lib/npsearch/signalp.rb in npsearch-2.1.2 vs lib/npsearch/signalp.rb in npsearch-2.1.3

@@ -6,30 +6,30 @@
 module NpSearch
   # A class to hold sequence data
   class Signalp
     class << self
       extend Forwardable
-      def_delegators NpSearch, :opt
+      def_delegators NpSearch, :opt, :logger
 
       def analyse_sequence(seq)
         sp_headers = %w(name cmax cmax_pos ymax ymax_pos smax smax_pos smean d
                         sp dmaxcut networks orf)
         seqs       = setup_analysis(seq)
         sp_results = []
-        seqs.each do |seq|
-          sp_results << run_signalp(seq, sp_headers)
+        seqs.each do |sequence|
+          sp_results << run_signalp(sequence, sp_headers)
         end
         sp_results.sort_by { |h| h[:d] }.reverse[0]
       end
 
       private
 
       def run_signalp(seq, sp_headers)
-        Timeout::timeout(300) do
+        timeout(300) do
           cmd = "echo '>seq\n#{seq}\n' | #{opt[:signalp_path]} -t euk" \
-                " -f short -U 0.34 -u 0.34"
-          stdin, stdout, stderr, wait_thr = Open3.popen3(cmd)
+                ' -f short -U 0.34 -u 0.34'
+          stdin, stdout, stderr = Open3.popen3(cmd)
           out = stdout.gets(nil).split("\n").delete_if { |l| l[0] == '#' }
           if out.nil? || out.empty?
             print stdout
             print stderr
             raise ArgumentError, 'Signalp failed to run sucessfully :('
@@ -38,16 +38,16 @@
             return Hash[sp_headers.map(&:to_sym).zip(result.split)]
           end
           stdin.close; stdout.close; stderr.close
         end
       rescue Timeout::Error
-        no_results = [0,0,1,1,1,1,1,1,1,'N',1,1, seq]
+        no_results = [0, 0, 1, 1, 1, 1, 1, 1, 1, 'N', 1, 1, seq]
         return Hash[sp_headers.map(&:to_sym).zip(no_results)]
       end
 
       def setup_analysis(seq)
         orfs = seq.scan(/(?=(M\w{#{opt[:min_orf_length]},}))./).flatten
-        (opt[:type] == :protein || orfs.empty? || orfs.nil?) ? [seq] : orfs
+        opt[:type] == :protein || orfs.empty? || orfs.nil? ? [seq] : orfs
       end
     end
   end
 end