bin/br_bioflat.rb in bio-0.7.1 vs bin/br_bioflat.rb in bio-1.0.0

@@ -1,27 +1,15 @@
 #!/usr/bin/env ruby
 # 
-# bioflat - OBDA flat file indexer (executable)
+# = bioflat - OBDA flat file indexer (executable)
 # 
-#   Copyright (C) 2002 GOTO Naohisa <[e-mail]> 
+# Copyright::   Copyright (C) 2002
+#               Naohisa Goto <[e-mail]>
+# License::     Ruby's
+#
+# $Id: br_bioflat.rb,v 1.16 2006/02/22 07:01:05 ngoto Exp $ 
 # 
-#  This program is free software; you can redistribute it and/or modify 
-#  it under the terms of the GNU General Public License as published by 
-#  the Free Software Foundation; either version 2 of the License, or 
-#  (at your option) any later version. 
-# 
-#  This program is distributed in the hope that it will be useful, 
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of 
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
-#  GNU General Public License for more details. 
-# 
-#  You should have received a copy of the GNU General Public License 
-#  along with this program; if not, write to the Free Software 
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA 
-# 
-#  $Id: br_bioflat.rb,v 1.14 2003/08/27 17:28:30 ng Exp $ 
-# 
 
 require 'bio'
 
 def usage
   print <<EOM
@@ -149,11 +137,11 @@
 
     when /^\-\-?renew/
       options['renew'] = true
 
     else
-      STDERR.print "Warning: ignoring invalid option #{x.inspect}\n"
+      $stderr.print "Warning: ignoring invalid option #{x.inspect}\n"
     end
   end
 
   dbpath = File.join(location, dbname) unless dbpath
   if mode == :update then
@@ -189,28 +177,28 @@
   end
   dbname = ARGV.shift unless dbname
   dbname = File.join(location, dbname) unless location.to_s.empty?
   db = Bio::FlatFileIndex.open(dbname)
   ARGV.each do |key|
-    STDERR.print "Searching for \'#{key}\'...\n"
+    $stderr.print "Searching for \'#{key}\'...\n"
     #r = db.search(key)
-    #STDERR.print "OK, #{r.size} entry found\n"
+    #$stderr.print "OK, #{r.size} entry found\n"
     #if r.size > 0 then
     #  print r
     #end
     begin
       if names.empty? then
 	r = db.include?(key)
       else
 	r = db.include_in_namespaces?(key, *names)
       end
     rescue RuntimeError
-      STDERR.print "ERROR: #{$!}\n"
+      $stderr.print "ERROR: #{$!}\n"
       next
     end
     r = [] unless r
-    STDERR.print "OK, #{r.size} entry found\n"
+    $stderr.print "OK, #{r.size} entry found\n"
     r.each do |i|
       print db.search_primary(i)
     end
   end
   db.close
@@ -250,17 +238,17 @@
     files.each do |x|
       k = Bio::FlatFile.autodetect_file(x)
       break if k
     end
     if k then
-      STDERR.print "Format: #{k.to_s}\n"
+      $stderr.print "Format: #{k.to_s}\n"
       format = k
     else
-      STDERR.print "ERROR: couldn't determine file format\n"
+      $stderr.print "ERROR: couldn't determine file format\n"
       return
     end
   end
-  STDERR.print "Namespaces: (first line: primary namespace)\n"
+  $stderr.print "Namespaces: (first line: primary namespace)\n"
   if format then
     parser = Bio::FlatFileIndex::Indexer::Parser.new(format)
     print parser.primary.name, "\n"
     puts parser.secondary.keys
   else