[BioRuby-cvs] bioruby/lib/bio/appl clustalw.rb, 1.11, 1.12 mafft.rb, 1.11, 1.12 sim4.rb, 1.6, 1.7
Naohisa Goto
ngoto at dev.open-bio.org
Thu Dec 14 14:54:53 UTC 2006
Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv13473/lib/bio/appl
Modified Files:
clustalw.rb mafft.rb sim4.rb
Log Message:
Changed to use Bio::Command in bio/command.rb instead of Open3.popen3.
Bio::(ClustalW|MAFFT|Sim4)#option is changed to #options.
Bio::ClustalW::errorlog and Bio::(MAFFT|Sim4)#log are deprecated and
there are no replacements for the methods.
Index: sim4.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** sim4.rb 30 Apr 2006 05:50:19 -0000 1.6
--- sim4.rb 14 Dec 2006 14:54:50 -0000 1.7
***************
*** 16,21 ****
#
- require 'open3'
require 'tempfile'
module Bio
--- 16,21 ----
#
require 'tempfile'
+ require 'bio/command'
module Bio
***************
*** 30,41 ****
# [+database+] Default file name of database('seq2').
# [+option+] Options (array of strings).
! def initialize(program = 'sim4', database = nil, option = [])
@program = program
! @option = option
@database = database #seq2
@command = nil
@output = nil
@report = nil
- @log = nil
end
--- 30,40 ----
# [+database+] Default file name of database('seq2').
# [+option+] Options (array of strings).
! def initialize(program = 'sim4', database = nil, opt = [])
@program = program
! @options = opt
@database = database #seq2
@command = nil
@output = nil
@report = nil
end
***************
*** 47,57 ****
# options
! attr_reader :option
# last command-line strings executed by the object
attr_reader :command
# last messages of program reported to the STDERR
! attr_reader :log
# last result text (String)
--- 46,70 ----
# options
! attr_accessor :options
!
! # option is deprecated. Instead, please use options.
! def option
! warn "option is deprecated. Please use options."
! options
! end
# last command-line strings executed by the object
attr_reader :command
+ #---
# last messages of program reported to the STDERR
! #attr_reader :log
! #+++
!
! #log is deprecated (no replacement) and returns empty string.
! def log
! warn "log is deprecated (no replacement) and returns empty string."
! ''
! end
# last result text (String)
***************
*** 97,112 ****
@command = [ @program, filename1, (filename2 or @database), *@option ]
@output = nil
- @log = nil
@report = nil
! Open3.popen3(*@command) do |din, dout, derr|
! din.close
! derr.sync = true
! t = Thread.start { @log = derr.read }
! begin
! @output = dout.read
! @report = Bio::Sim4::Report.new(@output)
! ensure
! t.join
! end
end
@report
--- 110,118 ----
@command = [ @program, filename1, (filename2 or @database), *@option ]
@output = nil
@report = nil
! Bio::Command.call_command(*@command) do |io|
! io.close_write
! @output = io.read
! @report = Bio::Sim4::Report.new(@output)
end
@report
Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** clustalw.rb 30 Apr 2006 05:50:19 -0000 1.11
--- clustalw.rb 14 Dec 2006 14:54:50 -0000 1.12
***************
*** 24,29 ****
require 'tempfile'
- require 'open3'
require 'bio/sequence'
require 'bio/alignment'
--- 24,29 ----
require 'tempfile'
+ require 'bio/command'
require 'bio/sequence'
require 'bio/alignment'
***************
*** 39,45 ****
# Creates a new CLUSTAL W execution wrapper object (alignment factory).
! def initialize(program = 'clustalw', option = [])
@program = program
! @option = option
@command = nil
@output = nil
--- 39,45 ----
# Creates a new CLUSTAL W execution wrapper object (alignment factory).
! def initialize(program = 'clustalw', opt = [])
@program = program
! @options = opt
@command = nil
@output = nil
***************
*** 52,56 ****
# options
! attr_accessor :option
# Returns last command-line strings executed by this factory.
--- 52,62 ----
# options
! attr_accessor :options
!
! # option is deprecated. Instead, please use options.
! def option
! warn "option is deprecated. Please use options."
! options
! end
# Returns last command-line strings executed by this factory.
***************
*** 144,149 ****
attr_reader :output_dnd
# Returns last error messages (to stderr) of CLUSTAL W execution.
! attr_reader :errorlog
private
--- 150,162 ----
attr_reader :output_dnd
+ #---
# Returns last error messages (to stderr) of CLUSTAL W execution.
! #attr_reader :errorlog
! #+++
! #errorlog is deprecated (no replacement) and returns empty string.
! def errorlog
! warn "errorlog is deprecated (no replacement) and returns empty string."
! ''
! end
private
***************
*** 154,170 ****
@log = nil
! Open3.popen3(*@command) do |din, dout, derr|
! din.close
! t = Thread.start do
! @errorlog = derr.read
! end
@log = dout.read
t.join
end
- # @command_string = @command.join(" ")
- # IO.popen(@command, "r") do |io|
- # io.sync = true
- # @log = io.read
- # end
@log
end
--- 167,175 ----
@log = nil
! Bio::Command.call_command(*@command) do |io|
! io.close_write
@log = dout.read
t.join
end
@log
end
Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** mafft.rb 25 Sep 2006 08:09:22 -0000 1.11
--- mafft.rb 14 Dec 2006 14:54:50 -0000 1.12
***************
*** 24,36 ****
#
require 'bio/db/fasta'
require 'bio/io/flatfile'
- #--
- # We use Open3.popen3, because MAFFT on win32 requires Cygwin.
- #++
- require 'open3'
- require 'tempfile'
-
module Bio
--- 24,34 ----
#
+ require 'tempfile'
+
+ require 'bio/command'
+
require 'bio/db/fasta'
require 'bio/io/flatfile'
module Bio
***************
*** 108,118 ****
# +program+ is the name of the program.
# +opt+ is options of the program.
! def initialize(program, option)
@program = program
! @option = option
@command = nil
@output = nil
@report = nil
- @log = nil
end
--- 106,115 ----
# +program+ is the name of the program.
# +opt+ is options of the program.
! def initialize(program, opt)
@program = program
! @options = opt
@command = nil
@output = nil
@report = nil
end
***************
*** 121,125 ****
# options
! attr_accessor :option
# Shows last command-line string. Returns nil or an array of String.
--- 118,128 ----
# options
! attr_accessor :options
!
! # option is deprecated. Instead, please use options.
! def option
! warn "option is deprecated. Please use options."
! options
! end
# Shows last command-line string. Returns nil or an array of String.
***************
*** 128,133 ****
attr_reader :command
# last message to STDERR when executing the program.
! attr_reader :log
# Shows latest raw alignment result.
--- 131,144 ----
attr_reader :command
+ #---
# last message to STDERR when executing the program.
! #attr_reader :log
! #+++
!
! #log is deprecated (no replacement) and returns empty string.
! def log
! warn "log is deprecated (no replacement) and returns empty string."
! ''
! end
# Shows latest raw alignment result.
***************
*** 189,204 ****
#STDERR.print "DEBUG: ", @command.join(" "), "\n"
@output = nil
! @log = nil
! Open3.popen3(*@command) do |din, dout, derr|
! din.close
! derr.sync = true
! t = Thread.start do
! @log = derr.read
! end
! ff = Bio::FlatFile.new(Bio::FastaFormat, dout)
@output = ff.to_a
- t.join
end
- @log
end
--- 200,208 ----
#STDERR.print "DEBUG: ", @command.join(" "), "\n"
@output = nil
! Bio::Command.call_command(*@command) do |io|
! io.close_write
! ff = Bio::FlatFile.new(Bio::FastaFormat, io)
@output = ff.to_a
end
end
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