renamed patternmatcher to dynamic

[biopieces.git] / bp_bin / assemble_seq_velvet

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index 71fc5c129c9972320fdc3d8d79976eca32fcfc58..98c0ba4486a23d47b6969cd9d56d2a4e1902f24b 100755 (executable)
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -161,10 +161,13 @@ Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
 file_fasta = File.join(options[:directory], "sequence_in.fna")
 
 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|
-                       fasta_io.puts record
-               end
+  Fasta.open(file_fasta, mode="w") do |fasta_io|
+    input.each_record do |record|
+      if record[:SEQ_NAME] and record[:SEQ]
+        seq = Seq.new_bp(record)
+        fasta_io.puts seq.to_fasta
+      end
+    end
        end
 
        unless File.size(file_fasta) == 0