--- /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 Ray.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'maasha/fasta'
+
+class Ray
+ def initialize(directory, sequence_file, options)
+ @directory = directory
+ @sequence_file = sequence_file
+ @options = options
+ end
+
+ def run
+ kmer = @options[:kmer_min]
+
+ if @options[:type] == "single"
+ type = "-s"
+ else
+ type = "-i"
+ end
+
+ while kmer <= @options[:kmer_max]
+ dir_ray = File.join(@directory, "Kmer_#{kmer}")
+
+ Dir.mkdir(dir_ray)
+
+ commands = []
+ commands << "nice -n 19"
+ commands << "mpirun"
+ commands << "-np #{@options[:cpus]}"
+ commands << "Ray"
+ commands << "-o " + File.join(dir_ray, "Ray")
+ commands << "-k #{kmer}"
+ commands << type
+ commands << @sequence_file
+
+ execute(commands)
+
+ kmer += 2
+ end
+ end
+
+ def pick_best_assembly
+ list = []
+
+ Dir.glob("#{@directory}/Kmer_*/*.fasta").each do |file|
+ n50 = fasta_n50(file)
+ list << [file, n50]
+ end
+
+ list.sort_by { |e| e.last }.last.first
+ end
+
+ private
+
+ def execute(commands)
+ commands.push "> /dev/null 2>&1" unless @options[:verbose]
+
+ command = commands.join(" ")
+
+ begin
+ system(command)
+ raise "Command failed: #{command}" unless $?.success?
+ rescue
+ $stderr.puts "Command failed: #{command}"
+ end
+ end
+
+ def fasta_n50(file)
+ total = 0
+ lengths = []
+ count = 0
+ n50 = 0
+
+ Fasta.open(file, mode="r") do |fasta_io|
+ fasta_io.each do |entry|
+ total += entry.length
+ lengths << entry.length
+ end
+ end
+
+ lengths.sort.reverse.each do |length|
+ count += length
+
+ if count >= total * 0.50
+ n50 = length
+ break
+ end
+ end
+
+ n50
+ end
+end
+
+casts = []
+casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'type', :short=>'t', :type=>'string', :mandatory=>true, :default=>'single', :allowed=>'single,paired', :disallowed=>nil}
+casts << {:long=>'cpus', :short=>'c', :type=>'uint', :mandatory=>true, :default=>1, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'kmer_min', :short=>'k', :type=>'uint', :mandatory=>true, :default=>19, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>true, :default=>31, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'clean', :short=>'X', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+raise ArgumentError, "kmer_min #{options[:kmer_min]} must be uneven." if options[:kmer_min].even?
+raise ArgumentError, "kmer_max #{options[:kmer_max]} must be uneven." if options[:kmer_max].even?
+raise ArgumentError, "kmer_min > kmer_max: #{options[:kmer_min]} > #{options[:kmer_max]}" if options[:kmer_min] > options[:kmer_max]
+
+Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
+
+file_fasta = File.join(options[:directory], "sequence_in.fasta")
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ Fasta.open(file_fasta, mode="w") do |fasta_io|
+ input.each_record do |record|
+ fasta_io.puts record
+ end
+ end
+
+ unless File.size(file_fasta) == 0
+ ray = Ray.new(options[:directory], file_fasta, options)
+ ray.run
+ file_contigs = ray.pick_best_assembly
+
+ Fasta.open(file_contigs, mode="r") do |fasta_io|
+ fasta_io.each do |entry|
+ output.puts entry.to_bp
+ end
+ end
+ end
+end
+
+FileUtils.remove_entry_secure file_fasta
+FileUtils.remove_entry_secure options[:directory] if options[:clean]
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__