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

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

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


require 'biopieces'
require 'seq'
require 'pp'

casts = []
casts << {:long=>'size', :short=>'s', :type=>'uint',   :mandatory=>false, :default=>4,     :allowed=>nil,               :disallowed=>'0'}
casts << {:long=>'type', :short=>'t', :type=>'string', :mandatory=>false, :default=>"dna", :allowed=>"dna,rna,protein", :disallowed=>nil}

bp = Biopieces.new

options = bp.parse(ARGV, casts)

oligos = Seq.generate_oligos(options[:size], options[:type])

bp.each_record do |record|
  if record.has_key? :SEQ
    kmers  = {}
    oligos.each { |oligo| kmers[oligo.upcase] = 0 }

    (0 ... record[:SEQ].length - options[:size]).each do |i|
      kmer = record[:SEQ][i .. i + options[:size] - 1].upcase
      kmers[kmer] += 1 if kmers[kmer]
    end

    record.merge! kmers
  end

  bp.puts record
end

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


__END__