lib/scaffolder/test/helpers.rb in scaffolder-test-helpers-0.1.0 vs lib/scaffolder/test/helpers.rb in scaffolder-test-helpers-0.2.0

@@ -1,37 +1,33 @@
 require 'tempfile'
 require 'bio'
 require 'scaffolder'
 
+require 'scaffolder/test/sequence'
+require 'scaffolder/test/unresolved'
+
 module Scaffolder::Test
   module Helpers
 
-    def write_sequence_file(entries,file = Tempfile.new("sequence").path)
-      File.open(file,'w') do |tmp|
-        make_sequence(entries).each do |entry|
-          seq = Bio::Sequence.new(entry[:sequence])
-          tmp.print(seq.output(:fasta,:header => entry[:name]))
-        end
-      end
-      file
+    def generate_scaffold_files(entries)
+      [write_scaffold_file(entries),write_sequence_file(entries)]
     end
 
     def write_scaffold_file(entries,file = Tempfile.new("scaffold").path)
-      File.open(file,'w'){|tmp| tmp.print(YAML.dump(make_scaffold(entries)))}
+      File.open(file,'w') do |tmp|
+        tmp.print(YAML.dump(entries.map{|e| e.to_hash }))
+      end
       file
     end
 
-    def make_scaffold(entries)
-      entries.map do |entry|
-        {'sequence' => {'source' => (entry['name'] || entry[:name]) }}
+    def write_sequence_file(entries,file = Tempfile.new("sequence").path)
+      File.open(file,'w') do |tmp|
+        entries.each do |entry|
+          tmp.puts(entry.to_fasta) if entry.respond_to? :to_fasta
+        end
       end
+      file
     end
 
-    def make_sequence(entries)
-      entries.map do |entry|
-        {:name => (entry['name'] || entry[:name]),
-          :sequence => (entry['nucleotides'] || entry[:nucleotides]) }
-      end.flatten
-    end
 
   end
 end