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

# Analyze assembled sequences in the stream and output stats.

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


require 'biopieces'
require 'fasta'
require 'prodigal'
require 'pp'

casts = []
casts << {:long=>'gene_cov',  :short=>'g', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
casts << {:long=>'procedure', :short=>'p', :type=>'string', :mandatory=>true,  :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
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}

bp = Biopieces.new

options = bp.parse(ARGV, casts)

options[:full] = true;

total   = 0
lengths = []
tmpdir  = bp.mktmpdir
infile  = "#{tmpdir}/in.fna"
outfile = "#{tmpdir}/out.prodigal"

Fasta.open(infile, mode="w") do |fasta_io|
  bp.each_record do |record|
    if record.has_key? :SEQ
      total   += record[:SEQ].length
      lengths << record[:SEQ].length
    end

    bp.puts record unless options[:no_stream]
    fasta_io.puts record
  end
end

if options[:gene_cov]
  prodigal = Prodigal.new(infile, outfile, options)
  prodigal.run
  gene_cov = prodigal.coverage
end

count = 0
n50   = 0

lengths.sort.reverse.each do |length|
  count += length

  if count >= total * 0.50
    n50 = length
    break
  end
end

bp.out = Stream.write(options[:data_out]) if options[:data_out]

new_record = {}
new_record[:N50]        = n50
new_record[:MAX]        = lengths.max
new_record[:MIN]        = lengths.min
new_record[:MEAN]       = (total.to_f / lengths.size.to_f).to_i
new_record[:TOTAL]      = total
new_record[:COUNT]      = lengths.size
new_record[:GENE_COV]   = gene_cov if options[:gene_cov]

bp.puts new_record

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


__END__