#!/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'

casts = []
casts << {:long=>'size', :short=>'s', :type=>'uint', :mandatory=>false, :default=>4, :allowed=>nil, :disallowed=>'0'}

options   = Biopieces.options_parse(ARGV, casts)

size      = options[:size]
kmer_hash = Hash.new { 0 }

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[:SEQ]
      seq = record[:SEQ].upcase

      (0 .. seq.length - size).each do |i|
        kmer = seq[i ... i + size]
        kmer_hash[kmer] += 1
      end
    end

    output.puts record
  end

  kmer_hash.each do |kmer, count|
    record = {
      :REC_TYPE => "KMER_FREQ",
      :KMER     => kmer,
      :COUNT    => count,
      :FREQ     => (count.to_f / kmer_hash.size).round(4)
    }

    output.puts record
  end
end


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


__END__