#!/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'

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=>'clean',       :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

unless File.size(file_fasta) == 0
  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?

  file_contig = [options[:directory], options[:name] ].join(File::SEPARATOR) + "-contig.fa"

  Fasta.open(file_contig, mode="r") do |fasta_io|
    fasta_io.each do |entry|
      bp.puts entry.to_bp
    end
  end
end

FileUtils.remove_entry_secure options[:directory] if options[:clean]


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


__END__