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

# Slice aligned sequences in the stream to obtain subsequences.

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

require 'maasha/biopieces'
require 'maasha/fasta'
require 'maasha/seq'

indels = Regexp.new(/-|\.|~/)

casts = []
casts << {long: 'beg',            short: 'b', type: 'uint',   mandatory: false, default: nil, allowed: nil, disallowed: "0"}
casts << {long: 'end',            short: 'e', type: 'uint',   mandatory: false, default: nil, allowed: nil, disallowed: "0"}
casts << {long: 'forward',        short: 'f', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'forward_rc',     short: 'F', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'reverse',        short: 'r', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'reverse_rc',     short: 'R', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'template_file',  short: 't', type: 'file!',  mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'mismatches',     short: 'm', type: 'uint',   mandatory: false, default: 2,   allowed: nil, disallowed: nil}
casts << {long: 'insertions',     short: 'i', type: 'uint',   mandatory: false, default: 1,   allowed: nil, disallowed: nil}
casts << {long: 'deletions',      short: 'd', type: 'uint',   mandatory: false, default: 1,   allowed: nil, disallowed: nil}

options = Biopieces.options_parse(ARGV, casts)

if options[:beg]
  raise "both --beg and --end must be speficied" unless options[:end]
  options[:beg] -= 1
  options[:end] -= 1
  raise "--beg (#{options[:beg]}) must be less than --end (#{options[:end]})" if options[:beg] > options[:end]
elsif options[:forward] or options[:forward_rc]
  raise "both --forward and --reverse or --reverse_rc must be specified" unless options[:reverse] or options[:reverse_rc]

  if options[:forward_rc]
    options[:forward] = Seq.new(seq: options[:forward_rc], type: :dna).reverse.complement.seq
  end

  if options[:reverse_rc]
    options[:reverse] = Seq.new(seq: options[:reverse_rc], type: :dna).reverse.complement.seq
  end
else
  raise "either --beg/--end or --forward/--reverse|--reverse_rc must be specified"
end

if options[:template_file]
  template = Fasta.open(options[:template_file]).get_entry

  if options[:beg]
    mbeg = options[:beg]
    mend = options[:end]
    i    = 0

    while template.seq[i]
      unless template.seq[i].match indels
        if mbeg > 0
          mbeg -= 1
          mend -= 1
        else
          options[:beg] = i
          break
        end
      end

      i += 1
    end

    while template.seq[i]
      unless template.seq[i].match indels
        if mend > 0
          mend -= 1
        else
          options[:end] = i
          break
        end
      end

      i += 1
    end
  end
end

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

      unless options[:beg]
        raise "template length != alignment length" if template and template.length != entry.length
        compact = template ? template : Seq.new(seq: entry.seq.dup)
        compact.seq.delete! "-.~"

        fmatch = compact.patmatch(options[:forward],
                                  max_mismatches: options[:mismatches],
                                  max_insertions: options[:insertions],
                                  max_deletions: options[:deletions])

        raise "forward primer: #{options[:forward]} not found" if fmatch.nil?

        rmatch = compact.patmatch(options[:reverse],
                                  max_mismatches: options[:mismatches],
                                  max_insertions: options[:insertions],
                                  max_deletions: options[:deletions])

        raise "reverse primer: #{options[:reverse]} not found" if rmatch.nil?

        mbeg = fmatch.pos
        mend = rmatch.pos + rmatch.length - 1

        i = 0

        while entry.seq[i]
          unless entry.seq[i].match indels
            if mbeg > 0
              mbeg -= 1
              mend -= 1
            else
              options[:beg] = i
              break
            end
          end

          i += 1
        end

        while entry.seq[i]
          unless entry.seq[i].match indels
            if mend > 0
              mend -= 1
            else
              options[:end] = i
              break
            end
          end

          i += 1
        end
      end

      record[:SEQ]     = entry[options[:beg] .. options[:end]].seq
      record[:SEQ_LEN] = record[:SEQ].length
    end

    output.puts record
  end
end


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


__END__