#!/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 Velvet.

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

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

class Velvet
  def initialize(directory, sequence_file, verbose)
    @directory     = directory
    @sequence_file = sequence_file
    @verbose       = verbose
  end

  def run_velveth(kmer_min, kmer_max, type)
    @kmer_min = kmer_min
    @kmer_max = kmer_max

    kmer = @kmer_min

    while kmer <= @kmer_max
      dir_velveth = File.join(@directory, "Kmer_#{kmer}")

      Dir.mkdir(dir_velveth)

      commands = []
      commands << "velveth"
      commands << dir_velveth
      commands << kmer
      commands << "-#{type}"
      commands << "-fasta"
      commands << @sequence_file

      execute(commands)

      kmer += 2
    end
  end

  def run_velvetg(cov_cutoffs, exp_cov)
    Dir.glob("#{@directory}/Kmer_*").each do |dir_velveth|
      files_velveth = Dir.glob("#{dir_velveth}/*")

      cov_cutoffs.each do |cov_cutoff|
        dir_velvetg = File.join(dir_velveth, "Cov_cutoff_#{cov_cutoff}")

        Dir.mkdir(dir_velvetg)
        FileUtils.cp_r files_velveth, dir_velvetg
        
        commands = []
        commands << "velvetg"
        commands << dir_velvetg
        commands << "-cov_cutoff #{cov_cutoff}"
        commands << "-exp_cov #{exp_cov}"
        commands << "-clean yes"

        execute(commands)
      end
    end
  end

  def pick_best_assembly
    list = []

    Dir.glob("#{@directory}/Kmer_*/Cov_cutoff_*/contigs.fa").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.unshift "nice -n 19"
    commands.push "> /dev/null 2>&1" unless @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

types       = 'short,shortPaired,long,longPaired'
cov_cutoffs = "2,4,8,16"

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=>'short',     :allowed=>types, :disallowed=>nil}
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=>'cov_cutoff', :short=>'c', :type=>'list',   :mandatory=>true,  :default=>cov_cutoffs, :allowed=>nil,   :disallowed=>nil}
casts << {:long=>'exp_cov',    :short=>'e', :type=>'float',  :mandatory=>true,  :default=>'auto',      :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]}" unless options[:kmer_max] > options[:kmer_min]

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

file_fasta = File.join(options[:directory], "sequence_in.fna")

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
		velvet = Velvet.new(options[:directory], file_fasta, options[:verbose])
		velvet.run_velveth(options[:kmer_min], options[:kmer_max], options[:type])
		velvet.run_velvetg(options[:cov_cutoff], options[:exp_cov])
		file_contigs = velvet.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__