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
  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/collection_without_thresholds.yaml CHANGED
@@ -1,185 +1,188 @@
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  table: {}
data/test/data/{medium_motif.pat → medium_motif.pwm} RENAMED
File without changes
data/test/data/{short_motif.pat → short_motif.pwm} RENAMED
File without changes