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')

Methods

goid2term new parse_goids

Attributes

header_lines	[R]	Returns a Hash instance of the header lines in ontology flatfile.
id2id	[R]
id2term	[R]

Public Class methods

new(str)

Bio::GO::Ontology.new(str) The DAG Edit format ontology data parser.

[Source]

    # File lib/bio/db/go.rb, line 69
69:     def initialize(str)
70:       @id2term      = {}
71:       @header_lines = {}
72:       @id2id        = {}
73:       adj_list = dag_edit_format_parser(str)
74:       super(adj_list)
75:     end

parse_goids(line)

Bio::GO::Ontology.parse_ogids(line)

Parsing GOID line in the DAGEdit format

 GO:ID[ ; GO:ID...]

[Source]

    # File lib/bio/db/go.rb, line 40
40:     def self.parse_goids(line)
41:       goids = []
42:       loop {
43:         if /^ *[$%<]\S.+?;/ =~ line
44:           endpoint = line.index(';') + 1
45:           line = line[endpoint..line.size]
46:         elsif /^,* GO:(\d{7}),*/ =~ line
47:           goids << $1.clone
48:           endpoint = line.index(goids.last) + goids.last.size
49:           line = line[endpoint..line.size]
50:         else
51:           break
52:         end
53:       }
54:       return goids
55:     end

Public Instance methods

goid2term(goid)

Returns a GO_Term correspondig with the given GO_ID.

[Source]

    # File lib/bio/db/go.rb, line 79
79:     def goid2term(goid)
80:       term = id2term[goid]
81:       term = id2term[id2id[goid]] if term == nil
82:       return term
83:     end