bioinform 0.1.7 → 0.1.8
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- data/TODO.txt +7 -2
- data/bin/merge_into_collection +4 -0
- data/bin/pcm2pwm +1 -1
- data/bin/split_motifs +1 -1
- data/bioinform.gemspec +2 -0
- data/lib/bioinform/cli/merge_into_collection.rb +76 -0
- data/lib/bioinform/cli/pcm2pwm.rb +20 -20
- data/lib/bioinform/cli/split_motifs.rb +21 -20
- data/lib/bioinform/cli.rb +16 -2
- data/lib/bioinform/data_models/collection.rb +13 -10
- data/lib/bioinform/data_models/pcm.rb +2 -2
- data/lib/bioinform/data_models/pm.rb +24 -37
- data/lib/bioinform/data_models/ppm.rb +2 -2
- data/lib/bioinform/data_models/pwm.rb +2 -2
- data/lib/bioinform/data_models.rb +8 -8
- data/lib/bioinform/parsers/parser.rb +10 -5
- data/lib/bioinform/parsers/splittable_parser.rb +57 -0
- data/lib/bioinform/parsers/string_fantom_parser.rb +3 -3
- data/lib/bioinform/parsers/string_parser.rb +5 -24
- data/lib/bioinform/parsers/trivial_parser.rb +19 -3
- data/lib/bioinform/parsers/yaml_parser.rb +35 -0
- data/lib/bioinform/parsers.rb +6 -4
- data/lib/bioinform/support/parameters.rb +19 -0
- data/lib/bioinform/support/partial_sums.rb +1 -1
- data/lib/bioinform/support.rb +11 -10
- data/lib/bioinform/version.rb +1 -1
- data/lib/bioinform.rb +5 -5
- data/spec/cli/cli_spec.rb +8 -7
- data/spec/cli/data/merge_into_collection/GABPA_f1.pwm +14 -0
- data/spec/cli/data/{KLF4_f2.pwm.result → merge_into_collection/KLF4_f2.pwm} +0 -0
- data/spec/cli/data/{SP1_f1.pwm.result → merge_into_collection/SP1_f1.pwm} +0 -0
- data/spec/cli/data/merge_into_collection/collection.txt.result +40 -0
- data/spec/cli/data/merge_into_collection/collection.yaml.result +185 -0
- data/spec/cli/data/merge_into_collection/collection_pwm.yaml.result +185 -0
- data/spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm +14 -0
- data/spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm +11 -0
- data/spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm +12 -0
- data/spec/cli/data/{KLF4 f2 spaced name.pcm → pcm2pwm/KLF4 f2 spaced name.pcm} +0 -0
- data/spec/cli/data/{KLF4_f2.pcm → pcm2pwm/KLF4_f2.pcm} +0 -0
- data/spec/cli/data/pcm2pwm/KLF4_f2.pwm.result +11 -0
- data/spec/cli/data/{SP1_f1.pcm → pcm2pwm/SP1_f1.pcm} +0 -0
- data/spec/cli/data/pcm2pwm/SP1_f1.pwm.result +12 -0
- data/spec/cli/data/split_motifs/GABPA_f1.mat.result +14 -0
- data/spec/cli/data/split_motifs/KLF4_f2.mat.result +11 -0
- data/spec/cli/data/split_motifs/SP1_f1.mat.result +12 -0
- data/spec/cli/data/split_motifs/collection.yaml +197 -0
- data/spec/cli/data/split_motifs/plain_collection.txt +38 -0
- data/spec/cli/merge_into_collection_spec.rb +100 -0
- data/spec/cli/pcm2pwm_spec.rb +3 -3
- data/spec/cli/split_motifs_spec.rb +74 -3
- data/spec/data_models/collection_spec.rb +2 -2
- data/spec/data_models/pcm_spec.rb +2 -2
- data/spec/data_models/pm_spec.rb +10 -27
- data/spec/data_models/ppm_spec.rb +2 -2
- data/spec/data_models/pwm_spec.rb +3 -3
- data/spec/fabricators/collection_fabricator.rb +8 -0
- data/spec/fabricators/pm_fabricator.rb +43 -0
- data/spec/parsers/parser_spec.rb +29 -37
- data/spec/parsers/string_fantom_parser_spec.rb +38 -35
- data/spec/parsers/string_parser_spec.rb +33 -66
- data/spec/parsers/trivial_parser_spec.rb +48 -6
- data/spec/parsers/yaml_parser_spec.rb +50 -0
- data/spec/spec_helper.rb +2 -6
- data/spec/support/advanced_scan_spec.rb +2 -2
- data/spec/support/array_product_spec.rb +2 -2
- data/spec/support/array_zip_spec.rb +2 -2
- data/spec/support/collect_hash_spec.rb +2 -2
- data/spec/support/delete_many_spec.rb +2 -2
- data/spec/support/inverf_spec.rb +2 -2
- data/spec/support/multiline_squish_spec.rb +2 -2
- data/spec/support/partial_sums_spec.rb +2 -2
- data/spec/support/same_by_spec.rb +2 -2
- metadata +86 -12
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bioinform
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.1.
|
4
|
+
version: 0.1.8
|
5
5
|
prerelease:
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
@@ -9,7 +9,7 @@ authors:
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|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2012-09-
|
12
|
+
date: 2012-09-15 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: activesupport
|
@@ -27,6 +27,22 @@ dependencies:
|
|
27
27
|
- - ! '>='
|
28
28
|
- !ruby/object:Gem::Version
|
29
29
|
version: 3.0.0
|
30
|
+
- !ruby/object:Gem::Dependency
|
31
|
+
name: docopt
|
32
|
+
requirement: !ruby/object:Gem::Requirement
|
33
|
+
none: false
|
34
|
+
requirements:
|
35
|
+
- - ! '>='
|
36
|
+
- !ruby/object:Gem::Version
|
37
|
+
version: 0.5.0
|
38
|
+
type: :runtime
|
39
|
+
prerelease: false
|
40
|
+
version_requirements: !ruby/object:Gem::Requirement
|
41
|
+
none: false
|
42
|
+
requirements:
|
43
|
+
- - ! '>='
|
44
|
+
- !ruby/object:Gem::Version
|
45
|
+
version: 0.5.0
|
30
46
|
- !ruby/object:Gem::Dependency
|
31
47
|
name: rspec
|
32
48
|
requirement: !ruby/object:Gem::Requirement
|
@@ -43,10 +59,27 @@ dependencies:
|
|
43
59
|
- - ! '>='
|
44
60
|
- !ruby/object:Gem::Version
|
45
61
|
version: '2.0'
|
62
|
+
- !ruby/object:Gem::Dependency
|
63
|
+
name: fabrication
|
64
|
+
requirement: !ruby/object:Gem::Requirement
|
65
|
+
none: false
|
66
|
+
requirements:
|
67
|
+
- - ! '>='
|
68
|
+
- !ruby/object:Gem::Version
|
69
|
+
version: 2.2.3
|
70
|
+
type: :development
|
71
|
+
prerelease: false
|
72
|
+
version_requirements: !ruby/object:Gem::Requirement
|
73
|
+
none: false
|
74
|
+
requirements:
|
75
|
+
- - ! '>='
|
76
|
+
- !ruby/object:Gem::Version
|
77
|
+
version: 2.2.3
|
46
78
|
description: A bunch of useful classes for bioinformatics
|
47
79
|
email:
|
48
80
|
- prijutme4ty@gmail.com
|
49
81
|
executables:
|
82
|
+
- merge_into_collection
|
50
83
|
- pcm2pwm
|
51
84
|
- split_motifs
|
52
85
|
extensions: []
|
@@ -58,11 +91,13 @@ files:
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|
58
91
|
- README.md
|
59
92
|
- Rakefile
|
60
93
|
- TODO.txt
|
94
|
+
- bin/merge_into_collection
|
61
95
|
- bin/pcm2pwm
|
62
96
|
- bin/split_motifs
|
63
97
|
- bioinform.gemspec
|
64
98
|
- lib/bioinform.rb
|
65
99
|
- lib/bioinform/cli.rb
|
100
|
+
- lib/bioinform/cli/merge_into_collection.rb
|
66
101
|
- lib/bioinform/cli/pcm2pwm.rb
|
67
102
|
- lib/bioinform/cli/split_motifs.rb
|
68
103
|
- lib/bioinform/data_models.rb
|
@@ -73,9 +108,11 @@ files:
|
|
73
108
|
- lib/bioinform/data_models/pwm.rb
|
74
109
|
- lib/bioinform/parsers.rb
|
75
110
|
- lib/bioinform/parsers/parser.rb
|
111
|
+
- lib/bioinform/parsers/splittable_parser.rb
|
76
112
|
- lib/bioinform/parsers/string_fantom_parser.rb
|
77
113
|
- lib/bioinform/parsers/string_parser.rb
|
78
114
|
- lib/bioinform/parsers/trivial_parser.rb
|
115
|
+
- lib/bioinform/parsers/yaml_parser.rb
|
79
116
|
- lib/bioinform/support.rb
|
80
117
|
- lib/bioinform/support/advanced_scan.rb
|
81
118
|
- lib/bioinform/support/array_product.rb
|
@@ -85,15 +122,31 @@ files:
|
|
85
122
|
- lib/bioinform/support/delete_many.rb
|
86
123
|
- lib/bioinform/support/inverf.rb
|
87
124
|
- lib/bioinform/support/multiline_squish.rb
|
125
|
+
- lib/bioinform/support/parameters.rb
|
88
126
|
- lib/bioinform/support/partial_sums.rb
|
89
127
|
- lib/bioinform/support/same_by.rb
|
90
128
|
- lib/bioinform/version.rb
|
91
129
|
- spec/cli/cli_spec.rb
|
92
|
-
- spec/cli/data/
|
93
|
-
- spec/cli/data/KLF4_f2.
|
94
|
-
- spec/cli/data/
|
95
|
-
- spec/cli/data/
|
96
|
-
- spec/cli/data/
|
130
|
+
- spec/cli/data/merge_into_collection/GABPA_f1.pwm
|
131
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+
- spec/cli/data/merge_into_collection/KLF4_f2.pwm
|
132
|
+
- spec/cli/data/merge_into_collection/SP1_f1.pwm
|
133
|
+
- spec/cli/data/merge_into_collection/collection.txt.result
|
134
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+
- spec/cli/data/merge_into_collection/collection.yaml.result
|
135
|
+
- 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
|
138
|
+
- spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm
|
139
|
+
- spec/cli/data/pcm2pwm/KLF4 f2 spaced name.pcm
|
140
|
+
- spec/cli/data/pcm2pwm/KLF4_f2.pcm
|
141
|
+
- spec/cli/data/pcm2pwm/KLF4_f2.pwm.result
|
142
|
+
- spec/cli/data/pcm2pwm/SP1_f1.pcm
|
143
|
+
- spec/cli/data/pcm2pwm/SP1_f1.pwm.result
|
144
|
+
- spec/cli/data/split_motifs/GABPA_f1.mat.result
|
145
|
+
- spec/cli/data/split_motifs/KLF4_f2.mat.result
|
146
|
+
- spec/cli/data/split_motifs/SP1_f1.mat.result
|
147
|
+
- spec/cli/data/split_motifs/collection.yaml
|
148
|
+
- spec/cli/data/split_motifs/plain_collection.txt
|
149
|
+
- spec/cli/merge_into_collection_spec.rb
|
97
150
|
- spec/cli/pcm2pwm_spec.rb
|
98
151
|
- spec/cli/split_motifs_spec.rb
|
99
152
|
- spec/data_models/collection_spec.rb
|
@@ -101,10 +154,13 @@ files:
|
|
101
154
|
- spec/data_models/pm_spec.rb
|
102
155
|
- spec/data_models/ppm_spec.rb
|
103
156
|
- spec/data_models/pwm_spec.rb
|
157
|
+
- spec/fabricators/collection_fabricator.rb
|
158
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+
- spec/fabricators/pm_fabricator.rb
|
104
159
|
- spec/parsers/parser_spec.rb
|
105
160
|
- spec/parsers/string_fantom_parser_spec.rb
|
106
161
|
- spec/parsers/string_parser_spec.rb
|
107
162
|
- spec/parsers/trivial_parser_spec.rb
|
163
|
+
- spec/parsers/yaml_parser_spec.rb
|
108
164
|
- spec/spec_helper.rb
|
109
165
|
- spec/support/advanced_scan_spec.rb
|
110
166
|
- spec/support/array_product_spec.rb
|
@@ -144,11 +200,26 @@ summary: Classes for work with different input formats of positional matrices an
|
|
144
200
|
symbols
|
145
201
|
test_files:
|
146
202
|
- spec/cli/cli_spec.rb
|
147
|
-
- spec/cli/data/
|
148
|
-
- spec/cli/data/KLF4_f2.
|
149
|
-
- spec/cli/data/
|
150
|
-
- spec/cli/data/
|
151
|
-
- spec/cli/data/
|
203
|
+
- spec/cli/data/merge_into_collection/GABPA_f1.pwm
|
204
|
+
- spec/cli/data/merge_into_collection/KLF4_f2.pwm
|
205
|
+
- spec/cli/data/merge_into_collection/SP1_f1.pwm
|
206
|
+
- spec/cli/data/merge_into_collection/collection.txt.result
|
207
|
+
- spec/cli/data/merge_into_collection/collection.yaml.result
|
208
|
+
- spec/cli/data/merge_into_collection/collection_pwm.yaml.result
|
209
|
+
- spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm
|
210
|
+
- spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm
|
211
|
+
- spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm
|
212
|
+
- spec/cli/data/pcm2pwm/KLF4 f2 spaced name.pcm
|
213
|
+
- spec/cli/data/pcm2pwm/KLF4_f2.pcm
|
214
|
+
- spec/cli/data/pcm2pwm/KLF4_f2.pwm.result
|
215
|
+
- spec/cli/data/pcm2pwm/SP1_f1.pcm
|
216
|
+
- spec/cli/data/pcm2pwm/SP1_f1.pwm.result
|
217
|
+
- spec/cli/data/split_motifs/GABPA_f1.mat.result
|
218
|
+
- spec/cli/data/split_motifs/KLF4_f2.mat.result
|
219
|
+
- spec/cli/data/split_motifs/SP1_f1.mat.result
|
220
|
+
- spec/cli/data/split_motifs/collection.yaml
|
221
|
+
- spec/cli/data/split_motifs/plain_collection.txt
|
222
|
+
- spec/cli/merge_into_collection_spec.rb
|
152
223
|
- spec/cli/pcm2pwm_spec.rb
|
153
224
|
- spec/cli/split_motifs_spec.rb
|
154
225
|
- spec/data_models/collection_spec.rb
|
@@ -156,10 +227,13 @@ test_files:
|
|
156
227
|
- spec/data_models/pm_spec.rb
|
157
228
|
- spec/data_models/ppm_spec.rb
|
158
229
|
- spec/data_models/pwm_spec.rb
|
230
|
+
- spec/fabricators/collection_fabricator.rb
|
231
|
+
- spec/fabricators/pm_fabricator.rb
|
159
232
|
- spec/parsers/parser_spec.rb
|
160
233
|
- spec/parsers/string_fantom_parser_spec.rb
|
161
234
|
- spec/parsers/string_parser_spec.rb
|
162
235
|
- spec/parsers/trivial_parser_spec.rb
|
236
|
+
- spec/parsers/yaml_parser_spec.rb
|
163
237
|
- spec/spec_helper.rb
|
164
238
|
- spec/support/advanced_scan_spec.rb
|
165
239
|
- spec/support/array_product_spec.rb
|