find_pairs added

[biopieces.git] / bp_bin / join_seq

diff --git a/bp_bin/join_seq b/bp_bin/join_seq
index f071f41d0dcc6a5165267a85f426a719f2a21fa8..ce36e5944a665753c2e43aae8b660a0935dcd81e 100755 (executable)
--- a/bp_bin/join_seq
+++ b/bp_bin/join_seq
@@ -33,9 +33,11 @@ require 'maasha/fasta'
 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|
@@ -44,13 +46,14 @@ 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