fixed assemblers

[biopieces.git] / bp_bin / assemble_seq_idba

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index 1f392e91184b94de637b43e7e4a4b32648db5085..2b655431a8a0154c4af8bc7005a8cf527668d24a 100755 (executable)
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -53,17 +53,21 @@ count = 0
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
        Fasta.open(file_fasta, mode="w") do |fasta_io|
                input.each_record do |record|
-      if options[:scaffold] # we need to fix the sequence name for mate-pair IDBA
-        if record[:SEQ_NAME] =~ /1$/
-          record[:SEQ_NAME] = "read#{count}/1"
-        else
-          record[:SEQ_NAME] = "read#{count}/2"
+      if record[:SEQ_NAME] and record[:SEQ]
+        seq = Seq.new_bp(record)
 
-          count += 1
+        if options[:scaffold] # we need to fix the sequence name for mate-pair IDBA
+          if seq.seq_name =~ /1$/
+            seq.seq_name = "read#{count}/1"
+          else
+            seq.seq_name = "read#{count}/2"
+
+            count += 1
+          end
         end
-      end
 
-                       fasta_io.puts record
+        fasta_io.puts seq.to_fasta
+      end
                end
        end