genomer-plugin-view 0.0.5 → 0.0.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/features/core.feature +16 -0
- data/features/table/cds_entries.feature +73 -0
- data/genomer-plugin-view.gemspec +2 -2
- data/lib/genomer-plugin-view/gff_record_helper.rb +1 -2
- data/lib/genomer-plugin-view/table.rb +20 -16
- data/lib/genomer-plugin-view/version.rb +1 -1
- data/lib/genomer-plugin-view.rb +16 -0
- data/man/genomer-view.ronn +4 -0
- data/spec/genomer-view-plugin/gff_record_helper_spec.rb +28 -25
- data/spec/genomer-view-plugin/table_spec.rb +79 -16
- data/spec/genomer-view-plugin_spec.rb +27 -7
- data/spec/spec_helper.rb +1 -1
- metadata +7 -7
data/features/core.feature
CHANGED
@@ -10,3 +10,19 @@ Feature: Producing different views of a genomes scaffold
|
|
10
10
|
Then the exit status should be 0
|
11
11
|
And the output should contain a valid man page
|
12
12
|
And the output should contain "GENOMER-VIEW(1)"
|
13
|
+
|
14
|
+
@disable-bundler
|
15
|
+
Scenario: Running `genomer view` without a subcommand
|
16
|
+
Given I create a new genomer project
|
17
|
+
When I run `genomer view`
|
18
|
+
Then the exit status should be 0
|
19
|
+
And the output should contain:
|
20
|
+
"""
|
21
|
+
Run `genomer man view COMMAND` to review available formats
|
22
|
+
Where COMMAND is one of the following:
|
23
|
+
agp
|
24
|
+
fasta
|
25
|
+
gff
|
26
|
+
mapping
|
27
|
+
table
|
28
|
+
"""
|
@@ -302,3 +302,76 @@ Feature: Producing cds annotation view from a scaffold
|
|
302
302
|
|
303
303
|
"""
|
304
304
|
|
305
|
+
@disable-bundler
|
306
|
+
Scenario: A CDS entry with a single DBxref attribute
|
307
|
+
Given I successfully run `genomer init project`
|
308
|
+
And I cd to "project"
|
309
|
+
And I write to "assembly/scaffold.yml" with:
|
310
|
+
"""
|
311
|
+
---
|
312
|
+
- sequence:
|
313
|
+
source: contig1
|
314
|
+
"""
|
315
|
+
And I write to "assembly/sequence.fna" with:
|
316
|
+
"""
|
317
|
+
>contig1
|
318
|
+
AAAAATTTTTGGGGGCCCCC
|
319
|
+
"""
|
320
|
+
And I write to "assembly/annotations.gff" with:
|
321
|
+
"""
|
322
|
+
##gff-version 3
|
323
|
+
contig1 . gene 1 3 . - 1 ID=gene1;DBxref=GO:000001
|
324
|
+
"""
|
325
|
+
And I append to "Gemfile" with:
|
326
|
+
"""
|
327
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
328
|
+
"""
|
329
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
330
|
+
Then the exit status should be 0
|
331
|
+
And the output should contain:
|
332
|
+
"""
|
333
|
+
>Feature genome annotation_table
|
334
|
+
3 1 gene
|
335
|
+
locus_tag gene1
|
336
|
+
3 1 CDS
|
337
|
+
protein_id gene1
|
338
|
+
db_xref GO:000001
|
339
|
+
|
340
|
+
"""
|
341
|
+
|
342
|
+
@disable-bundler
|
343
|
+
Scenario: A CDS entry with multiple DBxref attributes
|
344
|
+
Given I successfully run `genomer init project`
|
345
|
+
And I cd to "project"
|
346
|
+
And I write to "assembly/scaffold.yml" with:
|
347
|
+
"""
|
348
|
+
---
|
349
|
+
- sequence:
|
350
|
+
source: contig1
|
351
|
+
"""
|
352
|
+
And I write to "assembly/sequence.fna" with:
|
353
|
+
"""
|
354
|
+
>contig1
|
355
|
+
AAAAATTTTTGGGGGCCCCC
|
356
|
+
"""
|
357
|
+
And I write to "assembly/annotations.gff" with:
|
358
|
+
"""
|
359
|
+
##gff-version 3
|
360
|
+
contig1 . gene 1 3 . - 1 ID=gene1;DBxref=GO:000001;DBxref=InterPro:IPR000111
|
361
|
+
"""
|
362
|
+
And I append to "Gemfile" with:
|
363
|
+
"""
|
364
|
+
gem 'genomer-plugin-view', :path => '../../../'
|
365
|
+
"""
|
366
|
+
When I run `genomer view table --identifier=genome --generate_encoded_features`
|
367
|
+
Then the exit status should be 0
|
368
|
+
And the output should contain:
|
369
|
+
"""
|
370
|
+
>Feature genome annotation_table
|
371
|
+
3 1 gene
|
372
|
+
locus_tag gene1
|
373
|
+
3 1 CDS
|
374
|
+
protein_id gene1
|
375
|
+
db_xref GO:000001
|
376
|
+
db_xref InterPro:IPR000111
|
377
|
+
"""
|
data/genomer-plugin-view.gemspec
CHANGED
@@ -6,7 +6,7 @@ Gem::Specification.new do |s|
|
|
6
6
|
s.name = "genomer-plugin-view"
|
7
7
|
s.version = GenomerViewPlugin::VERSION
|
8
8
|
s.platform = Gem::Platform::RUBY
|
9
|
-
s.homepage = "http://
|
9
|
+
s.homepage = "http://next.gs"
|
10
10
|
s.license = "MIT"
|
11
11
|
s.authors = ["Michael Barton"]
|
12
12
|
s.email = ["mail@michaelbarton.me.uk"]
|
@@ -16,7 +16,7 @@ Gem::Specification.new do |s|
|
|
16
16
|
s.required_rubygems_version = "~> 1.8.0"
|
17
17
|
s.rubyforge_project = "genomer-view-plugin"
|
18
18
|
|
19
|
-
s.add_dependency "genomer", ">= 0.0.
|
19
|
+
s.add_dependency "genomer", ">= 0.0.10"
|
20
20
|
|
21
21
|
# Specs
|
22
22
|
s.add_development_dependency "rspec", "~> 2.9.0"
|
@@ -21,33 +21,37 @@ class GenomerPluginView::Table < Genomer::Plugin
|
|
21
21
|
def create_encoded_features(genes,prefix)
|
22
22
|
features = genes.map do |gene|
|
23
23
|
feature = gene.clone
|
24
|
-
attrs =
|
24
|
+
attrs = feature.attributes.clone
|
25
25
|
|
26
|
-
|
27
|
-
|
28
|
-
end
|
29
|
-
|
30
|
-
feature.feature = attrs['feature_type'] || 'CDS'
|
26
|
+
feature_type = attrs.detect{|k,v| k == 'feature_type'}
|
27
|
+
feature.feature = (feature_type ? feature_type.last : 'CDS')
|
31
28
|
|
32
29
|
unless SUPPORTED_FEATURE_TYPES.include?(feature.feature)
|
33
30
|
raise Genomer::Error, "Unknown feature_type '#{feature.feature}'"
|
34
31
|
end
|
35
32
|
|
33
|
+
attrs.map! do |(k,v)|
|
34
|
+
v = (k == 'ID' && prefix.instance_of?(String) ? prefix + v : v)
|
35
|
+
[k,v]
|
36
|
+
end
|
37
|
+
|
36
38
|
if feature.feature == "CDS"
|
37
|
-
name, prdt, ftn = attrs['Name'], attrs['product'], attrs['function']
|
38
39
|
|
39
|
-
if
|
40
|
-
|
41
|
-
|
42
|
-
|
43
|
-
end
|
40
|
+
if attrs.detect{|(k,v)| k == 'Name' }
|
41
|
+
attrs.map! do |(k,v)|
|
42
|
+
v = v.clone
|
43
|
+
v[0,1] = v[0,1].upcase if k == 'Name'
|
44
44
|
|
45
|
-
|
46
|
-
|
47
|
-
|
45
|
+
v = nil if k == 'function'
|
46
|
+
k = 'function' if k == 'product'
|
47
|
+
k = 'product' if k == 'Name'
|
48
|
+
[k,v]
|
49
|
+
end
|
50
|
+
end
|
51
|
+
#attrs.delete('Name')
|
48
52
|
end
|
49
53
|
|
50
|
-
feature.attributes = attrs.
|
54
|
+
feature.attributes = attrs.reject{|(_,value)| value.nil? }
|
51
55
|
feature
|
52
56
|
end
|
53
57
|
genes.zip(features).flatten
|
data/lib/genomer-plugin-view.rb
CHANGED
@@ -3,6 +3,7 @@ require 'genomer'
|
|
3
3
|
class GenomerPluginView < Genomer::Plugin
|
4
4
|
|
5
5
|
def run
|
6
|
+
return help if arguments.empty?
|
6
7
|
self.class.fetch_view(arguments.shift).new(arguments,flags).run
|
7
8
|
end
|
8
9
|
|
@@ -26,4 +27,19 @@ class GenomerPluginView < Genomer::Plugin
|
|
26
27
|
end
|
27
28
|
end
|
28
29
|
|
30
|
+
def help
|
31
|
+
message = <<-STRING.unindent
|
32
|
+
Run `genomer man view COMMAND` to review available formats
|
33
|
+
Where COMMAND is one of the following:
|
34
|
+
STRING
|
35
|
+
|
36
|
+
message + Dir[File.dirname(__FILE__) + '/genomer-plugin-view/*.rb'].
|
37
|
+
map{|f| File.basename(f).gsub('.rb','')}.
|
38
|
+
delete_if{|i| i == 'version'}.
|
39
|
+
delete_if{|i| i == 'gff_record_helper'}.
|
40
|
+
sort.
|
41
|
+
map{|i| " " * 2 + i}.
|
42
|
+
join("\n") + "\n"
|
43
|
+
end
|
44
|
+
|
29
45
|
end
|
data/man/genomer-view.ronn
CHANGED
@@ -68,6 +68,10 @@ begin with an upper case letter.
|
|
68
68
|
Used to populate the **Note** field for entries when the
|
69
69
|
`--generate_encoded_features` option is passed.
|
70
70
|
|
71
|
+
* `DBxref`: Used to link the annotation to other database references. This
|
72
|
+
field is added verbatim to generated output. Multiple entires of this
|
73
|
+
field may be used.
|
74
|
+
|
71
75
|
### GENOMER ATTRIBUTES
|
72
76
|
|
73
77
|
These attributes are specific to genomer and should begin with a lower case
|
@@ -68,7 +68,7 @@ describe GenomerPluginView::GffRecordHelper do
|
|
68
68
|
context "gene feature with attributes" do
|
69
69
|
|
70
70
|
let(:annotation) do
|
71
|
-
@attn.feature('gene').attributes('ID'
|
71
|
+
@attn.feature('gene').attributes([['ID', 'id']])
|
72
72
|
end
|
73
73
|
|
74
74
|
it "should return a table entry" do
|
@@ -189,7 +189,7 @@ describe GenomerPluginView::GffRecordHelper do
|
|
189
189
|
context "for a feature with an unknown attribute" do
|
190
190
|
|
191
191
|
let(:annotation) do
|
192
|
-
@attn.attributes('something'
|
192
|
+
@attn.attributes([['something','else']])
|
193
193
|
end
|
194
194
|
|
195
195
|
it "should return an empty array" do
|
@@ -199,34 +199,38 @@ describe GenomerPluginView::GffRecordHelper do
|
|
199
199
|
end
|
200
200
|
|
201
201
|
feature_keys = {
|
202
|
-
:gene =>
|
203
|
-
|
204
|
-
|
205
|
-
:tRNA =>
|
206
|
-
|
207
|
-
|
208
|
-
|
209
|
-
|
210
|
-
|
211
|
-
|
212
|
-
|
213
|
-
|
214
|
-
|
215
|
-
|
216
|
-
|
217
|
-
|
218
|
-
|
219
|
-
|
220
|
-
|
221
|
-
|
222
|
-
|
202
|
+
:gene => [
|
203
|
+
['Name', 'gene'],
|
204
|
+
['ID', 'locus_tag']],
|
205
|
+
:tRNA => [
|
206
|
+
['DBxref', 'db_xref'],
|
207
|
+
['product', 'product'],
|
208
|
+
['Note', 'note']],
|
209
|
+
:rRNA => [
|
210
|
+
['product', 'product'],
|
211
|
+
['Note', 'note']],
|
212
|
+
:miscRNA => [
|
213
|
+
['DBxref', 'db_xref'],
|
214
|
+
['product', 'product'],
|
215
|
+
['Note', 'note']],
|
216
|
+
:tmRNA => [
|
217
|
+
['DBxref', 'db_xref'],
|
218
|
+
['product', 'product'],
|
219
|
+
['Note', 'note']],
|
220
|
+
:CDS => [
|
221
|
+
['ec_number', 'EC_number'],
|
222
|
+
['DBxref', 'db_xref'],
|
223
|
+
['function', 'function'],
|
224
|
+
['product', 'product'],
|
225
|
+
['Note', 'note'],
|
226
|
+
['ID', 'protein_id' ]]}
|
223
227
|
|
224
228
|
feature_keys.each do |type,mappings|
|
225
229
|
mappings.each do |a,b|
|
226
230
|
context "#{type.to_s} feature" do
|
227
231
|
|
228
232
|
let(:annotation) do
|
229
|
-
@attn.feature(type.to_s).attributes(a
|
233
|
+
@attn.feature(type.to_s).attributes([[a, :value]])
|
230
234
|
end
|
231
235
|
|
232
236
|
it "should return #{b} for the attribute #{a}" do
|
@@ -238,7 +242,6 @@ describe GenomerPluginView::GffRecordHelper do
|
|
238
242
|
end
|
239
243
|
end
|
240
244
|
|
241
|
-
|
242
245
|
end
|
243
246
|
|
244
247
|
end
|
@@ -73,7 +73,7 @@ describe GenomerPluginView::Table do
|
|
73
73
|
|
74
74
|
let(:flags){ {:generate_encoded_features => 'pre_'} }
|
75
75
|
|
76
|
-
let(:annotations){ [gene({:attributes =>
|
76
|
+
let(:annotations){ [gene({:attributes => [['ID', '1']]})] }
|
77
77
|
|
78
78
|
it "should call the to_genbank_features method " do
|
79
79
|
subject.run.should == <<-EOS.unindent
|
@@ -91,9 +91,9 @@ describe GenomerPluginView::Table do
|
|
91
91
|
|
92
92
|
let(:flags){ {:generate_encoded_features => 'pre_'} }
|
93
93
|
|
94
|
-
let(:annotations){ [gene({:attributes =>
|
95
|
-
'feature_type'
|
96
|
-
'product'
|
94
|
+
let(:annotations){ [gene({:attributes => [['ID', '1'],
|
95
|
+
['feature_type', 'tRNA'],
|
96
|
+
['product', 'tRNA-Gly']]})] }
|
97
97
|
|
98
98
|
it "should call the to_genbank_features method " do
|
99
99
|
subject.run.should == <<-EOS.unindent
|
@@ -112,7 +112,7 @@ describe GenomerPluginView::Table do
|
|
112
112
|
describe "#create_encoded_features" do
|
113
113
|
|
114
114
|
let(:prefix) do
|
115
|
-
|
115
|
+
true
|
116
116
|
end
|
117
117
|
|
118
118
|
subject do
|
@@ -143,10 +143,26 @@ describe GenomerPluginView::Table do
|
|
143
143
|
|
144
144
|
end
|
145
145
|
|
146
|
+
describe "passed a gene with an ID attributes" do
|
147
|
+
|
148
|
+
let(:attributes) do
|
149
|
+
[['ID', 'something']]
|
150
|
+
end
|
151
|
+
|
152
|
+
let(:annotations) do
|
153
|
+
[gene({:attributes => attributes})]
|
154
|
+
end
|
155
|
+
|
156
|
+
it "should not change the attributes" do
|
157
|
+
subject.attributes.should == attributes
|
158
|
+
end
|
159
|
+
|
160
|
+
end
|
161
|
+
|
146
162
|
describe "passed a gene with a known feature_type attribute" do
|
147
163
|
|
148
164
|
let(:attributes) do
|
149
|
-
|
165
|
+
[['feature_type', 'tRNA']]
|
150
166
|
end
|
151
167
|
|
152
168
|
let(:annotations) do
|
@@ -162,7 +178,7 @@ describe GenomerPluginView::Table do
|
|
162
178
|
describe "passed a gene with an unknown feature_type attribute" do
|
163
179
|
|
164
180
|
let(:attributes) do
|
165
|
-
|
181
|
+
[['feature_type', 'unknown']]
|
166
182
|
end
|
167
183
|
|
168
184
|
let(:annotations) do
|
@@ -176,10 +192,26 @@ describe GenomerPluginView::Table do
|
|
176
192
|
|
177
193
|
end
|
178
194
|
|
195
|
+
describe "passed a gene with a duplicate attribute" do
|
196
|
+
|
197
|
+
let(:attributes) do
|
198
|
+
[['product', 'abcd'],['product', 'efgh']]
|
199
|
+
end
|
200
|
+
|
201
|
+
let(:annotations) do
|
202
|
+
[gene({:attributes => attributes})]
|
203
|
+
end
|
204
|
+
|
205
|
+
it "should not change attributes" do
|
206
|
+
subject.should have_identical_attributes cds({:attributes => attributes})
|
207
|
+
end
|
208
|
+
|
209
|
+
end
|
210
|
+
|
179
211
|
describe "passed a gene with a Name attribute" do
|
180
212
|
|
181
213
|
let(:attributes) do
|
182
|
-
|
214
|
+
[['Name', 'abcD']]
|
183
215
|
end
|
184
216
|
|
185
217
|
let(:annotations) do
|
@@ -187,7 +219,7 @@ describe GenomerPluginView::Table do
|
|
187
219
|
end
|
188
220
|
|
189
221
|
it "should set the capitalise value to the product key" do
|
190
|
-
subject.should have_identical_attributes cds({:attributes =>
|
222
|
+
subject.should have_identical_attributes cds({:attributes => [['product', 'AbcD']]})
|
191
223
|
end
|
192
224
|
|
193
225
|
end
|
@@ -195,7 +227,7 @@ describe GenomerPluginView::Table do
|
|
195
227
|
describe "passed a gene with a product attribute" do
|
196
228
|
|
197
229
|
let(:attributes) do
|
198
|
-
|
230
|
+
[['product', 'abcd']]
|
199
231
|
end
|
200
232
|
|
201
233
|
let(:annotations) do
|
@@ -211,7 +243,7 @@ describe GenomerPluginView::Table do
|
|
211
243
|
describe "passed a gene with a function attribute" do
|
212
244
|
|
213
245
|
let(:attributes) do
|
214
|
-
|
246
|
+
[['function', 'abcd']]
|
215
247
|
end
|
216
248
|
|
217
249
|
let(:annotations) do
|
@@ -227,7 +259,7 @@ describe GenomerPluginView::Table do
|
|
227
259
|
describe "passed a gene with product and function attributes" do
|
228
260
|
|
229
261
|
let(:attributes) do
|
230
|
-
|
262
|
+
[['product', 'abcd'], ['function', 'efgh']]
|
231
263
|
end
|
232
264
|
|
233
265
|
let(:annotations) do
|
@@ -243,7 +275,7 @@ describe GenomerPluginView::Table do
|
|
243
275
|
describe "passed a gene with Name and product attributes" do
|
244
276
|
|
245
277
|
let(:attributes) do
|
246
|
-
|
278
|
+
[['Name', 'abcD'], ['product', 'efgh']]
|
247
279
|
end
|
248
280
|
|
249
281
|
let(:annotations) do
|
@@ -252,7 +284,7 @@ describe GenomerPluginView::Table do
|
|
252
284
|
|
253
285
|
it "should map Name to product and product to function" do
|
254
286
|
subject.should have_identical_attributes cds({:attributes =>
|
255
|
-
|
287
|
+
[['product', 'AbcD'], ['function', 'efgh']]})
|
256
288
|
end
|
257
289
|
|
258
290
|
end
|
@@ -260,7 +292,7 @@ describe GenomerPluginView::Table do
|
|
260
292
|
describe "passed a gene with Name, product and function attributes" do
|
261
293
|
|
262
294
|
let(:attributes) do
|
263
|
-
|
295
|
+
[['Name', 'abcD'], ['product', 'efgh'], ['function', 'ijkl']]
|
264
296
|
end
|
265
297
|
|
266
298
|
let(:annotations) do
|
@@ -269,11 +301,42 @@ describe GenomerPluginView::Table do
|
|
269
301
|
|
270
302
|
it "should map Name to product and product to function" do
|
271
303
|
subject.should have_identical_attributes cds({:attributes =>
|
272
|
-
|
304
|
+
[['product', 'AbcD'], ['function', 'efgh']]})
|
273
305
|
end
|
274
306
|
|
275
307
|
end
|
276
308
|
|
309
|
+
describe "passed a gene with a single db_xref attribute" do
|
310
|
+
|
311
|
+
let(:attributes) do
|
312
|
+
{'db_xref' => 'InterPro:IPR000111'}
|
313
|
+
end
|
314
|
+
|
315
|
+
let(:annotations) do
|
316
|
+
[gene({:attributes => attributes})]
|
317
|
+
end
|
318
|
+
|
319
|
+
it "should not change attributes" do
|
320
|
+
subject.should have_identical_attributes cds({:attributes => attributes})
|
321
|
+
end
|
322
|
+
|
323
|
+
end
|
324
|
+
|
325
|
+
describe "passed a gene with multiple db_xref attribute" do
|
326
|
+
|
327
|
+
let(:attributes) do
|
328
|
+
{'db_xref' => 'InterPro:IPR000111','db_xref' => 'GO:000001'}
|
329
|
+
end
|
330
|
+
|
331
|
+
let(:annotations) do
|
332
|
+
[gene({:attributes => attributes})]
|
333
|
+
end
|
334
|
+
|
335
|
+
it "should not change attributes" do
|
336
|
+
subject.should have_identical_attributes cds({:attributes => attributes})
|
337
|
+
end
|
338
|
+
|
339
|
+
end
|
277
340
|
end
|
278
341
|
|
279
342
|
end
|
@@ -16,18 +16,38 @@ describe GenomerPluginView do
|
|
16
16
|
GenomerPluginView::Example = Class.new(GenomerPluginView)
|
17
17
|
end
|
18
18
|
|
19
|
-
|
20
|
-
|
21
|
-
|
19
|
+
context "with a view argument passed" do
|
20
|
+
|
21
|
+
before do
|
22
|
+
mock(described_class).fetch_view('example') do
|
23
|
+
example
|
24
|
+
end
|
22
25
|
end
|
26
|
+
|
27
|
+
it "should initialize and run the required view plugin" do
|
28
|
+
mock.proxy(example).new([:arg],:flags) do |instance|
|
29
|
+
mock(instance).run
|
30
|
+
end
|
31
|
+
|
32
|
+
described_class.new(['example',:arg],:flags).run
|
33
|
+
end
|
34
|
+
|
23
35
|
end
|
24
36
|
|
25
|
-
|
26
|
-
|
27
|
-
|
37
|
+
context "with no argument passed" do
|
38
|
+
|
39
|
+
it "should return help information" do
|
40
|
+
described_class.new([],[]).run.should ==<<-STRING.unindent
|
41
|
+
Run `genomer man view COMMAND` to review available formats
|
42
|
+
Where COMMAND is one of the following:
|
43
|
+
agp
|
44
|
+
fasta
|
45
|
+
gff
|
46
|
+
mapping
|
47
|
+
table
|
48
|
+
STRING
|
28
49
|
end
|
29
50
|
|
30
|
-
described_class.new(['example',:arg],:flags).run
|
31
51
|
end
|
32
52
|
|
33
53
|
end
|
data/spec/spec_helper.rb
CHANGED
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: genomer-plugin-view
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.6
|
5
5
|
prerelease:
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
@@ -9,7 +9,7 @@ authors:
|
|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2013-
|
12
|
+
date: 2013-03-11 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: genomer
|
@@ -18,7 +18,7 @@ dependencies:
|
|
18
18
|
requirements:
|
19
19
|
- - ! '>='
|
20
20
|
- !ruby/object:Gem::Version
|
21
|
-
version: 0.0.
|
21
|
+
version: 0.0.10
|
22
22
|
type: :runtime
|
23
23
|
prerelease: false
|
24
24
|
version_requirements: !ruby/object:Gem::Requirement
|
@@ -26,7 +26,7 @@ dependencies:
|
|
26
26
|
requirements:
|
27
27
|
- - ! '>='
|
28
28
|
- !ruby/object:Gem::Version
|
29
|
-
version: 0.0.
|
29
|
+
version: 0.0.10
|
30
30
|
- !ruby/object:Gem::Dependency
|
31
31
|
name: rspec
|
32
32
|
requirement: !ruby/object:Gem::Requirement
|
@@ -172,7 +172,7 @@ files:
|
|
172
172
|
- spec/genomer-view-plugin/table_spec.rb
|
173
173
|
- spec/genomer-view-plugin_spec.rb
|
174
174
|
- spec/spec_helper.rb
|
175
|
-
homepage: http://
|
175
|
+
homepage: http://next.gs
|
176
176
|
licenses:
|
177
177
|
- MIT
|
178
178
|
post_install_message:
|
@@ -187,7 +187,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
187
187
|
version: '0'
|
188
188
|
segments:
|
189
189
|
- 0
|
190
|
-
hash:
|
190
|
+
hash: 390518256786568765
|
191
191
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
192
192
|
none: false
|
193
193
|
requirements:
|
@@ -196,7 +196,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
196
196
|
version: 1.8.0
|
197
197
|
requirements: []
|
198
198
|
rubyforge_project: genomer-view-plugin
|
199
|
-
rubygems_version: 1.8.
|
199
|
+
rubygems_version: 1.8.25
|
200
200
|
signing_key:
|
201
201
|
specification_version: 3
|
202
202
|
summary: Provide different views of scaffold.
|