ruby-ensembl-api 0.9.6

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Files changed (54) hide show
  1. data/TUTORIAL.rdoc +623 -0
  2. data/bin/ensembl +40 -0
  3. data/lib/ensembl.rb +64 -0
  4. data/lib/ensembl/core/activerecord.rb +1914 -0
  5. data/lib/ensembl/core/collection.rb +60 -0
  6. data/lib/ensembl/core/project.rb +264 -0
  7. data/lib/ensembl/core/slice.rb +693 -0
  8. data/lib/ensembl/core/transcript.rb +425 -0
  9. data/lib/ensembl/core/transform.rb +97 -0
  10. data/lib/ensembl/db_connection.rb +216 -0
  11. data/lib/ensembl/variation/activerecord.rb +253 -0
  12. data/lib/ensembl/variation/variation.rb +163 -0
  13. data/test/unit/data/seq_c6qbl.fa +10 -0
  14. data/test/unit/data/seq_cso19_coding.fa +16 -0
  15. data/test/unit/data/seq_cso19_transcript.fa +28 -0
  16. data/test/unit/data/seq_drd3_gene.fa +838 -0
  17. data/test/unit/data/seq_drd3_transcript.fa +22 -0
  18. data/test/unit/data/seq_drd4_transcript.fa +24 -0
  19. data/test/unit/data/seq_forward_composite.fa +1669 -0
  20. data/test/unit/data/seq_par_boundary.fa +169 -0
  21. data/test/unit/data/seq_rnd3_transcript.fa +47 -0
  22. data/test/unit/data/seq_ub2r1_coding.fa +13 -0
  23. data/test/unit/data/seq_ub2r1_gene.fa +174 -0
  24. data/test/unit/data/seq_ub2r1_transcript.fa +26 -0
  25. data/test/unit/data/seq_y.fa +2 -0
  26. data/test/unit/ensembl_genomes/test_collection.rb +51 -0
  27. data/test/unit/ensembl_genomes/test_gene.rb +52 -0
  28. data/test/unit/ensembl_genomes/test_slice.rb +71 -0
  29. data/test/unit/ensembl_genomes/test_variation.rb +17 -0
  30. data/test/unit/release_50/core/test_project.rb +215 -0
  31. data/test/unit/release_50/core/test_project_human.rb +58 -0
  32. data/test/unit/release_50/core/test_relationships.rb +66 -0
  33. data/test/unit/release_50/core/test_sequence.rb +175 -0
  34. data/test/unit/release_50/core/test_slice.rb +121 -0
  35. data/test/unit/release_50/core/test_transcript.rb +108 -0
  36. data/test/unit/release_50/core/test_transform.rb +223 -0
  37. data/test/unit/release_50/variation/test_activerecord.rb +143 -0
  38. data/test/unit/release_50/variation/test_variation.rb +84 -0
  39. data/test/unit/release_53/core/test_gene.rb +66 -0
  40. data/test/unit/release_53/core/test_project.rb +96 -0
  41. data/test/unit/release_53/core/test_project_human.rb +65 -0
  42. data/test/unit/release_53/core/test_slice.rb +47 -0
  43. data/test/unit/release_53/core/test_transform.rb +63 -0
  44. data/test/unit/release_53/variation/test_activerecord.rb +145 -0
  45. data/test/unit/release_53/variation/test_variation.rb +71 -0
  46. data/test/unit/release_56/core/test_gene.rb +66 -0
  47. data/test/unit/release_56/core/test_project.rb +96 -0
  48. data/test/unit/release_56/core/test_slice.rb +54 -0
  49. data/test/unit/release_56/core/test_transform.rb +63 -0
  50. data/test/unit/release_56/variation/test_activerecord.rb +142 -0
  51. data/test/unit/release_56/variation/test_variation.rb +68 -0
  52. data/test/unit/test_connection.rb +66 -0
  53. data/test/unit/test_releases.rb +136 -0
  54. metadata +128 -0
metadata ADDED
@@ -0,0 +1,128 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: ruby-ensembl-api
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+ version: !ruby/object:Gem::Version
4
+ version: 0.9.6
5
+ platform: ruby
6
+ authors:
7
+ - Jan Aerts
8
+ - Francesco Strozzi
9
+ autorequire: ensembl
10
+ bindir: bin
11
+ cert_chain: []
12
+
13
+ date: 2010-02-10 00:00:00 +09:00
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+ default_executable: ensembl
15
+ dependencies:
16
+ - !ruby/object:Gem::Dependency
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+ name: bio
18
+ type: :runtime
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+ version_requirement:
20
+ version_requirements: !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: "1"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: activerecord
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
32
+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
36
+ description: ruby-ensembl-api provides a ruby API to the Ensembl databases (http://www.ensembl.org)
37
+ email:
38
+ - jan.aerts@gmail.com
39
+ - francesco.strozzi@gmail.com
40
+ executables:
41
+ - ensembl
42
+ extensions: []
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+
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+ extra_rdoc_files:
45
+ - TUTORIAL.rdoc
46
+ files:
47
+ - lib/ensembl/core/activerecord.rb
48
+ - lib/ensembl/core/collection.rb
49
+ - lib/ensembl/core/project.rb
50
+ - lib/ensembl/core/slice.rb
51
+ - lib/ensembl/core/transcript.rb
52
+ - lib/ensembl/core/transform.rb
53
+ - lib/ensembl/db_connection.rb
54
+ - lib/ensembl/variation/activerecord.rb
55
+ - lib/ensembl/variation/variation.rb
56
+ - lib/ensembl.rb
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+ - bin/ensembl
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+ - TUTORIAL.rdoc
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+ has_rdoc: true
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+ homepage: http://github.com/jandot/ruby-ensembl-api
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+ licenses: []
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+
63
+ post_install_message:
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+ rdoc_options: []
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+
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+ require_paths:
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+ - lib
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+ required_ruby_version: !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"
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+ version:
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+ required_rubygems_version: !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"
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+ version:
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+ requirements: []
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+
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+ rubyforge_project:
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+ rubygems_version: 1.3.5
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+ signing_key:
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+ specification_version: 3
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+ summary: API to Ensembl databases
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+ test_files:
88
+ - test/unit/data/seq_c6qbl.fa
89
+ - test/unit/data/seq_cso19_coding.fa
90
+ - test/unit/data/seq_cso19_transcript.fa
91
+ - test/unit/data/seq_drd3_gene.fa
92
+ - test/unit/data/seq_drd3_transcript.fa
93
+ - test/unit/data/seq_drd4_transcript.fa
94
+ - test/unit/data/seq_forward_composite.fa
95
+ - test/unit/data/seq_par_boundary.fa
96
+ - test/unit/data/seq_rnd3_transcript.fa
97
+ - test/unit/data/seq_ub2r1_coding.fa
98
+ - test/unit/data/seq_ub2r1_gene.fa
99
+ - test/unit/data/seq_ub2r1_transcript.fa
100
+ - test/unit/data/seq_y.fa
101
+ - test/unit/ensembl_genomes/test_collection.rb
102
+ - test/unit/ensembl_genomes/test_gene.rb
103
+ - test/unit/ensembl_genomes/test_slice.rb
104
+ - test/unit/ensembl_genomes/test_variation.rb
105
+ - test/unit/release_50/core/test_project.rb
106
+ - test/unit/release_50/core/test_project_human.rb
107
+ - test/unit/release_50/core/test_relationships.rb
108
+ - test/unit/release_50/core/test_sequence.rb
109
+ - test/unit/release_50/core/test_slice.rb
110
+ - test/unit/release_50/core/test_transcript.rb
111
+ - test/unit/release_50/core/test_transform.rb
112
+ - test/unit/release_50/variation/test_activerecord.rb
113
+ - test/unit/release_50/variation/test_variation.rb
114
+ - test/unit/release_53/core/test_gene.rb
115
+ - test/unit/release_53/core/test_project.rb
116
+ - test/unit/release_53/core/test_project_human.rb
117
+ - test/unit/release_53/core/test_slice.rb
118
+ - test/unit/release_53/core/test_transform.rb
119
+ - test/unit/release_53/variation/test_activerecord.rb
120
+ - test/unit/release_53/variation/test_variation.rb
121
+ - test/unit/release_56/core/test_gene.rb
122
+ - test/unit/release_56/core/test_project.rb
123
+ - test/unit/release_56/core/test_slice.rb
124
+ - test/unit/release_56/core/test_transform.rb
125
+ - test/unit/release_56/variation/test_activerecord.rb
126
+ - test/unit/release_56/variation/test_variation.rb
127
+ - test/unit/test_connection.rb
128
+ - test/unit/test_releases.rb