class PlasmoDB

Provides fast indexed access to a swissprot database in a flat .dat file

Public Class Methods

new(env=nil) click to toggle source
# File lib/protk/plasmodb.rb, line 10
def initialize(env=nil)
  if ( env!=nil)
    @genv=env
  else
    @genv=Constants.instance
  end

  database_file="#{@genv.protein_database_root}/#{@genv.plasmodb_annotation_database}/raw.txt"

  throw "The plasmodb database at \"#{database_file}\" does not exist"  if ( database_file==nil || !FileTest.exist?(database_file) )

  @db_object=EuPathDBGeneInformationFileExtractor.new(database_file)

end

Public Instance Methods

get_entry_for_name(name) click to toggle source
# File lib/protk/plasmodb.rb, line 26
def get_entry_for_name(name)
  
  @genv.log("Getting entry for #{name}",:info)
  
  begin
    result=nil 
    result=@db_object.extract_gene_info(name,10000)
    
  rescue
    
    
    if result==nil
      if ( @genv!=nil)
        @genv.log("Failed to find PlasmoDB entry for gene named #{name} in database",:warn)
      end
    end
    
    
    return result
  end
    
    
end