lib/genevalidator/validation_duplication.rb in genevalidator-1.6.2 vs lib/genevalidator/validation_duplication.rb in genevalidator-1.6.3

@@ -2,10 +2,11 @@
 require 'forwardable'
 require 'statsample'
 
 require 'genevalidator/exceptions'
 require 'genevalidator/ext/array'
+require 'genevalidator/get_raw_sequences'
 require 'genevalidator/validation_report'
 require 'genevalidator/validation_test'
 
 module GeneValidator
   ##
@@ -111,39 +112,28 @@
     # Check duplication in the first n hits
     # Output:
     # +DuplicationValidationOutput+ object
     def run(n = 10)
       fail NotEnoughHitsError unless hits.length >= 5
-      fail Exception unless prediction.is_a?(Sequence) &&
-                            !prediction.raw_sequence.nil? &&
-                            hits[0].is_a?(Sequence)
+      fail unless prediction.is_a?(Query) && !prediction.raw_sequence.nil? &&
+                  hits[0].is_a?(Query)
 
       start = Time.new
       # get the first n hits
       less_hits = @hits[0..[n - 1, @hits.length].min]
       useless_hits = []
-
       # get raw sequences for less_hits
       less_hits.map do |hit|
-        # get gene by accession number
         next unless hit.raw_sequence.nil?
-
-        hit.get_sequence_from_index_file(@raw_seq_file, @index_file_name,
-                                         hit.identifier, @raw_seq_file_load)
-
-        if hit.raw_sequence.nil? || hit.raw_sequence.empty?
-          seq_type = (hit.type == :protein) ? 'protein' : 'nucleotide'
-          hit.get_sequence_by_accession_no(hit.accession_no, seq_type, @db)
-        end
-
+        hit.raw_sequence = FetchRawSequences.run(hit.identifier,
+                                                 hit.accession_no)
         useless_hits.push(hit) if hit.raw_sequence.nil?
-        useless_hits.push(hit) if hit.raw_sequence.empty?
       end
 
       useless_hits.each { |hit| less_hits.delete(hit) }
 
-      fail NoInternetError if less_hits.length.nil?
+      fail NoInternetError if less_hits.length == 0
 
       averages = []
 
       less_hits.each do |hit|
         coverage = Array.new(hit.length_protein, 0)
@@ -183,11 +173,11 @@
               align     = []
 
               raw_align.each { |seq| align.push(seq.to_s) }
               hit_alignment   = align[0]
               query_alignment = align[1]
-            rescue Exception
+            rescue
               raise NoMafftInstallationError
             end
           end
 
           # check multiple coverage
@@ -248,10 +238,10 @@
     rescue NoInternetError
       @validation_report = ValidationReport.new('Internet error', :error,
                                                 @short_header, @header,
                                                 @description)
       @validation_report.errors.push NoInternetError
-    rescue Exception
+    rescue
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
                                                 @description)
       @validation_report.errors.push 'Unexpected Error'
     end