#!/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 'maasha/biopieces'
require 'maasha/fasta'

casts = []
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=>'metagenome', :short=>'m', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint', :mandatory=>false, :default=>25,  :allowed=>nil, :disallowed=>nil}
casts << {:long=>'kmer_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=>'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") + ".fna"

count = 0

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|
      if record[:SEQ_NAME] and record[:SEQ]
        seq = Seq.new_bp(record)

        if options[:scaffold] # we need to fix the sequence name for mate-pair IDBA
          if seq.seq_name =~ /1$/
            seq.seq_name = "read#{count}/1"
          else
            seq.seq_name = "read#{count}/2"

            count += 1
          end
        end

        fasta_io.puts seq.to_fasta
      end
		end
	end

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

		commands = []
		commands << "nice -n 19"

    if options[:metagenome]
		  commands << "metaidba"
    else
		  commands << "idba"
    end

		commands << "--read #{file_fasta}"
		commands << "--output #{prefix}"
		commands << "--scaffold" if options[:scaffold]
		commands << "--mink #{options[:kmer_min]}"
		commands << "--maxk #{options[:kmer_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(" ")

		begin
			system(command)
			raise "Command failed: #{command}" unless $?.success?
		rescue
			$stderr.puts "Command failed: #{command}"
		end

    if options[:scaffold]
		  file_contig = File.join(options[:directory], "IDBA") + "-contig-mate.fa"
    else
		  file_contig = File.join(options[:directory], "IDBA") + "-contig.fa"
    end

		Fasta.open(file_contig, 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__