Class: Taxonifi::Export::OboNomenclature

Inherits:
Base
  • Object
show all
Defined in:
lib/taxonifi/export/format/obo_nomenclature.rb

Overview

Writes a OBO formatted file for all names in a name collection. !! Does not write synonyms out. Follows the TTO example.

Constant Summary

Constants inherited from Base

Base::EXPORT_BASE, Base::TAXRANKS

Instance Attribute Summary collapse

Attributes inherited from Base

#base_export_path, #export_folder

Instance Method Summary collapse

Methods inherited from Base

#configure_folders, #export_path, #new_output_file, #sanitize, #sql_insert_statement, #sqlize, #write_file

Constructor Details

#initialize(options = {}) ⇒ OboNomenclature

Returns a new instance of OboNomenclature.

Raises:



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# File 'lib/taxonifi/export/format/obo_nomenclature.rb', line 11

def initialize(options = {})
  opts = {
    :nc => Taxonifi::Model::NameCollection.new,
    :export_folder => 'obo_nomenclature',
    :starting_id => 1,
    :namespace => 'XYZ'
  }.merge!(options)

  super(opts)
  raise Taxonifi::Export::ExportError, 'NameCollection not passed to OboNomenclature export.' if ! opts[:nc].class == Taxonifi::Model::NameCollection
  @name_collection = opts[:nc]
  @namespace = opts[:namespace]
  @time = Time.now.strftime("%D %T").gsub('/',":") 
  @empty_quotes = "" 
end

Instance Attribute Details

#name_collection ⇒ Object

Returns the value of attribute name_collection.



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# File 'lib/taxonifi/export/format/obo_nomenclature.rb', line 9

def name_collection
  @name_collection
end

#namespace ⇒ Object

Returns the value of attribute namespace.



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# File 'lib/taxonifi/export/format/obo_nomenclature.rb', line 9

def namespace
  @namespace
end

Instance Method Details

#export ⇒ Object

Writes the file.



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# File 'lib/taxonifi/export/format/obo_nomenclature.rb', line 28

def export()
  super
  f = new_output_file('obo_nomenclature.obo') 
 
  # header 
  f.puts 'format-version: 1.2'
  f.puts "date: #{@time}"
  f.puts 'saved-by: someone'
  f.puts 'auto-generated-by: Taxonifi'
  f.puts 'synonymtypedef: COMMONNAME "common name"'
  f.puts 'synonymtypedef: MISSPELLING "misspelling" EXACT'
  f.puts 'synonymtypedef: TAXONNAMEUSAGE "name with (author year)" NARROW'
  f.puts "default-namespace: #{@namespace}"
  f.puts "ontology: FIX-ME-taxonifi-ontology\n\n" 

  # terms
  @name_collection.collection.each do |n|
    f.puts '[Term]'
    f.puts "id: #{id_string(n)}"
    f.puts "name: #{n.name}"
    f.puts "is_a: #{id_string(n.parent)} ! #{n.parent.name}" if n.parent
    f.puts "property_value: has_rank #{rank_string(n)}"
    f.puts
  end

  # typedefs
  f.puts "[Typedef]"
  f.puts "id: has_rank"
  f.puts "name: has taxonomic rank"
  f.puts "is_metadata_tag: true"

  true
end

#id_string(name) ⇒ Object 



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# File 'lib/taxonifi/export/format/obo_nomenclature.rb', line 66

def id_string(name)
  "#{@namespace}:#{name.id.to_s.rjust(7,"0")}"
end

#rank_string(name) ⇒ Object 



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# File 'lib/taxonifi/export/format/obo_nomenclature.rb', line 62

def rank_string(name)    
  "TAXRANK:#{TAXRANKS[name.rank].to_s.rjust(7,"0")}"
end