bio-rdf 0.0.1.pre1 → 0.0.1

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Files changed (17) hide show
  1. data/Gemfile +4 -1
  2. data/README.md +53 -3
  3. data/VERSION +1 -1
  4. data/bin/bio-rdf +35 -4
  5. data/doc/design.md +20 -0
  6. data/features/parse_broad_gsea_cls.feature +18 -0
  7. data/features/parse_broad_gsea_cls.rb +13 -0
  8. data/features/parse_broad_gsea_results.feature +29 -0
  9. data/features/parse_broad_gsea_results.rb +59 -0
  10. data/features/support/env.rb +13 -0
  11. data/lib/bio-rdf.rb +2 -1
  12. data/lib/bio-rdf/parsers/gsea/broadgsea.rb +161 -0
  13. data/spec/spec_helper.rb +12 -0
  14. data/test/data/parsers/gsea/Run1_C2.SUMMARY.RESULTS.REPORT.0.txt +1066 -0
  15. data/test/data/parsers/gsea/Run1_C2.SUMMARY.RESULTS.REPORT.1.txt +474 -0
  16. metadata +62 -21
  17. data/README.rdoc +0 -46
metadata CHANGED
@@ -1,8 +1,8 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-rdf
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  version: !ruby/object:Gem::Version
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- version: 0.0.1.pre1
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- prerelease: 6
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+ version: 0.0.1
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+ prerelease:
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  platform: ruby
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  authors:
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  - Pjotr Prins
@@ -10,11 +10,22 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-04-07 00:00:00.000000000Z
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+ date: 2012-05-01 00:00:00.000000000Z
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  dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: bio-logger
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+ requirement: &15565000 !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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+ prerelease: false
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+ version_requirements: *15565000
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  - !ruby/object:Gem::Dependency
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  name: shoulda
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- requirement: &16197900 !ruby/object:Gem::Requirement
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+ requirement: &15564160 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -22,10 +33,32 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *16197900
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+ version_requirements: *15564160
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+ - !ruby/object:Gem::Dependency
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+ name: rspec
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+ requirement: &15562720 !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: *15562720
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+ - !ruby/object:Gem::Dependency
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+ name: cucumber
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+ requirement: &15560480 !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: *15560480
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  - !ruby/object:Gem::Dependency
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  name: rdoc
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- requirement: &16196760 !ruby/object:Gem::Requirement
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+ requirement: &15559440 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -33,21 +66,21 @@ dependencies:
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  version: '3.12'
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  type: :development
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  prerelease: false
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- version_requirements: *16196760
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+ version_requirements: *15559440
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &16195560 !ruby/object:Gem::Requirement
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+ requirement: &15558220 !ruby/object:Gem::Requirement
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  none: false
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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: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: *16195560
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+ version_requirements: *15558220
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &16194300 !ruby/object:Gem::Requirement
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+ requirement: &15557260 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -55,10 +88,10 @@ dependencies:
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  version: 1.8.3
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  type: :development
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  prerelease: false
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- version_requirements: *16194300
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+ version_requirements: *15557260
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  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &16193260 !ruby/object:Gem::Requirement
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+ requirement: &15515240 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -66,10 +99,10 @@ dependencies:
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  version: 1.4.2
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  type: :development
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  prerelease: false
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- version_requirements: *16193260
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+ version_requirements: *15515240
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  - !ruby/object:Gem::Dependency
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  name: rdoc
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- requirement: &16192040 !ruby/object:Gem::Requirement
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+ requirement: &15514680 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -77,7 +110,7 @@ dependencies:
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  version: '3.12'
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  type: :development
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  prerelease: false
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- version_requirements: *16192040
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+ version_requirements: *15514680
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  description: Store relationships in a triple-store, such as gene enrichment and QTL,
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  and use this information for inference and causality
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  email: pjotr.public01@thebird.nl
@@ -87,19 +120,27 @@ extensions: []
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  extra_rdoc_files:
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  - LICENSE.txt
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  - README.md
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- - README.rdoc
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  files:
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  - .document
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  - .travis.yml
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  - Gemfile
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  - LICENSE.txt
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  - README.md
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- - README.rdoc
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  - Rakefile
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  - VERSION
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  - bin/bio-rdf
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+ - doc/design.md
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+ - features/parse_broad_gsea_cls.feature
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+ - features/parse_broad_gsea_cls.rb
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+ - features/parse_broad_gsea_results.feature
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+ - features/parse_broad_gsea_results.rb
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+ - features/support/env.rb
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  - lib/bio-rdf.rb
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+ - lib/bio-rdf/parsers/gsea/broadgsea.rb
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  - lib/bio-rdf/rdf.rb
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+ - spec/spec_helper.rb
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+ - test/data/parsers/gsea/Run1_C2.SUMMARY.RESULTS.REPORT.0.txt
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+ - test/data/parsers/gsea/Run1_C2.SUMMARY.RESULTS.REPORT.1.txt
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  - test/helper.rb
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  - test/test_bio-rdf.rb
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  homepage: http://github.com/pjotrp/bioruby-rdf
@@ -117,13 +158,13 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
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- hash: -868237054466869818
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+ hash: 4447990018592781869
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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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+ - - ! '>='
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  - !ruby/object:Gem::Version
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- version: 1.3.1
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+ version: '0'
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  requirements: []
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  rubyforge_project:
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  rubygems_version: 1.8.10
data/README.rdoc DELETED
@@ -1,46 +0,0 @@
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- = bio-rdf
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-
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- {<img
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- src="https://secure.travis-ci.org/pjotrp/bioruby-rdf.png"
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- />}[http://travis-ci.org/#!/pjotrp/bioruby-rdf]
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-
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- Full description goes here
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-
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- Note: this software is under active development!
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-
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- == Installation
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-
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- gem install bio-rdf
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-
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- == Usage
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-
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- == Developers
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-
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- To use the library
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-
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- require 'bio-rdf
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-
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- The API doc is online. For more code examples see also the test files in
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- the source tree.
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-
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- == Project home page
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-
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- Information on the source tree, documentation, issues and how to contribute, see
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-
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- http://github.com/pjotrp/bioruby-rdf
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-
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- == Cite
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-
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- If you use this software, please cite one of
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-
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- * [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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- * [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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-
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- == Biogems.info
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-
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- This Biogem is published at http://biogems.info/index.html#bio-rdf
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-
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- == Copyright
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-
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- Copyright (c) 2012 Pjotr Prins. See LICENSE.txt for further details.
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-