#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Run Uclust on sequences in the stream.

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

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

SORT_LIMIT = 2_000_000_000   # use mergesort for files biggern than 2Gb.

class Uclust
  include Enumerable

  def initialize(infile, outfile, options)
    @infile  = infile
    @outfile = outfile
    @options = options
    @command = []
  end

  # Method that calls Usearch sorting for sorting a FASTA file
  # according to decending sequence length.
  def sort
    # usearch -sort seqs.fasta -output seqs.sorted.fasta
    if File.size(@infile) < SORT_LIMIT
      @command << "usearch --sort #{@infile} --output #{@infile}.sort"
    else
      @command << "usearch --mergesort #{@infile} --output #{@infile}.sort"
    end

		execute

    File.rename "#{@infile}.sort", @infile
  end

	# Method to execute clustering de novo.
  def cluster
    @command << "usearch --cluster #{@infile} --uc #{@outfile} --id #{@options[:identity]}"

		execute
  end

	# Method to parse a Uclust .uc file and for each line of data
	# yield a Biopiece record.
  def each
    record = {}

    File.open(@outfile, mode="r") do |ios|
      ios.each_line do |line|
        if line !~ /^#/
          fields = line.chomp.split("\t")

          next if fields[0] == 'C'

          record[:TYPE]     = fields[0]
          record[:CLUSTER]  = fields[1].to_i
          record[:IDENT]    = fields[3].to_f
          record[:Q_ID]     = fields[8]

          yield record
        end
      end
    end

    self # conventionally
  end

  private

	# Method to execute a command using a system() call.
	# The command is composed of bits from the @command variable.
	def execute
		@command.unshift "nice -n 19"
    @command << "--rev" if @options[:comp]
		@command << "> /dev/null 2>&1" unless @options[:verbose]
		command = @command.join(" ")
    system(command)
    raise "Command failed: #{command}" unless $?.success?

		@command = []
	end
end

casts = []
casts << {:long=>'no_sort',  :short=>'n', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,        :disallowed=>nil}
casts << {:long=>'comp',     :short=>'c', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,        :disallowed=>nil}
casts << {:long=>'identity', :short=>'i', :type=>'float',  :mandatory=>true,  :default=>0.9,      :allowed=>nil,        :disallowed=>nil}

options = Biopieces.options_parse(ARGV, casts)

tmpdir       = Biopieces.mktmpdir
file_records = File.join(tmpdir, "data.stream")
file_fasta   = File.join(tmpdir, "in.fna")
file_uclust  = File.join(tmpdir, "out.uc")

Biopieces.open(options[:stream_in], file_records) do |input, output|
  Fasta.open(file_fasta, mode="w") do |fasta_io|
    input.each_record do |record|
      output.puts record

      if record.has_key? :SEQ_NAME and record.has_key? :SEQ
        fasta_io.puts Seq.new_bp(record).to_fasta
      end
    end
  end
end

uc = Uclust.new(file_fasta, file_uclust, options)
uc.sort unless options[:no_sort]
uc.cluster

hash = {}

uc.each do |record|
  hash[record[:Q_ID].to_sym] = record.dup
end

Biopieces.open(file_records, options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record.has_key? :SEQ_NAME and record.has_key? :SEQ
      if hash.has_key? record[:SEQ_NAME].to_sym
        uc = hash[record[:SEQ_NAME].to_sym]
        record[:CLUSTER] = uc[:CLUSTER].to_i
        record[:IDENT]   = uc[:IDENT].to_i
        record[:IDENT] = '*' if uc[:TYPE] == 'S'
      end
    end

    output.puts record
  end
end


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


__END__