lib/bio/db/rebase.rb in bio-1.2.1 vs lib/bio/db/rebase.rb in bio-1.3.0

@@ -3,19 +3,18 @@
 #
 # Author::    Trevor Wennblom  <mailto:[e-mail]>
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: rebase.rb,v 1.8 2007/04/05 23:35:40 trevor Exp $
+#  $Id:$
 #
 
-autoload :YAML, 'yaml'
+require 'yaml'
+require 'bio/reference'
 
-module Bio #:nodoc:
+module Bio
 
-autoload :Reference, 'bio/reference'
-
 #
 # bio/db/rebase.rb - Interface for EMBOSS formatted REBASE files
 #
 # Author::    Trevor Wennblom  <mailto:[e-mail]>
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
@@ -314,11 +313,11 @@
   #   :c3 => Second 5' cut
   #   :c4 => Seocnd 3' cut
   def parse_enzymes( lines )
     data = {}
     return data if lines == nil
-    lines.each do |line|
+    lines.each_line do |line|
       next if line[0].chr == '#'
       line.chomp!
       
       a = line.split("\s")
       
@@ -345,11 +344,11 @@
     return data if lines == nil
     index = 1
     h = {}
     references_left = 0
 
-    lines.each do |line|
+    lines.each_line do |line|
       next if line[0].chr == '#'  # Comment
       next if line[0..1] == '//'  # End of entry marker
       line.chomp!
 
       if (1..7).include?( index )
@@ -387,10 +386,10 @@
   #   data[supplier_code]
   #   returns the suppliers name
   def parse_suppliers( lines )
     data = {}
     return data if lines == nil
-    lines.each do |line|
+    lines.each_line do |line|
       next if line[0].chr == '#'
       data[$1] = $2 if line =~ %r{(.+?)\s(.+)}
     end
     data
   end