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

# Usearch sequences in the stream against a specified database.

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

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

class Usearch
  include Enumerable

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

  # Method to execute database search.
  def usearch
    @command << "usearch --query #{@infile} --db #{@options[:database]} --userout #{@outfile}"
    @command << "--userfields target+tloz+thiz+query+bits+strand"
    @command << "--id #{@options[:identity]}"  if @options.has_key? :identity
    @command << "--evalue #{@options[:e_val]}" if @options.has_key? :e_val

		execute
  end

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

    File.open(@outfile, mode="r") do |ios|
      ios.gets   # skip comment line
      ios.each_line do |line|
        fields = line.chomp.split("\t")

        record[:REC_TYPE] = "USEARCH"
        record[:S_ID]     = fields[0]
        record[:S_BEG]    = fields[1].to_i
        record[:S_END]    = fields[2].to_i
        record[:Q_ID]     = fields[3]
        record[:SCORE]    = fields[4].to_f
        record[:STRAND]   = fields[5]

        yield record
      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=>'database', :short=>'d', :type=>'file!', :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=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'e_val',    :short=>'e', :type=>'float', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}

options = Biopieces.options_parse(ARGV, casts)

raise ArgumentError, "--identity or --e_val must be specified" unless options[:identity] or options[:e_val]

tmpdir  = Biopieces.mktmpdir
infile  = File.join(tmpdir, "in.fna")
outfile = File.join(tmpdir, "out.uc")

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  Fasta.open(infile, 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

  uc = Usearch.new(infile, outfile, options)

  uc.usearch

  uc.each do |record|
    output.puts record
  end
end


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


__END__