[BioRuby-cvs] bioruby/lib/bio/appl emboss.rb,1.2,1.3

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory pub.open-bio.org:/tmp/cvs-serv4775/lib/bio/appl

Modified Files:
	emboss.rb 
Log Message:
* entret/seqret commands in EMBOSS are supported
  * Bio::EMBOSS.seqret(usa), Bio::EMBOSS.entret(usa)
  * bioruby> seqret(usa), entret(usa)
* obj() method is added in addition to seq() and ent() methods.


Index: emboss.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/emboss.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** emboss.rb	8 Sep 2005 01:22:08 -0000	1.2
--- emboss.rb	28 Jan 2006 06:46:42 -0000	1.3
***************
*** 1,6 ****
  #
! # bio/appl/emboss.rb - EMBOSS wrapper
  # 
! #   Copyright (C) 2002 KATAYAMA Toshiaki <k at bioruby.org>
  #
  #  This library is free software; you can redistribute it and/or
--- 1,16 ----
  #
! # = bio/appl/emboss.rb - EMBOSS wrapper
  # 
! # Copyright::	Copyright (C) 2002, 2005
! #		KATAYAMA Toshiaki <k at bioruby.org>
! # License::	LGPL
! #
! # $Id$
! #
! # == References
! #
! # * http://www.emboss.org
! #
! #--
  #
  #  This library is free software; you can redistribute it and/or
***************
*** 18,68 ****
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #  $Id$
  #
  
  module Bio
  
!   class EMBOSS
  
!     def initialize(cmd_line)
!       @cmd_line = cmd_line + ' -stdout'
!     end
  
!     def exec
!       begin
!         @io = IO.popen(@cmd_line, "w+")
!         @result = @io.read
!         return @result
!       ensure
!         @io.close
!       end
!     end
!     attr_reader :io, :result
  
    end
  
! end
! 
! =begin
! 
! = Bio::EMBOSS
! 
! EMBOSS wrapper.
  
!   #!/usr/bin/env ruby
!   require 'bio'
  
!   emboss = Bio::EMBOSS.new("getorf -sequence ~/xlrhodop -outseq stdout")
!   puts emboss.exec
  
! --- Bio::EMBOSS.new(command_line)
  
! --- Bio::EMBOSS#exec
! --- Bio::EMBOSS#io
! --- Bio::EMBOSS#result
  
! === SEE ALSO
  
! * http://www.emboss.org
  
- =end
--- 28,79 ----
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
  
  module Bio
  
! autoload :Command, 'bio/command'
  
! class EMBOSS
  
!   extend Bio::Command::Tools
  
+   def self.seqret(arg)
+     str = self.retrieve('seqret', arg)
    end
  
!   def self.entret(arg)
!     str = self.retrieve('entret', arg)
!   end
  
!   def initialize(cmd_line)
!     @cmd_line = cmd_line + ' -stdout -auto'
!   end
  
!   def exec
!     begin
!       @io = IO.popen(@cmd_line, "w+")
!       @result = @io.read
!       return @result
!     ensure
!       @io.close
!     end
!   end
!   attr_reader :io, :result
  
!   private
  
!   def self.retrieve(cmd, arg)
!     cmd = [ cmd, arg, '-auto', '-stdout' ]
!     str = ''
!     call_command_local(cmd) do |inn, out|
!       inn.close_write
!       str = out.read
!     end
!     return str
!   end
  
! end # EMBOSS
  
! end # Bio