RubyGems - macroape - Versions diffs - 4.0.2 → 4.1.0 - Mend

macroape 4.0.2 → 4.1.0

Files changed (74) hide show

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

metadata CHANGED

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: macroape
 version: !ruby/object:Gem::Version
-  version: 4.0.2
+  version: 4.1.0
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2013-09-30 00:00:00.000000000 Z
+date: 2014-07-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bioinform
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.1.10
+        version: 0.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.1.10
+        version: 0.2.0
 description: Macroape is an abbreviation for MAtrix CompaRisOn by Approximate P-value
   Estimation. It's a bioinformatic tool for evaluating similarity measure and best
   alignment between a pair of Position Weight Matrices(PWM), finding thresholds by
@@ -67,12 +67,18 @@ files:
 - lib/macroape/cli/find_threshold.rb
 - lib/macroape/cli/preprocess_collection.rb
 - lib/macroape/cli/scan_collection.rb
-- lib/macroape/counting.rb
+- lib/macroape/collection.rb
+- lib/macroape/motif_with_thresholds.rb
 - lib/macroape/pwm_compare.rb
 - lib/macroape/pwm_compare_aligned.rb
+- lib/macroape/pwm_counting.rb
+- lib/macroape/support/inverf.rb
+- lib/macroape/support/partial_sums.rb
 - lib/macroape/version.rb
 - macroape.gemspec
 - spec/count_distribution_spec.rb
+- spec/inverf_spec.rb
+- spec/partial_sums_spec.rb
 - spec/spec_helper.rb
 - test/align_motifs_test.rb
 - test/data/AHR_si.pwm
@@ -88,8 +94,6 @@ files:
 - test/data/SP1_f1.pwm
 - test/data/SP1_f1_revcomp.pcm
 - test/data/SP1_f1_revcomp.pwm
-- test/data/collection_pcm_without_thresholds.yaml
-- test/data/collection_without_thresholds.yaml
 - test/data/medium_motif.pwm
 - test/data/short_motif.pwm
 - test/data/test_collection.yaml
@@ -128,12 +132,14 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project:
-rubygems_version: 2.1.5
+rubygems_version: 2.3.0
 signing_key:
 specification_version: 4
 summary: PWM comparison tool using MACROAPE approach
 test_files:
 - spec/count_distribution_spec.rb
+- spec/inverf_spec.rb
+- spec/partial_sums_spec.rb
 - spec/spec_helper.rb
 - test/align_motifs_test.rb
 - test/data/AHR_si.pwm
@@ -149,8 +155,6 @@ test_files:
 - test/data/SP1_f1.pwm
 - test/data/SP1_f1_revcomp.pcm
 - test/data/SP1_f1_revcomp.pwm
-- test/data/collection_pcm_without_thresholds.yaml
-- test/data/collection_without_thresholds.yaml
 - test/data/medium_motif.pwm
 - test/data/short_motif.pwm
 - test/data/test_collection.yaml

data/test/data/collection_pcm_without_thresholds.yaml DELETED

@@ -1,188 +0,0 @@
---- !ruby/object:Bioinform::Collection
-container:
-- !ruby/object:Bioinform::Motif
-  parameters: !ruby/object:OpenStruct
-    table:
-      :original_data_model: :pcm
-      :pcm: !ruby/object:Bioinform::PCM
-        parameters: !ruby/object:OpenStruct
-          table:
-            :name: GABPA_f1
-            :background:
-            - 1
-            - 1
-            - 1
-            - 1
-          modifiable: true
-        matrix:
-        - - 615.2572649050138
-          - 697.0698715160123
-          - 1261.1903440712872
-          - 176.43506582414153
-        - - 996.4929869323321
-          - 805.1878697364007
-          - 693.7695793644275
-          - 254.5021102832924
-        - - 1106.9888035794224
-          - 508.19444415177276
-          - 1029.8329748714536
-          - 104.93632371380718
-        - - 143.7121486195701
-          - 2086.4279160661263
-          - 518.37507049306
-          - 1.4374111377025893
-        - - 362.9541452731307
-          - 2369.473894845734
-          - 17.23702397004065
-          - 0.2874822275405179
-        - - 0.0
-          - 0.0
-          - 2749.952546316428
-          - 0.0
-        - - 0.0
-          - 0.0
-          - 2749.952546316428
-          - 0.0
-        - - 2748.2567506938462
-          - 1.695795622582083
-          - 0.0
-          - 0.0
-        - - 2726.6484322711017
-          - 1.1499289101620715
-          - 1.1499289101620715
-          - 21.00425622500253
-        - - 202.05697400573305
-          - 28.799402471063658
-          - 2518.808687612104
-          - 0.2874822275405179
-        - - 172.92889618879767
-          - 521.1240363384483
-          - 106.38197600987633
-          - 1949.517637779338
-        - - 398.1679460365911
-          - 424.20938204069563
-          - 1706.4024212088275
-          - 221.17279703034018
-        - - 764.2587933951809
-          - 675.0883944902433
-          - 1066.5413633225007
-          - 244.06399510852864
-    modifiable: true
-- !ruby/object:Bioinform::Motif
-  parameters: !ruby/object:OpenStruct
-    table:
-      :original_data_model: :pcm
-      :pcm: !ruby/object:Bioinform::PCM
-        parameters: !ruby/object:OpenStruct
-          table:
-            :name: KLF4_f2
-            :background:
-            - 1
-            - 1
-            - 1
-            - 1
-          modifiable: true
-        matrix:
-        - - 1233.46088405354
-          - 93.18173277811673
-          - 1036.6014857092885
-          - 1258.2948629970272
-        - - 263.979242343185
-          - 5.314520555872139
-          - 3347.5949971525274
-          - 4.650205486388122
-        - - 76.7700780003465
-          - 6.643150694840173
-          - 3529.4896409394937
-          - 8.636095903292224
-        - - 57.86097393406657
-          - 18.102585643439472
-          - 3520.3342027139347
-          - 25.24120324653207
-        - - 518.1947904009378
-          - 1545.9062946905135
-          - 22.396758181071043
-          - 1535.0411222654507
-        - - 137.98151691820345
-          - 9.300410972776241
-          - 3456.320530770924
-          - 17.936506876068467
-        - - 115.27647661640499
-          - 81.51802997128804
-          - 1861.9425868567278
-          - 1562.801872093553
-        - - 227.8095486111286
-          - 42.84555258785854
-          - 3278.6396005325996
-          - 72.244263806387
-        - - 108.73384179997886
-          - 134.47328134862394
-          - 3162.880454846513
-          - 215.45138754285665
-        - - 238.49636899561344
-          - 2225.9561104691043
-          - 402.40727964384774
-          - 754.6792064294074
-    modifiable: true
-- !ruby/object:Bioinform::Motif
-  parameters: !ruby/object:OpenStruct
-    table:
-      :original_data_model: :pcm
-      :pcm: !ruby/object:Bioinform::PCM
-        parameters: !ruby/object:OpenStruct
-          table:
-            :name: SP1_f1
-            :background:
-            - 1
-            - 1
-            - 1
-            - 1
-          modifiable: true
-        matrix:
-        - - 682.6436366358055
-          - 443.1455214015781
-          - 2075.655346294993
-          - 287.211468117951
-        - - 299.8883246804867
-          - 103.74338315843572
-          - 2613.8927022405364
-          - 471.1315623708902
-        - - 591.4892493324709
-          - 42.631827541794564
-          - 2845.1654083148564
-          - 9.36948726124641
-        - - 7.071084742361592
-          - 45.29093411231232
-          - 3432.8847704374107
-          - 3.409183158303573
-        - - 91.308984085713
-          - 19.1536481364332
-          - 3373.656949880137
-          - 4.5363903481026
-        - - 809.2082973387932
-          - 2246.941954176211
-          - 61.30766021687515
-          - 371.19806071846244
-        - - 120.56476435866055
-          - 42.4349244403591
-          - 3242.1560628684038
-          - 83.50022078295852
-        - - 13.72524477409959
-          - 35.858220519297525
-          - 3332.4066864946167
-          - 106.66582066236779
-        - - 558.1188080161639
-          - 90.0084504200356
-          - 2694.854973210736
-          - 145.67374080342415
-        - - 264.0088462230318
-          - 254.7175868081866
-          - 2796.88087480315
-          - 173.0486646159857
-        - - 519.46013914282
-          - 1874.9349086474765
-          - 654.5411208373813
-          - 439.7198038226514
-    modifiable: true
-parameters: !ruby/object:OpenStruct
-  table: {}

data/test/data/collection_without_thresholds.yaml DELETED

@@ -1,188 +0,0 @@
---- !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:
-            - 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
-    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:
-            - 1
-            - 1
-            - 1
-            - 1
-          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
-    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:
-            - 1
-            - 1
-            - 1
-            - 1
-          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
-    modifiable: true
-parameters: !ruby/object:OpenStruct
-  table: {}