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

# Shred sequences in the stream into subsequences.

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


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

class Seq
  # Method that shreds the sequence of a sequence object into
  # random subsequences of a specified size. Subsequences are
  # alternatly picked from the + or - strand (i.e. reverse complemented)
  # until the specified coverage is reached.
  #
  # seq.shred { |subseq| } -> Seq
  # seq.shred              -> []
  def shred(size, max_cov)
    raise SeqError, "Size: #{size} < 1"            if size    < 1
    raise SeqError, "Max coverage: #{max_cov} < 1" if max_cov < 1

    entries = []
    sum     = 0
    strand  = '+'

    while coverage(sum) < max_cov
      entry = self.subseq_rand(size)
      entry.reverse!.complement! if strand == '-'

      if block_given?
        yield entry
      else
        entries << entry
      end
      
      strand = (strand == '+') ? '-' : '+'

      sum += size
    end

    entries
  end

  private

  # Method that returns the coverage of subsequences.
  def coverage(sum)
    sum / self.seq.length
  end
end

casts = []
casts << {:long=>'size',     :short=>'s', :type=>'uint', :mandatory=>true, :default=>500, :allowed=>nil, :disallowed=>'0'}
casts << {:long=>'coverage', :short=>'c', :type=>'uint', :mandatory=>true, :default=>100, :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|
    if record[:SEQ] and record[:SEQ].length >= options[:size]
      entry      = Seq.new_bp(record)
      entry.type = :dna

      entry.shred(options[:size], options[:coverage]) do |subentry|
        output.puts subentry.to_bp
      end
    end
  end
end


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


__END__