lib/bio/shell/plugin/entry.rb in bio-0.7.1 vs lib/bio/shell/plugin/entry.rb in bio-1.0.0

@@ -1,32 +1,14 @@
 #
 # = bio/shell/plugin/entry.rb - extract entry and sequence
 #
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <[e-mail]>
-# License::	LGPL
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <[e-mail]>
+# License::     Ruby's
 #
-# $Id: entry.rb,v 1.4 2005/12/07 05:12:07 k Exp $
+# $Id: entry.rb,v 1.8 2006/02/27 09:37:14 k Exp $
 #
-#--
-#
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library 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
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#++
-#
 
 module Bio::Shell
 
   private
 
@@ -56,30 +38,57 @@
     elsif ent.respond_to?(:aaseq)
       seq = ent.aaseq
     end
 
     if tmp and tmp.is_a?(String) and not tmp.empty?
-      seq = Bio::Sequence.auto(tmp)
+      seq = Bio::Sequence.auto(tmp).seq
     end
     return seq
   end
 
   # Obtain a database entry from
   #   * IO          -- IO object (first entry only)
   #   * "filename"  -- local file (first entry only)
-  #   * "db:entry"  -- local bioflat, OBDA, KEGG API
+  #   * "db:entry"  -- local BioFlat, OBDA, EMBOSS, KEGG API
   def ent(arg)
     entry = ""
     db, entry_id = arg.to_s.strip.split(/:/)
+
+    # local file
     if arg.respond_to?(:gets) or File.exists?(arg)
+      puts "Retrieving entry from file (#{arg})"
       entry = flatfile(arg)
+
+    # BioFlat in ./.bioruby/bioflat/ or ~/.bioinformatics/.bioruby/bioflat/
     elsif Bio::Shell.find_flat_dir(db)
+      puts "Retrieving entry from local BioFlat database (#{arg})"
       entry = flatsearch(db, entry_id)
+
+    # OBDA in ~/.bioinformatics/seqdatabase.ini
     elsif obdadbs.include?(db)
+      puts "Retrieving entry from OBDA (#{arg})"
       entry = obdaentry(db, entry_id)
+
     else
-      entry = bget(arg)
+      # EMBOSS USA in ~/.embossrc
+      str = entret(arg)
+      if $?.exitstatus == 0 and str.length != 0
+        puts "Retrieving entry from EMBOSS (#{arg})"
+        entry = str
+
+      # KEGG API at http://www.genome.jp/kegg/soap/
+      else
+        puts "Retrieving entry from KEGG API (#{arg})"
+        entry = bget(arg)
+      end
     end
+
     return entry
+  end
+
+  # Obtain a parsed object from sources that ent() supports.
+  def obj(arg)
+    str = ent(arg)
+    flatparse(str)
   end
 
 end