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/table/core.feature ADDED
@@ -0,0 +1,302 @@
1
+ Feature: Producing a annotation view of a scaffold
2
+ In order to submit genome annotations
3
+ A user can use the "table" command
4
+ to generate the genbank annotation table format
5
+
6
+ @disable-bundler
7
+ Scenario: Generating a table file from a single annotation
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+ Given I successfully run `genomer init project`
9
+ And I cd to "project"
10
+ And I write to "assembly/scaffold.yml" with:
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+ """
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+ ---
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+ - sequence:
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+ source: contig1
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+ """
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+ And I write to "assembly/sequence.fna" with:
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+ """
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+ >contig1
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+ AAAAATTTTTGGGGGCCCCC
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+ """
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+ And I write to "assembly/annotations.gff" with:
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+ """
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+ ##gff-version 3
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+ contig1 . gene 1 3 . + 1 .
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+ """
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+ And I append to "Gemfile" with:
27
+ """
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+ gem 'genomer-plugin-view', :path => '../../../'
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+ """
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+ When I run `genomer view table --identifier=genome`
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+ Then the exit status should be 0
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+ And the output should contain:
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+ """
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+ >Feature genome annotation_table
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+ 1 3 gene
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+
37
+ """
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+
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+ @disable-bundler
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+ Scenario: Generating a table file from two annotations
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+ Given I successfully run `genomer init project`
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+ And I cd to "project"
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+ And I write to "assembly/scaffold.yml" with:
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+ """
45
+ ---
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+ - sequence:
47
+ source: contig1
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+ """
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+ And I write to "assembly/sequence.fna" with:
50
+ """
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+ >contig1
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+ AAAAATTTTTGGGGGCCCCC
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+ """
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+ And I write to "assembly/annotations.gff" with:
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+ """
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+ ##gff-version 3
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+ contig1 . gene 1 3 . + 1
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+ contig1 . gene 4 6 . + 1
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+ """
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+ And I append to "Gemfile" with:
61
+ """
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+ gem 'genomer-plugin-view', :path => '../../../'
63
+ """
64
+ When I run `genomer view table --identifier=genome`
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+ Then the exit status should be 0
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+ And the output should contain:
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+ """
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+ >Feature genome annotation_table
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+ 1 3 gene
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+ 4 6 gene
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+
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+ """
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+
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+ @disable-bundler
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+ Scenario: Generating a table file from a gene with ID attribute
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+ Given I successfully run `genomer init project`
77
+ And I cd to "project"
78
+ And I write to "assembly/scaffold.yml" with:
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+ """
80
+ ---
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+ - sequence:
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+ source: contig1
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+ """
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+ And I write to "assembly/sequence.fna" with:
85
+ """
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+ >contig1
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+ AAAAATTTTTGGGGGCCCCC
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+ """
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+ And I write to "assembly/annotations.gff" with:
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+ """
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+ ##gff-version 3
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+ contig1 . gene 1 3 . - 1 ID=gene1
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+ """
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+ And I append to "Gemfile" with:
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+ """
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+ gem 'genomer-plugin-view', :path => '../../../'
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+ """
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+ When I run `genomer view table --identifier=genome`
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+ Then the exit status should be 0
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+ And the output should contain:
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+ """
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+ >Feature genome annotation_table
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+ 3 1 gene
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+ locus_tag gene1
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+
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+ """
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+
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+ @disable-bundler
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+ Scenario: Generating a table file from a gene with ID and name attributes
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+ Given I successfully run `genomer init project`
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+ And I cd to "project"
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+ And I write to "assembly/scaffold.yml" with:
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+ """
114
+ ---
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+ - sequence:
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+ source: contig1
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+ """
118
+ And I write to "assembly/sequence.fna" with:
119
+ """
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+ >contig1
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+ AAAAATTTTTGGGGGCCCCC
122
+ """
123
+ And I write to "assembly/annotations.gff" with:
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+ """
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+ ##gff-version 3
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+ contig1 . gene 1 3 . - 1 ID=gene1;Name=abcd
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+ """
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+ And I append to "Gemfile" with:
129
+ """
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+ gem 'genomer-plugin-view', :path => '../../../'
131
+ """
132
+ When I run `genomer view table --identifier=genome`
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+ Then the exit status should be 0
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+ And the output should contain:
135
+ """
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+ >Feature genome annotation_table
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+ 3 1 gene
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+ locus_tag gene1
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+ gene abcd
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+
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+ """
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+
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+ @disable-bundler
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+ Scenario: Reseting locus tag numbering at the scaffold origin
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+ Given I successfully run `genomer init project`
146
+ And I cd to "project"
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+ And I write to "assembly/scaffold.yml" with:
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+ """
149
+ ---
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+ - sequence:
151
+ source: contig1
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+ """
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+ And I write to "assembly/sequence.fna" with:
154
+ """
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+ >contig1
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+ AAAAATTTTTGGGGGCCCCC
157
+ """
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+ And I write to "assembly/annotations.gff" with:
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+ """
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+ ##gff-version 3
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+ contig1 . gene 1 3 . + 1 ID=gene1
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+ contig1 . gene 4 6 . + 1 ID=gene2
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+ """
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+ And I append to "Gemfile" with:
165
+ """
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+ gem 'genomer-plugin-view', :path => '../../../'
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+ """
168
+ When I run `genomer view table --identifier=genome --reset_locus_numbering`
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+ Then the exit status should be 0
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+ And the output should contain:
171
+ """
172
+ >Feature genome annotation_table
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+ 1 3 gene
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+ locus_tag 000001
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+ 4 6 gene
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+ locus_tag 000002
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+
178
+ """
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+ @disable-bundler
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+ Scenario: Reseting locus tag numbering at specified start value
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+ Given I successfully run `genomer init project`
182
+ And I cd to "project"
183
+ And I write to "assembly/scaffold.yml" with:
184
+ """
185
+ ---
186
+ - sequence:
187
+ source: contig1
188
+ """
189
+ And I write to "assembly/sequence.fna" with:
190
+ """
191
+ >contig1
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+ AAAAATTTTTGGGGGCCCCC
193
+ """
194
+ And I write to "assembly/annotations.gff" with:
195
+ """
196
+ ##gff-version 3
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+ contig1 . gene 1 3 . + 1 ID=gene1
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+ contig1 . gene 4 6 . + 1 ID=gene2
199
+ """
200
+ And I append to "Gemfile" with:
201
+ """
202
+ gem 'genomer-plugin-view', :path => '../../../'
203
+ """
204
+ When I run `genomer view table --identifier=genome --reset_locus_numbering=5`
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+ Then the exit status should be 0
206
+ And the output should contain:
207
+ """
208
+ >Feature genome annotation_table
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+ 1 3 gene
210
+ locus_tag 000005
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+ 4 6 gene
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+ locus_tag 000006
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+
214
+ """
215
+
216
+ @disable-bundler
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+ Scenario: Reseting locus tag at the scaffold origin with unordered annotations
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+ Given I successfully run `genomer init project`
219
+ And I cd to "project"
220
+ And I write to "assembly/scaffold.yml" with:
221
+ """
222
+ ---
223
+ - sequence:
224
+ source: contig1
225
+ """
226
+ And I write to "assembly/sequence.fna" with:
227
+ """
228
+ >contig1
229
+ AAAAATTTTTGGGGGCCCCC
230
+ """
231
+ And I write to "assembly/annotations.gff" with:
232
+ """
233
+ ##gff-version 3
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+ contig1 . gene 10 12 . + 1 ID=gene4
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+ contig1 . gene 4 6 . + 1 ID=gene2
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+ contig1 . gene 1 3 . + 1 ID=gene1
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+ contig1 . gene 7 9 . + 1 ID=gene3
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+ """
239
+ And I append to "Gemfile" with:
240
+ """
241
+ gem 'genomer-plugin-view', :path => '../../../'
242
+ """
243
+ When I run `genomer view table --identifier=genome --reset_locus_numbering`
244
+ Then the exit status should be 0
245
+ And the output should contain:
246
+ """
247
+ >Feature genome annotation_table
248
+ 1 3 gene
249
+ locus_tag 000001
250
+ 4 6 gene
251
+ locus_tag 000002
252
+ 7 9 gene
253
+ locus_tag 000003
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+ 10 12 gene
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+ locus_tag 000004
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+
257
+ """
258
+
259
+ @disable-bundler
260
+ Scenario: Adding a prefix to annotation locus tags
261
+ Given I successfully run `genomer init project`
262
+ And I cd to "project"
263
+ And I write to "assembly/scaffold.yml" with:
264
+ """
265
+ ---
266
+ - sequence:
267
+ source: contig1
268
+ """
269
+ And I write to "assembly/sequence.fna" with:
270
+ """
271
+ >contig1
272
+ AAAAATTTTTGGGGGCCCCC
273
+ """
274
+ And I write to "assembly/annotations.gff" with:
275
+ """
276
+ ##gff-version 3
277
+ contig1 . gene 10 12 . + 1 ID=gene4
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+ contig1 . gene 4 6 . + 1 ID=gene2
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+ contig1 . gene 1 3 . + 1 ID=gene1
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+ contig1 . gene 7 9 . + 1 ID=gene3
281
+ """
282
+ And I append to "Gemfile" with:
283
+ """
284
+ gem 'genomer-plugin-view', :path => '../../../'
285
+ """
286
+ When I run `genomer view table --identifier=genome --prefix=pre_`
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+ Then the exit status should be 0
288
+ And the output should contain:
289
+ """
290
+ >Feature genome annotation_table
291
+ 1 3 gene
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+ locus_tag pre_gene1
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+ 4 6 gene
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+ locus_tag pre_gene2
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+ 7 9 gene
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+ locus_tag pre_gene3
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+ 10 12 gene
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+ locus_tag pre_gene4
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+
300
+ """
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+
302
+
data/features/table/feature_type.feature ADDED
@@ -0,0 +1,180 @@
1
+ Feature: Producing an table view of alternate entries
2
+ In order to submit non-CDS genome annotations
3
+ A user can use the "table" command with --generate_encoded_features
4
+ to generate the genbank annotation table format with non-CDS
5
+
6
+ @disable-bundler
7
+ Scenario: Creating an unknown feature type using 'feature_type'
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
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+ contig1 . gene 1 3 . - 1 ID=gene1;feature_type=unknown;product=something
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+ """
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 1
32
+ And the output should contain:
33
+ """
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+ Error. Unknown feature_type 'unknown'
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+ """
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+
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+ @disable-bundler
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+ Scenario: Creating a tRNA entry from using the 'feature_type' field
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+ Given I successfully run `genomer init project`
40
+ And I cd to "project"
41
+ And I write to "assembly/scaffold.yml" with:
42
+ """
43
+ ---
44
+ - sequence:
45
+ source: contig1
46
+ """
47
+ And I write to "assembly/sequence.fna" with:
48
+ """
49
+ >contig1
50
+ AAAAATTTTTGGGGGCCCCC
51
+ """
52
+ And I write to "assembly/annotations.gff" with:
53
+ """
54
+ ##gff-version 3
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+ contig1 . gene 1 3 . - 1 ID=gene1;feature_type=tRNA;product=tRNA-Gly;Note=something
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+ """
57
+ And I append to "Gemfile" with:
58
+ """
59
+ gem 'genomer-plugin-view', :path => '../../../'
60
+ """
61
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
62
+ Then the exit status should be 0
63
+ And the output should contain:
64
+ """
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+ 3 1 gene
66
+ locus_tag gene1
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+ 3 1 tRNA
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+ product tRNA-Gly
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+ note something
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+
71
+ """
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+
73
+ @disable-bundler
74
+ Scenario: Creating a rRNA entry from using the 'feature_type' field
75
+ Given I successfully run `genomer init project`
76
+ And I cd to "project"
77
+ And I write to "assembly/scaffold.yml" with:
78
+ """
79
+ ---
80
+ - sequence:
81
+ source: contig1
82
+ """
83
+ And I write to "assembly/sequence.fna" with:
84
+ """
85
+ >contig1
86
+ AAAAATTTTTGGGGGCCCCC
87
+ """
88
+ And I write to "assembly/annotations.gff" with:
89
+ """
90
+ ##gff-version 3
91
+ contig1 . gene 1 3 . - 1 ID=gene1;feature_type=rRNA;product=ribosomal RNA;Note=something
92
+ """
93
+ And I append to "Gemfile" with:
94
+ """
95
+ gem 'genomer-plugin-view', :path => '../../../'
96
+ """
97
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
98
+ Then the exit status should be 0
99
+ And the output should contain:
100
+ """
101
+ 3 1 gene
102
+ locus_tag gene1
103
+ 3 1 rRNA
104
+ product ribosomal RNA
105
+ note something
106
+
107
+ """
108
+
109
+ @disable-bundler
110
+ Scenario: Creating a tmRNA entry from using the 'feature_type' field
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 1 3 . - 1 ID=gene1;feature_type=tmRNA;product=tmRNA;Note=something
128
+ """
129
+ And I append to "Gemfile" with:
130
+ """
131
+ gem 'genomer-plugin-view', :path => '../../../'
132
+ """
133
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
134
+ Then the exit status should be 0
135
+ And the output should contain:
136
+ """
137
+ 3 1 gene
138
+ locus_tag gene1
139
+ 3 1 tmRNA
140
+ product tmRNA
141
+ note something
142
+
143
+ """
144
+
145
+ @disable-bundler
146
+ Scenario: Creating a miscRNA entry from using the 'feature_type' field
147
+ Given I successfully run `genomer init project`
148
+ And I cd to "project"
149
+ And I write to "assembly/scaffold.yml" with:
150
+ """
151
+ ---
152
+ - sequence:
153
+ source: contig1
154
+ """
155
+ And I write to "assembly/sequence.fna" with:
156
+ """
157
+ >contig1
158
+ AAAAATTTTTGGGGGCCCCC
159
+ """
160
+ And I write to "assembly/annotations.gff" with:
161
+ """
162
+ ##gff-version 3
163
+ contig1 . gene 1 3 . - 1 ID=gene1;feature_type=miscRNA;product=RNA signal;Note=something
164
+ """
165
+ And I append to "Gemfile" with:
166
+ """
167
+ gem 'genomer-plugin-view', :path => '../../../'
168
+ """
169
+ When I run `genomer view table --identifier=genome --generate_encoded_features`
170
+ Then the exit status should be 0
171
+ And the output should contain:
172
+ """
173
+ 3 1 gene
174
+ locus_tag gene1
175
+ 3 1 miscRNA
176
+ product RNA signal
177
+ note something
178
+
179
+ """
180
+