macroape 3.3.7 → 3.3.8

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Files changed (46) hide show
  1. data/README.md +2 -2
  2. data/Rakefile.rb +6 -6
  3. data/TODO.txt +23 -3
  4. data/benchmark/similarity_benchmark.rb +18 -18
  5. data/lib/macroape/aligned_pair_intersection.rb +4 -4
  6. data/lib/macroape/cli/align_motifs.rb +34 -28
  7. data/lib/macroape/cli/eval_alignment.rb +73 -47
  8. data/lib/macroape/cli/eval_similarity.rb +65 -40
  9. data/lib/macroape/cli/find_pvalue.rb +30 -34
  10. data/lib/macroape/cli/find_threshold.rb +52 -41
  11. data/lib/macroape/cli/preprocess_collection.rb +68 -58
  12. data/lib/macroape/cli/scan_collection.rb +89 -73
  13. data/lib/macroape/cli.rb +184 -1
  14. data/lib/macroape/counting.rb +31 -5
  15. data/lib/macroape/pwm_compare.rb +8 -2
  16. data/lib/macroape/pwm_compare_aligned.rb +15 -10
  17. data/lib/macroape/version.rb +2 -1
  18. data/macroape.gemspec +2 -1
  19. data/spec/count_distribution_spec.rb +11 -11
  20. data/test/align_motifs_test.rb +16 -4
  21. data/test/data/{AHR_si.pat → AHR_si.pwm} +0 -0
  22. data/test/data/{KLF3_f1.pat → KLF3_f1.pwm} +0 -0
  23. data/test/data/{KLF4_f2.pat → KLF4_f2.pwm} +0 -0
  24. data/test/data/KLF4_f2_scan_results_all.txt +1 -2
  25. data/test/data/KLF4_f2_scan_results_default_cutoff.txt +1 -2
  26. data/test/data/KLF4_f2_scan_results_precise_mode.txt +1 -2
  27. data/test/data/KLF4_f2_scan_results_weak_threshold.txt +2 -0
  28. data/test/data/{SP1_f1.pat → SP1_f1.pwm} +0 -0
  29. data/test/data/{SP1_f1_revcomp.pat → SP1_f1_revcomp.pwm} +0 -0
  30. data/test/data/collection_pcm_without_thresholds.yaml +186 -183
  31. data/test/data/collection_without_thresholds.yaml +186 -183
  32. data/test/data/{medium_motif.pat → medium_motif.pwm} +0 -0
  33. data/test/data/{short_motif.pat → short_motif.pwm} +0 -0
  34. data/test/data/test_collection/{GABPA_f1.pat → GABPA_f1.pwm} +0 -0
  35. data/test/data/test_collection/{KLF4_f2.pat → KLF4_f2.pwm} +0 -0
  36. data/test/data/test_collection/{SP1_f1.pat → SP1_f1.pwm} +0 -0
  37. data/test/data/test_collection.yaml +179 -176
  38. data/test/data/test_collection_weak.yaml +214 -0
  39. data/test/eval_alignment_test.rb +97 -21
  40. data/test/eval_similarity_test.rb +104 -26
  41. data/test/find_pvalue_test.rb +22 -9
  42. data/test/find_threshold_test.rb +76 -25
  43. data/test/preprocess_collection_test.rb +16 -21
  44. data/test/scan_collection_test.rb +26 -14
  45. data/test/test_helper.rb +96 -12
  46. metadata +44 -24
data/test/data/test_collection.yaml CHANGED
@@ -1,73 +1,73 @@
1
- --- &19230696 !ruby/object:Bioinform::Collection
2
- collection:
3
- - - !ruby/object:Bioinform::PWM
4
- parameters: !ruby/object:OpenStruct
5
- table:
6
- :name: GABPA_f1
7
- :tags:
8
- - *19230696
9
- :background: &19231104
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- - 1
11
- - 1
12
- - 1
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- - 1
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- modifiable: true
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- matrix:
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- - - -0.1106670158341858
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- - 0.013801606113892391
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- - 0.6054596108973699
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- - -1.3518085041421573
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- - - 0.37030668921643345
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- - 0.15761121480429963
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- - 0.009069314183831202
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- - -0.9888619717703562
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- - - 0.47526546359546684
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- - -0.3011678534572083
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- - 0.4031522994412777
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- - - -1.5544255540164373
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- - -0.2814091552834454
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- - - -0.6362037835776368
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- - 0.4381106695354074
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- - -1.0304105539540915
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- max_hash_size: 1000000
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- - !ruby/object:OpenStruct
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+ --- !ruby/object:Bioinform::Collection
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+ container:
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+ - !ruby/object:Bioinform::Motif
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+ parameters: !ruby/object:OpenStruct
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  table:
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+ :original_data_model: :pwm
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+ :pwm: !ruby/object:Bioinform::PWM
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+ parameters: !ruby/object:OpenStruct
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+ table:
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+ :name: GABPA_f1
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+ :background: &15478152
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+ - 1
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+ - 1
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+ - 1
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+ :max_hash_size: 1000000
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+ modifiable: true
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+ matrix:
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+ - 0.6054596108973699
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+ - 0.009069314183831202
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+ - -5.852906870733575
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+ - 1.3841383838057746
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  :rough:
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  5.0e-05: 16.1
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  0.0001: 15.1
@@ -76,58 +76,59 @@ collection:
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  5.0e-05: 8.61
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  0.0001: 7.609999999999999
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  0.0005: 4.51
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- - - !ruby/object:Bioinform::PWM
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- parameters: !ruby/object:OpenStruct
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- table:
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- :name: KLF4_f2
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- :tags:
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- - *19230696
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- :background: *19231104
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- modifiable: true
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- matrix:
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- - - 0.30861857265872605
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- max_hash_size: 1000000
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- - !ruby/object:OpenStruct
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+ modifiable: true
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+ - !ruby/object:Bioinform::Motif
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+ parameters: !ruby/object:OpenStruct
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82
  table:
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+ :original_data_model: :pwm
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+ :pwm: !ruby/object:Bioinform::PWM
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+ parameters: !ruby/object:OpenStruct
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+ table:
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+ :name: KLF4_f2
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+ :background: *15478152
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+ :max_hash_size: 1000000
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+ modifiable: true
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+ matrix:
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  :rough:
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  5.0e-05: 14.1
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  0.0001: 13.1
@@ -136,62 +137,63 @@ collection:
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  5.0e-05: 8.51
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  0.0001: 7.909999999999999
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  0.0005: 5.8100000000000005
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- - - !ruby/object:Bioinform::PWM
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- parameters: !ruby/object:OpenStruct
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- table:
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- :name: SP1_f1
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- :tags:
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- :background: *19231104
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- modifiable: true
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- - !ruby/object:OpenStruct
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  table:
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  5.0e-05: 8.51
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  0.0001: 7.709999999999999
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  0.0005: 5.61
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+ modifiable: true
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  parameters: !ruby/object:OpenStruct
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  table:
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- :background: *19231104
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  - 0.0005
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data/test/data/test_collection_weak.yaml ADDED
@@ -0,0 +1,214 @@
1
+ --- !ruby/object:Bioinform::Collection
2
+ container:
3
+ - !ruby/object:Bioinform::Motif
4
+ parameters: !ruby/object:OpenStruct
5
+ table:
6
+ :original_data_model: :pwm
7
+ :pwm: !ruby/object:Bioinform::PWM
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+ parameters: !ruby/object:OpenStruct
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+ table:
10
+ :name: GABPA_f1
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+ modifiable: true
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