bioinform 0.1.8 → 0.1.9

Sign up to get free protection for your applications and to get access to all the features.
Files changed (60) hide show
  1. data/.gitignore +1 -0
  2. data/Gemfile +12 -0
  3. data/Guardfile +9 -0
  4. data/README.md +7 -1
  5. data/TODO.txt +8 -0
  6. data/bioinform.gemspec +7 -5
  7. data/lib/bioinform.rb +1 -0
  8. data/lib/bioinform/cli.rb +12 -3
  9. data/lib/bioinform/cli/convert_motif.rb +108 -0
  10. data/lib/bioinform/cli/merge_into_collection.rb +6 -2
  11. data/lib/bioinform/cli/pcm2pwm.rb +1 -1
  12. data/lib/bioinform/cli/split_motifs.rb +1 -1
  13. data/lib/bioinform/conversion_algorithms/pcm2ppm_converter.rb +19 -0
  14. data/lib/bioinform/conversion_algorithms/pcm2pwm_converter.rb +20 -0
  15. data/lib/bioinform/conversion_algorithms/pcm2pwm_mara_converter.rb +0 -0
  16. data/lib/bioinform/conversion_algorithms/ppm2pcm_converter.rb +0 -0
  17. data/lib/bioinform/conversion_algorithms/ppm2pwm_converter.rb +0 -0
  18. data/lib/bioinform/data_models/collection.rb +21 -35
  19. data/lib/bioinform/data_models/motif.rb +56 -0
  20. data/lib/bioinform/data_models/pcm.rb +4 -8
  21. data/lib/bioinform/data_models/pm.rb +19 -48
  22. data/lib/bioinform/data_models/pwm.rb +16 -0
  23. data/lib/bioinform/formatters.rb +2 -0
  24. data/lib/bioinform/formatters/raw_formatter.rb +41 -0
  25. data/lib/bioinform/formatters/transfac_formatter.rb +39 -0
  26. data/lib/bioinform/parsers.rb +2 -1
  27. data/lib/bioinform/parsers/jaspar_parser.rb +35 -0
  28. data/lib/bioinform/parsers/string_parser.rb +1 -1
  29. data/lib/bioinform/parsers/trivial_parser.rb +2 -1
  30. data/lib/bioinform/parsers/yaml_parser.rb +1 -1
  31. data/lib/bioinform/support.rb +2 -1
  32. data/lib/bioinform/support/parameters.rb +27 -18
  33. data/lib/bioinform/support/strip_doc.rb +9 -0
  34. data/lib/bioinform/version.rb +1 -1
  35. data/spec/cli/convert_motif_spec.rb +107 -0
  36. data/spec/cli/data/merge_into_collection/collection.yaml.result +186 -183
  37. data/spec/cli/data/merge_into_collection/collection_pwm.yaml.result +186 -183
  38. data/spec/cli/data/split_motifs/collection.yaml +184 -193
  39. data/spec/cli/shared_examples/convert_motif/motif_list_empty.rb +18 -0
  40. data/spec/cli/shared_examples/convert_motif/several_motifs_specified.rb +14 -0
  41. data/spec/cli/shared_examples/convert_motif/single_motif_specified.rb +50 -0
  42. data/spec/cli/shared_examples/convert_motif/yield_help_string.rb +5 -0
  43. data/spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb +4 -0
  44. data/spec/data_models/collection_spec.rb +36 -34
  45. data/spec/data_models/motif_spec.rb +224 -0
  46. data/spec/data_models/pcm_spec.rb +28 -17
  47. data/spec/data_models/pm_spec.rb +83 -121
  48. data/spec/data_models/pwm_spec.rb +38 -0
  49. data/spec/fabricators/collection_fabricator.rb +2 -2
  50. data/spec/fabricators/motif_fabricator.rb +33 -0
  51. data/spec/fabricators/motif_formats_fabricator.rb +125 -0
  52. data/spec/fabricators/pcm_fabricator.rb +25 -0
  53. data/spec/fabricators/pm_fabricator.rb +10 -1
  54. data/spec/fabricators/ppm_fabricator.rb +14 -0
  55. data/spec/fabricators/pwm_fabricator.rb +16 -0
  56. data/spec/parsers/trivial_parser_spec.rb +12 -12
  57. data/spec/parsers/yaml_parser_spec.rb +11 -11
  58. data/spec/spec_helper.rb +19 -49
  59. data/spec/spec_helper_source.rb +59 -0
  60. metadata +78 -7
data/lib/bioinform/support/strip_doc.rb ADDED
@@ -0,0 +1,9 @@
1
+ def strip_doc(doc)
2
+ doc.strip_doc
3
+ end
4
+
5
+ class String
6
+ def strip_doc
7
+ gsub(/^#{self[/\A +/]}/,'')
8
+ end
9
+ end
data/lib/bioinform/version.rb CHANGED
@@ -1,3 +1,3 @@
1
1
  module Bioinform
2
- VERSION = "0.1.8"
2
+ VERSION = "0.1.9"
3
3
  end
data/spec/cli/convert_motif_spec.rb ADDED
@@ -0,0 +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
107
+ end
data/spec/cli/data/merge_into_collection/collection.yaml.result CHANGED
@@ -1,185 +1,188 @@
1
- --- &19257216 !ruby/object:Bioinform::Collection
2
- collection:
3
- - - !ruby/object:Bioinform::PM
4
- parameters: !ruby/object:OpenStruct
5
- table:
6
- :name: GABPA_f1
7
- :tags:
8
- - *19257216
9
- :background:
10
- - 1
11
- - 1
12
- - 1
13
- - 1
14
- modifiable: true
15
- matrix:
16
- - - -0.1106670158341858
17
- - 0.013801606113892391
18
- - 0.6054596108973699
19
- - -1.3518085041421573
20
- - - 0.37030668921643345
21
- - 0.15761121480429963
22
- - 0.009069314183831202
23
- - -0.9888619717703562
24
- - - 0.47526546359546684
25
- - -0.3011678534572083
26
- - 0.4031522994412777
27
- - -1.8638752827041059
28
- - - -1.5544255540164373
29
- - 1.1082369687811506
30
- - -0.2814091552834454
31
- - -5.30708531823271
32
- - - -0.6362037835776368
33
- - 1.235338189985594
34
- - -3.5801322928552253
35
- - -5.717323067092849
36
- - - -5.852906870733575
37
- - -5.852906870733575
38
- - 1.3841383838057746
39
- - -5.852906870733575
40
- - - -5.852906870733575
41
- - -5.852906870733575
42
- - 1.3841383838057746
43
- - -5.852906870733575
44
- - - 1.3835219739184708
45
- - -5.2341956006430985
46
- - -5.852906870733575
47
- - -5.852906870733575
48
- - - 1.3756340514956562
49
- - -5.394962755562375
50
- - -5.394962755562375
51
- - -3.401117964959733
52
- - - -1.2176198315414444
53
- - -3.109079898175411
54
- - 1.2964067931472216
55
- - -5.717323067092849
56
- - - -1.3716559438167257
57
- - -0.2761401935045069
58
- - -1.8504445165866068
59
- - 1.0404320473626856
60
- - - -0.5440863133031895
61
- - -0.48103682561971345
62
- - 0.907381908447086
63
- - -1.1280642594012078
64
- - - 0.10557340209290218
65
- - -0.01814819455289191
66
- - 0.4381106695354074
67
- - -1.0304105539540915
68
- - !ruby/object:OpenStruct
69
- table: {}
70
- - - !ruby/object:Bioinform::PM
71
- parameters: !ruby/object:OpenStruct
72
- table:
73
- :name: KLF4_f2
74
- :tags:
75
- - *19257216
76
- :background:
77
- - 1
78
- - 1
79
- - 1
80
- - 1
81
- modifiable: true
82
- matrix:
83
- - - 0.30861857265872605
84
- - -2.254321000121579
85
- - 0.13505703522674192
86
- - 0.3285194224375633
87
- - - -1.227018967707036
88
- - -4.814127713368663
89
- - 1.3059890687390967
90
- - -4.908681463544344
91
- - - -2.443469374521196
92
- - -4.648238485031404
93
- - 1.3588686548279805
94
- - -4.441801801188402
95
- - - -2.7177827948276123
96
- - -3.8073538975356565
97
- - 1.356272809724262
98
- - -3.504104725510225
99
- - - -0.5563232977367343
100
- - 0.5340697765121405
101
- - -3.61417723090579
102
- - 0.5270259776377405
103
- - - -1.8687622060887386
104
- - -4.381483976582316
105
- - 1.337932245336098
106
- - -3.815629658877517
107
- - - -2.045671123823928
108
- - -2.384975142213679
109
- - 0.7198551207724355
110
- - 0.5449254135616948
111
- - - -1.373157530374372
112
- - -3.0063112097748217
113
- - 1.285188335493552
114
- - -2.5026044231773543
115
- - - -2.1030513122772208
116
- - -1.8941348100402244
117
- - 1.249265758393991
118
- - -1.4284210948906104
119
- - - -1.3277128628152939
120
- - 0.8982415633049462
121
- - -0.8080773665408135
122
- - -0.18161647647456935
123
- - !ruby/object:OpenStruct
124
- table: {}
125
- - - !ruby/object:Bioinform::PM
126
- parameters: !ruby/object:OpenStruct
127
- table:
128
- :name: SP1_f1
129
- :tags:
130
- - *19257216
131
- :background:
132
- - 1
133
- - 1
134
- - 1
135
- - 1
136
- modifiable: true
137
- matrix:
138
- - - -0.24435707885585292
139
- - -0.674823404693731
140
- - 0.8657012535789866
141
- - -1.1060188862599287
142
- - - -1.0631255752097797
143
- - -2.111925969423868
144
- - 1.0960627561110403
145
- - -0.6138563775211977
146
- - - -0.3872276234760535
147
- - -2.9739851913218045
148
- - 1.1807800242010378
149
- - -4.338927525031566
150
- - - -4.563896055436894
151
- - -2.9161633002532277
152
- - 1.3684371349982638
153
- - -5.077972423609655
154
- - - -2.2369752892820083
155
- - -3.7196436313301846
156
- - 1.3510439136452734
157
- - -4.889930670508233
158
- - - -0.07473964149330865
159
- - 0.944919654762011
160
- - -2.6246857648086044
161
- - -0.8510983487822436
162
- - - -1.9643526491643322
163
- - -2.978402770880115
164
- - 1.3113096718240573
165
- - -2.324334259499025
166
- - - -4.0155484139655835
167
- - -3.1384268078096667
168
- - 1.3387488589788057
169
- - -2.084673903537648
170
- - - -0.44509385828355363
171
- - -2.2510053061629702
172
- - 1.1265431574368685
173
- - -1.7780413702431372
174
- - - -1.1896356092245048
175
- - -1.2251832285630027
176
- - 1.1636760063747527
177
- - -1.6080243648157353
178
- - - -0.5166047365590571
179
- - 0.7641033353626657
180
- - -0.2862677570028208
181
- - -0.68254820978656
182
- - !ruby/object:OpenStruct
183
- table: {}
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:
12
+ - 1
13
+ - 1
14
+ - 1
15
+ - 1
16
+ modifiable: true
17
+ matrix:
18
+ - - -0.1106670158341858
19
+ - 0.013801606113892391
20
+ - 0.6054596108973699
21
+ - -1.3518085041421573
22
+ - - 0.37030668921643345
23
+ - 0.15761121480429963
24
+ - 0.009069314183831202
25
+ - -0.9888619717703562
26
+ - - 0.47526546359546684
27
+ - -0.3011678534572083
28
+ - 0.4031522994412777
29
+ - -1.8638752827041059
30
+ - - -1.5544255540164373
31
+ - 1.1082369687811506
32
+ - -0.2814091552834454
33
+ - -5.30708531823271
34
+ - - -0.6362037835776368
35
+ - 1.235338189985594
36
+ - -3.5801322928552253
37
+ - -5.717323067092849
38
+ - - -5.852906870733575
39
+ - -5.852906870733575
40
+ - 1.3841383838057746
41
+ - -5.852906870733575
42
+ - - -5.852906870733575
43
+ - -5.852906870733575
44
+ - 1.3841383838057746
45
+ - -5.852906870733575
46
+ - - 1.3835219739184708
47
+ - -5.2341956006430985
48
+ - -5.852906870733575
49
+ - -5.852906870733575
50
+ - - 1.3756340514956562
51
+ - -5.394962755562375
52
+ - -5.394962755562375
53
+ - -3.401117964959733
54
+ - - -1.2176198315414444
55
+ - -3.109079898175411
56
+ - 1.2964067931472216
57
+ - -5.717323067092849
58
+ - - -1.3716559438167257
59
+ - -0.2761401935045069
60
+ - -1.8504445165866068
61
+ - 1.0404320473626856
62
+ - - -0.5440863133031895
63
+ - -0.48103682561971345
64
+ - 0.907381908447086
65
+ - -1.1280642594012078
66
+ - - 0.10557340209290218
67
+ - -0.01814819455289191
68
+ - 0.4381106695354074
69
+ - -1.0304105539540915
70
+ 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
+ - - 0.30861857265872605
87
+ - -2.254321000121579
88
+ - 0.13505703522674192
89
+ - 0.3285194224375633
90
+ - - -1.227018967707036
91
+ - -4.814127713368663
92
+ - 1.3059890687390967
93
+ - -4.908681463544344
94
+ - - -2.443469374521196
95
+ - -4.648238485031404
96
+ - 1.3588686548279805
97
+ - -4.441801801188402
98
+ - - -2.7177827948276123
99
+ - -3.8073538975356565
100
+ - 1.356272809724262
101
+ - -3.504104725510225
102
+ - - -0.5563232977367343
103
+ - 0.5340697765121405
104
+ - -3.61417723090579
105
+ - 0.5270259776377405
106
+ - - -1.8687622060887386
107
+ - -4.381483976582316
108
+ - 1.337932245336098
109
+ - -3.815629658877517
110
+ - - -2.045671123823928
111
+ - -2.384975142213679
112
+ - 0.7198551207724355
113
+ - 0.5449254135616948
114
+ - - -1.373157530374372
115
+ - -3.0063112097748217
116
+ - 1.285188335493552
117
+ - -2.5026044231773543
118
+ - - -2.1030513122772208
119
+ - -1.8941348100402244
120
+ - 1.249265758393991
121
+ - -1.4284210948906104
122
+ - - -1.3277128628152939
123
+ - 0.8982415633049462
124
+ - -0.8080773665408135
125
+ - -0.18161647647456935
126
+ modifiable: true
127
+ - !ruby/object:Bioinform::Motif
128
+ parameters: !ruby/object:OpenStruct
129
+ table:
130
+ :original_data_model: :pm
131
+ :pm: !ruby/object:Bioinform::PM
132
+ parameters: !ruby/object:OpenStruct
133
+ table:
134
+ :name: SP1_f1
135
+ :background:
136
+ - 1
137
+ - 1
138
+ - 1
139
+ - 1
140
+ modifiable: true
141
+ matrix:
142
+ - - -0.24435707885585292
143
+ - -0.674823404693731
144
+ - 0.8657012535789866
145
+ - -1.1060188862599287
146
+ - - -1.0631255752097797
147
+ - -2.111925969423868
148
+ - 1.0960627561110403
149
+ - -0.6138563775211977
150
+ - - -0.3872276234760535
151
+ - -2.9739851913218045
152
+ - 1.1807800242010378
153
+ - -4.338927525031566
154
+ - - -4.563896055436894
155
+ - -2.9161633002532277
156
+ - 1.3684371349982638
157
+ - -5.077972423609655
158
+ - - -2.2369752892820083
159
+ - -3.7196436313301846
160
+ - 1.3510439136452734
161
+ - -4.889930670508233
162
+ - - -0.07473964149330865
163
+ - 0.944919654762011
164
+ - -2.6246857648086044
165
+ - -0.8510983487822436
166
+ - - -1.9643526491643322
167
+ - -2.978402770880115
168
+ - 1.3113096718240573
169
+ - -2.324334259499025
170
+ - - -4.0155484139655835
171
+ - -3.1384268078096667
172
+ - 1.3387488589788057
173
+ - -2.084673903537648
174
+ - - -0.44509385828355363
175
+ - -2.2510053061629702
176
+ - 1.1265431574368685
177
+ - -1.7780413702431372
178
+ - - -1.1896356092245048
179
+ - -1.2251832285630027
180
+ - 1.1636760063747527
181
+ - -1.6080243648157353
182
+ - - -0.5166047365590571
183
+ - 0.7641033353626657
184
+ - -0.2862677570028208
185
+ - -0.68254820978656
186
+ modifiable: true
184
187
  parameters: !ruby/object:OpenStruct
185
188
  table: {}