Module: GO

Defined in:
lib/rbbt/sources/go.rb

Overview

This module holds helper methods to deal with the Gene Ontology files. Right now all it does is provide a translation form id to the actual names.

Constant Summary collapse

MULTIPLE_VALUE_FIELDS = 
%w(is_a)
TSV_GENE_ONTOLOGY = 
File.join(Persist.cachedir, 'gene_ontology')

Class Method Summary collapse

Class Method Details

.goterms ⇒ Object 



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# File 'lib/rbbt/sources/go.rb', line 47

def self.goterms
  info.keys
end

.id2ancestors(id) ⇒ Object 



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# File 'lib/rbbt/sources/go.rb', line 60

def self.id2ancestors(id)
  if id.kind_of? Array
    info.values_at(*id).
      select{|i| ! i['is_a'].nil?}.
      collect{|i| i['is_a'].collect{|id| 
      id.match(/(GO:\d+)/)[1] if id.match(/(GO:\d+)/)
    }.compact
    }
  else
    return [] if id.nil? or info[id].nil? or info[id]['is_a'].nil?
    info[id]['is_a'].
      collect{|id| 
      id.match(/(GO:\d+)/)[1] if id.match(/(GO:\d+)/)
    }.compact
  end
end

.id2name(id) ⇒ Object 



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# File 'lib/rbbt/sources/go.rb', line 51

def self.id2name(id)
  if id.kind_of? Array
    info.values_at(*id).collect{|i| i['name'] if i}
  else
    return nil if info[id].nil?
    info[id]['name']
  end
end

.id2namespace(id) ⇒ Object 



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# File 'lib/rbbt/sources/go.rb', line 77

def self.id2namespace(id)
  self.init unless info
  if id.kind_of? Array
    info.values_at(*id).collect{|i| i['namespace'] if i}
  else
    return nil if info[id].nil?
    info[id]['namespace']
  end
end

.info ⇒ Object 



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# File 'lib/rbbt/sources/go.rb', line 43

def self.info
  @@info ||= self.init
end

.init ⇒ Object

This method needs to be called before any translations can be made, it is called automatically the first time the id2name method is called. It loads the gene_ontology.obo file and extracts all the fields, although right now, only the name field is used.



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# File 'lib/rbbt/sources/go.rb', line 19

def self.init
  Persist.persist_tsv(nil, 'gene_ontology', {}, :persist => true) do |info|
    info.serializer = :marshal if info.respond_to? :serializer
    Rbbt.share.databases.GO.gene_ontology.read.split(/\[Term\]/).each{|term| 
      term_info = {}

      term.split(/\n/). select{|l| l =~ /:/}.each{|l| 
        key, value = l.chomp.match(/(.*?):(.*)/).values_at(1,2)
        if MULTIPLE_VALUE_FIELDS.include? key.strip
          term_info[key.strip] ||= []
          term_info[key.strip] << value.strip
        else
          term_info[key.strip] = value.strip
        end
      }

      next if term_info["id"].nil?
      info[term_info["id"]] = term_info
    }

    info
  end.tap{|o| o.unnamed = true}
end