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

# Write sequences from stream in FASTA format.

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

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

casts = []
casts << {long: 'no_stream', short: 'x', type: 'flag',   mandatory: false, default: nil, allowed: nil,               disallowed: nil}
casts << {long: 'data_out',  short: 'o', type: 'file',   mandatory: false, default: nil, allowed: nil,               disallowed: nil}
casts << {long: 'wrap',      short: 'w', type: 'uint',   mandatory: false, default: nil, allowed: nil,               disallowed: "0"}
casts << {long: 'compress',  short: 'Z', type: 'string', mandatory: false, default: nil, allowed: "gzip,bzip,bzip2", disallowed: nil}

options = Biopieces.options_parse(ARGV, casts)

compress = options[:compress] ? options[:compress].to_sym : nil

raise "--data_out is mandatory for compressed output" if compress and not options[:data_out]

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  fasta_out = options[:data_out] ? Fasta.open(options[:data_out], 'w', compress: compress) : STDOUT

  input.each do |record|
    if record[:SEQ_NAME] and record[:SEQ]
      entry = Seq.new_bp(record)

      fasta_out.puts entry.to_fasta(options[:wrap])
    end

    output.puts record unless options[:no_stream]
  end

  fasta_out.close
end


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


__END__