refactoring of assemble_pairs

[biopieces.git] / bp_bin / find_genes

diff --git a/bp_bin/find_genes b/bp_bin/find_genes
index a7dda28bcb13fe139edc0d6c40c368cbb50efc75..88dacf2ddee0c7ec899a13cf6f008a7b6380e61b 100755 (executable)
--- a/bp_bin/find_genes
+++ b/bp_bin/find_genes
@@ -44,10 +44,14 @@ infile  = File.join(tmpdir, "in.fna")
 outfile = File.join(tmpdir, "out.prodigal")
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  Fasta.open(infile, mode="w") do |fasta_io|
+  Fasta.open(infile, "w") do |fasta_io|
     input.each_record do |record|
       output.puts record
-      fasta_io.puts record
+
+      if record[:SEQ_NAME] and record[:SEQ]
+        seq = Seq.new_bp(record)
+        fasta_io.puts seq.to_fasta
+      end
     end
   end
 
@@ -55,10 +59,6 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   prodigal.run
 
   prodigal.each do |record|
-    record[:DEFINITION].match /seqhdr="([^"]+)/ do |m| 
-      record[:S_ID] = $1
-    end
-
     output.puts record
   end
 end