X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fjoin_seq;h=b2749e984aea9d94e533cf444dde24290681ff94;hb=2f0fd91b461033529a4a72e161bd133252a22eb6;hp=de80ad2a53246c67385bc4c3a0d28a9f721e87f4;hpb=494dc53ebd515b1e3e9b91bbebf43059899ca4ce;p=biopieces.git

diff --git a/bp_bin/join_seq b/bp_bin/join_seq
index de80ad2..b2749e9 100755
--- a/bp_bin/join_seq
+++ b/bp_bin/join_seq
@@ -33,29 +33,33 @@ require 'maasha/fasta'
 require 'maasha/seq'
 
 casts = []
+casts << {:long=>'delimiter', :short=>'d', :type=>'string', :mandatory=>true, :default=>"", :allowed=>nil, :disallowed=>nil}
 
-bp = Biopieces.new
-
-options = bp.parse(ARGV, casts)
+options = Biopieces.options_parse(ARGV, casts)
 
+sequences = []
 seq = Seq.new(nil, "")
 
-bp.each_record do |record|
-  if record.has_key? :SEQ
-    unless seq.seq_name 
-      seq.seq_name = record[:SEQ_NAME]
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    if record[:SEQ]
+      unless seq.seq_name 
+        seq.seq_name = record[:SEQ_NAME]
+      end
+      sequences << record[:SEQ]
     end
-    seq.seq << record[:SEQ]
+
+    output.puts record
   end
 
-  bp.puts record
+  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
+  end
 end
 
-if seq.seq != ""
-  new_record = seq.to_bp
-  new_record[:REC_TYPE] = "JOIN"
-  bp.puts new_record
-end
 
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