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#
# = bio/appl/tcoffee.rb - T-Coffee application wrapper class
#
# Copyright:: Copyright (C) 2006-2007
# Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu>
# Naohisa Goto <ng@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
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