output.rb in neurohmmer-0.1.1

- old
+ new

@@ -1,20 +1,22 @@
-require 'slim'
 require 'forwardable'
+require 'slim'
 
+require 'neurohmmer/signalp'
+
 # Top level module / namespace.
 module Neurohmmer
   # A class that holds methods related to Output
   class Output
     class <<self
       extend Forwardable
-      def_delegators Neurohmmer, :conf
+      def_delegators Neurohmmer, :opt, :conf
 
       def to_html(hmm_results)
         @html_results = format_seqs_for_html(hmm_results)
-        template_path = File.expand_path(File.join(__FILE__, '../../../',
-                                                   'template/contents.slim'))
+        template_path = File.expand_path('../../../template/contents.slim',
+                                         __FILE__)
         contents_temp = File.read(template_path)
         html_content = Slim::Template.new { contents_temp }.render(self)
         File.open(conf[:html_output], 'w') { |f| f.puts html_content }
       end
 
@@ -33,18 +35,46 @@
 
       private
 
       def format_html_seq(seq, flatseq)
         seq.gsub!("\n", '')
+        signalp_output = Signalp.analyse_sequence(seq) if opt[:type] == :protein
         flatseq.each do |hsp|
           seq.gsub!(/#{hsp.gsub('-', '')}/i, '<span class=hsp>\0</span>')
         end
+        seq = format_signal_peptide(seq, signalp_output)
         seq.gsub(/KR|KK|RR/i, '<span class=clv>\0</span>')
           .gsub(/(K|R)<span class=hsp>(K|R)/i, '<span class=clv>\1</span>' \
                 '<span class=clv_i>\2</span><span class=hsp>')
           .gsub('<span class=clv>R</span><span class=clv_i>K</span><span' \
                 ' class=hsp>', 'R<span class=hsp>K')
           .gsub(/G<span class=clv>/, '<span class=gly>G</span><span class=clv>')
+      end
+
+      def format_signal_peptide(seq, sp)
+        return seq if opt[:type] == :genetic || sp[:sp] == 'N'
+        add_signalp_formatting(seq, sp[:ymax_pos].to_i - 1)
+      end
+
+      def add_signalp_formatting(seq, sp_cut_off)
+        s1 = seq[0, sp_cut_off]
+        if s1 =~ /^</
+          s = seq.gsub(/^<span class=hsp>/, '<span class=sp_hsp>')
+          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>')
+        elsif s1 =~ /</
+          s = s1.gsub(/<.+$/, '</span><span class=sp_hsp>') +
+              seq[sp_cut_off..-1].gsub(/^\w+?>/,'')
+          return s.insert(0, '<span class=sp>')
+                  .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
     end
   end
 end