lib/neurohmmer/output.rb in neurohmmer-0.1.1 vs lib/neurohmmer/output.rb in neurohmmer-0.1.2

@@ -9,10 +9,24 @@
   class Output
     class <<self
       extend Forwardable
       def_delegators Neurohmmer, :opt, :conf
 
+      def to_fasta(hmm_results)
+        File.open(conf[:fasta_output], 'w') do |file|
+          hmm_results.each do |query, hits|
+            next if hits.length == 0
+            file.puts # a blank line
+            file.puts '# ' + query
+            hits.each do |hit|
+              file.puts '>' + hit[:id]
+              file.puts hit[:seq]
+            end
+          end
+        end
+      end
+
       def to_html(hmm_results)
         @html_results = format_seqs_for_html(hmm_results)
         template_path = File.expand_path('../../../template/contents.slim',
                                          __FILE__)
         contents_temp = File.read(template_path)
@@ -62,15 +76,15 @@
           return s.insert(sp_cut_off + 19, '</span><span class=hsp>')
         elsif s1 =~ /<span class=hsp>/
           s = s1.gsub(/<span class=hsp>/, '</span><span class=sp_hsp>') +
               seq[sp_cut_off..-1]
           return s.insert(0, '<span class=sp>')
-                  .insert(sp_cut_off + 41, '</span><span class=hsp>')
+            .insert(sp_cut_off + 41, '</span><span class=hsp>')
         elsif s1 =~ /</
-          s = s1.gsub(/<.+$/, '</span><span class=sp_hsp>') +
-              seq[sp_cut_off..-1].gsub(/^\w+?>/,'')
+          s = s1.gsub(/<.*?$/, '</span><span class=sp_hsp>') +
+              seq[sp_cut_off..-1].gsub(/^.*?>/, '')
           return s.insert(0, '<span class=sp>')
-                  .insert(sp_cut_off + 41, '</span><span class=hsp>')
+            .insert(sp_cut_off + 41, '</span><span class=hsp>')
         else
           return seq.insert(0, '<span class=sp>').insert(sp_cut_off + 15,
                                                          '</span>')
         end
       end