bio-maf 0.2.0-java → 0.3.0-java
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- data/.gitignore +1 -0
- data/Gemfile +3 -1
- data/README.md +98 -29
- data/Rakefile +6 -2
- data/bin/maf_tile +59 -35
- data/bio-maf.gemspec +4 -3
- data/features/block-joining.feature +32 -0
- data/features/dir-access.feature +46 -0
- data/features/maf-indexing.feature +23 -0
- data/features/maf-to-fasta.feature +9 -0
- data/features/slice.feature +54 -0
- data/features/step_definitions/dir-access_steps.rb +15 -0
- data/features/step_definitions/file_steps.rb +7 -0
- data/features/step_definitions/gap_removal_steps.rb +4 -0
- data/features/step_definitions/index_steps.rb +3 -3
- data/features/step_definitions/output_steps.rb +9 -1
- data/features/step_definitions/parse_steps.rb +13 -2
- data/features/step_definitions/query_steps.rb +7 -6
- data/features/step_definitions/slice_steps.rb +15 -0
- data/features/step_definitions/{gap-filling_steps.rb → tiling_steps.rb} +0 -0
- data/features/support/aruba.rb +1 -0
- data/features/support/env.rb +3 -1
- data/features/{gap-filling.feature → tiling.feature} +85 -0
- data/lib/bio/maf/index.rb +223 -11
- data/lib/bio/maf/maf.rb +209 -0
- data/lib/bio/maf/parser.rb +190 -111
- data/lib/bio/maf/tiler.rb +33 -6
- data/man/maf_index.1 +1 -1
- data/man/maf_tile.1 +7 -7
- data/man/maf_tile.1.ronn +21 -13
- data/man/maf_to_fasta.1 +1 -1
- data/spec/bio/maf/index_spec.rb +99 -0
- data/spec/bio/maf/maf_spec.rb +184 -0
- data/spec/bio/maf/parser_spec.rb +75 -115
- data/spec/bio/maf/tiler_spec.rb +44 -0
- data/test/data/chr22_ieq2.maf +11 -0
- data/test/data/gap-1.kct +0 -0
- data/test/data/gap-1.maf +9 -0
- data/test/data/gap-filled1.fa +6 -0
- data/test/data/gap-sp1.fa.gz +0 -0
- data/test/data/mm8_chr7_tiny_slice1.maf +9 -0
- data/test/data/mm8_chr7_tiny_slice2.maf +10 -0
- data/test/data/mm8_chr7_tiny_slice3.maf +10 -0
- data/test/data/mm8_chrM_tiny.kct +0 -0
- data/test/data/mm8_chrM_tiny.maf +1000 -0
- metadata +65 -16
metadata
CHANGED
@@ -2,30 +2,44 @@
|
|
2
2
|
name: bio-maf
|
3
3
|
version: !ruby/object:Gem::Version
|
4
4
|
prerelease:
|
5
|
-
version: 0.
|
5
|
+
version: 0.3.0
|
6
6
|
platform: java
|
7
7
|
authors:
|
8
8
|
- Clayton Wheeler
|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2012-
|
12
|
+
date: 2012-07-18 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
|
+
- !ruby/object:Gem::Dependency
|
15
|
+
name: bio-alignment
|
16
|
+
version_requirements: !ruby/object:Gem::Requirement
|
17
|
+
requirements:
|
18
|
+
- - ~>
|
19
|
+
- !ruby/object:Gem::Version
|
20
|
+
version: 0.0.7
|
21
|
+
none: false
|
22
|
+
requirement: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - ~>
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: 0.0.7
|
27
|
+
none: false
|
28
|
+
prerelease: false
|
29
|
+
type: :runtime
|
14
30
|
- !ruby/object:Gem::Dependency
|
15
31
|
name: bio-bigbio
|
16
32
|
version_requirements: !ruby/object:Gem::Requirement
|
17
33
|
requirements:
|
18
34
|
- - ! '>='
|
19
35
|
- !ruby/object:Gem::Version
|
20
|
-
version:
|
21
|
-
MA==
|
36
|
+
version: '0'
|
22
37
|
none: false
|
23
38
|
requirement: !ruby/object:Gem::Requirement
|
24
39
|
requirements:
|
25
40
|
- - ! '>='
|
26
41
|
- !ruby/object:Gem::Version
|
27
|
-
version:
|
28
|
-
MA==
|
42
|
+
version: '0'
|
29
43
|
none: false
|
30
44
|
prerelease: false
|
31
45
|
type: :runtime
|
@@ -51,13 +65,13 @@ dependencies:
|
|
51
65
|
requirements:
|
52
66
|
- - ~>
|
53
67
|
- !ruby/object:Gem::Version
|
54
|
-
version: 0.
|
68
|
+
version: 0.3.0
|
55
69
|
none: false
|
56
70
|
requirement: !ruby/object:Gem::Requirement
|
57
71
|
requirements:
|
58
72
|
- - ~>
|
59
73
|
- !ruby/object:Gem::Version
|
60
|
-
version: 0.
|
74
|
+
version: 0.3.0
|
61
75
|
none: false
|
62
76
|
prerelease: false
|
63
77
|
type: :runtime
|
@@ -106,22 +120,29 @@ files:
|
|
106
120
|
- bin/maf_write
|
107
121
|
- bin/random_ranges
|
108
122
|
- bio-maf.gemspec
|
109
|
-
- features/
|
123
|
+
- features/block-joining.feature
|
124
|
+
- features/dir-access.feature
|
110
125
|
- features/gap-removal.feature
|
111
126
|
- features/maf-indexing.feature
|
112
127
|
- features/maf-output.feature
|
113
128
|
- features/maf-parsing.feature
|
114
129
|
- features/maf-querying.feature
|
115
130
|
- features/maf-to-fasta.feature
|
131
|
+
- features/slice.feature
|
116
132
|
- features/step_definitions/convert_steps.rb
|
117
|
-
- features/step_definitions/
|
133
|
+
- features/step_definitions/dir-access_steps.rb
|
134
|
+
- features/step_definitions/file_steps.rb
|
118
135
|
- features/step_definitions/gap_removal_steps.rb
|
119
136
|
- features/step_definitions/index_steps.rb
|
120
137
|
- features/step_definitions/output_steps.rb
|
121
138
|
- features/step_definitions/parse_steps.rb
|
122
139
|
- features/step_definitions/query_steps.rb
|
140
|
+
- features/step_definitions/slice_steps.rb
|
141
|
+
- features/step_definitions/tiling_steps.rb
|
123
142
|
- features/step_definitions/ucsc_bin_steps.rb
|
143
|
+
- features/support/aruba.rb
|
124
144
|
- features/support/env.rb
|
145
|
+
- features/tiling.feature
|
125
146
|
- features/ucsc-bins.feature
|
126
147
|
- lib/bio-maf.rb
|
127
148
|
- lib/bio-maf/maf.rb
|
@@ -144,18 +165,29 @@ files:
|
|
144
165
|
- man/maf_to_fasta.1
|
145
166
|
- man/maf_to_fasta.1.ronn
|
146
167
|
- spec/bio/maf/index_spec.rb
|
168
|
+
- spec/bio/maf/maf_spec.rb
|
147
169
|
- spec/bio/maf/parser_spec.rb
|
148
170
|
- spec/bio/maf/struct_spec.rb
|
149
171
|
- spec/bio/maf/tiler_spec.rb
|
150
172
|
- spec/spec_helper.rb
|
151
173
|
- test/data/big-block.maf
|
152
174
|
- test/data/chr22_ieq.maf
|
175
|
+
- test/data/chr22_ieq2.maf
|
153
176
|
- test/data/chrY-1block.maf
|
154
177
|
- test/data/empty
|
155
178
|
- test/data/empty.db
|
179
|
+
- test/data/gap-1.kct
|
180
|
+
- test/data/gap-1.maf
|
181
|
+
- test/data/gap-filled1.fa
|
156
182
|
- test/data/gap-sp1.fa
|
183
|
+
- test/data/gap-sp1.fa.gz
|
157
184
|
- test/data/mm8_chr7_tiny.kct
|
158
185
|
- test/data/mm8_chr7_tiny.maf
|
186
|
+
- test/data/mm8_chr7_tiny_slice1.maf
|
187
|
+
- test/data/mm8_chr7_tiny_slice2.maf
|
188
|
+
- test/data/mm8_chr7_tiny_slice3.maf
|
189
|
+
- test/data/mm8_chrM_tiny.kct
|
190
|
+
- test/data/mm8_chrM_tiny.maf
|
159
191
|
- test/data/mm8_mod_a.maf
|
160
192
|
- test/data/mm8_single.maf
|
161
193
|
- test/data/mm8_subset_a.maf
|
@@ -182,15 +214,13 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
182
214
|
segments:
|
183
215
|
- 0
|
184
216
|
hash: 2
|
185
|
-
version:
|
186
|
-
MA==
|
217
|
+
version: '0'
|
187
218
|
none: false
|
188
219
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
189
220
|
requirements:
|
190
221
|
- - ! '>='
|
191
222
|
- !ruby/object:Gem::Version
|
192
|
-
version:
|
193
|
-
MA==
|
223
|
+
version: '0'
|
194
224
|
none: false
|
195
225
|
requirements: []
|
196
226
|
rubyforge_project:
|
@@ -199,36 +229,54 @@ signing_key:
|
|
199
229
|
specification_version: 3
|
200
230
|
summary: MAF parser for BioRuby
|
201
231
|
test_files:
|
202
|
-
- features/
|
232
|
+
- features/block-joining.feature
|
233
|
+
- features/dir-access.feature
|
203
234
|
- features/gap-removal.feature
|
204
235
|
- features/maf-indexing.feature
|
205
236
|
- features/maf-output.feature
|
206
237
|
- features/maf-parsing.feature
|
207
238
|
- features/maf-querying.feature
|
208
239
|
- features/maf-to-fasta.feature
|
240
|
+
- features/slice.feature
|
209
241
|
- features/step_definitions/convert_steps.rb
|
210
|
-
- features/step_definitions/
|
242
|
+
- features/step_definitions/dir-access_steps.rb
|
243
|
+
- features/step_definitions/file_steps.rb
|
211
244
|
- features/step_definitions/gap_removal_steps.rb
|
212
245
|
- features/step_definitions/index_steps.rb
|
213
246
|
- features/step_definitions/output_steps.rb
|
214
247
|
- features/step_definitions/parse_steps.rb
|
215
248
|
- features/step_definitions/query_steps.rb
|
249
|
+
- features/step_definitions/slice_steps.rb
|
250
|
+
- features/step_definitions/tiling_steps.rb
|
216
251
|
- features/step_definitions/ucsc_bin_steps.rb
|
252
|
+
- features/support/aruba.rb
|
217
253
|
- features/support/env.rb
|
254
|
+
- features/tiling.feature
|
218
255
|
- features/ucsc-bins.feature
|
219
256
|
- spec/bio/maf/index_spec.rb
|
257
|
+
- spec/bio/maf/maf_spec.rb
|
220
258
|
- spec/bio/maf/parser_spec.rb
|
221
259
|
- spec/bio/maf/struct_spec.rb
|
222
260
|
- spec/bio/maf/tiler_spec.rb
|
223
261
|
- spec/spec_helper.rb
|
224
262
|
- test/data/big-block.maf
|
225
263
|
- test/data/chr22_ieq.maf
|
264
|
+
- test/data/chr22_ieq2.maf
|
226
265
|
- test/data/chrY-1block.maf
|
227
266
|
- test/data/empty
|
228
267
|
- test/data/empty.db
|
268
|
+
- test/data/gap-1.kct
|
269
|
+
- test/data/gap-1.maf
|
270
|
+
- test/data/gap-filled1.fa
|
229
271
|
- test/data/gap-sp1.fa
|
272
|
+
- test/data/gap-sp1.fa.gz
|
230
273
|
- test/data/mm8_chr7_tiny.kct
|
231
274
|
- test/data/mm8_chr7_tiny.maf
|
275
|
+
- test/data/mm8_chr7_tiny_slice1.maf
|
276
|
+
- test/data/mm8_chr7_tiny_slice2.maf
|
277
|
+
- test/data/mm8_chr7_tiny_slice3.maf
|
278
|
+
- test/data/mm8_chrM_tiny.kct
|
279
|
+
- test/data/mm8_chrM_tiny.maf
|
232
280
|
- test/data/mm8_mod_a.maf
|
233
281
|
- test/data/mm8_single.maf
|
234
282
|
- test/data/mm8_subset_a.maf
|
@@ -238,3 +286,4 @@ test_files:
|
|
238
286
|
- test/data/t1a.maf
|
239
287
|
- test/helper.rb
|
240
288
|
- test/test_bio-maf.rb
|
289
|
+
...
|