Class: WingenderTFClass::OBO::TFClassification

Inherits:
Object
  • Object
show all
Defined in:
lib/WingenderTFClass/obo/tf_classification.rb

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ TFClassification

terms by ids



19
20
21
22
23
24
25
26
27
 
# File 'lib/WingenderTFClass/obo/tf_classification.rb', line 19

def initialize()
  @terms_by_id = {}
  @children_by_id = Hash.new{|h,k| h[k] = [] }
  @terms_by_name = Hash.new{|h,k| h[k] = [] }
  # @terms_by_id.each{|term_id, term|
  #   @children_by_id[term.parent_id] << term  if term.parent_id
  # }
  self << Term.new(self, '', '', 'Root', '', nil, [], [])
end

Class Method Details

.by_species(species) ⇒ Object 



7
8
9
10
11
12
13
14
15
16
 
# File 'lib/WingenderTFClass/obo/tf_classification.rb', line 7

def self.by_species(species)
  case species.to_s.downcase
  when 'human'
    OBO::TFClassification.from_file(FilePaths::TFOntologyHuman)
  when 'mouse'
    OBO::TFClassification.from_file(FilePaths::TFOntologyMouse)
  else
    raise "Unknown species `#{species}`"
  end
end

.from_file(filename) ⇒ Object 



36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
 
# File 'lib/WingenderTFClass/obo/tf_classification.rb', line 36

def self.from_file(filename)
  tf_ontology = self.new
  terms = File.readlines(filename)
    .map(&:chomp)
    .slice_before{|line|
      line.start_with?('[Term]')
    }.drop(1)
    .map{|enumerator|
       Term.from_line_array(tf_ontology, enumerator.to_a)
    }
  terms.each{|term|
    tf_ontology << term
  }
  tf_ontology
end

Instance Method Details

#<<(term) ⇒ Object 



29
30
31
32
33
34
 
# File 'lib/WingenderTFClass/obo/tf_classification.rb', line 29

def <<(term)
  raise "Duplicate id #{term.id}"  if @terms_by_id[term.id]
  @terms_by_id[term.id] = term
  @terms_by_name[term.name] << term
  @children_by_id[term.parent_id] << term  if term.parent_id
end

#children(term_id) ⇒ Object 



60
61
62
 
# File 'lib/WingenderTFClass/obo/tf_classification.rb', line 60

def children(term_id)
  @children_by_id[term_id]
end

#leaf?(term_id) ⇒ Boolean 



68
69
70
71
 
# File 'lib/WingenderTFClass/obo/tf_classification.rb', line 68

def leaf?(term_id)
  raise "Term #{term_id} does not exist"  unless @terms_by_id[term_id]
  @children_by_id[term_id].empty?
end

#root ⇒ Object 



64
65
66
 
# File 'lib/WingenderTFClass/obo/tf_classification.rb', line 64

def root
  term('')
end

#term(term_id) ⇒ Object 



56
57
58
 
# File 'lib/WingenderTFClass/obo/tf_classification.rb', line 56

def term(term_id)
  @terms_by_id[term_id]
end

#term_by_name(name) ⇒ Object 



52
53
54
 
# File 'lib/WingenderTFClass/obo/tf_classification.rb', line 52

def term_by_name(name)
  @terms_by_name[name]
end

#tf_groups(slice_deepness) ⇒ Object 



73
74
75
76
77
78
79
 
# File 'lib/WingenderTFClass/obo/tf_classification.rb', line 73

def tf_groups(slice_deepness)
  @terms_by_id.each_value.select{|term|
    term.deepness >= slice_deepness && (!term.parent || term.parent.deepness < slice_deepness)
  }.map{|term|
    [term, term.subtree_nodes]
  }.to_h
end