adding bzip2 support in ruby

[biopieces.git] / bp_bin / write_fasta_files

diff --git a/bp_bin/write_fasta_files b/bp_bin/write_fasta_files
index 3ffeb82c5608eff45e7b72e53ad49484b4540152..36011ed411fad74d891f2f12f7108bfc02eb91a2 100755 (executable)
--- a/bp_bin/write_fasta_files
+++ b/bp_bin/write_fasta_files
@@ -46,15 +46,17 @@ fh_hash = {}
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
     if record[:SEQ_NAME] and record[:SEQ] and record[key]
-      if fh_hash.has_key? record[key].to_sym
+      seq = Seq.new_bp(record)
+
+      if fh_hash[record[key].to_sym]
         fasta_io = fh_hash[record[key].to_sym]
       else
-        mid_file = File.join(options[:dir], record[key] + ".fasta")
-        fasta_io = Fasta.open(mid_file, "w")
+        fasta_file = File.join(options[:dir], record[key] + ".fasta")
+        fasta_io   = Fasta.open(fasta_file, "w")
         fh_hash[record[key].to_sym] = fasta_io
       end
 
-      fasta_io.puts record
+      fasta_io.puts seq.to_fasta
     end
 
     output.puts record unless options[:no_stream]