options = Biopieces.options_parse(ARGV, casts)
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
- input.each_record do |record|
- output.puts record
+ unless options[:data_in] and options[:data_in].first == '-'
+ input.each_record do |record|
+ output.puts record
+ end
end
num = 0
last = false
- if options.has_key? :data_in
+ if options[: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
+ if options[:num] and options[:num] == num
last = true
break
end