-#!/usr/bin/env perl
+#!/usr/bin/env ruby
-use warnings;
-use strict;
+# Copyright (C) 2007-2011 Martin A. Hansen.
-use Maasha::BioRun;
+# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read EMBL entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'maasha/embl'
+
+casts = []
+casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'num', :short=>'n', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'keys', :short=>'k', :type=>'list', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'features', :short=>'f', :type=>'list', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'qualifiers', :short=>'q', :type=>'list', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+hash_keys = options[:keys].inject(Hash.new) { |h,k| h[k.upcase.to_sym] = true; h } if options[:keys]
+hash_feats = options[:features].inject(Hash.new) { |h,k| h[k.upcase.to_sym] = true; h } if options[:features]
+hash_quals = options[:qualifiers].inject(Hash.new) { |h,k| h[k.upcase.to_sym] = true; h } if options[:qualifiers]
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ output.puts record
+ end
+
+ num = 0
+ last = false
+
+ if options.has_key? :data_in
+ options[:data_in].each do |file|
+ EMBL.open(file, mode='r') do |embl_io|
+ embl_io.each(hash_keys, hash_feats, hash_quals) do |entry|
+ output.puts entry
+
+ num += 1
+
+ if options.has_key? :num and options[:num] == num
+ last = true
+ break
+ end
+ end
+ end
+
+ break if last
+ end
+ end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__