rbfam 0.1.3 → 0.2.0

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Files changed (20) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +19 -0
  3. data/Gemfile +4 -0
  4. data/Gemfile.lock +95 -0
  5. data/Rakefile +3 -0
  6. data/db/config.yml +5 -0
  7. data/db/migrate/20140114232757_add_alignment_table.rb +14 -0
  8. data/db/migrate/20140114232805_add_sequence_table.rb +17 -0
  9. data/db/migrate/20140114232810_add_family_table.rb +15 -0
  10. data/db/schema.rb +44 -0
  11. data/lib/rbfam.rb +10 -3
  12. data/lib/rbfam/modules/alignment.rb +15 -17
  13. data/lib/rbfam/modules/family.rb +17 -19
  14. data/lib/rbfam/modules/sequence.rb +4 -14
  15. data/lib/rbfam/scripts/sequences_in_mysql.rb +38 -21
  16. data/lib/rbfam/version.rb +3 -0
  17. data/load_rbfam_seed.rb +28 -0
  18. data/rbfam.gemspec +34 -0
  19. data/rfam_12.seed.utf8 +139884 -0
  20. metadata +169 -22
metadata CHANGED
@@ -1,77 +1,221 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: rbfam
3
3
  version: !ruby/object:Gem::Version
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- version: 0.1.3
4
+ version: 0.2.0
5
5
  platform: ruby
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  authors:
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  - Evan Senter
8
8
  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2013-04-29 00:00:00.000000000 Z
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+ date: 2014-12-11 00:00:00.000000000 Z
12
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  dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: standalone_migrations
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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: '2.1'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 2.1.5
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+ type: :development
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+ prerelease: false
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+ 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: '2.1'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 2.1.5
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+ - !ruby/object:Gem::Dependency
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+ name: activerecord
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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'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
43
+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: activesupport
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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'
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+ type: :runtime
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+ prerelease: false
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+ 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: '0'
13
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  - !ruby/object:Gem::Dependency
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  name: bio
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  requirement: !ruby/object:Gem::Requirement
16
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  requirements:
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- - - '>='
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.4'
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 1.4.2
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
24
- - - '>='
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.4'
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 1.4.2
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+ - !ruby/object:Gem::Dependency
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+ name: bio-stockholm
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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'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 0.0.1
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+ type: :runtime
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+ prerelease: false
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+ 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: '0.0'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 0.0.1
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  - !ruby/object:Gem::Dependency
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  name: entrez
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '0.5'
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 0.5.8.1
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '0.5'
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 0.5.8.1
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  - !ruby/object:Gem::Dependency
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  name: httparty
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '0.8'
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 0.8.3
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '0.8'
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 0.8.3
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  - !ruby/object:Gem::Dependency
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- name: vienna_rna
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+ name: mysql2
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: 0.1.3
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+ version: '0.3'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 0.3.14
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '0.3'
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+ - - ">="
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  - !ruby/object:Gem::Version
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- version: 0.1.3
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+ version: 0.3.14
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+ - !ruby/object:Gem::Dependency
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+ name: nokogiri
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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: '1.6'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 1.6.1
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+ type: :runtime
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+ prerelease: false
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+ 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: '1.6'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 1.6.1
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+ - !ruby/object:Gem::Dependency
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+ name: parallel
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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: '1.3'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 1.3.2
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+ type: :runtime
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+ prerelease: false
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+ 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: '1.3'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 1.3.2
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  description: Light wrapper for RFam data in Ruby.
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- email: evansenter@gmail.com
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+ email:
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+ - evansenter@gmail.com
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  executables: []
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  extensions: []
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  extra_rdoc_files: []
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  files:
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+ - ".gitignore"
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+ - Gemfile
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+ - Gemfile.lock
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+ - README.md
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+ - Rakefile
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+ - db/config.yml
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+ - db/migrate/20140114232757_add_alignment_table.rb
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+ - db/migrate/20140114232805_add_sequence_table.rb
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+ - db/migrate/20140114232810_add_family_table.rb
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+ - db/schema.rb
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+ - lib/rbfam.rb
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  - lib/rbfam/helpers/common.rb
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  - lib/rbfam/helpers/simple_names.json
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  - lib/rbfam/modules/alignment.rb
@@ -79,10 +223,13 @@ files:
79
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  - lib/rbfam/modules/sequence.rb
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  - lib/rbfam/modules/utils.rb
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  - lib/rbfam/scripts/sequences_in_mysql.rb
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- - lib/rbfam.rb
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- - README.md
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- homepage: http://rubygems.org/gems/rbfam
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- licenses: []
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+ - lib/rbfam/version.rb
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+ - load_rbfam_seed.rb
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+ - rbfam.gemspec
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+ - rfam_12.seed.utf8
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+ homepage: ''
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+ licenses:
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+ - MIT
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  metadata: {}
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  post_install_message:
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  rdoc_options: []
@@ -90,17 +237,17 @@ require_paths:
90
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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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+ - - ">="
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: '2.0'
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 2.0.2
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+ rubygems_version: 2.4.4
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  signing_key:
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  specification_version: 4
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  summary: Bindings to Rfam.