Container class for ontologies in the DAG Edit format.
c_data = File.open('component.oontology').read go_c = Bio::GO::Ontology.new(c_data) p go_c.bfs_shortest_path('0003673','0005632')
Bio::GO::Ontology.new(str) The DAG Edit format ontology data parser.
# File lib/bio/db/go.rb, line 69 def initialize(str) @id2term = {} @header_lines = {} @id2id = {} adj_list = dag_edit_format_parser(str) super(adj_list) end
Bio::GO::Ontology.parse_ogids(line)
Parsing GOID line in the DAGEdit format
GO:ID[ ; GO:ID...]
# File lib/bio/db/go.rb, line 40 def self.parse_goids(line) goids = [] loop { if /^ *[$%<]\S.+?;/ =~ line endpoint = line.index(';') + 1 line = line[endpoint..line.size] elsif /^,* GO:(\d{7}),*/ =~ line goids << $1.clone endpoint = line.index(goids.last) + goids.last.size line = line[endpoint..line.size] else break end } return goids end
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