bio-maf 0.2.0-java → 0.3.0-java

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Files changed (46) hide show
  1. data/.gitignore +1 -0
  2. data/Gemfile +3 -1
  3. data/README.md +98 -29
  4. data/Rakefile +6 -2
  5. data/bin/maf_tile +59 -35
  6. data/bio-maf.gemspec +4 -3
  7. data/features/block-joining.feature +32 -0
  8. data/features/dir-access.feature +46 -0
  9. data/features/maf-indexing.feature +23 -0
  10. data/features/maf-to-fasta.feature +9 -0
  11. data/features/slice.feature +54 -0
  12. data/features/step_definitions/dir-access_steps.rb +15 -0
  13. data/features/step_definitions/file_steps.rb +7 -0
  14. data/features/step_definitions/gap_removal_steps.rb +4 -0
  15. data/features/step_definitions/index_steps.rb +3 -3
  16. data/features/step_definitions/output_steps.rb +9 -1
  17. data/features/step_definitions/parse_steps.rb +13 -2
  18. data/features/step_definitions/query_steps.rb +7 -6
  19. data/features/step_definitions/slice_steps.rb +15 -0
  20. data/features/step_definitions/{gap-filling_steps.rb → tiling_steps.rb} +0 -0
  21. data/features/support/aruba.rb +1 -0
  22. data/features/support/env.rb +3 -1
  23. data/features/{gap-filling.feature → tiling.feature} +85 -0
  24. data/lib/bio/maf/index.rb +223 -11
  25. data/lib/bio/maf/maf.rb +209 -0
  26. data/lib/bio/maf/parser.rb +190 -111
  27. data/lib/bio/maf/tiler.rb +33 -6
  28. data/man/maf_index.1 +1 -1
  29. data/man/maf_tile.1 +7 -7
  30. data/man/maf_tile.1.ronn +21 -13
  31. data/man/maf_to_fasta.1 +1 -1
  32. data/spec/bio/maf/index_spec.rb +99 -0
  33. data/spec/bio/maf/maf_spec.rb +184 -0
  34. data/spec/bio/maf/parser_spec.rb +75 -115
  35. data/spec/bio/maf/tiler_spec.rb +44 -0
  36. data/test/data/chr22_ieq2.maf +11 -0
  37. data/test/data/gap-1.kct +0 -0
  38. data/test/data/gap-1.maf +9 -0
  39. data/test/data/gap-filled1.fa +6 -0
  40. data/test/data/gap-sp1.fa.gz +0 -0
  41. data/test/data/mm8_chr7_tiny_slice1.maf +9 -0
  42. data/test/data/mm8_chr7_tiny_slice2.maf +10 -0
  43. data/test/data/mm8_chr7_tiny_slice3.maf +10 -0
  44. data/test/data/mm8_chrM_tiny.kct +0 -0
  45. data/test/data/mm8_chrM_tiny.maf +1000 -0
  46. 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: 0.2.0
5
+ version: 0.3.0
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  platform: java
7
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  authors:
8
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  - Clayton Wheeler
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-06-29 00:00:00.000000000 Z
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+ date: 2012-07-18 00:00:00.000000000 Z
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  dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: bio-alignment
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
18
+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 0.0.7
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+ none: false
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 0.0.7
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+ none: false
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+ prerelease: false
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+ type: :runtime
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  - !ruby/object:Gem::Dependency
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  name: bio-bigbio
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
18
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: !binary |-
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- MA==
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+ version: '0'
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  none: false
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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- version: !binary |-
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- MA==
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+ version: '0'
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  none: false
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  prerelease: false
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  type: :runtime
@@ -51,13 +65,13 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 0.2.0
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+ version: 0.3.0
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  none: false
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 0.2.0
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+ version: 0.3.0
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  none: false
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  prerelease: false
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  type: :runtime
@@ -106,22 +120,29 @@ files:
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  - bin/maf_write
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  - bin/random_ranges
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  - bio-maf.gemspec
109
- - features/gap-filling.feature
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/gap-filling_steps.rb
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:
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  - man/maf_to_fasta.1
145
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  - 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
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  - spec/bio/maf/tiler_spec.rb
150
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  - spec/spec_helper.rb
151
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  - test/data/big-block.maf
152
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  - test/data/chr22_ieq.maf
175
+ - test/data/chr22_ieq2.maf
153
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  - test/data/chrY-1block.maf
154
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  - 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
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  - test/data/mm8_mod_a.maf
160
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  - test/data/mm8_single.maf
161
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  - test/data/mm8_subset_a.maf
@@ -182,15 +214,13 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  segments:
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  - 0
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  hash: 2
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- version: !binary |-
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- MA==
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+ version: '0'
187
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  none: false
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  required_rubygems_version: !ruby/object:Gem::Requirement
189
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  requirements:
190
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  - - ! '>='
191
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  - !ruby/object:Gem::Version
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- version: !binary |-
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- MA==
223
+ version: '0'
194
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  none: false
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  requirements: []
196
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  rubyforge_project:
@@ -199,36 +229,54 @@ signing_key:
199
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  specification_version: 3
200
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  summary: MAF parser for BioRuby
201
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  test_files:
202
- - features/gap-filling.feature
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/gap-filling_steps.rb
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
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  - 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
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  - 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
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  - 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
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  - test/data/mm8_subset_a.maf
@@ -238,3 +286,4 @@ test_files:
238
286
  - test/data/t1a.maf
239
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  - test/helper.rb
240
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  - test/test_bio-maf.rb
289
+ ...