#!/usr/bin/env ruby

# Copyright (C) 2007-2012 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Determine the frequencies for k-mers in sequences in the stream.

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


require 'maasha/biopieces'
require 'maasha/seq'

codons_start = "ATG,GTG,AUG,GUG"
codons_stop  = "TAA,TGA,TAG,UAA,UGA,UAG"

casts = []
casts << {:long=>'start_codons',  :short=>'s', :type=>'list', :mandatory=>true,  :default=>codons_start, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'stop_codons',   :short=>'S', :type=>'list', :mandatory=>true,  :default=>codons_stop,  :allowed=>nil, :disallowed=>nil}
casts << {:long=>'min_size',      :short=>'m', :type=>'uint', :mandatory=>true,  :default=>50,           :allowed=>nil, :disallowed=>'0'}
casts << {:long=>'max_size',      :short=>'M', :type=>'uint', :mandatory=>true,  :default=>10_000,       :allowed=>nil, :disallowed=>'0'}
casts << {:long=>'non_redundant', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil,          :allowed=>nil, :disallowed=>'0'}

options = Biopieces.options_parse(ARGV, casts)

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    output.puts record

    if record[:SEQ]
      entry = Seq.new_bp(record)

      entry.each_orf(options[:min_size], options[:max_size], options[:start_codons], options[:stop_codons], options[:non_redundant]) do |orf, orf_beg, orf_end|
        new_record = {}
        new_record[:REC_TYPE] = "ORF"
        new_record.merge!(orf.to_bp)
        new_record[:S_BEG] = orf_beg
        new_record[:S_END] = orf_end

        output.puts new_record
      end
    end
  end
end


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


__END__