ collection:
         5.0e-05: 8.51
         0.0001: 7.909999999999999
         0.0005: 5.8100000000000005
-- - !ruby/object:Bioinform::PWM
-    parameters: !ruby/object:OpenStruct
-      table:
-        :name: SP1_f1
-        :tags:
-        - *19230696
-        :background: *19231104
-      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
-    max_hash_size: 1000000
-  - !ruby/object:OpenStruct
+    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: *15478152
+            :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: 14.1
         0.0001: 14.1
@@ -200,11 +202,12 @@ collection:
         5.0e-05: 8.51
         0.0001: 7.709999999999999
         0.0005: 5.61
+    modifiable: true
 parameters: !ruby/object:OpenStruct
   table:
     :rough_discretization: 1
     :precise_discretization: 10
-    :background: *19231104
+    :background: *15478152
     :pvalues:
     - 0.0005
     - 0.0001

data/test/data/test_collection_weak.yaml ADDED Viewed

@@ -0,0 +1,214 @@
+--- !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