[BioRuby-cvs] bioruby/lib/bio/appl clustalw.rb,1.7,1.8
Naohisa Goto
ngoto at pub.open-bio.org
Mon Oct 31 14:46:21 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory pub.open-bio.org:/tmp/cvs-serv4526
Modified Files:
clustalw.rb
Log Message:
Changed document format from RD to RDoc.
Added references in document.
Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** clustalw.rb 9 Sep 2005 15:52:57 -0000 1.7
--- clustalw.rb 31 Oct 2005 19:46:19 -0000 1.8
***************
*** 1,7 ****
#
! # bio/appl/clustalw.rb - CLUSTAL W wrapper class
#
! # Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
--- 1,9 ----
#
! # = bio/appl/clustalw.rb - CLUSTAL W wrapper class
#
! # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # Licence:: LGPL
#
+ #--
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
***************
*** 17,23 ****
--- 19,41 ----
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ #++
#
# $Id$
#
+ # Bio::ClustalW is a CLUSTAL W execution wrapper class.
+ # Its object is also called an alignment factory.
+ # CLUSTAL W is a very popular software for multiple sequence alignment.
+ #
+ # == References
+ #
+ # * Thompson,J.D., Higgins,D.G. and Gibson,T.J..
+ # CLUSTAL W: improving the sensitivity of progressive multiple sequence
+ # alignment through sequence weighting, position-specific gap penalties
+ # and weight matrix choice. Nucleic Acids Research, 22:4673-4680, 1994.
+ # http://nar.oxfordjournals.org/cgi/content/abstract/22/22/4673
+ # * http://www.ebi.ac.uk/clustalw/
+ # * ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
+ #
+
require 'tempfile'
***************
*** 27,35 ****
require 'bio/alignment'
! module Bio
class ClustalW
autoload :Report, 'bio/appl/clustalw/report'
def initialize(program = 'clustalw', option = [])
@program = program
--- 45,58 ----
require 'bio/alignment'
! module Bio #:nodoc:
!
! # Bio::ClustalW is a CLUSTAL W execution wrapper class.
! # Its object is also called an alignment factory.
! # CLUSTAL W is a very popular software for multiple sequence alignment.
class ClustalW
autoload :Report, 'bio/appl/clustalw/report'
+ # Creates a new CLUSTAL W execution wrapper object (alignment factory).
def initialize(program = 'clustalw', option = [])
@program = program
***************
*** 40,47 ****
@log = nil
end
- attr_accessor :program, :option
- attr_reader :command, :log
- attr_reader :output, :report
def query(seqs)
if seqs then
--- 63,92 ----
@log = nil
end
+ # name of the program (usually 'clustalw' in UNIX)
+ attr_accessor :program
+
+ # options
+ attr_accessor :option
+
+ # Returns last command-line strings executed by this factory.
+ # Note that filenames described in the command-line may already
+ # be removed because they are temporary files.
+ # Returns an array.
+ attr_reader :command
+
+ # Returns last messages of CLUSTAL W execution.
+ attr_reader :log
+
+ # Returns last raw alignment result (String).
+ attr_reader :output
+
+ # Returns last alignment result.
+ # Returns a Bio::ClustalW::Report object.
+ attr_reader :report
+
+ # Executes the program(clustalw).
+ # If +seqs+ is not nil, perform alignment for seqs.
+ # If +seqs+ is nil, simply executes CLUSTAL W.
def query(seqs)
if seqs then
***************
*** 52,57 ****
end
def query_align(seqs)
- # seqs should be Bio::Alignment or Array of sequences or nil
seqtype = nil
unless seqs.is_a?(Bio::Alignment)
--- 97,103 ----
end
+ # Performs alignment for +seqs+.
+ # +seqs+ should be Bio::Alignment or Array of sequences or nil.
def query_align(seqs)
seqtype = nil
unless seqs.is_a?(Bio::Alignment)
***************
*** 69,72 ****
--- 115,120 ----
end
+ # Performs alignment for +str+.
+ # +str+ should be a string that can be recognized by CLUSTAL W.
def query_string(str, *arg)
begin
***************
*** 81,84 ****
--- 129,133 ----
end
+ # Performs alignment of sequences in the file named +path+.
def query_by_filename(path, seqtype = nil)
require 'bio/appl/clustalw/report'
***************
*** 107,114 ****
--- 156,168 ----
@report
end
+
+ # Returns last alignment guild-tree (file.dnd).
attr_reader :output_dnd
+ # Returns last error messages (to stderr) of CLUSTAL W execution.
attr_reader :errorlog
+
private
+ # Executes the program in the local machine.
def exec_local(opt)
@command = [ @program, *opt ]
***************
*** 136,198 ****
end #module Bio
- =begin
-
- = Bio::ClustalW
-
- --- Bio::ClustalW.new(path_to_clustalw = 'clustalw', option = [])
-
- Creates new alignment factory.
-
- --- Bio::ClustalW#program
- --- Bio::ClustalW#option
-
- Access to the variables specified in Bio::ClustalW.new.
-
- --- Bio::ClustalW#query(seqs)
-
- Executes the program(clustalw).
- If 'seqs' is not nil, perform alignment for seqs.
- If 'seqs' is nil, simply executes CLUSTAL W.
-
- --- Bio::ClustalW#query_align(seqs)
-
- Performs alignment for seqs.
-
- --- Bio::ClustalW#query_string(str)
-
- Performs alignment for str.
- Str should be a string that can be recognized by CLUSTAL W.
-
- --- Bio::ClustalW#query_by_filename(filename)
-
- Performs alignment of sequences in the file named filename.
-
- --- Bio::ClustalW#command
-
- Shows latest command-line executed by this factory.
- Note that filenames described in the command-line may already
- be removed because they are temporary files.
- Returns an array.
-
- --- Bio::ClustalW#log
-
- Shows latest messages of CLUSTAL W execution.
-
- --- Bio::ClustalW#report
-
- Shows latest alignment result (instance of Bio::ClustalW::Report)
- performed by this factory.
-
- --- Bio::ClustalW#output
-
- Shows latest raw alignment result (String).
-
- --- Bio::ClustalW#output_dnd
-
- Shows latest alignment guild-tree (filename.dnd).
-
- --- Bio::ClustalW#errorlog
-
- Shows latest error messages (thourgh stderr) of CLUSTAL W execution.
-
- =end
--- 190,191 ----
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