validation_duplication.rb in genevalidator-1.6.2

- old
+ new

@@ -1,8 +1,14 @@
-require 'genevalidator/validation_report'
+require 'bio'
+require 'forwardable'
+require 'statsample'
+
 require 'genevalidator/exceptions'
 require 'genevalidator/ext/array'
+require 'genevalidator/validation_report'
+require 'genevalidator/validation_test'
+
 module GeneValidator
   ##
   # Class that stores the validation output information
   class DuplicationValidationOutput < ValidationReport
     attr_reader :pvalue
@@ -69,28 +75,31 @@
 
   ##
   # This class contains the methods necessary for
   # finding duplicated subsequences in the predicted gene
   class DuplicationValidation < ValidationTest
+    extend Forwardable
+    def_delegators GeneValidator, :opt, :config
+
     attr_reader :raw_seq_file
     attr_reader :index_file_name
     attr_reader :raw_seq_file_load
 
-    def initialize(type, prediction, hits, raw_seq_file, index_file_name,
-                   raw_seq_file_load, db, num_threads)
+    def initialize(prediction, hits)
       super
       @short_header      = 'Duplication'
       @header            = 'Duplication'
       @description       = 'Check whether there is a duplicated subsequence' \
                            ' in the predicted gene by counting the hsp' \
                            ' residue coverage of the prediction, for each hit.'
       @cli_name          = 'dup'
-      @raw_seq_file      = raw_seq_file
-      @index_file_name   = index_file_name
-      @raw_seq_file_load = raw_seq_file_load
-      @db                = db
-      @num_threads       = num_threads
+      @raw_seq_file      = opt[:raw_sequences]
+      @index_file_name   = config[:raw_seq_file_index]
+      @raw_seq_file_load = config[:raw_seq_file_load]
+      @db                = opt[:db]
+      @num_threads       = opt[:num_threads]
+      @type              = config[:type]
     end
 
     def in_range?(ranges, idx)
       ranges.each do |range|
         return (range.member?(idx)) ? true : false
@@ -212,52 +221,47 @@
       if averages.reject { |x| x == 1 } == []
         @validation_report = DuplicationValidationOutput.new(@short_header,
                                                              @header,
                                                              @description, 1,
                                                              averages)
-        @validation_report.running_time = Time.now - start
+        @validation_report.run_time = Time.now - start
         return @validation_report
       end
 
       pval = wilcox_test(averages)
 
       @validation_report = DuplicationValidationOutput.new(@short_header,
                                                            @header,
                                                            @description, pval,
                                                            averages)
-      @running_time = Time.now - start
+      @run_time = Time.now - start
       @validation_report
 
     rescue NotEnoughHitsError
       @validation_report = ValidationReport.new('Not enough evidence', :warning,
                                                 @short_header, @header,
-                                                @description, @explanation,
-                                                @conclusion)
+                                                @description)
     rescue NoMafftInstallationError
       @validation_report = ValidationReport.new('Mafft error', :error,
                                                 @short_header, @header,
-                                                @description, @explanation,
-                                                @conclusion)
+                                                @description)
       @validation_report.errors.push NoMafftInstallationError
     rescue NoInternetError
       @validation_report = ValidationReport.new('Internet error', :error,
                                                 @short_header, @header,
-                                                @description, @explanation,
-                                                @conclusion)
+                                                @description)
       @validation_report.errors.push NoInternetError
     rescue Exception
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
-                                                @description, @explanation,
-                                                @conclusion)
+                                                @description)
       @validation_report.errors.push 'Unexpected Error'
     end
 
     ##
     # wilcox test implementation from statsample ruby gem
     # many thanks to Claudio for helping us with the implementation!
     def wilcox_test(averages)
-      require 'statsample'
       wilcox = Statsample::Test.wilcoxon_signed_rank(averages.to_scale,
                                                      Array.new(averages.length,
                                                                1).to_scale)
 
       (averages.length < 15) ? wilcox.probability_exact : wilcox.probability_z