#!/usr/bin/env ruby

# Copyright (C) 2007-2010 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Find and count MID tags in sequences in the stream.

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


require 'maasha/biopieces'

MID_LEN = 10

mids = %w{ ACGAGTGCGT ACGCTCGACA AGACGCACTC AGCACTGTAG ATCAGACACG
           ATATCGCGAG CGTGTCTCTA CTCGCGTGTC TAGTATCAGC TCTCTATGCG
           TGATACGTCT TACTGAGCTA CATAGTAGTG CGAGAGATAC ATACGACGTA
           TCACGTACTA CGTCTAGTAC TCTACGTAGC TGTACTACTC ACGACTACAG
           CGTAGACTAG TACGAGTATG TACTCTCGTG TAGAGACGAG TCGTCGCTCG
           ACATACGCGT ACGCGAGTAT ACTACTATGT ACTGTACAGT AGACTATACT
           AGCGTCGTCT AGTACGCTAT ATAGAGTACT CACGCTACGT CAGTAGACGT
           CGACGTGACT TACACACACT TACACGTGAT TACAGATCGT TACGCTGTCT
           TAGTGTAGAT TCGATCACGT TCGCACTAGT TCTAGCGACT TCTATACTAT
           TGACGTATGT TGTGAGTAGT ACAGTATATA ACGCGATCGA ACTAGCAGTA
           AGCTCACGTA AGTATACATA AGTCGAGAGA AGTGCTACGA CGATCGTATA
           CGCAGTACGA CGCGTATACA CGTACAGTCA CGTACTCAGA CTACGCTCTA
           CTATAGCGTA TACGTCATCA TAGTCGCATA TATATATACA TATGCTAGTA
           TCACGCGAGA TCGATAGTGA TCGCTGCGTA TCTGACGTCA TGAGTCAGTA
           TGTAGTGTGA TGTCACACGA TGTCGTCGCA ACACATACGC ACAGTCGTGC
           ACATGACGAC ACGACAGCTC ACGTCTCATC ACTCATCTAC ACTCGCGCAC
           AGAGCGTCAC AGCGACTAGC AGTAGTGATC AGTGACACAC AGTGTATGTC
           ATAGATAGAC ATATAGTCGC ATCTACTGAC CACGTAGATC CACGTGTCGC
           CATACTCTAC CGACACTATC CGAGACGCGC CGTATGCGAC CGTCGATCTC
           CTACGACTGC CTAGTCACTC CTCTACGCTC CTGTACATAC TAGACTGCAC
           TAGCGCGCGC TAGCTCTATC TATAGACATC TATGATACGC TCACTCATAC
           TCATCGAGTC TCGAGCTCTC TCGCAGACAC TCTGTCTCGC TGAGTGACGC
           TGATGTGTAC TGCTATAGAC TGCTCGCTAC ACGTGCAGCG ACTCACAGAG
           AGACTCAGCG AGAGAGTGTG AGCTATCGCG AGTCTGACTG AGTGAGCTCG
           ATAGCTCTCG ATCACGTGCG ATCGTAGCAG ATCGTCTGTG ATGTACGATG
           ATGTGTCTAG CACACGATAG CACTCGCACG CAGACGTCTG CAGTACTGCG
           CGACAGCGAG CGATCTGTCG CGCGTGCTAG CGCTCGAGTG CGTGATGACG
           CTATGTACAG CTCGATATAG CTCGCACGCG CTGCGTCACG CTGTGCGTCG
           TAGCATACTG TATACATGTG TATCACTCAG TATCTGATAG TCGTGACATG
           TCTGATCGAG TGACATCTCG TGAGCTAGAG TGATAGAGCG TGCGTGTGCG
           TGCTAGTCAG TGTATCACAG TGTGCGCGTG ACACGACGAC ACACGTAGTA
           ACACTACTCG ACGACACGTA ACGAGTAGAC ACGCGTCTAG ACGTACACAC
           ACGTACTGTG ACGTAGATCG ACTACGTCTC ACTATACGAG ACTCGCGTCG
}


count_hash = Hash.new { |hash, key| hash[key] = 0 }
mid_hash   = {}

mids.each_with_index do |mid, i|
  mid_hash[mid] = true
end

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

options = Biopieces.options_parse(ARGV, casts)

pos = options[:pos]

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record.has_key? :SEQ
      tag = record[:SEQ][pos ... pos + MID_LEN].upcase

      if mid_hash.has_key? tag
        count_hash[tag] += 1
      end
    end
    output.puts record
  end

  mids.each_with_index do |mid, i|
    if count_hash[mid] > 0
      record = {}
      record[:REC_TYPE]  = "MID"
      record[:MID_NUM]   = i + 1
      record[:MID_COUNT] = count_hash[mid]
      record[:MID_SEQ]   = mid
      output.puts record
    end
  end
end


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


__END__