[BioRuby-cvs] bioruby/lib/bio/io fastacmd.rb,1.6,1.7

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv9033/lib/bio/io

Modified Files:
	fastacmd.rb 
Log Message:
	* lib/bio/command.rb
	
	  Newly added Bio::Command::Tools module.
  	  Bio::Command::Tools is a collection of useful methods
  	  for execution of external commands.

  	* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
	  lib/bio/appl/hmmer.rb, lib/bio/io/fastacmd.rb

  	  For security reason, shell special characters are escaped.

  	* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb, lib/bio/appl/hmmer.rb

	  Options are stored with an array (@options).
  	  #options and #opions= methods are added.
										  	* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb

	  Bio::Blast.remote and Bio::Fasta.remote did not work
  	  due to the change of the GenomeNet.


Index: fastacmd.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/fastacmd.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** fastacmd.rb	10 Aug 2005 12:55:06 -0000	1.6
--- fastacmd.rb	16 Aug 2005 09:38:34 -0000	1.7
***************
*** 24,28 ****
  require 'bio/db/fasta'
  require 'bio/io/flatfile'
! require 'open3'
  
  module Bio
--- 24,28 ----
  require 'bio/db/fasta'
  require 'bio/io/flatfile'
! require 'bio/command'
  
  module Bio
***************
*** 32,35 ****
--- 32,36 ----
  
    include Enumerable
+   include Bio::Command::Tools
  
    def initialize(db)
***************
*** 52,95 ****
      end
  
!     if RUBY_PLATFORM[/mswin32|bccwin32/]	 # replace with appl/factory.rb
!       cmd = "#{@fastacmd} -d #{@database} -s #{entry_id}"
!       IO.popen(cmd, "r") do |io|
!         io.sync = true
!         results = Bio::FlatFile.new(Bio::FastaFormat, io).to_a
!       end
!     else
!       cmd = [ @fastacmd, '-d', @database, '-s', entry_id ]
!       Open3.popen3(*cmd) do |inn, out, err|
!         inn.close
!         t = Thread.start { @errorlog = err.read }
!         results = Bio::FlatFile.new(Bio::FastaFormat, out).to_a
!         t.join
!         results
!       end
      end
    end
  
    def each_entry
!     if RUBY_PLATFORM[/mswin32|bccwin32/]	 # replace with appl/factory.rb
!       cmd = "#{@fastacmd} -d #{@database} -D T"
!       IO.popen(cmd, "r") do |io|
!         io.sync = true
!         Bio::FlatFile.open(Bio::FastaFormat, io) do |f|
!           f.each_entry do |e|
!             yield e
!           end
!         end
!       end
!     else
!       cmd = [ @fastacmd, '-d', @database, '-D', 'T' ]
!       Open3.popen3(*cmd) do |inn, out, err|
!         inn.close
!         t = Thread.start { @errorlog = err.read }
!         Bio::FlatFile.open(Bio::FastaFormat, out) do |f|
!           f.each_entry do |e|
!             yield e
!           end
          end
-         t.join
        end
      end
--- 53,71 ----
      end
  
!     cmd = [ @fastacmd, '-d', @database, '-s', entry_id ]
!     call_command_local(cmd) do |inn, out|
!       inn.close_write
!       Bio::FlatFile.new(Bio::FastaFormat, out).to_a
      end
    end
  
    def each_entry
!     cmd = [ @fastacmd, '-d', @database, '-D', 'T' ]
!     call_command_local(cmd) do |inn, out|
!       inn.close_write
!       Bio::FlatFile.open(Bio::FastaFormat, out) do |f|
!         f.each_entry do |e|
!           yield e
          end
        end
      end