bioinform 0.1.17 → 0.2.0

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Files changed (145) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +3 -3
  3. data/LICENSE +0 -1
  4. data/README.md +1 -1
  5. data/TODO.txt +23 -30
  6. data/bin/convert_motif +4 -0
  7. data/bin/pcm2pwm +1 -1
  8. data/bin/split_motifs +1 -1
  9. data/bioinform.gemspec +0 -2
  10. data/lib/bioinform.rb +54 -16
  11. data/lib/bioinform/alphabet.rb +85 -0
  12. data/lib/bioinform/background.rb +90 -0
  13. data/lib/bioinform/cli.rb +1 -2
  14. data/lib/bioinform/cli/convert_motif.rb +52 -17
  15. data/lib/bioinform/cli/pcm2pwm.rb +32 -26
  16. data/lib/bioinform/cli/split_motifs.rb +31 -30
  17. data/lib/bioinform/conversion_algorithms.rb +6 -0
  18. data/lib/bioinform/conversion_algorithms/pcm2ppm_converter.rb +13 -11
  19. data/lib/bioinform/conversion_algorithms/pcm2pwm_converter.rb +39 -11
  20. data/lib/bioinform/conversion_algorithms/pcm2pwm_mara_converter.rb +26 -0
  21. data/lib/bioinform/conversion_algorithms/ppm2pcm_converter.rb +30 -0
  22. data/lib/bioinform/conversion_algorithms/pwm2iupac_pwm_converter.rb +23 -0
  23. data/lib/bioinform/conversion_algorithms/pwm2pcm_converter.rb +85 -0
  24. data/lib/bioinform/data_models.rb +1 -7
  25. data/lib/bioinform/data_models/named_model.rb +38 -0
  26. data/lib/bioinform/data_models/pcm.rb +18 -28
  27. data/lib/bioinform/data_models/pm.rb +73 -170
  28. data/lib/bioinform/data_models/ppm.rb +11 -24
  29. data/lib/bioinform/data_models/pwm.rb +30 -56
  30. data/lib/bioinform/errors.rb +17 -0
  31. data/lib/bioinform/formatters.rb +4 -2
  32. data/lib/bioinform/formatters/consensus_formatter.rb +35 -0
  33. data/lib/bioinform/formatters/motif_formatter.rb +69 -0
  34. data/lib/bioinform/formatters/pretty_matrix_formatter.rb +36 -0
  35. data/lib/bioinform/formatters/transfac_formatter.rb +29 -37
  36. data/lib/bioinform/parsers.rb +1 -8
  37. data/lib/bioinform/parsers/matrix_parser.rb +44 -36
  38. data/lib/bioinform/parsers/motif_splitter.rb +45 -0
  39. data/lib/bioinform/support.rb +46 -14
  40. data/lib/bioinform/support/strip_doc.rb +1 -1
  41. data/lib/bioinform/version.rb +1 -1
  42. data/spec/alphabet_spec.rb +79 -0
  43. data/spec/background_spec.rb +57 -0
  44. data/spec/cli/cli_spec.rb +6 -6
  45. data/spec/cli/convert_motif_spec.rb +88 -88
  46. data/spec/cli/data/pcm2pwm/KLF4_f2.pwm.result +9 -9
  47. data/spec/cli/data/pcm2pwm/SP1_f1.pwm.result +11 -11
  48. data/spec/cli/pcm2pwm_spec.rb +22 -23
  49. data/spec/cli/shared_examples/convert_motif/motif_list_empty.rb +1 -1
  50. data/spec/cli/shared_examples/convert_motif/several_motifs_specified.rb +1 -1
  51. data/spec/cli/shared_examples/convert_motif/single_motif_specified.rb +5 -5
  52. data/spec/cli/shared_examples/convert_motif/yield_help_string.rb +2 -2
  53. data/spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb +3 -3
  54. data/spec/cli/split_motifs_spec.rb +6 -21
  55. data/spec/converters/pcm2ppm_converter_spec.rb +32 -0
  56. data/spec/converters/pcm2pwm_converter_spec.rb +71 -0
  57. data/spec/converters/ppm2pcm_converter_spec.rb +32 -0
  58. data/spec/converters/pwm2iupac_pwm_converter_spec.rb +65 -0
  59. data/spec/converters/pwm2pcm_converter_spec.rb +57 -0
  60. data/spec/data_models/named_model_spec.rb +41 -0
  61. data/spec/data_models/pcm_spec.rb +114 -45
  62. data/spec/data_models/pm_spec.rb +132 -333
  63. data/spec/data_models/ppm_spec.rb +47 -44
  64. data/spec/data_models/pwm_spec.rb +85 -77
  65. data/spec/fabricators/motif_formats_fabricator.rb +116 -116
  66. data/spec/formatters/consensus_formatter_spec.rb +26 -0
  67. data/spec/formatters/raw_formatter_spec.rb +169 -0
  68. data/spec/parsers/matrix_parser_spec.rb +216 -0
  69. data/spec/parsers/motif_splitter_spec.rb +87 -0
  70. data/spec/spec_helper.rb +2 -2
  71. data/spec/spec_helper_source.rb +25 -5
  72. data/spec/support_spec.rb +31 -0
  73. metadata +43 -124
  74. data/bin/merge_into_collection +0 -4
  75. data/lib/bioinform/cli/merge_into_collection.rb +0 -80
  76. data/lib/bioinform/conversion_algorithms/ppm2pwm_converter.rb +0 -0
  77. data/lib/bioinform/data_models/collection.rb +0 -75
  78. data/lib/bioinform/data_models/motif.rb +0 -56
  79. data/lib/bioinform/formatters/raw_formatter.rb +0 -41
  80. data/lib/bioinform/parsers/jaspar_parser.rb +0 -35
  81. data/lib/bioinform/parsers/parser.rb +0 -92
  82. data/lib/bioinform/parsers/splittable_parser.rb +0 -57
  83. data/lib/bioinform/parsers/string_fantom_parser.rb +0 -35
  84. data/lib/bioinform/parsers/string_parser.rb +0 -72
  85. data/lib/bioinform/parsers/trivial_parser.rb +0 -34
  86. data/lib/bioinform/parsers/yaml_parser.rb +0 -35
  87. data/lib/bioinform/support/advanced_scan.rb +0 -8
  88. data/lib/bioinform/support/array_product.rb +0 -6
  89. data/lib/bioinform/support/array_zip.rb +0 -6
  90. data/lib/bioinform/support/collect_hash.rb +0 -7
  91. data/lib/bioinform/support/deep_dup.rb +0 -5
  92. data/lib/bioinform/support/delete_many.rb +0 -14
  93. data/lib/bioinform/support/inverf.rb +0 -13
  94. data/lib/bioinform/support/multiline_squish.rb +0 -6
  95. data/lib/bioinform/support/parameters.rb +0 -28
  96. data/lib/bioinform/support/partial_sums.rb +0 -16
  97. data/lib/bioinform/support/same_by.rb +0 -12
  98. data/lib/bioinform/support/third_part/active_support/core_ext/array/extract_options.rb +0 -29
  99. data/lib/bioinform/support/third_part/active_support/core_ext/hash/indifferent_access.rb +0 -23
  100. data/lib/bioinform/support/third_part/active_support/core_ext/hash/keys.rb +0 -54
  101. data/lib/bioinform/support/third_part/active_support/core_ext/module/attribute_accessors.rb +0 -64
  102. data/lib/bioinform/support/third_part/active_support/core_ext/object/try.rb +0 -57
  103. data/lib/bioinform/support/third_part/active_support/core_ext/string/access.rb +0 -99
  104. data/lib/bioinform/support/third_part/active_support/core_ext/string/behavior.rb +0 -6
  105. data/lib/bioinform/support/third_part/active_support/core_ext/string/filters.rb +0 -49
  106. data/lib/bioinform/support/third_part/active_support/core_ext/string/multibyte.rb +0 -72
  107. data/lib/bioinform/support/third_part/active_support/hash_with_indifferent_access.rb +0 -181
  108. data/lib/bioinform/support/third_part/active_support/multibyte.rb +0 -44
  109. data/lib/bioinform/support/third_part/active_support/multibyte/chars.rb +0 -476
  110. data/lib/bioinform/support/third_part/active_support/multibyte/exceptions.rb +0 -8
  111. data/lib/bioinform/support/third_part/active_support/multibyte/unicode.rb +0 -393
  112. data/lib/bioinform/support/third_part/active_support/multibyte/utils.rb +0 -60
  113. data/spec/cli/data/merge_into_collection/GABPA_f1.pwm +0 -14
  114. data/spec/cli/data/merge_into_collection/KLF4_f2.pwm +0 -11
  115. data/spec/cli/data/merge_into_collection/SP1_f1.pwm +0 -12
  116. data/spec/cli/data/merge_into_collection/collection.txt.result +0 -40
  117. data/spec/cli/data/merge_into_collection/collection.yaml.result +0 -188
  118. data/spec/cli/data/merge_into_collection/collection_pwm.yaml.result +0 -188
  119. data/spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm +0 -14
  120. data/spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm +0 -11
  121. data/spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm +0 -12
  122. data/spec/cli/data/split_motifs/collection.yaml +0 -188
  123. data/spec/cli/merge_into_collection_spec.rb +0 -100
  124. data/spec/data_models/collection_spec.rb +0 -98
  125. data/spec/data_models/motif_spec.rb +0 -224
  126. data/spec/fabricators/collection_fabricator.rb +0 -8
  127. data/spec/fabricators/motif_fabricator.rb +0 -33
  128. data/spec/fabricators/pcm_fabricator.rb +0 -25
  129. data/spec/fabricators/pm_fabricator.rb +0 -52
  130. data/spec/fabricators/ppm_fabricator.rb +0 -14
  131. data/spec/fabricators/pwm_fabricator.rb +0 -16
  132. data/spec/parsers/parser_spec.rb +0 -152
  133. data/spec/parsers/string_fantom_parser_spec.rb +0 -70
  134. data/spec/parsers/string_parser_spec.rb +0 -77
  135. data/spec/parsers/trivial_parser_spec.rb +0 -64
  136. data/spec/parsers/yaml_parser_spec.rb +0 -50
  137. data/spec/support/advanced_scan_spec.rb +0 -32
  138. data/spec/support/array_product_spec.rb +0 -15
  139. data/spec/support/array_zip_spec.rb +0 -15
  140. data/spec/support/collect_hash_spec.rb +0 -15
  141. data/spec/support/delete_many_spec.rb +0 -44
  142. data/spec/support/inverf_spec.rb +0 -19
  143. data/spec/support/multiline_squish_spec.rb +0 -25
  144. data/spec/support/partial_sums_spec.rb +0 -30
  145. data/spec/support/same_by_spec.rb +0 -36
data/spec/cli/data/merge_into_collection/GABPA_f1.pwm DELETED
@@ -1,14 +0,0 @@
1
- GABPA_f1
2
- -0.1106670158341858 0.013801606113892391 0.6054596108973699 -1.3518085041421573
3
- 0.37030668921643345 0.15761121480429963 0.009069314183831202 -0.9888619717703562
4
- 0.47526546359546684 -0.3011678534572083 0.4031522994412777 -1.8638752827041059
5
- -1.5544255540164373 1.1082369687811506 -0.2814091552834454 -5.30708531823271
6
- -0.6362037835776368 1.235338189985594 -3.5801322928552253 -5.717323067092849
7
- -5.852906870733575 -5.852906870733575 1.3841383838057746 -5.852906870733575
8
- -5.852906870733575 -5.852906870733575 1.3841383838057746 -5.852906870733575
9
- 1.3835219739184708 -5.2341956006430985 -5.852906870733575 -5.852906870733575
10
- 1.3756340514956562 -5.394962755562375 -5.394962755562375 -3.401117964959733
11
- -1.2176198315414444 -3.109079898175411 1.2964067931472216 -5.717323067092849
12
- -1.3716559438167257 -0.2761401935045069 -1.8504445165866068 1.0404320473626856
13
- -0.5440863133031895 -0.48103682561971345 0.907381908447086 -1.1280642594012078
14
- 0.10557340209290218 -0.01814819455289191 0.4381106695354074 -1.0304105539540915
data/spec/cli/data/merge_into_collection/KLF4_f2.pwm DELETED
@@ -1,11 +0,0 @@
1
- KLF4_f2
2
- 0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
3
- -1.227018967707036 -4.814127713368663 1.3059890687390967 -4.908681463544344
4
- -2.443469374521196 -4.648238485031404 1.3588686548279805 -4.441801801188402
5
- -2.7177827948276123 -3.8073538975356565 1.356272809724262 -3.504104725510225
6
- -0.5563232977367343 0.5340697765121405 -3.61417723090579 0.5270259776377405
7
- -1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
8
- -2.045671123823928 -2.384975142213679 0.7198551207724355 0.5449254135616948
9
- -1.373157530374372 -3.0063112097748217 1.285188335493552 -2.5026044231773543
10
- -2.1030513122772208 -1.8941348100402244 1.249265758393991 -1.4284210948906104
11
- -1.3277128628152939 0.8982415633049462 -0.8080773665408135 -0.18161647647456935
data/spec/cli/data/merge_into_collection/SP1_f1.pwm DELETED
@@ -1,12 +0,0 @@
1
- SP1_f1
2
- -0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
3
- -1.0631255752097797 -2.111925969423868 1.0960627561110403 -0.6138563775211977
4
- -0.3872276234760535 -2.9739851913218045 1.1807800242010378 -4.338927525031566
5
- -4.563896055436894 -2.9161633002532277 1.3684371349982638 -5.077972423609655
6
- -2.2369752892820083 -3.7196436313301846 1.3510439136452734 -4.889930670508233
7
- -0.07473964149330865 0.944919654762011 -2.6246857648086044 -0.8510983487822436
8
- -1.9643526491643322 -2.978402770880115 1.3113096718240573 -2.324334259499025
9
- -4.0155484139655835 -3.1384268078096667 1.3387488589788057 -2.084673903537648
10
- -0.44509385828355363 -2.2510053061629702 1.1265431574368685 -1.7780413702431372
11
- -1.1896356092245048 -1.2251832285630027 1.1636760063747527 -1.6080243648157353
12
- -0.5166047365590571 0.7641033353626657 -0.2862677570028208 -0.68254820978656
data/spec/cli/data/merge_into_collection/collection.txt.result DELETED
@@ -1,40 +0,0 @@
1
- GABPA_f1
2
- -0.1106670158341858 0.013801606113892391 0.6054596108973699 -1.3518085041421573
3
- 0.37030668921643345 0.15761121480429963 0.009069314183831202 -0.9888619717703562
4
- 0.47526546359546684 -0.3011678534572083 0.4031522994412777 -1.8638752827041059
5
- -1.5544255540164373 1.1082369687811506 -0.2814091552834454 -5.30708531823271
6
- -0.6362037835776368 1.235338189985594 -3.5801322928552253 -5.717323067092849
7
- -5.852906870733575 -5.852906870733575 1.3841383838057746 -5.852906870733575
8
- -5.852906870733575 -5.852906870733575 1.3841383838057746 -5.852906870733575
9
- 1.3835219739184708 -5.2341956006430985 -5.852906870733575 -5.852906870733575
10
- 1.3756340514956562 -5.394962755562375 -5.394962755562375 -3.401117964959733
11
- -1.2176198315414444 -3.109079898175411 1.2964067931472216 -5.717323067092849
12
- -1.3716559438167257 -0.2761401935045069 -1.8504445165866068 1.0404320473626856
13
- -0.5440863133031895 -0.48103682561971345 0.907381908447086 -1.1280642594012078
14
- 0.10557340209290218 -0.01814819455289191 0.4381106695354074 -1.0304105539540915
15
-
16
- KLF4_f2
17
- 0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633
18
- -1.227018967707036 -4.814127713368663 1.3059890687390967 -4.908681463544344
19
- -2.443469374521196 -4.648238485031404 1.3588686548279805 -4.441801801188402
20
- -2.7177827948276123 -3.8073538975356565 1.356272809724262 -3.504104725510225
21
- -0.5563232977367343 0.5340697765121405 -3.61417723090579 0.5270259776377405
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- -1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517
23
- -2.045671123823928 -2.384975142213679 0.7198551207724355 0.5449254135616948
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- -1.373157530374372 -3.0063112097748217 1.285188335493552 -2.5026044231773543
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- -2.1030513122772208 -1.8941348100402244 1.249265758393991 -1.4284210948906104
26
- -1.3277128628152939 0.8982415633049462 -0.8080773665408135 -0.18161647647456935
27
-
28
- SP1_f1
29
- -0.24435707885585292 -0.674823404693731 0.8657012535789866 -1.1060188862599287
30
- -1.0631255752097797 -2.111925969423868 1.0960627561110403 -0.6138563775211977
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- -0.3872276234760535 -2.9739851913218045 1.1807800242010378 -4.338927525031566
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- -4.563896055436894 -2.9161633002532277 1.3684371349982638 -5.077972423609655
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- -2.2369752892820083 -3.7196436313301846 1.3510439136452734 -4.889930670508233
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- -0.07473964149330865 0.944919654762011 -2.6246857648086044 -0.8510983487822436
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- -4.0155484139655835 -3.1384268078096667 1.3387488589788057 -2.084673903537648
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- -0.44509385828355363 -2.2510053061629702 1.1265431574368685 -1.7780413702431372
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- -1.1896356092245048 -1.2251832285630027 1.1636760063747527 -1.6080243648157353
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- -0.5166047365590571 0.7641033353626657 -0.2862677570028208 -0.68254820978656
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-
data/spec/cli/data/merge_into_collection/collection.yaml.result DELETED
@@ -1,188 +0,0 @@
1
- --- !ruby/object:Bioinform::Collection
2
- container:
3
- - !ruby/object:Bioinform::Motif
4
- parameters: !ruby/object:OpenStruct
5
- table:
6
- :original_data_model: :pm
7
- :pm: !ruby/object:Bioinform::PM
8
- parameters: !ruby/object:OpenStruct
9
- table:
10
- :name: GABPA_f1
11
- :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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- matrix:
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- - - -0.1106670158341858
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- - 0.6054596108973699
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- - -1.3518085041421573
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- - - 0.37030668921643345
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- - -0.9888619717703562
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- - - 0.47526546359546684
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- - -1.8638752827041059
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- - - -1.5544255540164373
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- - -0.2814091552834454
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- - -5.30708531823271
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- - - -0.6362037835776368
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- - - -5.852906870733575
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- - -5.852906870733575
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- - - -5.852906870733575
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- - -5.852906870733575
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- - 1.3841383838057746
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- - -5.852906870733575
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- - - 1.3835219739184708
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- - -5.2341956006430985
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- - -5.852906870733575
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- - -5.852906870733575
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- - - 1.3756340514956562
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- - -5.394962755562375
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- - -3.401117964959733
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- - - -1.2176198315414444
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- - -3.109079898175411
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- - 1.2964067931472216
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- - -5.717323067092849
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- - - -1.3716559438167257
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- - -0.2761401935045069
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- - 1.0404320473626856
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- - - -0.5440863133031895
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- - -0.48103682561971345
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- - 0.907381908447086
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- - -1.1280642594012078
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- - - 0.10557340209290218
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- - -0.01814819455289191
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- - 0.4381106695354074
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- - -1.0304105539540915
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- modifiable: true
71
- - !ruby/object:Bioinform::Motif
72
- parameters: !ruby/object:OpenStruct
73
- table:
74
- :original_data_model: :pm
75
- :pm: !ruby/object:Bioinform::PM
76
- parameters: !ruby/object:OpenStruct
77
- table:
78
- :name: KLF4_f2
79
- :background:
80
- - 1
81
- - 1
82
- - 1
83
- - 1
84
- modifiable: true
85
- matrix:
86
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