class Bio::GO::Ontology
Bio::GO::Ontology¶ ↑
Container class for ontologies in the DAG Edit format.
Example¶ ↑
c_data = File.open('component.oontology').read go_c = Bio::GO::Ontology.new(c_data) p go_c.bfs_shortest_path('0003673','0005632')
Attributes
Returns a Hash instance of the header lines in ontology flatfile.
Public Class Methods
Source
# File lib/bio/db/go.rb 68 def initialize(str) 69 @id2term = {} 70 @header_lines = {} 71 @id2id = {} 72 adj_list = dag_edit_format_parser(str) 73 super(adj_list) 74 end
Bio::GO::Ontology.new(str) The DAG Edit format ontology data parser.
Calls superclass method
Bio::Pathway::new
Source
# File lib/bio/db/go.rb 39 def self.parse_goids(line) 40 goids = [] 41 loop { 42 if /^ *[$%<]\S.+?;/ =~ line 43 endpoint = line.index(';') + 1 44 line = line[endpoint..line.size] 45 elsif /^,* GO:(\d{7}),*/ =~ line 46 goids << $1.clone 47 endpoint = line.index(goids.last) + goids.last.size 48 line = line[endpoint..line.size] 49 else 50 break 51 end 52 } 53 return goids 54 end
Bio::GO::Ontology.parse_ogids(line)
Parsing GOID line in the DAGEdit format
GO:ID[ ; GO:ID...]
Public Instance Methods
Source
# File lib/bio/db/go.rb 78 def goid2term(goid) 79 term = id2term[goid] 80 term = id2term[id2id[goid]] if term == nil 81 return term 82 end
Returns a GO_Term correspondig with the given GO_ID.