--- /dev/null
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Assemble sequences in the stream using IDBA.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'biopieces'
+require 'fasta'
+require 'pp'
+
+ok_methods = "ublast,usearch,uclust,usearch_uclust"
+
+casts = []
+casts << {:long=>'name', :short=>'n', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'scaffold', :short=>'s', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'k_value_min', :short=>'k', :type=>'uint', :mandatory=>false, :default=>25, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'k_value_max', :short=>'K', :type=>'uint', :mandatory=>false, :default=>50, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'count_min', :short=>'c', :type=>'uint', :mandatory=>false, :default=>2, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cover', :short=>'C', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'pairs_min', :short=>'p', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'prefix_len', :short=>'P', :type=>'uint', :mandatory=>false, :default=>3, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
+
+file_fasta = [options[:directory], options[:name] ].join(File::SEPARATOR) + ".fna"
+
+Fasta.open(file_fasta, mode="w") do |fasta_io|
+ bp.each_record do |record|
+ fasta_io.puts record
+ end
+end
+
+output = [options[:directory], options[:name] ].join(File::SEPARATOR)
+
+commands = []
+commands << "nice -n 19"
+commands << "idba"
+commands << "--read #{file_fasta}"
+commands << "--output #{output}"
+commands << "--scaffold" if options[:scaffold]
+commands << "--mink #{options[:k_value_min]}"
+commands << "--maxk #{options[:k_value_max]}"
+commands << "--minCount #{options[:count_min]}"
+commands << "--cover #{options[:cover]}"
+commands << "--minPairs #{options[:pairs_min]}"
+commands << "--prefixLength #{options[:prefix_len]}"
+commands << "> /dev/null 2>&1" unless options[:verbose]
+
+command = commands.join(" ")
+system(command)
+raise "Command failed: #{command}" unless $?.success?
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__