made find_orfs run on DNA or RNA

[biopieces.git] / bp_bin / blast_seq_pair

diff --git a/bp_bin/blast_seq_pair b/bp_bin/blast_seq_pair
index 18b2b5bd404a6fab75f3cf638463a6e08e32f84d..d0488c2571a492fcf4f6e3729c3a465f069e9fcb 100755 (executable)
--- a/bp_bin/blast_seq_pair
+++ b/bp_bin/blast_seq_pair
@@ -165,9 +165,11 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     output.puts record
 
     if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+      seq = Seq.new_bp(record)
+
       unless got1
         Fasta.open(infile1, mode="w") do |fasta_io|
-          fasta_io.puts record
+          fasta_io.puts seq.to_fasta
         end
 
         got1  = true
@@ -177,7 +179,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
       unless got2
         Fasta.open(infile2, mode="w") do |fasta_io|
-          fasta_io.puts record
+          fasta_io.puts seq.to_fasta
         end
 
         got2  = true