+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Determine the frequencies for k-mers in sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'maasha/biopieces'
+require 'maasha/seq'
+
+casts = []
+casts << {:long=>'start_codons', :short=>'s', :type=>'list', :mandatory=>true, :default=>"AUG,GUG", :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'stop_codons', :short=>'S', :type=>'list', :mandatory=>true, :default=>"UAA,UGA,UAG", :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'min_size', :short=>'m', :type=>'uint', :mandatory=>true, :default=>50, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'max_size', :short=>'M', :type=>'uint', :mandatory=>true, :default=>10_000, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'non_redundant', :short=>'r', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ if record[:SEQ]
+ entry = Seq.new_bp(record)
+
+ entry.each_orf(options[:min_size], options[:max_size], options[:start_codons], options[:stop_codons], options[:non_redundant]) do |orf, orf_beg, orf_end|
+ new_record = {}
+ new_record[:REC_TYPE] = "ORF"
+ new_record.merge!(orf.to_bp)
+ new_record[:S_BEG] = orf_beg
+ new_record[:S_END] = orf_end
+
+ output.puts new_record
+ end
+
+ exit
+ end
+
+ output.puts record
+ end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__