obo_parser 0.4.1 → 0.4.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/README.md +1 -7
- data/lib/obo_parser/utilities/viz.rb +1 -1
- data/lib/obo_parser/version.rb +1 -1
- metadata +1 -1
checksums.yaml
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data.tar.gz: ae3a82ba6cb523277e7615608393bb7259ee8ec6140becf4330ffbeb12d4d20fd0bb69523cef9c8e489306c527518bc71d4b02ac0a7edefaff53335834a9d908
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data/Gemfile.lock
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data/README.md
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@@ -12,8 +12,6 @@ A simple Ruby gem for parsing OBO 1.2 (?4) formatted ontology files. Useful for
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## Use
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### General
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require 'rubygems'
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require 'obo_parser'
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o = parse_obo_file(File.read('my_ontology.obo')) # => An OboParser instance
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first_term = o.terms.first # => An OboParser#Term instance
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See also /test/test_obo_parser.rb
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##
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## Utilities
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A small set of methods (e.g. comparing OBO ontologies) utilizing the gem are included in /lib/utilities.rb. For example: 1) shared labels across sets of ontologies can be found and returned, 2) ontologies can be dumped into a simple Cytoscape node/edge format; 3) given a set of correspondances between two ontologies various reports can be made.
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OboParser::Utilities::Viz.mock_coordinate_space(o, size: 100) # => STDOUT tab delimited table with x, y, z, identifier, label
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## Documentation
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Code documentation is slowly being formalized using Yard.
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## Contributing
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Fork, test, code, test, pull request.
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edge_length = (size / 2) - (size * 0.2)
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total_terms = ontology.terms.size
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grid_length = Math.cbrt(total_terms).ceil.to_i
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cutoff ||=
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cutoff ||= data.count + 1
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data.each_with_index do |row, i|
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break if i > cutoff
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data/lib/obo_parser/version.rb
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