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
data/spec/cli/convert_motif_spec.rb CHANGED
@@ -1,107 +1,107 @@
1
- require 'shellwords'
2
- require_relative '../spec_helper'
3
- require_relative '../../lib/bioinform/cli/convert_motif'
4
- require_relative 'shared_examples/convert_motif/single_motif_specified'
5
- require_relative 'shared_examples/convert_motif/several_motifs_specified'
6
- require_relative 'shared_examples/convert_motif/motif_list_empty'
7
- require_relative 'shared_examples/convert_motif/yield_motif_conversion_error'
8
-
9
- def make_option_list(options = {})
10
- result = []
11
- result << '--from' << options[:model_from] if options[:model_from]
12
- result << '--to' << options[:model_to] if options[:model_to]
13
- result << '--parser' << options[:parser] if options[:parser]
14
- result << '--formatter' << options[:formatter] if options[:formatter]
15
- result << (options[:silent] ? '--silent' : '--no-silent') if options.has_key?(:silent)
16
- result << (options[:force] ? '--force' : '--no-force') if options.has_key?(:force)
17
- result << '--save' << options[:filename_format] if options[:filename_format]
18
- result << '--algorithm' << options[:algorithm] if options[:algorithm]
19
- result
20
- end
21
-
22
-
23
- shared_context 'most common options' do
24
- Given(:parser) { 'plain' }
25
- Given(:formatter) { 'plain' }
26
- Given(:silent) { true }
27
- Given(:force) { false }
28
- Given(:filename_format) { nil }
29
- Given(:algorithm) { nil }
30
- end
31
-
32
- shared_context 'completely specified option list' do
33
- Given(:options) {
34
- make_option_list( model_from: model_from, model_to: model_to,
35
- parser: parser, formatter: formatter,
36
- silent: silent, force: force,
37
- filename_format: filename_format,
38
- algorithm: algorithm ).shelljoin
39
- }
40
- end
41
-
42
- shared_context 'input filenames are motif_name.motif_type' do
43
- Given(:input_filenames) { motif_list.map{|motif| motif_filename(motif, model_from) }.shelljoin }
44
- end
45
-
46
- ##################################
47
-
48
- describe Bioinform::CLI::ConvertMotif do
49
- include FakeFS::SpecHelpers
50
- Given(:resulting_stdout) { resulting_io[:stdout] }
51
- Given(:resulting_stderr) { resulting_io[:stderr] }
52
-
53
- Given(:command) { options.shellsplit + arguments.shellsplit }
54
-
55
- Given(:sp1_f1){ Fabricate(:SP1_f1_plain_text) }
56
- Given(:klf4_f2){ Fabricate(:KLF4_f2_plain_text) }
57
-
58
- ########################################################
59
-
60
- context 'when program not piped' do
61
- Given(:arguments) { input_filenames }
62
- Given(:resulting_io) {
63
- capture_io{
64
- Bioinform::CLI::ConvertMotif.main(command)
65
- }
66
- }
67
- include_context 'input filenames are motif_name.motif_type'
68
-
69
- context 'with most options specified' do
70
- include_context 'completely specified option list'
71
- include_context 'most common options'
72
-
73
- include_examples 'single motif specified'
74
- include_examples 'several motifs specified'
75
- end
76
-
77
- include_examples 'motif list is empty'
78
- end
79
-
80
- ########################################################
81
-
82
- context 'when program is piped' do
83
- # include_context 'completely specified option list'
84
- # include_context 'most common options'
85
- include_context 'input filenames are motif_name.motif_type'
86
-
87
- Given(:tty){ false }
88
- Given(:stdin_data) { input_filenames }
89
- Given(:arguments) { '' }
90
- Given(:resulting_io) {
91
- capture_io{
92
- provide_stdin(stdin_data, tty) {
93
- Bioinform::CLI::ConvertMotif.main(command)
94
- }
95
- }
96
- }
97
-
98
- include_examples 'motif list is empty'
99
- context 'with most options specified' do
100
- include_context 'completely specified option list'
101
- include_context 'most common options'
102
-
103
- include_examples 'single motif specified'
104
- include_examples 'several motifs specified'
105
- end
106
- end
1
+ require 'shellwords'
2
+ require_relative '../spec_helper'
3
+ require_relative '../../lib/bioinform/cli/convert_motif'
4
+ require_relative 'shared_examples/convert_motif/single_motif_specified'
5
+ require_relative 'shared_examples/convert_motif/several_motifs_specified'
6
+ require_relative 'shared_examples/convert_motif/motif_list_empty'
7
+ require_relative 'shared_examples/convert_motif/yield_motif_conversion_error'
8
+
9
+ def make_option_list(options = {})
10
+ result = []
11
+ result << '--from' << options[:model_from] if options[:model_from]
12
+ result << '--to' << options[:model_to] if options[:model_to]
13
+ result << '--parser' << options[:parser] if options[:parser]
14
+ result << '--formatter' << options[:formatter] if options[:formatter]
15
+ result << (options[:silent] ? '--silent' : '--no-silent') if options.has_key?(:silent)
16
+ result << (options[:force] ? '--force' : '--no-force') if options.has_key?(:force)
17
+ result << '--save' << options[:filename_format] if options[:filename_format]
18
+ result << '--algorithm' << options[:algorithm] if options[:algorithm]
19
+ result
20
+ end
21
+
22
+
23
+ shared_context 'most common options' do
24
+ Given(:parser) { 'plain' }
25
+ Given(:formatter) { 'plain' }
26
+ Given(:silent) { true }
27
+ Given(:force) { false }
28
+ Given(:filename_format) { nil }
29
+ Given(:algorithm) { nil }
30
+ end
31
+
32
+ shared_context 'completely specified option list' do
33
+ Given(:options) {
34
+ make_option_list( model_from: model_from, model_to: model_to,
35
+ parser: parser, formatter: formatter,
36
+ silent: silent, force: force,
37
+ filename_format: filename_format,
38
+ algorithm: algorithm ).shelljoin
39
+ }
40
+ end
41
+
42
+ shared_context 'input filenames are motif_name.motif_type' do
43
+ Given(:input_filenames) { motif_list.map{|motif| motif_filename(motif, model_from) }.shelljoin }
44
+ end
45
+
46
+ ##################################
47
+
48
+ describe Bioinform::CLI::ConvertMotif do
49
+ include FakeFS::SpecHelpers
50
+ Given(:resulting_stdout) { resulting_io[:stdout] }
51
+ Given(:resulting_stderr) { resulting_io[:stderr] }
52
+
53
+ Given(:command) { options.shellsplit + arguments.shellsplit }
54
+
55
+ Given(:sp1_f1){ Fabricate(:SP1_f1_plain_text) }
56
+ Given(:klf4_f2){ Fabricate(:KLF4_f2_plain_text) }
57
+
58
+ ########################################################
59
+
60
+ context 'when program not piped' do
61
+ Given(:arguments) { input_filenames }
62
+ Given(:resulting_io) {
63
+ capture_io{
64
+ Bioinform::CLI::ConvertMotif.main(command)
65
+ }
66
+ }
67
+ include_context 'input filenames are motif_name.motif_type'
68
+
69
+ context 'with most options specified' do
70
+ include_context 'completely specified option list'
71
+ include_context 'most common options'
72
+
73
+ include_examples 'single motif specified'
74
+ include_examples 'several motifs specified'
75
+ end
76
+
77
+ include_examples 'motif list is empty'
78
+ end
79
+
80
+ ########################################################
81
+
82
+ context 'when program is piped' do
83
+ # include_context 'completely specified option list'
84
+ # include_context 'most common options'
85
+ include_context 'input filenames are motif_name.motif_type'
86
+
87
+ Given(:tty){ false }
88
+ Given(:stdin_data) { input_filenames }
89
+ Given(:arguments) { '' }
90
+ Given(:resulting_io) {
91
+ capture_io{
92
+ provide_stdin(stdin_data, tty) {
93
+ Bioinform::CLI::ConvertMotif.main(command)
94
+ }
95
+ }
96
+ }
97
+
98
+ include_examples 'motif list is empty'
99
+ context 'with most options specified' do
100
+ include_context 'completely specified option list'
101
+ include_context 'most common options'
102
+
103
+ include_examples 'single motif specified'
104
+ include_examples 'several motifs specified'
105
+ end
106
+ end
107
107
  end
data/spec/cli/data/merge_into_collection/GABPA_f1.pwm CHANGED
@@ -1,14 +1,14 @@
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
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 CHANGED
@@ -1,11 +1,11 @@
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
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 CHANGED
@@ -1,12 +1,12 @@
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
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1
+ SP1_f1
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data/spec/cli/data/merge_into_collection/collection.txt.result CHANGED
@@ -1,40 +1,40 @@
1
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- KLF4_f2
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-
1
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+
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+ KLF4_f2
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