utils.rb in big_simon-0.2.0

- old
+ new

@@ -68,10 +68,11 @@
 
     def self.scale_log_likelihood ll
       1 - Math.exp(ll)
     end
 
+    # @note I also rename all the sequences in the tmp fasta files with the new ID.
     def self.set_up_tmp_dirs fastas, tmpdir, which
       Object::FileUtils.mkdir_p tmpdir
 
       name_map = {}
       all_ids  = Set.new
@@ -90,10 +91,10 @@
             name_map[new_id] = rec.id
 
             outfname = File.join tmpdir, "#{new_id}.fa"
 
             File.open(outfname, "w") do |f|
-              f.puts rec
+              f.puts ">#{new_id}\n#{rec.seq}" # TODO HERE
             end
           end
         end
       end
 
\ No newline at end of file