[BioRuby-cvs] bioruby/lib/bio/appl muscle.rb, NONE, 1.1 probcons.rb, NONE, 1.1 tcoffee.rb, NONE, 1.1

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv19995/lib/bio/appl

Added Files:
	muscle.rb probcons.rb tcoffee.rb 
Log Message:
New classess Bio::Muscle, Bio::Probcons, and Bio::Tcoffee are added
for MUSCLE, ProbCons, and T-Coffee multiple alignment programs.
Contributed by Jeffrey Blakeslee and colleagues.


--- NEW FILE: tcoffee.rb ---
#
# = bio/appl/tcoffee.rb - T-Coffee application wrapper class
#
# Copyright:: Copyright (C) 2006-2007
#             Jeffrey Blakeslee and John Conery University of Oregon <jeffb at uoregon.edu>
#             Naohisa Goto <ng at bioruby.org>
# License::   The Ruby License
#
#  $Id: tcoffee.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
#
# Bio::Tcoffee is a wrapper class to execute T-Coffee.
#
# == References
#
# * http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
# * Notredame, C., Higgins, D.G. and Heringa, J.
#   T-Coffee: A novel method for fast and accurate multiple sequence
#   alignment. J. Mol. Biol. 302: 205-217, 2000.
#


module Bio

  # Bio::Tcoffee is a wrapper class to execute t-coffee.
  #
  # Please refer documents in bio/apple/tcoffee.rb for references.
  class Tcoffee < Bio::Alignment::FactoryTemplate::FileInFileOutWithTree

    # default program name
    DEFAULT_PROGRAM = 't_coffee'.freeze

    # default report parser
    DEFAULT_PARSER = Bio::ClustalW::Report

    private
    # generates options specifying input filename.
    # returns an array of string
    def _option_input_file(fn)
      [ '-infile', fn ]
    end

    # generates options specifying output filename.
    # returns an array of string
    def _option_output_file(fn)
      [ '-outfile', fn ]
    end

    # generates options specifying output filename.
    # returns an array of string
    def _option_output_dndfile(fn)
      [ '-newtree', fn ]
    end
  end #class TCoffee

end #module Bio

--- NEW FILE: muscle.rb ---
#
# = bio/appl/muscle.rb - MUSCLE application wrapper class
#
# Copyright:: Copyright (C) 2006-2007
#             Jeffrey Blakeslee and John Conery University of Oregon <jeffb at uoregon.edu>
#             Naohisa Goto <ng at bioruby.org>
# License::   The Ruby License
#
#  $Id: muscle.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
#
#
# Bio::Muscle is a wrapper class to execute MUSCLE.
#
# == References
#
# * http://www.drive5.com/muscle/
# * Edgar R.C.
#   MUSCLE: multiple sequence alignment with high accuracy and
#   high throughput. Nucleic Acids Res. 32: 1792-1797, 2004.
# * Edgar, R.C.
#   MUSCLE: a multiple sequence alignment method with reduced time
#   and space complexity. BMC Bioinformatics 5: 113, 2004.
#

module Bio

  # Bio::Muscle is a wrapper class to execute MUSCLE.
  #
  # Please refer documents in bio/apple/muscle.rb for references.
  class Muscle < Bio::Alignment::FactoryTemplate::StdinInFileOut

    # default program name
    DEFAULT_PROGRAM = 'muscle'.freeze

    # default report parser
    DEFAULT_PARSER = Bio::Alignment::MultiFastaFormat

    private
    # generates options specifying input filename.
    # returns an array of string
    def _option_input_file(fn)
      [ '-in', fn ]
    end

    # generates options specifying output filename.
    # returns an array of string
    def _option_output_file(fn)
      [ '-out', fn ]
    end
  end #class Muscle

end #module Bio

--- NEW FILE: probcons.rb ---
#
# = bio/appl/probcons.rb - ProbCons application wrapper class
#
# Copyright:: Copyright (C) 2006-2007
#             Jeffrey Blakeslee and John Conery University of Oregon <jeffb at uoregon.edu>
#             Naohisa Goto <ng at bioruby.org>
# License::   The Ruby License
#
#  $Id: probcons.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
#
# Bio::Probcons is a wrapper class to execute ProbCons
# (Probabilistic Consistency-based Multiple Alignment
# of Amino Acid Sequences).
#
# == References
# 
# * http://probcons.stanford.edu/
# * Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S.
#   ProbCons: Probabilistic Consistency-based Multiple Sequence Alignment.
#   Genome Research 15: 330-340, 2005.
#


module Bio

  # Bio::Probcons is a wrapper class to execute PROBCONS
  # (Probabilistic Consistency-based Multiple Alignment
  # of Amino Acid Sequences).
  #
  # Please refer documents in bio/apple/probcons.rb for references.
  class Probcons < Bio::Alignment::FactoryTemplate::FileInStdoutOut

    # default program name
    DEFAULT_PROGRAM = 'probcons'.freeze

    # default report parser
    DEFAULT_PARSER = Bio::Alignment::MultiFastaFormat

  end #class Probcons

end #module Bio