require 'maasha/seq'
casts = []
+casts << {:long=>'delimiter', :short=>'d', :type=>'string', :mandatory=>true, :default=>"", :allowed=>nil, :disallowed=>nil}
options = Biopieces.options_parse(ARGV, casts)
+sequences = []
seq = Seq.new(nil, "")
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
unless seq.seq_name
seq.seq_name = record[:SEQ_NAME]
end
- seq.seq << record[:SEQ]
+ sequences << record[:SEQ]
end
output.puts record
end
- if seq.seq != ""
+ unless sequences.empty?
+ seq.seq = sequences.join(options[:delimiter].to_s)
new_record = seq.to_bp
new_record[:REC_TYPE] = "JOIN"
output.puts new_record