preprocess_collection.rb in macroape-4.0.1

- old
+ new

@@ -24,11 +24,11 @@
           Example:
             #{run_tool_cmd} ./motifs  collection.yaml -p 0.001,0.0005,0.0001 -d 1,10 -b 0.2,0.3,0.3,0.2
         EOS
 
         if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts doc
+          $stderr.puts doc
           exit
         end
 
         data_model = argv.delete('--pcm') ? Bioinform::PCM : Bioinform::PWM
 
@@ -97,11 +97,11 @@
         end
 
         pwms = motifs.map(&:to_pwm)
 
         pwms.each_with_index do |pwm,index|
-          STDERR.puts "Motif #{pwm.name}, length: #{pwm.length} (#{index+1} of #{pwms.size}, #{index*100/pwms.size}% complete)"  unless silent
+          $stderr.puts "Motif #{pwm.name}, length: #{pwm.length} (#{index+1} of #{pwms.size}, #{index*100/pwms.size}% complete)"  unless silent
 
           # When support of onefile collections is introduced - then here should be check if name exists.
           # Otherwise it should skip motif and tell you about this
           # Also two command line options to fail on skipping or to skip silently should be included
 
@@ -138,11 +138,11 @@
           else
             pwm.discrete(precise_discretization).weak_thresholds(*pvalues,&fill_precise_infos)
           end
           collection.add_pm(pwm, info)  unless skip_motif
         end
-        STDERR.puts "100% complete. Saving results"  unless silent
+        $stderr.puts "100% complete. Saving results"  unless silent
         File.open(output_file, 'w') do |f|
           f.puts(collection.to_yaml)
         end
         puts OutputInformation.new{|infos|
           infos.add_parameter('P', 'P-value list', pvalues.join(','))
@@ -150,10 +150,10 @@
           infos.add_parameter('VP', 'discretization value, precise', precise_discretization)
           infos.add_parameter('PB', 'P-value boundary', pvalue_boundary)
           infos.background_parameter('B', 'background', background)
         }.result
       rescue => err
-        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
+        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
       end
 
     end
   end
 end
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