#!/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: 'program',    short: 'p', type: 'string', mandatory: false, default: 'global', allowed: "local,global", disallowed: nil}
casts << {long: 'database',   short: 'd', type: 'file!',  mandatory: true,  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}
casts << {long: 'cpus',       short: 'c', type: 'uint',   mandatory: false, default: 1,        allowed: nil,            disallowed: "0"}
casts << {long: 'maxaccepts', short: 'm', type: 'uint',   mandatory: false, default: 0,        allowed: nil,            disallowed: nil}

options = Biopieces.options_parse(ARGV, casts)

if options[:program] == 'global'
  raise ArgumentError, "--identity be specified for global search" unless options[:identity]
  raise ArgumentError, "--e_val is invalid for global search" if options[:e_val]
else
  raise ArgumentError, "--identity or --e_val must be specified" unless options[:identity] or options[:e_val]
end

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, "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

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

  case options[:program]
  when "local"  then us.usearch_local
  when "global" then us.usearch_global
  else raise "no such program #{options[:program]}"
  end

  us.each_hit do |record|
    output.puts record
  end
end


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


__END__