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

# Replace values to a specied key for each record in the stream.

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

require 'maasha/biopieces'

casts = []
casts << {:long=>'key',         :short=>'k', :type=>'string', :mandatory=>true,  :default=>nil,   :allowed=>nil, :disallowed=>nil}
casts << {:long=>'search',      :short=>'s', :type=>'string', :mandatory=>false, :default=>nil,   :allowed=>nil, :disallowed=>nil}
casts << {:long=>'replace',     :short=>'r', :type=>'string', :mandatory=>false, :default=>nil,   :allowed=>nil, :disallowed=>nil}
casts << {:long=>'file',        :short=>'f', :type=>'file!',  :mandatory=>false, :default=>nil,   :allowed=>nil, :disallowed=>nil}
casts << {:long=>'search_col',  :short=>'S', :type=>'uint',   :mandatory=>false, :default=>1,     :allowed=>nil, :disallowed=>"0"}
casts << {:long=>'replace_col', :short=>'R', :type=>'uint',   :mandatory=>false, :default=>2,     :allowed=>nil, :disallowed=>"0"}
casts << {:long=>'delimiter',   :short=>'d', :type=>'string', :mandatory=>false, :default=>'\s+', :allowed=>nil, :disallowed=>nil}

options   = Biopieces.options_parse(ARGV, casts)
key       = options[:key].to_sym
delimiter = Regexp.new(options[:delimiter])

raise ArgumentError, "both --search and --replace must be specified" if options[:search]  and not options[:replace]
raise ArgumentError, "both --search and --replace must be specified" if options[:replace] and not options[:search]

replace_hash = {}

if options[:search]
  replace_hash[options[:search].to_s] = options[:replace].to_s
end

if options[:file]
  File.open(options[:file], "r") do |ios|
    ios.each_line do |line|
      unless line[0] == '#'
        fields = line.chomp.split(delimiter)
        k      = fields[options[:search_col] - 1]
        v      = fields[options[:replace_col] - 1]

        raise RuntimeError, "duplicate key: #{k} found in file" if replace_hash[k]

        replace_hash[k] = v
      end
    end
  end
end

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[key]
      if replace_hash[record[key]]
        record[key] = replace_hash[record[key]]
      end
    end

    output.puts record
  end
end

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


__END__