#!/usr/bin/env ruby

# Copyright (C) 2007-2012 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-UD.

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

require 'maasha/biopieces'
require 'maasha/fasta'

casts = []
casts << {:long=>'directory',  :short=>'d', :type=>'dir',  :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint', :mandatory=>false, :default=>20,  :allowed=>nil, :disallowed=>nil}
casts << {:long=>'kmer_max',   :short=>'K', :type=>'uint', :mandatory=>false, :default=>100, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'count_min',  :short=>'c', :type=>'uint', :mandatory=>false, :default=>2,   :allowed=>nil, :disallowed=>nil}
casts << {:long=>'pairs_min',  :short=>'p', :type=>'uint', :mandatory=>false, :default=>3,   :allowed=>nil, :disallowed=>nil}
casts << {:long=>'prefix_len', :short=>'P', :type=>'uint', :mandatory=>false, :default=>3,   :allowed=>nil, :disallowed=>nil}
casts << {:long=>'cpus',       :short=>'C', :type=>'uint', :mandatory=>false, :default=>0,   :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)

Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])

file_fasta = File.join(options[:directory], "IDBA-UD") + ".fna"

count = 0

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
	Fasta.open(file_fasta, "w") do |fasta_io|
		input.each_record do |record|
      if record[:SEQ_NAME] and record[:SEQ]
        seq = Seq.new_bp(record)

        fasta_io.puts seq.to_fasta
      end
		end
	end

	unless File.size(file_fasta) == 0
		prefix = File.join(options[:directory], "IDBA-UD")

		commands = []
		commands << "nice -n 19"
		commands << "idba_ud"
		commands << "--read #{file_fasta}"
		commands << "--out #{prefix}"
		commands << "--mink #{options[:kmer_min]}"
		commands << "--maxk #{options[:kmer_max]}"
		commands << "--min_count #{options[:count_min]}"
		commands << "--min_pairs #{options[:pairs_min]}"
		commands << "--prefix #{options[:prefix_len]}"
		commands << "--num_threads #{options[:cpus]}"
		commands << "> /dev/null 2>&1" unless options[:verbose]

		command = commands.join(" ")

	  system(command)
	  raise "Command failed: #{command}" unless $?.success?

    file_contig = File.join(options[:directory], "IDBA-UD", "contig.fa")

		Fasta.open(file_contig, "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__