bioinform 0.1.7 → 0.1.8

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Files changed (73) hide show
  1. data/TODO.txt +7 -2
  2. data/bin/merge_into_collection +4 -0
  3. data/bin/pcm2pwm +1 -1
  4. data/bin/split_motifs +1 -1
  5. data/bioinform.gemspec +2 -0
  6. data/lib/bioinform/cli/merge_into_collection.rb +76 -0
  7. data/lib/bioinform/cli/pcm2pwm.rb +20 -20
  8. data/lib/bioinform/cli/split_motifs.rb +21 -20
  9. data/lib/bioinform/cli.rb +16 -2
  10. data/lib/bioinform/data_models/collection.rb +13 -10
  11. data/lib/bioinform/data_models/pcm.rb +2 -2
  12. data/lib/bioinform/data_models/pm.rb +24 -37
  13. data/lib/bioinform/data_models/ppm.rb +2 -2
  14. data/lib/bioinform/data_models/pwm.rb +2 -2
  15. data/lib/bioinform/data_models.rb +8 -8
  16. data/lib/bioinform/parsers/parser.rb +10 -5
  17. data/lib/bioinform/parsers/splittable_parser.rb +57 -0
  18. data/lib/bioinform/parsers/string_fantom_parser.rb +3 -3
  19. data/lib/bioinform/parsers/string_parser.rb +5 -24
  20. data/lib/bioinform/parsers/trivial_parser.rb +19 -3
  21. data/lib/bioinform/parsers/yaml_parser.rb +35 -0
  22. data/lib/bioinform/parsers.rb +6 -4
  23. data/lib/bioinform/support/parameters.rb +19 -0
  24. data/lib/bioinform/support/partial_sums.rb +1 -1
  25. data/lib/bioinform/support.rb +11 -10
  26. data/lib/bioinform/version.rb +1 -1
  27. data/lib/bioinform.rb +5 -5
  28. data/spec/cli/cli_spec.rb +8 -7
  29. data/spec/cli/data/merge_into_collection/GABPA_f1.pwm +14 -0
  30. data/spec/cli/data/{KLF4_f2.pwm.result → merge_into_collection/KLF4_f2.pwm} +0 -0
  31. data/spec/cli/data/{SP1_f1.pwm.result → merge_into_collection/SP1_f1.pwm} +0 -0
  32. data/spec/cli/data/merge_into_collection/collection.txt.result +40 -0
  33. data/spec/cli/data/merge_into_collection/collection.yaml.result +185 -0
  34. data/spec/cli/data/merge_into_collection/collection_pwm.yaml.result +185 -0
  35. data/spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm +14 -0
  36. data/spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm +11 -0
  37. data/spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm +12 -0
  38. data/spec/cli/data/{KLF4 f2 spaced name.pcm → pcm2pwm/KLF4 f2 spaced name.pcm} +0 -0
  39. data/spec/cli/data/{KLF4_f2.pcm → pcm2pwm/KLF4_f2.pcm} +0 -0
  40. data/spec/cli/data/pcm2pwm/KLF4_f2.pwm.result +11 -0
  41. data/spec/cli/data/{SP1_f1.pcm → pcm2pwm/SP1_f1.pcm} +0 -0
  42. data/spec/cli/data/pcm2pwm/SP1_f1.pwm.result +12 -0
  43. data/spec/cli/data/split_motifs/GABPA_f1.mat.result +14 -0
  44. data/spec/cli/data/split_motifs/KLF4_f2.mat.result +11 -0
  45. data/spec/cli/data/split_motifs/SP1_f1.mat.result +12 -0
  46. data/spec/cli/data/split_motifs/collection.yaml +197 -0
  47. data/spec/cli/data/split_motifs/plain_collection.txt +38 -0
  48. data/spec/cli/merge_into_collection_spec.rb +100 -0
  49. data/spec/cli/pcm2pwm_spec.rb +3 -3
  50. data/spec/cli/split_motifs_spec.rb +74 -3
  51. data/spec/data_models/collection_spec.rb +2 -2
  52. data/spec/data_models/pcm_spec.rb +2 -2
  53. data/spec/data_models/pm_spec.rb +10 -27
  54. data/spec/data_models/ppm_spec.rb +2 -2
  55. data/spec/data_models/pwm_spec.rb +3 -3
  56. data/spec/fabricators/collection_fabricator.rb +8 -0
  57. data/spec/fabricators/pm_fabricator.rb +43 -0
  58. data/spec/parsers/parser_spec.rb +29 -37
  59. data/spec/parsers/string_fantom_parser_spec.rb +38 -35
  60. data/spec/parsers/string_parser_spec.rb +33 -66
  61. data/spec/parsers/trivial_parser_spec.rb +48 -6
  62. data/spec/parsers/yaml_parser_spec.rb +50 -0
  63. data/spec/spec_helper.rb +2 -6
  64. data/spec/support/advanced_scan_spec.rb +2 -2
  65. data/spec/support/array_product_spec.rb +2 -2
  66. data/spec/support/array_zip_spec.rb +2 -2
  67. data/spec/support/collect_hash_spec.rb +2 -2
  68. data/spec/support/delete_many_spec.rb +2 -2
  69. data/spec/support/inverf_spec.rb +2 -2
  70. data/spec/support/multiline_squish_spec.rb +2 -2
  71. data/spec/support/partial_sums_spec.rb +2 -2
  72. data/spec/support/same_by_spec.rb +2 -2
  73. metadata +86 -12
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: bioinform
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  version: !ruby/object:Gem::Version
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- version: 0.1.7
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+ version: 0.1.8
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  prerelease:
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  platform: ruby
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  authors:
@@ -9,7 +9,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-09-11 00:00:00.000000000 Z
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+ date: 2012-09-15 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: activesupport
@@ -27,6 +27,22 @@ dependencies:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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  version: 3.0.0
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+ - !ruby/object:Gem::Dependency
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+ name: docopt
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+ requirement: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: 0.5.0
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: 0.5.0
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  - !ruby/object:Gem::Dependency
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  name: rspec
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  requirement: !ruby/object:Gem::Requirement
@@ -43,10 +59,27 @@ dependencies:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '2.0'
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+ - !ruby/object:Gem::Dependency
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+ name: fabrication
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+ requirement: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: 2.2.3
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: 2.2.3
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  description: A bunch of useful classes for bioinformatics
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  email:
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  - prijutme4ty@gmail.com
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  executables:
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+ - merge_into_collection
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  - pcm2pwm
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  - split_motifs
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  extensions: []
@@ -58,11 +91,13 @@ files:
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  - README.md
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  - Rakefile
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  - TODO.txt
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+ - bin/merge_into_collection
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  - bin/pcm2pwm
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  - bin/split_motifs
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  - bioinform.gemspec
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  - lib/bioinform.rb
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  - lib/bioinform/cli.rb
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+ - lib/bioinform/cli/merge_into_collection.rb
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  - lib/bioinform/cli/pcm2pwm.rb
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  - lib/bioinform/cli/split_motifs.rb
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  - lib/bioinform/data_models.rb
@@ -73,9 +108,11 @@ files:
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  - lib/bioinform/data_models/pwm.rb
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  - lib/bioinform/parsers.rb
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  - lib/bioinform/parsers/parser.rb
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+ - lib/bioinform/parsers/splittable_parser.rb
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  - lib/bioinform/parsers/string_fantom_parser.rb
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  - lib/bioinform/parsers/string_parser.rb
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  - lib/bioinform/parsers/trivial_parser.rb
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+ - lib/bioinform/parsers/yaml_parser.rb
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  - lib/bioinform/support.rb
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  - lib/bioinform/support/advanced_scan.rb
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  - lib/bioinform/support/array_product.rb
@@ -85,15 +122,31 @@ files:
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  - lib/bioinform/support/delete_many.rb
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  - lib/bioinform/support/inverf.rb
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  - lib/bioinform/support/multiline_squish.rb
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+ - lib/bioinform/support/parameters.rb
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  - lib/bioinform/support/partial_sums.rb
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  - lib/bioinform/support/same_by.rb
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  - lib/bioinform/version.rb
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  - spec/cli/cli_spec.rb
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- - spec/cli/data/KLF4 f2 spaced name.pcm
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- - spec/cli/data/KLF4_f2.pcm
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- - spec/cli/data/KLF4_f2.pwm.result
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- - spec/cli/data/SP1_f1.pcm
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- - spec/cli/data/SP1_f1.pwm.result
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+ - spec/cli/data/merge_into_collection/GABPA_f1.pwm
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+ - spec/cli/data/merge_into_collection/KLF4_f2.pwm
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+ - spec/cli/data/merge_into_collection/SP1_f1.pwm
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+ - spec/cli/data/merge_into_collection/collection.txt.result
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+ - spec/cli/data/merge_into_collection/collection.yaml.result
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+ - spec/cli/data/merge_into_collection/collection_pwm.yaml.result
136
+ - spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm
137
+ - spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm
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+ - spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm
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+ - spec/cli/data/pcm2pwm/KLF4 f2 spaced name.pcm
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+ - spec/cli/data/pcm2pwm/KLF4_f2.pcm
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+ - spec/cli/data/pcm2pwm/KLF4_f2.pwm.result
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+ - spec/cli/data/pcm2pwm/SP1_f1.pcm
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+ - spec/cli/data/pcm2pwm/SP1_f1.pwm.result
144
+ - spec/cli/data/split_motifs/GABPA_f1.mat.result
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+ - spec/cli/data/split_motifs/KLF4_f2.mat.result
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+ - spec/cli/data/split_motifs/SP1_f1.mat.result
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+ - spec/cli/data/split_motifs/collection.yaml
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+ - spec/cli/data/split_motifs/plain_collection.txt
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+ - spec/cli/merge_into_collection_spec.rb
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  - spec/cli/pcm2pwm_spec.rb
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  - spec/cli/split_motifs_spec.rb
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  - spec/data_models/collection_spec.rb
@@ -101,10 +154,13 @@ files:
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  - spec/data_models/pm_spec.rb
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  - spec/data_models/ppm_spec.rb
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  - spec/data_models/pwm_spec.rb
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+ - spec/fabricators/collection_fabricator.rb
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+ - spec/fabricators/pm_fabricator.rb
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  - spec/parsers/parser_spec.rb
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  - spec/parsers/string_fantom_parser_spec.rb
106
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  - spec/parsers/string_parser_spec.rb
107
162
  - spec/parsers/trivial_parser_spec.rb
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+ - spec/parsers/yaml_parser_spec.rb
108
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  - spec/spec_helper.rb
109
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  - spec/support/advanced_scan_spec.rb
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  - spec/support/array_product_spec.rb
@@ -144,11 +200,26 @@ summary: Classes for work with different input formats of positional matrices an
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  symbols
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  test_files:
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  - spec/cli/cli_spec.rb
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- - spec/cli/data/KLF4 f2 spaced name.pcm
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- - spec/cli/data/KLF4_f2.pcm
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- - spec/cli/data/KLF4_f2.pwm.result
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- - spec/cli/data/SP1_f1.pcm
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- - spec/cli/data/SP1_f1.pwm.result
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+ - spec/cli/data/merge_into_collection/GABPA_f1.pwm
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+ - spec/cli/data/merge_into_collection/KLF4_f2.pwm
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+ - spec/cli/data/merge_into_collection/SP1_f1.pwm
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+ - spec/cli/data/merge_into_collection/collection.txt.result
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+ - spec/cli/data/merge_into_collection/collection.yaml.result
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+ - spec/cli/data/merge_into_collection/collection_pwm.yaml.result
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+ - spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm
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+ - spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm
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+ - spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm
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+ - spec/cli/data/pcm2pwm/KLF4 f2 spaced name.pcm
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+ - spec/cli/data/pcm2pwm/KLF4_f2.pcm
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+ - spec/cli/data/pcm2pwm/KLF4_f2.pwm.result
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+ - spec/cli/data/pcm2pwm/SP1_f1.pcm
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+ - spec/cli/data/pcm2pwm/SP1_f1.pwm.result
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+ - spec/cli/data/split_motifs/GABPA_f1.mat.result
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+ - spec/cli/data/split_motifs/KLF4_f2.mat.result
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+ - spec/cli/data/split_motifs/SP1_f1.mat.result
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+ - spec/cli/data/split_motifs/collection.yaml
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+ - spec/cli/data/split_motifs/plain_collection.txt
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+ - spec/cli/merge_into_collection_spec.rb
152
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  - spec/cli/pcm2pwm_spec.rb
153
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  - spec/cli/split_motifs_spec.rb
154
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  - spec/data_models/collection_spec.rb
@@ -156,10 +227,13 @@ test_files:
156
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  - spec/data_models/pm_spec.rb
157
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  - spec/data_models/ppm_spec.rb
158
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  - spec/data_models/pwm_spec.rb
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+ - spec/fabricators/collection_fabricator.rb
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+ - spec/fabricators/pm_fabricator.rb
159
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  - spec/parsers/parser_spec.rb
160
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  - spec/parsers/string_fantom_parser_spec.rb
161
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  - spec/parsers/string_parser_spec.rb
162
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  - spec/parsers/trivial_parser_spec.rb
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+ - spec/parsers/yaml_parser_spec.rb
163
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  - spec/spec_helper.rb
164
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  - spec/support/advanced_scan_spec.rb
165
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  - spec/support/array_product_spec.rb