obo_parser 0.4.1 → 0.4.2
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- 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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metadata.gz: 5c50158118a407e908f7c6ab46830ea21d6b87fb7c73898418883759a91a1b17771c86956a7bb9cb81f2fdefc6079b70eb52687d9689fc3b6bf0c9a7b6ee871b
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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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@@ -14,7 +14,7 @@ module OboParser
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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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