#!/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'
require 'maasha/usearch'

casts = []
casts << {:long=>'database', :short=>'d', :type=>'file!', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}

options = Biopieces.options_parse(ARGV, casts)

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

Biopieces.open(options[:stream_in], tmpfile) do |input, output|
  Fasta.open(infile, "w") do |fasta_io|
    input.each_record do |record|
      output.puts record

      if record[:SEQ_NAME] and record[:SEQ]
        fasta_io.puts Seq.new_bp(record).to_fasta
      end
    end
  end
end

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

us.uchime

lookup = {}

File.open(outfile, 'r') do |ios|
  while ! ios.eof?
    line   = ios.readline.chomp
    fields = line.split("\t")

    q_id = fields[1]
    chim = fields[-1]

    if chim == 'Y'
      lookup[q_id] = 'YES'
    else
      lookup[q_id] = 'NO'
    end
  end
end

Biopieces.open(tmpfile, options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[:SEQ_NAME] and record[:SEQ]
      record[:CHIMERIC] = lookup[record[:SEQ_NAME]];
    end
    
    output.puts record
  end
end

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


__END__