biointerchange 1.0.0 → 1.0.1

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Files changed (27) hide show
  1. checksums.yaml +7 -0
  2. data/.travis.yml +2 -2
  3. data/README.md +7 -6
  4. data/VERSION +1 -1
  5. data/examples/ReaderModelWriterSequenceDiagram.graffle +3073 -0
  6. data/examples/ReaderModelWriterSequenceDiagram.png +0 -0
  7. data/lib/biointerchange/core.rb +63 -58
  8. data/lib/biointerchange/faldo.rb +125 -35
  9. data/lib/biointerchange/genomics/gff3_feature_sequence.rb +36 -0
  10. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +254 -147
  11. data/lib/biointerchange/genomics/gff3_reader.rb +22 -3
  12. data/lib/biointerchange/genomics/locations.rb +30 -0
  13. data/lib/biointerchange/gfvo.rb +1072 -0
  14. data/lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb +6 -5
  15. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +7 -4
  16. data/lib/biointerchange/writer.rb +138 -2
  17. data/spec/gff3_rdfwriter_spec.rb +5 -6
  18. data/spec/gvf_rdfwriter_spec.rb +5 -6
  19. data/spec/phylogenetics_spec.rb +1 -1
  20. data/web/images/BioInterchange120.png +0 -0
  21. data/web/images/BioInterchange120inv.png +0 -0
  22. data/web/images/BioInterchange160.png +0 -0
  23. data/web/images/BioInterchange160inv.png +0 -0
  24. data/web/images/BioInterchange300inv.png +0 -0
  25. data/web/index.html +5 -1
  26. data/web/ontologies.html +1538 -21
  27. metadata +31 -46
metadata CHANGED
@@ -1,8 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: biointerchange
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3
  version: !ruby/object:Gem::Version
4
- version: 1.0.0
5
- prerelease:
4
+ version: 1.0.1
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  platform: ruby
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  authors:
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  - Joachim Baran
@@ -13,92 +12,81 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2013-06-08 00:00:00.000000000 Z
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+ date: 2013-08-19 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rdf
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  requirement: !ruby/object:Gem::Requirement
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- none: false
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  requirements:
23
- - - ! '>='
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+ - - '>='
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  - !ruby/object:Gem::Version
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23
  version: 0.3.4.1
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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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- 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: 0.3.4.1
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  - !ruby/object:Gem::Dependency
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  name: json
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  requirement: !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: 1.6.4
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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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- 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: 1.6.4
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  - !ruby/object:Gem::Dependency
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  name: getopt
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  requirement: !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: 1.4.1
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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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- 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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  - !ruby/object:Gem::Dependency
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  name: addressable
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  requirement: !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: 2.3.2
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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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- 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: 2.3.2
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  - !ruby/object:Gem::Dependency
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  name: bio
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  requirement: !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: 1.4.2
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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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- none: false
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  requirements:
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- - - ! '>='
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  - !ruby/object:Gem::Version
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  version: 1.4.2
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  - !ruby/object:Gem::Dependency
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  name: rspec
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  requirement: !ruby/object:Gem::Requirement
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- none: false
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  - !ruby/object:Gem::Version
@@ -106,7 +94,6 @@ dependencies:
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  version_requirements: !ruby/object:Gem::Requirement
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@@ -114,23 +101,20 @@ dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bundler
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  requirement: !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: 1.1.5
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  type: :development
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  version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- - - ! '>='
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  - !ruby/object:Gem::Version
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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  requirement: !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
@@ -138,7 +122,6 @@ dependencies:
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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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- none: false
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -146,23 +129,20 @@ dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio
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  requirement: !ruby/object:Gem::Requirement
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- none: false
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  requirements:
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- - - ! '>='
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  prerelease: false
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  version_requirements: !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: 1.4.2
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  - !ruby/object:Gem::Dependency
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  name: rdoc
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  requirement: !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
@@ -170,7 +150,6 @@ dependencies:
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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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- none: false
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
@@ -195,6 +174,8 @@ files:
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  - VERSION
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  - bin/biointerchange
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  - examples/BovineGenomeChrX.gff3.gz
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+ - examples/ReaderModelWriterSequenceDiagram.graffle
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+ - examples/ReaderModelWriterSequenceDiagram.png
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  - examples/Saccharomyces_cerevisiae_incl_consequences.gvf.gz
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  - examples/bininda_emonds_mammals.new
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  - examples/chromosome_BF.gff
@@ -219,6 +200,7 @@ files:
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  - lib/biointerchange/exceptions.rb
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  - lib/biointerchange/faldo.rb
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  - lib/biointerchange/genomics/gff3_feature.rb
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+ - lib/biointerchange/genomics/gff3_feature_sequence.rb
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  - lib/biointerchange/genomics/gff3_feature_set.rb
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  - lib/biointerchange/genomics/gff3_pragmas.rb
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  - lib/biointerchange/genomics/gff3_rdf_ntriples.rb
@@ -227,7 +209,9 @@ files:
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  - lib/biointerchange/genomics/gvf_feature_set.rb
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  - lib/biointerchange/genomics/gvf_pragmas.rb
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  - lib/biointerchange/genomics/gvf_reader.rb
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+ - lib/biointerchange/genomics/locations.rb
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  - lib/biointerchange/gff3o.rb
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+ - lib/biointerchange/gfvo.rb
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  - lib/biointerchange/goxref.rb
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  - lib/biointerchange/gvf1o.rb
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  - lib/biointerchange/model.rb
@@ -293,7 +277,12 @@ files:
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  - web/cli.html
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  - web/css/rdoc-style.css
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  - web/css/rdoc.css
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+ - web/images/BioInterchange120.png
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+ - web/images/BioInterchange120inv.png
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+ - web/images/BioInterchange160.png
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+ - web/images/BioInterchange160inv.png
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  - web/images/BioInterchange300.png
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+ - web/images/BioInterchange300inv.png
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  - web/index.html
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  - web/ontologies.html
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  - web/service/rdfizer.fcgi
@@ -301,30 +290,26 @@ files:
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  homepage: http://www.biointerchange.org
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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: []
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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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- 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: '0'
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- segments:
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- hash: 3715660603784796436
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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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  requirements: []
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  rubyforge_project:
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- rubygems_version: 1.8.23
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+ rubygems_version: 2.0.5
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  signing_key:
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- specification_version: 3
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+ specification_version: 4
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  summary: An open source framework for transforming heterogeneous data formats into
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  RDF.
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  test_files: []