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'}
-bp = Biopieces.new
+options = Biopieces.options_parse(ARGV, casts)
-options = bp.parse(ARGV, casts)
-
-bp.each_record do |record|
- bp.puts record
-end
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ unless options[:data_in] and options[:data_in].first == '-'
+ input.each_record do |record|
+ output.puts record
+ end
+ end
-num = 0
-last = false
+ num = 0
+ last = false
-if options.has_key? :data_in
- options[:data_in].each do |file|
- Fasta.open(file, mode='r') do |fasta|
- fasta.each do |entry|
- bp.puts entry.to_bp
- num += 1
+ if options.has_key? :data_in
+ options[:data_in].each do |file|
+ Fasta.open(file, mode='r') do |fasta|
+ fasta.each do |entry|
+ output.puts entry.to_bp
+ num += 1
- if options.has_key? :num and options[:num] == num
- last = true
- break
+ if options.has_key? :num and options[:num] == num
+ last = true
+ break
+ end
end
end
- end
- break if last
+ break if last
+ end
end
end