Class: Bio::Ngs::Ontology

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/ngs/ontology.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(gene_id, go = [], library = nil) ⇒ Ontology

Constructor for Bio::Ngs::Ontology instances



61
62
63
64
65
 
# File 'lib/bio/ngs/ontology.rb', line 61

def initialize(gene_id,go=[],library=nil)
  @gene_id = gene_id
  @go = go
  @library = library
end

Instance Attribute Details

#gene_id ⇒ Object

Returns the value of attribute gene_id.



59
60
61
 
# File 'lib/bio/ngs/ontology.rb', line 59

def gene_id
  @gene_id
end

#go ⇒ Object

Returns the value of attribute go.



59
60
61
 
# File 'lib/bio/ngs/ontology.rb', line 59

def go
  @go
end

#library ⇒ Object

Returns the value of attribute library.



59
60
61
 
# File 'lib/bio/ngs/ontology.rb', line 59

def library
  @library
end

Class Method Details

.go_import(file, yaml_file = nil) ⇒ Object

Method to import a GO OBO file into Go table created according to ActiveRecord model Params: GO OBO file, YAML file for db connection



15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
 
# File 'lib/bio/ngs/ontology.rb', line 15

def self.go_import(file,yaml_file=nil)
  db = Bio::Ngs::Db.new :ontology,yaml_file
  inserts = []
  file = File.open(file)
  file.each do |line|
    if line.start_with? "[Term]"
      block = file.gets("\n\n")
      is_a = []
      data = []
      block.split("\n").each do |elem|
        if elem.start_with? "id: "
          data << elem.gsub("id: ","")
        elsif elem.start_with? "name: "
          data << elem.gsub("name: ","")
        elsif elem.start_with? "is_a"
          is_a << elem.gsub("is_a: ","").split("!").first
        elsif elem.start_with? "namespace: "
          data << elem.gsub("namespace: ","")
        end
      end
      data << is_a.join(" ")
      inserts << data
      if inserts.size == 1000
        db.insert_many(:go,"INSERT INTO go(go_id,name,namespace,is_a) VALUES(?,?,?,?)",inserts)
        inserts = []
      end
    end
  end
  db.insert_many(:go,"INSERT INTO go(go_id,name,namespace,is_a) VALUES(?,?,?,?)",inserts) if inserts.size > 0
end

.load_go_genes(file, yaml_file = nil) ⇒ Object

Method to lood the Gene-GO associations from a JSON file into the Ontology db Params: JSON file name, YAML file for db connection (optional)



48
49
50
51
52
53
54
55
56
 
# File 'lib/bio/ngs/ontology.rb', line 48

def self.load_go_genes(file,yaml_file=nil)
  db = Bio::Ngs::Db.new :ontology, yaml_file
  list = JSON.load File.read(file)
  ontologies = Bio::Ngs::OntologyCollection.new
  list.each_with_index do |gene,index|
    ontologies << Bio::Ngs::Ontology.new(gene["gene_id"],gene["go"],gene["library"])
  end
  ontologies.to_db(yaml_file)
end

Instance Method Details

#to_db(yaml_file = nil) ⇒ Object

Method to store a single Bio::Ngs::Ontology object into the Ontology db

Raises:

  • (RuntimeError) 


68
69
70
71
72
73
74
75
 
# File 'lib/bio/ngs/ontology.rb', line 68

def to_db(yaml_file=nil)
  raise RuntimeError,"You must initialize the Ontolgy db with biongs ontology:db:init" if Go.count == 0
  db = Bio::Ngs::Db.new :ontology,yaml_file
  g = Gene.create(:gene_id => @gene_id, :library => @library)
  Go.where({:go_id => @go}).all.each do |go|
    g.gene_gos.create(:go_id => go.id)
  end
end