gistfile1.rb

  def parse(signalp_hash, open_reading_frames_condensed, motif)
      signalp_with_seq = {}
      signalp_hash.each do |id, h|
          current_orf = open_reading_frames_condensed[id]
          sequence = current_orf.to_s.gsub('["', '').gsub('"]', '')
          sp_clv = h[0][:cut_off].to_i - 1
          signalp = sequence[0,sp_clv]
          seq_end = sequence[sp_clv+1, sequence.length - (sp_clv+1)]
           if seq_end.match(/#{motif}/)
                signalp_with_seq[id + "~- S.P. Cleavage Site: #{sp_clv}:" \
                    "#{h[0][:cut_off]} - S.P. D-value: #{h[0][:d_value]}"] = \
                    "#{signalp}~#{seq_end}" 
            
          
          end 
        end
      end
      return signalp_with_seq
  end