bio-ensembl 1.1.0
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- data/.document +5 -0
- data/Gemfile +20 -0
- data/Gemfile.lock +40 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +19 -0
- data/Rakefile +71 -0
- data/VERSION +1 -0
- data/bin/ensembl +40 -0
- data/bin/variation_effect_predictor +106 -0
- data/bio-ensembl.gemspec +190 -0
- data/lib/bio-ensembl.rb +65 -0
- data/lib/bio-ensembl/core/activerecord.rb +1812 -0
- data/lib/bio-ensembl/core/collection.rb +64 -0
- data/lib/bio-ensembl/core/project.rb +262 -0
- data/lib/bio-ensembl/core/slice.rb +657 -0
- data/lib/bio-ensembl/core/transcript.rb +409 -0
- data/lib/bio-ensembl/core/transform.rb +95 -0
- data/lib/bio-ensembl/db_connection.rb +205 -0
- data/lib/bio-ensembl/variation/activerecord.rb +536 -0
- data/lib/bio-ensembl/variation/variation_feature.rb +376 -0
- data/lib/bio-ensembl/variation/variation_feature62.rb +444 -0
- data/samples/ensembl_genomes_example.rb +60 -0
- data/samples/examples_perl_tutorial.rb +125 -0
- data/samples/small_example_ruby_api.rb +34 -0
- data/samples/variation_effect_predictor_data.txt +4 -0
- data/samples/variation_example.rb +67 -0
- data/test/data/seq_c6qbl.fa +10 -0
- data/test/data/seq_cso19_coding.fa +16 -0
- data/test/data/seq_cso19_transcript.fa +28 -0
- data/test/data/seq_drd3_gene.fa +838 -0
- data/test/data/seq_drd3_transcript.fa +22 -0
- data/test/data/seq_drd4_transcript.fa +24 -0
- data/test/data/seq_forward_composite.fa +1669 -0
- data/test/data/seq_par_boundary.fa +169 -0
- data/test/data/seq_rnd3_transcript.fa +47 -0
- data/test/data/seq_ub2r1_coding.fa +13 -0
- data/test/data/seq_ub2r1_gene.fa +174 -0
- data/test/data/seq_ub2r1_transcript.fa +26 -0
- data/test/data/seq_y.fa +2 -0
- data/test/default/test_connection.rb +60 -0
- data/test/default/test_releases.rb +130 -0
- data/test/ensembl_genomes/test_collection.rb +122 -0
- data/test/ensembl_genomes/test_gene.rb +46 -0
- data/test/ensembl_genomes/test_slice.rb +65 -0
- data/test/ensembl_genomes/test_variation.rb +38 -0
- data/test/helper.rb +18 -0
- data/test/release_50/core/test_project.rb +210 -0
- data/test/release_50/core/test_project_human.rb +52 -0
- data/test/release_50/core/test_relationships.rb +72 -0
- data/test/release_50/core/test_sequence.rb +170 -0
- data/test/release_50/core/test_slice.rb +116 -0
- data/test/release_50/core/test_transcript.rb +125 -0
- data/test/release_50/core/test_transform.rb +217 -0
- data/test/release_50/variation/test_activerecord.rb +138 -0
- data/test/release_50/variation/test_variation.rb +79 -0
- data/test/release_53/core/test_gene.rb +61 -0
- data/test/release_53/core/test_project.rb +91 -0
- data/test/release_53/core/test_project_human.rb +61 -0
- data/test/release_53/core/test_slice.rb +42 -0
- data/test/release_53/core/test_transform.rb +57 -0
- data/test/release_53/variation/test_activerecord.rb +137 -0
- data/test/release_53/variation/test_variation.rb +66 -0
- data/test/release_56/core/test_gene.rb +61 -0
- data/test/release_56/core/test_project.rb +91 -0
- data/test/release_56/core/test_slice.rb +49 -0
- data/test/release_56/core/test_transform.rb +57 -0
- data/test/release_56/variation/test_activerecord.rb +141 -0
- data/test/release_56/variation/test_consequence.rb +131 -0
- data/test/release_56/variation/test_variation.rb +63 -0
- data/test/release_60/core/test_gene.rb +61 -0
- data/test/release_60/core/test_project_human.rb +34 -0
- data/test/release_60/core/test_slice.rb +42 -0
- data/test/release_60/core/test_transcript.rb +120 -0
- data/test/release_60/core/test_transform.rb +57 -0
- data/test/release_60/variation/test_activerecord.rb +216 -0
- data/test/release_60/variation/test_consequence.rb +153 -0
- data/test/release_60/variation/test_variation.rb +64 -0
- data/test/release_62/core/test_gene.rb +42 -0
- data/test/release_62/variation/test_activerecord.rb +86 -0
- data/test/release_62/variation/test_consequence.rb +191 -0
- metadata +287 -0
metadata
ADDED
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@@ -0,0 +1,287 @@
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--- !ruby/object:Gem::Specification
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name: bio-ensembl
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3
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version: !ruby/object:Gem::Version
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version: 1.1.0
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5
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prerelease:
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platform: ruby
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7
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authors:
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8
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- Jan Aerts
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9
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- Francesco Strozzi
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autorequire:
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11
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bindir: bin
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12
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cert_chain: []
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date: 2011-12-06 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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requirement: &2161899320 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: 1.4.1
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type: :runtime
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prerelease: false
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version_requirements: *2161899320
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- !ruby/object:Gem::Dependency
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name: mysql
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requirement: &2161898840 !ruby/object:Gem::Requirement
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none: false
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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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35
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prerelease: false
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version_requirements: *2161898840
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37
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- !ruby/object:Gem::Dependency
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name: activerecord
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requirement: &2161914720 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - =
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- !ruby/object:Gem::Version
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version: 3.0.0
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type: :runtime
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46
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prerelease: false
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version_requirements: *2161914720
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48
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- !ruby/object:Gem::Dependency
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49
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name: shoulda
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requirement: &2161914240 !ruby/object:Gem::Requirement
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51
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none: false
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requirements:
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53
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- - ! '>='
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54
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- !ruby/object:Gem::Version
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55
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version: '0'
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56
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type: :development
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57
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prerelease: false
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58
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version_requirements: *2161914240
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59
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- !ruby/object:Gem::Dependency
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60
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name: bundler
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requirement: &2161913760 !ruby/object:Gem::Requirement
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none: false
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requirements:
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+
- - ~>
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- !ruby/object:Gem::Version
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version: 1.0.0
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type: :development
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68
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prerelease: false
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version_requirements: *2161913760
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- !ruby/object:Gem::Dependency
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name: jeweler
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requirement: &2161913280 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.5.2
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type: :development
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prerelease: false
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version_requirements: *2161913280
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- !ruby/object:Gem::Dependency
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name: rcov
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requirement: &2161912800 !ruby/object:Gem::Requirement
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none: false
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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: :development
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prerelease: false
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version_requirements: *2161912800
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- !ruby/object:Gem::Dependency
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name: bio
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requirement: &2161912320 !ruby/object:Gem::Requirement
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none: false
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requirements:
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+
- - ! '>='
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- !ruby/object:Gem::Version
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version: 1.4.1
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100
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type: :development
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101
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prerelease: false
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102
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version_requirements: *2161912320
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103
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- !ruby/object:Gem::Dependency
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name: mysql
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requirement: &2161911840 !ruby/object:Gem::Requirement
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none: false
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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: :development
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prerelease: false
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version_requirements: *2161911840
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114
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- !ruby/object:Gem::Dependency
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name: activerecord
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requirement: &2161911360 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - =
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- !ruby/object:Gem::Version
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version: 3.0.0
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type: :development
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prerelease: false
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version_requirements: *2161911360
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125
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description: This API provides a complete set of methods and classes to access the
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126
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Ensembl database using Ruby programming language
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email:
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- jan.aerts@gmail.com
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- francesco.strozzi@gmail.com
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executables:
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- ensembl
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- variation_effect_predictor
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extensions: []
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extra_rdoc_files:
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- LICENSE.txt
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- README.rdoc
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files:
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- .document
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- Gemfile
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- Gemfile.lock
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- LICENSE.txt
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- README.rdoc
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- Rakefile
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- VERSION
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- bin/ensembl
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- bin/variation_effect_predictor
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- bio-ensembl.gemspec
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- lib/bio-ensembl.rb
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- lib/bio-ensembl/core/activerecord.rb
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- lib/bio-ensembl/core/collection.rb
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151
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- lib/bio-ensembl/core/project.rb
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- lib/bio-ensembl/core/slice.rb
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- lib/bio-ensembl/core/transcript.rb
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- lib/bio-ensembl/core/transform.rb
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- lib/bio-ensembl/db_connection.rb
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- lib/bio-ensembl/variation/activerecord.rb
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157
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- lib/bio-ensembl/variation/variation_feature.rb
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158
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- lib/bio-ensembl/variation/variation_feature62.rb
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159
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- samples/ensembl_genomes_example.rb
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160
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- samples/examples_perl_tutorial.rb
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161
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- samples/small_example_ruby_api.rb
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162
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- samples/variation_effect_predictor_data.txt
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163
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- samples/variation_example.rb
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164
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- test/data/seq_c6qbl.fa
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165
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- test/data/seq_cso19_coding.fa
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166
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- test/data/seq_cso19_transcript.fa
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167
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- test/data/seq_drd3_gene.fa
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168
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- test/data/seq_drd3_transcript.fa
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169
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- test/data/seq_drd4_transcript.fa
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170
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- test/data/seq_forward_composite.fa
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- test/data/seq_par_boundary.fa
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- test/data/seq_rnd3_transcript.fa
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- test/data/seq_ub2r1_coding.fa
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174
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- test/data/seq_ub2r1_gene.fa
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- test/data/seq_ub2r1_transcript.fa
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- test/data/seq_y.fa
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- test/default/test_connection.rb
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- test/default/test_releases.rb
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- test/ensembl_genomes/test_collection.rb
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- test/ensembl_genomes/test_gene.rb
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- test/ensembl_genomes/test_slice.rb
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- test/ensembl_genomes/test_variation.rb
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183
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- test/helper.rb
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- test/release_50/core/test_project.rb
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- test/release_50/core/test_project_human.rb
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- test/release_50/core/test_relationships.rb
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187
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- test/release_50/core/test_sequence.rb
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- test/release_50/core/test_slice.rb
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- test/release_50/core/test_transcript.rb
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190
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- test/release_50/core/test_transform.rb
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191
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- test/release_50/variation/test_activerecord.rb
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192
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- test/release_50/variation/test_variation.rb
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- test/release_53/core/test_gene.rb
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194
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- test/release_53/core/test_project.rb
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195
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- test/release_53/core/test_project_human.rb
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- test/release_53/core/test_slice.rb
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- test/release_53/core/test_transform.rb
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- test/release_53/variation/test_activerecord.rb
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- test/release_53/variation/test_variation.rb
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200
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- test/release_56/core/test_gene.rb
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- test/release_56/core/test_project.rb
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202
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- test/release_56/core/test_slice.rb
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- test/release_56/core/test_transform.rb
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- test/release_56/variation/test_activerecord.rb
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205
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- test/release_56/variation/test_consequence.rb
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206
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- test/release_56/variation/test_variation.rb
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207
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- test/release_60/core/test_gene.rb
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208
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- test/release_60/core/test_project_human.rb
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209
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- test/release_60/core/test_slice.rb
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210
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- test/release_60/core/test_transcript.rb
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- test/release_60/core/test_transform.rb
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212
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- test/release_60/variation/test_activerecord.rb
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- test/release_60/variation/test_consequence.rb
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214
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- test/release_60/variation/test_variation.rb
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215
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- test/release_62/core/test_gene.rb
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216
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- test/release_62/variation/test_activerecord.rb
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217
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- test/release_62/variation/test_consequence.rb
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218
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homepage: http://github.com/fstrozzi/bioruby-ensembl
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licenses:
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220
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- MIT
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post_install_message:
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222
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rdoc_options: []
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223
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require_paths:
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224
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
|
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228
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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segments:
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- 0
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hash: 3215180575419888787
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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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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240
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requirements: []
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rubyforge_project:
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242
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rubygems_version: 1.8.12
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signing_key:
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244
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specification_version: 3
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summary: A Ruby API to the Ensembl database
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test_files:
|
|
247
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- test/default/test_connection.rb
|
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248
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- test/default/test_releases.rb
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249
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+
- test/ensembl_genomes/test_collection.rb
|
|
250
|
+
- test/ensembl_genomes/test_gene.rb
|
|
251
|
+
- test/ensembl_genomes/test_slice.rb
|
|
252
|
+
- test/ensembl_genomes/test_variation.rb
|
|
253
|
+
- test/helper.rb
|
|
254
|
+
- test/release_50/core/test_project.rb
|
|
255
|
+
- test/release_50/core/test_project_human.rb
|
|
256
|
+
- test/release_50/core/test_relationships.rb
|
|
257
|
+
- test/release_50/core/test_sequence.rb
|
|
258
|
+
- test/release_50/core/test_slice.rb
|
|
259
|
+
- test/release_50/core/test_transcript.rb
|
|
260
|
+
- test/release_50/core/test_transform.rb
|
|
261
|
+
- test/release_50/variation/test_activerecord.rb
|
|
262
|
+
- test/release_50/variation/test_variation.rb
|
|
263
|
+
- test/release_53/core/test_gene.rb
|
|
264
|
+
- test/release_53/core/test_project.rb
|
|
265
|
+
- test/release_53/core/test_project_human.rb
|
|
266
|
+
- test/release_53/core/test_slice.rb
|
|
267
|
+
- test/release_53/core/test_transform.rb
|
|
268
|
+
- test/release_53/variation/test_activerecord.rb
|
|
269
|
+
- test/release_53/variation/test_variation.rb
|
|
270
|
+
- test/release_56/core/test_gene.rb
|
|
271
|
+
- test/release_56/core/test_project.rb
|
|
272
|
+
- test/release_56/core/test_slice.rb
|
|
273
|
+
- test/release_56/core/test_transform.rb
|
|
274
|
+
- test/release_56/variation/test_activerecord.rb
|
|
275
|
+
- test/release_56/variation/test_consequence.rb
|
|
276
|
+
- test/release_56/variation/test_variation.rb
|
|
277
|
+
- test/release_60/core/test_gene.rb
|
|
278
|
+
- test/release_60/core/test_project_human.rb
|
|
279
|
+
- test/release_60/core/test_slice.rb
|
|
280
|
+
- test/release_60/core/test_transcript.rb
|
|
281
|
+
- test/release_60/core/test_transform.rb
|
|
282
|
+
- test/release_60/variation/test_activerecord.rb
|
|
283
|
+
- test/release_60/variation/test_consequence.rb
|
|
284
|
+
- test/release_60/variation/test_variation.rb
|
|
285
|
+
- test/release_62/core/test_gene.rb
|
|
286
|
+
- test/release_62/variation/test_activerecord.rb
|
|
287
|
+
- test/release_62/variation/test_consequence.rb
|