#!/usr/bin/env ruby

# Copyright (C) 2007-2013 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Create bowtie2 index from sequences in the stream.

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

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=>'directory',  :short=>'d', :type=>'dir',    :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'index_name', :short=>'i', :type=>'string', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}

options = Biopieces.options_parse(ARGV, casts)

unless File.directory? options[:directory]
  Dir.mkdir options[:directory]
end

tmpdir  = Biopieces.mktmpdir
tmpfile = File.join(tmpdir, "tmp.fna")

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  Fasta.open(tmpfile, "w") do |fasta_io|
    input.each_record do |record|
      output.puts record unless options[:no_stream]

      if record[:SEQ_NAME] and record[:SEQ]
        fasta_io.puts Seq.new_bp(record).to_fasta
      end
    end
  end
end

cmd = []
cmd << "bowtie2-build"
cmd << "-q" unless options[:verbose]
cmd << tmpfile
cmd << File.join(options[:directory], options[:index_name])

c = cmd.join(" ")

$stderr.puts c if options[:verbose]

system(c)

raise "Error: executing #{c}" unless $?.success?


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


__END__