lib/bio/appl/meme/mast.rb in bio-1.4.3.0001 vs lib/bio/appl/meme/mast.rb in bio-1.5.0

@@ -92,11 +92,11 @@
     # * (required) _mast_location_: String
     # *Raises*:: ArgumentError if mast program is not found
     # *Returns*:: a Bio::Meme::Mast object
     
     def initialize(mast_location, options = {})
-      unless File.exists?(mast_location)
+      unless File.exist?(mast_location)
         raise ArgumentError.new("mast: command not found : #{mast_location}")
       end
       @binary = mast_location
       options.empty? ? config(DEFAULT_OPTIONS) : config(options)
     end
@@ -135,12 +135,12 @@
     
     def check_options
       @options.each_key do |k|
         raise ArgumentError.new("Invalid option: #{k}") unless DEFAULT_OPTIONS.has_key?(k)
       end
-      raise ArgumentError.new("Motif file not found: #{@options[:mfile]}") if @options[:mfile].nil? or !File.exists?(@options[:mfile])
-      raise ArgumentError.new("Database not found: #{@options[:d]}") if @options[:d].nil? or !File.exists?(@options[:d])
+      raise ArgumentError.new("Motif file not found: #{@options[:mfile]}") if @options[:mfile].nil? or !File.exist?(@options[:mfile])
+      raise ArgumentError.new("Database not found: #{@options[:d]}") if @options[:d].nil? or !File.exist?(@options[:d])
     end
 
     # Run the mast program
     # ---
     # *Returns*:: Bio::Meme::Mast::Report object
@@ -151,6 +151,6 @@
       Report.new(@output)
     end
     
   end # End class Mast
 end # End module Meme
-end # End module Bio
\ No newline at end of file
+end # End module Bio