bioinform 0.1.12 → 0.1.13

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Files changed (110) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +17 -17
  3. data/Gemfile +16 -16
  4. data/LICENSE +21 -21
  5. data/README.md +35 -35
  6. data/Rakefile +4 -4
  7. data/TODO.txt +37 -37
  8. data/bin/merge_into_collection +3 -3
  9. data/bin/pcm2pwm +3 -3
  10. data/bin/split_motifs +3 -3
  11. data/bioinform.gemspec +19 -19
  12. data/lib/bioinform/cli/convert_motif.rb +107 -107
  13. data/lib/bioinform/cli/merge_into_collection.rb +79 -79
  14. data/lib/bioinform/cli/pcm2pwm.rb +46 -46
  15. data/lib/bioinform/cli/split_motifs.rb +46 -46
  16. data/lib/bioinform/cli.rb +29 -29
  17. data/lib/bioinform/conversion_algorithms/pcm2ppm_converter.rb +18 -18
  18. data/lib/bioinform/conversion_algorithms/pcm2pwm_converter.rb +19 -19
  19. data/lib/bioinform/data_models/collection.rb +74 -74
  20. data/lib/bioinform/data_models/motif.rb +55 -55
  21. data/lib/bioinform/data_models/pcm.rb +23 -23
  22. data/lib/bioinform/data_models/pm.rb +169 -169
  23. data/lib/bioinform/data_models/ppm.rb +9 -9
  24. data/lib/bioinform/data_models/pwm.rb +55 -55
  25. data/lib/bioinform/data_models.rb +10 -10
  26. data/lib/bioinform/formatters/raw_formatter.rb +40 -40
  27. data/lib/bioinform/formatters/transfac_formatter.rb +38 -38
  28. data/lib/bioinform/formatters.rb +1 -1
  29. data/lib/bioinform/parsers/jaspar_parser.rb +34 -34
  30. data/lib/bioinform/parsers/parser.rb +87 -87
  31. data/lib/bioinform/parsers/splittable_parser.rb +56 -56
  32. data/lib/bioinform/parsers/string_fantom_parser.rb +34 -34
  33. data/lib/bioinform/parsers/string_parser.rb +71 -71
  34. data/lib/bioinform/parsers/trivial_parser.rb +33 -33
  35. data/lib/bioinform/parsers/yaml_parser.rb +34 -34
  36. data/lib/bioinform/parsers.rb +6 -6
  37. data/lib/bioinform/support/array_product.rb +5 -5
  38. data/lib/bioinform/support/array_zip.rb +5 -5
  39. data/lib/bioinform/support/collect_hash.rb +6 -6
  40. data/lib/bioinform/support/deep_dup.rb +4 -4
  41. data/lib/bioinform/support/delete_many.rb +13 -13
  42. data/lib/bioinform/support/inverf.rb +12 -12
  43. data/lib/bioinform/support/multiline_squish.rb +5 -5
  44. data/lib/bioinform/support/parameters.rb +27 -27
  45. data/lib/bioinform/support/partial_sums.rb +15 -15
  46. data/lib/bioinform/support/same_by.rb +12 -12
  47. data/lib/bioinform/support/strip_doc.rb +8 -8
  48. data/lib/bioinform/support/third_part/active_support/hash_with_indifferent_access.rb +3 -0
  49. data/lib/bioinform/support.rb +17 -17
  50. data/lib/bioinform/version.rb +3 -3
  51. data/lib/bioinform.rb +10 -10
  52. data/spec/cli/cli_spec.rb +13 -13
  53. data/spec/cli/convert_motif_spec.rb +106 -106
  54. data/spec/cli/data/merge_into_collection/GABPA_f1.pwm +14 -14
  55. data/spec/cli/data/merge_into_collection/KLF4_f2.pwm +11 -11
  56. data/spec/cli/data/merge_into_collection/SP1_f1.pwm +12 -12
  57. data/spec/cli/data/merge_into_collection/collection.txt.result +40 -40
  58. data/spec/cli/data/merge_into_collection/collection.yaml.result +188 -188
  59. data/spec/cli/data/merge_into_collection/collection_pwm.yaml.result +188 -188
  60. data/spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm +14 -14
  61. data/spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm +11 -11
  62. data/spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm +12 -12
  63. data/spec/cli/data/pcm2pwm/KLF4 f2 spaced name.pcm +11 -11
  64. data/spec/cli/data/pcm2pwm/KLF4_f2.pcm +11 -11
  65. data/spec/cli/data/pcm2pwm/KLF4_f2.pwm.result +11 -11
  66. data/spec/cli/data/pcm2pwm/SP1_f1.pcm +12 -12
  67. data/spec/cli/data/pcm2pwm/SP1_f1.pwm.result +12 -12
  68. data/spec/cli/data/split_motifs/GABPA_f1.mat.result +14 -14
  69. data/spec/cli/data/split_motifs/KLF4_f2.mat.result +11 -11
  70. data/spec/cli/data/split_motifs/SP1_f1.mat.result +12 -12
  71. data/spec/cli/data/split_motifs/collection.yaml +188 -188
  72. data/spec/cli/data/split_motifs/plain_collection.txt +38 -38
  73. data/spec/cli/merge_into_collection_spec.rb +99 -99
  74. data/spec/cli/pcm2pwm_spec.rb +79 -79
  75. data/spec/cli/shared_examples/convert_motif/motif_list_empty.rb +17 -17
  76. data/spec/cli/shared_examples/convert_motif/several_motifs_specified.rb +14 -14
  77. data/spec/cli/shared_examples/convert_motif/single_motif_specified.rb +49 -49
  78. data/spec/cli/shared_examples/convert_motif/yield_help_string.rb +4 -4
  79. data/spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb +3 -3
  80. data/spec/cli/split_motifs_spec.rb +76 -76
  81. data/spec/data_models/collection_spec.rb +97 -97
  82. data/spec/data_models/motif_spec.rb +223 -223
  83. data/spec/data_models/pcm_spec.rb +55 -55
  84. data/spec/data_models/pm_spec.rb +359 -359
  85. data/spec/data_models/ppm_spec.rb +7 -7
  86. data/spec/data_models/pwm_spec.rb +82 -82
  87. data/spec/fabricators/collection_fabricator.rb +7 -7
  88. data/spec/fabricators/motif_fabricator.rb +32 -32
  89. data/spec/fabricators/motif_formats_fabricator.rb +124 -124
  90. data/spec/fabricators/pcm_fabricator.rb +24 -24
  91. data/spec/fabricators/pm_fabricator.rb +51 -51
  92. data/spec/fabricators/ppm_fabricator.rb +13 -13
  93. data/spec/fabricators/pwm_fabricator.rb +16 -16
  94. data/spec/parsers/parser_spec.rb +152 -152
  95. data/spec/parsers/string_fantom_parser_spec.rb +69 -69
  96. data/spec/parsers/string_parser_spec.rb +76 -76
  97. data/spec/parsers/trivial_parser_spec.rb +63 -63
  98. data/spec/parsers/yaml_parser_spec.rb +50 -50
  99. data/spec/spec_helper.rb +10 -10
  100. data/spec/spec_helper_source.rb +59 -59
  101. data/spec/support/advanced_scan_spec.rb +31 -31
  102. data/spec/support/array_product_spec.rb +14 -14
  103. data/spec/support/array_zip_spec.rb +14 -14
  104. data/spec/support/collect_hash_spec.rb +14 -14
  105. data/spec/support/delete_many_spec.rb +43 -43
  106. data/spec/support/inverf_spec.rb +18 -18
  107. data/spec/support/multiline_squish_spec.rb +24 -24
  108. data/spec/support/partial_sums_spec.rb +30 -30
  109. data/spec/support/same_by_spec.rb +35 -35
  110. metadata +3 -3
@@ -1,12 +1,12 @@
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- SP1_f1
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- -0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
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- -1.0631255752097797 -2.111925969423868 1.0960627561110403 -0.6138563775211977
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+ SP1_f1
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+ -0.5166047365590571 0.7641033353626657 -0.2862677570028208 -0.68254820978656
@@ -1,188 +1,188 @@
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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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+ table:
130
+ :original_data_model: :pwm
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+ :pwm: !ruby/object:Bioinform::PWM
132
+ parameters: !ruby/object:OpenStruct
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+ table:
134
+ :name: SP1_f1
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+ :background:
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+ - 1
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+ - 1
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+ - 1
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+ - 1
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+ modifiable: true
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+ modifiable: true
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+ parameters: !ruby/object:OpenStruct
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+ table: {}
@@ -1,38 +1,38 @@
1
- > SP1_f1
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13
-
14
- KLF4_f2
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24
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25
- GABPA_f1
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13
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14
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