genomer-plugin-view 0.0.2

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Files changed (32) hide show
  1. data/.document +5 -0
  2. data/.gitignore +52 -0
  3. data/Gemfile +2 -0
  4. data/LICENSE.txt +20 -0
  5. data/README.rdoc +19 -0
  6. data/Rakefile +9 -0
  7. data/features/agp/generation.feature +285 -0
  8. data/features/fasta/contigs.feature +173 -0
  9. data/features/fasta/single_sequence.feature +144 -0
  10. data/features/mappings/core.feature +181 -0
  11. data/features/support/env.rb +13 -0
  12. data/features/table/cds_entries.feature +304 -0
  13. data/features/table/core.feature +302 -0
  14. data/features/table/feature_type.feature +180 -0
  15. data/genomer-plugin-view.gemspec +34 -0
  16. data/lib/genomer-plugin-view/agp.rb +62 -0
  17. data/lib/genomer-plugin-view/fasta.rb +36 -0
  18. data/lib/genomer-plugin-view/gff_record_helper.rb +61 -0
  19. data/lib/genomer-plugin-view/mapping.rb +14 -0
  20. data/lib/genomer-plugin-view/table.rb +56 -0
  21. data/lib/genomer-plugin-view/version.rb +3 -0
  22. data/lib/genomer-plugin-view.rb +29 -0
  23. data/man/genomer-view-agp.ronn +46 -0
  24. data/man/genomer-view.ronn +153 -0
  25. data/spec/genomer-view-plugin/agp_spec.rb +79 -0
  26. data/spec/genomer-view-plugin/fasta_spec.rb +96 -0
  27. data/spec/genomer-view-plugin/gff_record_helper_spec.rb +244 -0
  28. data/spec/genomer-view-plugin/mapping_spec.rb +89 -0
  29. data/spec/genomer-view-plugin/table_spec.rb +279 -0
  30. data/spec/genomer-view-plugin_spec.rb +103 -0
  31. data/spec/spec_helper.rb +32 -0
  32. metadata +192 -0
data/features/fasta/single_sequence.feature ADDED
@@ -0,0 +1,144 @@
1
+ Feature: Producing a fasta view of a scaffold
2
+ In order to produce fasta output from a scaffold
3
+ A user can use the "view" command
4
+ to generate the required fasta output
5
+
6
+ @disable-bundler
7
+ Scenario: Generating simple fasta
8
+ Given I successfully run `genomer init project`
9
+ And I cd to "project"
10
+ And I write to "assembly/scaffold.yml" with:
11
+ """
12
+ ---
13
+ -
14
+ sequence:
15
+ source: "contig00001"
16
+ """
17
+ And I write to "assembly/sequence.fna" with:
18
+ """
19
+ >contig00001
20
+ ATGGC
21
+ """
22
+ And I append to "Gemfile" with:
23
+ """
24
+ gem 'genomer-plugin-view', :path => '../../../'
25
+ """
26
+ When I run `genomer view fasta`
27
+ Then the exit status should be 0
28
+ And the output should contain:
29
+ """
30
+ >.
31
+ ATGGC
32
+ """
33
+
34
+ @disable-bundler
35
+ Scenario: Generating simple fasta with a sequence identifier
36
+ Given I successfully run `genomer init project`
37
+ And I cd to "project"
38
+ And I write to "assembly/scaffold.yml" with:
39
+ """
40
+ ---
41
+ -
42
+ sequence:
43
+ source: "contig00001"
44
+ """
45
+ And I write to "assembly/sequence.fna" with:
46
+ """
47
+ >contig00001
48
+ ATGGC
49
+ """
50
+ And I append to "Gemfile" with:
51
+ """
52
+ gem 'genomer-plugin-view', :path => '../../../'
53
+ """
54
+ When I run `genomer view fasta --identifier=scaffold`
55
+ Then the exit status should be 0
56
+ And the output should contain:
57
+ """
58
+ >scaffold
59
+ ATGGC
60
+ """
61
+
62
+ @disable-bundler
63
+ Scenario: Generating fasta with a organism name modifier
64
+ Given I successfully run `genomer init project`
65
+ And I cd to "project"
66
+ And I write to "assembly/scaffold.yml" with:
67
+ """
68
+ ---
69
+ -
70
+ sequence:
71
+ source: "contig00001"
72
+ """
73
+ And I write to "assembly/sequence.fna" with:
74
+ """
75
+ >contig00001
76
+ ATGGC
77
+ """
78
+ And I append to "Gemfile" with:
79
+ """
80
+ gem 'genomer-plugin-view', :path => '../../../'
81
+ """
82
+ When I run `genomer view fasta --organism='genus species'`
83
+ Then the exit status should be 0
84
+ And the output should contain:
85
+ """
86
+ >. [organism=genus species]
87
+ ATGGC
88
+ """
89
+
90
+ @disable-bundler
91
+ Scenario: Generating fasta with a strain modifier
92
+ Given I successfully run `genomer init project`
93
+ And I cd to "project"
94
+ And I write to "assembly/scaffold.yml" with:
95
+ """
96
+ ---
97
+ -
98
+ sequence:
99
+ source: "contig00001"
100
+ """
101
+ And I write to "assembly/sequence.fna" with:
102
+ """
103
+ >contig00001
104
+ ATGGC
105
+ """
106
+ And I append to "Gemfile" with:
107
+ """
108
+ gem 'genomer-plugin-view', :path => '../../../'
109
+ """
110
+ When I run `genomer view fasta --strain=strain_name`
111
+ Then the exit status should be 0
112
+ And the output should contain:
113
+ """
114
+ >. [strain=strain_name]
115
+ ATGGC
116
+ """
117
+
118
+ @disable-bundler
119
+ Scenario: Generating fasta with identifier and strain modifier
120
+ Given I successfully run `genomer init project`
121
+ And I cd to "project"
122
+ And I write to "assembly/scaffold.yml" with:
123
+ """
124
+ ---
125
+ -
126
+ sequence:
127
+ source: "contig00001"
128
+ """
129
+ And I write to "assembly/sequence.fna" with:
130
+ """
131
+ >contig00001
132
+ ATGGC
133
+ """
134
+ And I append to "Gemfile" with:
135
+ """
136
+ gem 'genomer-plugin-view', :path => '../../../'
137
+ """
138
+ When I run `genomer view fasta --strain=strain_name --identifier=name`
139
+ Then the exit status should be 0
140
+ And the output should contain:
141
+ """
142
+ >name [strain=strain_name]
143
+ ATGGC
144
+ """
data/features/mappings/core.feature ADDED
@@ -0,0 +1,181 @@
1
+ Feature: Producing a map of annotations IDs
2
+ In order to use map annotation IDs between versions
3
+ A user can use the "mapping" command
4
+ to generate a list of the original and updated annotations
5
+
6
+ @disable-bundler
7
+ Scenario: Two genes with locus tag numbering reset at the scaffold origin
8
+ Given I successfully run `genomer init project`
9
+ And I cd to "project"
10
+ And I write to "assembly/scaffold.yml" with:
11
+ """
12
+ ---
13
+ - sequence:
14
+ source: contig1
15
+ """
16
+ And I write to "assembly/sequence.fna" with:
17
+ """
18
+ >contig1
19
+ AAAAATTTTTGGGGGCCCCC
20
+ """
21
+ And I write to "assembly/annotations.gff" with:
22
+ """
23
+ ##gff-version 3
24
+ contig1 . gene 1 3 . + 1 ID=gene1
25
+ contig1 . gene 4 6 . + 1 ID=gene2
26
+ """
27
+ And I append to "Gemfile" with:
28
+ """
29
+ gem 'genomer-plugin-view', :path => '../../../'
30
+ """
31
+ When I run `genomer view mapping --reset_locus_numbering`
32
+ Then the exit status should be 0
33
+ And the output should contain:
34
+ """
35
+ gene1 000001
36
+ gene2 000002
37
+ """
38
+
39
+ @disable-bundler
40
+ Scenario: Two genes with locus tag numbering reset at specified start value
41
+ Given I successfully run `genomer init project`
42
+ And I cd to "project"
43
+ And I write to "assembly/scaffold.yml" with:
44
+ """
45
+ ---
46
+ - sequence:
47
+ source: contig1
48
+ """
49
+ And I write to "assembly/sequence.fna" with:
50
+ """
51
+ >contig1
52
+ AAAAATTTTTGGGGGCCCCC
53
+ """
54
+ And I write to "assembly/annotations.gff" with:
55
+ """
56
+ ##gff-version 3
57
+ contig1 . gene 1 3 . + 1 ID=gene1
58
+ contig1 . gene 4 6 . + 1 ID=gene2
59
+ """
60
+ And I append to "Gemfile" with:
61
+ """
62
+ gem 'genomer-plugin-view', :path => '../../../'
63
+ """
64
+ When I run `genomer view mapping --reset_locus_numbering=5`
65
+ Then the exit status should be 0
66
+ And the output should contain:
67
+ """
68
+ gene1 000005
69
+ gene2 000006
70
+ """
71
+
72
+ @disable-bundler
73
+ Scenario: Four unordered genes with locus tag reset at the scaffold origin
74
+ Given I successfully run `genomer init project`
75
+ And I cd to "project"
76
+ And I write to "assembly/scaffold.yml" with:
77
+ """
78
+ ---
79
+ - sequence:
80
+ source: contig1
81
+ """
82
+ And I write to "assembly/sequence.fna" with:
83
+ """
84
+ >contig1
85
+ AAAAATTTTTGGGGGCCCCC
86
+ """
87
+ And I write to "assembly/annotations.gff" with:
88
+ """
89
+ ##gff-version 3
90
+ contig1 . gene 10 12 . + 1 ID=gene4
91
+ contig1 . gene 4 6 . + 1 ID=gene2
92
+ contig1 . gene 1 3 . + 1 ID=gene1
93
+ contig1 . gene 7 9 . + 1 ID=gene3
94
+ """
95
+ And I append to "Gemfile" with:
96
+ """
97
+ gem 'genomer-plugin-view', :path => '../../../'
98
+ """
99
+ When I run `genomer view mapping --reset_locus_numbering`
100
+ Then the exit status should be 0
101
+ And the output should contain:
102
+ """
103
+ gene1 000001
104
+ gene2 000002
105
+ gene3 000003
106
+ gene4 000004
107
+ """
108
+
109
+ @disable-bundler
110
+ Scenario: Four genes with a prefix added to the locus tags
111
+ Given I successfully run `genomer init project`
112
+ And I cd to "project"
113
+ And I write to "assembly/scaffold.yml" with:
114
+ """
115
+ ---
116
+ - sequence:
117
+ source: contig1
118
+ """
119
+ And I write to "assembly/sequence.fna" with:
120
+ """
121
+ >contig1
122
+ AAAAATTTTTGGGGGCCCCC
123
+ """
124
+ And I write to "assembly/annotations.gff" with:
125
+ """
126
+ ##gff-version 3
127
+ contig1 . gene 10 12 . + 1 ID=gene4
128
+ contig1 . gene 4 6 . + 1 ID=gene2
129
+ contig1 . gene 1 3 . + 1 ID=gene1
130
+ contig1 . gene 7 9 . + 1 ID=gene3
131
+ """
132
+ And I append to "Gemfile" with:
133
+ """
134
+ gem 'genomer-plugin-view', :path => '../../../'
135
+ """
136
+ When I run `genomer view mapping --prefix=pre_`
137
+ Then the exit status should be 0
138
+ And the output should contain:
139
+ """
140
+ gene1 pre_gene1
141
+ gene2 pre_gene2
142
+ gene3 pre_gene3
143
+ gene4 pre_gene4
144
+ """
145
+
146
+ @disable-bundler
147
+ Scenario: Four genes prefixes and locus tag reset at the scaffold origin
148
+ Given I successfully run `genomer init project`
149
+ And I cd to "project"
150
+ And I write to "assembly/scaffold.yml" with:
151
+ """
152
+ ---
153
+ - sequence:
154
+ source: contig1
155
+ """
156
+ And I write to "assembly/sequence.fna" with:
157
+ """
158
+ >contig1
159
+ AAAAATTTTTGGGGGCCCCC
160
+ """
161
+ And I write to "assembly/annotations.gff" with:
162
+ """
163
+ ##gff-version 3
164
+ contig1 . gene 10 12 . + 1 ID=gene4
165
+ contig1 . gene 4 6 . + 1 ID=gene2
166
+ contig1 . gene 1 3 . + 1 ID=gene1
167
+ contig1 . gene 7 9 . + 1 ID=gene3
168
+ """
169
+ And I append to "Gemfile" with:
170
+ """
171
+ gem 'genomer-plugin-view', :path => '../../../'
172
+ """
173
+ When I run `genomer view mapping --reset_locus_numbering=5 --prefix=pre_`
174
+ Then the exit status should be 0
175
+ And the output should contain:
176
+ """
177
+ gene1 pre_000005
178
+ gene2 pre_000006
179
+ gene3 pre_000007
180
+ gene4 pre_000008
181
+ """
data/features/support/env.rb ADDED
@@ -0,0 +1,13 @@
1
+ require 'bundler'
2
+ begin
3
+ Bundler.setup(:default, :development)
4
+ rescue Bundler::BundlerError => e
5
+ $stderr.puts e.message
6
+ $stderr.puts "Run `bundle install` to install missing gems"
7
+ exit e.status_code
8
+ end
9
+
10
+ $LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
11
+ $LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../spec')
12
+
13
+ require 'aruba/cucumber'
data/features/table/cds_entries.feature ADDED
@@ -0,0 +1,304 @@
1
+ Feature: Producing cds annotation view from a scaffold
2
+ In order to submit CDS genome annotations
3
+ A user can use the "table" command with --generate_encoded_features
4
+ to generate the genbank annotation table format with CDS
5
+
6
+ @disable-bundler
7
+ Scenario: A CDS entry with no attributes
8
+ Given I successfully run `genomer init project`
9
+ And I cd to "project"
10
+ And I write to "assembly/scaffold.yml" with:
11
+ """
12
+ ---
13
+ - sequence:
14
+ source: contig1
15
+ """
16
+ And I write to "assembly/sequence.fna" with:
17
+ """
18
+ >contig1
19
+ AAAAATTTTTGGGGGCCCCC
20
+ """
21
+ And I write to "assembly/annotations.gff" with:
22
+ """
23
+ ##gff-version 3
24
+ contig1 . gene 1 3 . + 1 .
25
+ """
26
+ And I append to "Gemfile" with:
27
+ """
28
+ gem 'genomer-plugin-view', :path => '../../../'
29
+ """
30
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
31
+ Then the exit status should be 0
32
+ And the output should contain:
33
+ """
34
+ >Feature genome annotation_table
35
+ 1 3 gene
36
+ 1 3 CDS
37
+
38
+ """
39
+
40
+ @disable-bundler
41
+ Scenario: A CDS entry with a prefixed ID
42
+ Given I successfully run `genomer init project`
43
+ And I cd to "project"
44
+ And I write to "assembly/scaffold.yml" with:
45
+ """
46
+ ---
47
+ - sequence:
48
+ source: contig1
49
+ """
50
+ And I write to "assembly/sequence.fna" with:
51
+ """
52
+ >contig1
53
+ AAAAATTTTTGGGGGCCCCC
54
+ """
55
+ And I write to "assembly/annotations.gff" with:
56
+ """
57
+ ##gff-version 3
58
+ contig1 . gene 1 3 . - 1 ID=gene1
59
+ """
60
+ And I append to "Gemfile" with:
61
+ """
62
+ gem 'genomer-plugin-view', :path => '../../../'
63
+ """
64
+ When I run `genomer view table --identifier=genome --generate_encoded_features=pre_`
65
+ Then the exit status should be 0
66
+ And the output should contain:
67
+ """
68
+ >Feature genome annotation_table
69
+ 3 1 gene
70
+ locus_tag gene1
71
+ 3 1 CDS
72
+ protein_id pre_gene1
73
+
74
+ """
75
+
76
+ @disable-bundler
77
+ Scenario: A CDS entry with a Name attribute
78
+ Given I successfully run `genomer init project`
79
+ And I cd to "project"
80
+ And I write to "assembly/scaffold.yml" with:
81
+ """
82
+ ---
83
+ - sequence:
84
+ source: contig1
85
+ """
86
+ And I write to "assembly/sequence.fna" with:
87
+ """
88
+ >contig1
89
+ AAAAATTTTTGGGGGCCCCC
90
+ """
91
+ And I write to "assembly/annotations.gff" with:
92
+ """
93
+ ##gff-version 3
94
+ contig1 . gene 4 6 . + 1 ID=gene2;Name=defg
95
+ """
96
+ And I append to "Gemfile" with:
97
+ """
98
+ gem 'genomer-plugin-view', :path => '../../../'
99
+ """
100
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
101
+ Then the exit status should be 0
102
+ And the output should contain:
103
+ """
104
+ >Feature genome annotation_table
105
+ 4 6 gene
106
+ locus_tag gene2
107
+ gene defg
108
+ 4 6 CDS
109
+ protein_id gene2
110
+ product Defg
111
+
112
+ """
113
+
114
+ @disable-bundler
115
+ Scenario: A CDS entry with a product attribute
116
+ Given I successfully run `genomer init project`
117
+ And I cd to "project"
118
+ And I write to "assembly/scaffold.yml" with:
119
+ """
120
+ ---
121
+ - sequence:
122
+ source: contig1
123
+ """
124
+ And I write to "assembly/sequence.fna" with:
125
+ """
126
+ >contig1
127
+ AAAAATTTTTGGGGGCCCCC
128
+ """
129
+ And I write to "assembly/annotations.gff" with:
130
+ """
131
+ ##gff-version 3
132
+ contig1 . gene 4 6 . + 1 ID=gene2;product=defg
133
+ """
134
+ And I append to "Gemfile" with:
135
+ """
136
+ gem 'genomer-plugin-view', :path => '../../../'
137
+ """
138
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
139
+ Then the exit status should be 0
140
+ And the output should contain:
141
+ """
142
+ >Feature genome annotation_table
143
+ 4 6 gene
144
+ locus_tag gene2
145
+ 4 6 CDS
146
+ protein_id gene2
147
+ product defg
148
+
149
+ """
150
+
151
+ @disable-bundler
152
+ Scenario: A CDS entry with Name and product attributes
153
+ Given I successfully run `genomer init project`
154
+ And I cd to "project"
155
+ And I write to "assembly/scaffold.yml" with:
156
+ """
157
+ ---
158
+ - sequence:
159
+ source: contig1
160
+ """
161
+ And I write to "assembly/sequence.fna" with:
162
+ """
163
+ >contig1
164
+ AAAAATTTTTGGGGGCCCCC
165
+ """
166
+ And I write to "assembly/annotations.gff" with:
167
+ """
168
+ ##gff-version 3
169
+ contig1 . gene 4 6 . + 1 ID=gene2;Name=defg;product=xyz
170
+ """
171
+ And I append to "Gemfile" with:
172
+ """
173
+ gem 'genomer-plugin-view', :path => '../../../'
174
+ """
175
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
176
+ Then the exit status should be 0
177
+ And the output should contain:
178
+ """
179
+ >Feature genome annotation_table
180
+ 4 6 gene
181
+ locus_tag gene2
182
+ gene defg
183
+ 4 6 CDS
184
+ protein_id gene2
185
+ product Defg
186
+ function xyz
187
+
188
+ """
189
+
190
+ @disable-bundler
191
+ Scenario: A CDS entry with product and function attributes
192
+ Given I successfully run `genomer init project`
193
+ And I cd to "project"
194
+ And I write to "assembly/scaffold.yml" with:
195
+ """
196
+ ---
197
+ - sequence:
198
+ source: contig1
199
+ """
200
+ And I write to "assembly/sequence.fna" with:
201
+ """
202
+ >contig1
203
+ AAAAATTTTTGGGGGCCCCC
204
+ """
205
+ And I write to "assembly/annotations.gff" with:
206
+ """
207
+ ##gff-version 3
208
+ contig1 . gene 4 6 . + 1 ID=gene2;product=defg;function=xyz
209
+ """
210
+ And I append to "Gemfile" with:
211
+ """
212
+ gem 'genomer-plugin-view', :path => '../../../'
213
+ """
214
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
215
+ Then the exit status should be 0
216
+ And the output should contain:
217
+ """
218
+ >Feature genome annotation_table
219
+ 4 6 gene
220
+ locus_tag gene2
221
+ 4 6 CDS
222
+ protein_id gene2
223
+ product defg
224
+ function xyz
225
+
226
+ """
227
+
228
+ @disable-bundler
229
+ Scenario: A CDS entry with Name, product and function attributes
230
+ Given I successfully run `genomer init project`
231
+ And I cd to "project"
232
+ And I write to "assembly/scaffold.yml" with:
233
+ """
234
+ ---
235
+ - sequence:
236
+ source: contig1
237
+ """
238
+ And I write to "assembly/sequence.fna" with:
239
+ """
240
+ >contig1
241
+ AAAAATTTTTGGGGGCCCCC
242
+ """
243
+ And I write to "assembly/annotations.gff" with:
244
+ """
245
+ ##gff-version 3
246
+ contig1 . gene 4 6 . + 1 ID=gene2;Name=abcd;product=efgh;function=ijkl
247
+ """
248
+ And I append to "Gemfile" with:
249
+ """
250
+ gem 'genomer-plugin-view', :path => '../../../'
251
+ """
252
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
253
+ Then the exit status should be 0
254
+ And the output should contain:
255
+ """
256
+ >Feature genome annotation_table
257
+ 4 6 gene
258
+ locus_tag gene2
259
+ gene abcd
260
+ 4 6 CDS
261
+ protein_id gene2
262
+ product Abcd
263
+ function efgh
264
+
265
+ """
266
+
267
+ @disable-bundler
268
+ Scenario: A CDS entry with ec_number and note attributes
269
+ Given I successfully run `genomer init project`
270
+ And I cd to "project"
271
+ And I write to "assembly/scaffold.yml" with:
272
+ """
273
+ ---
274
+ - sequence:
275
+ source: contig1
276
+ """
277
+ And I write to "assembly/sequence.fna" with:
278
+ """
279
+ >contig1
280
+ AAAAATTTTTGGGGGCCCCC
281
+ """
282
+ And I write to "assembly/annotations.gff" with:
283
+ """
284
+ ##gff-version 3
285
+ contig1 . gene 1 3 . - 1 ID=gene1;ec_number=3.5.2.3;Note=my protein
286
+ """
287
+ And I append to "Gemfile" with:
288
+ """
289
+ gem 'genomer-plugin-view', :path => '../../../'
290
+ """
291
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
292
+ Then the exit status should be 0
293
+ And the output should contain:
294
+ """
295
+ >Feature genome annotation_table
296
+ 3 1 gene
297
+ locus_tag gene1
298
+ 3 1 CDS
299
+ protein_id gene1
300
+ EC_number 3.5.2.3
301
+ note my protein
302
+
303
+ """
304
+