genevalidator 1.6.1 → 1.6.2

data/lib/genevalidator/validation_length_rank.rb

@@ -1,7 +1,10 @@
-require 'genevalidator/validation_report'
-require 'genevalidator/validation_test'
+require 'forwardable'
+
 require 'genevalidator/exceptions'
 require 'genevalidator/ext/array'
+require 'genevalidator/validation_report'
+require 'genevalidator/validation_test'
+
 module GeneValidator
   ##
   # Class that stores the validation output information
@@ -81,11 +84,9 @@ module GeneValidator
     ##
     # Initializes the object
     # Params:
-    # +hits+: a vector of +Sequence+ objects (representing blast hits)
     # +prediction+: a +Sequence+ object representing the blast query
-    # +threshold+: threshold below which the prediction length rank is
-    # considered to be inadequate
-    def initialize(type, prediction, hits)
+    # +hits+: a vector of +Sequence+ objects (representing blast hits)
+    def initialize(prediction, hits)
       super
       @short_header = 'LengthRank'
       @header       = 'Length Rank'
@@ -143,19 +144,17 @@ module GeneValidator
                                                           largest_hit,
                                                           extreme_hits,
                                                           percentage)
-      @validation_report.running_time = Time.now - start
+      @validation_report.run_time = Time.now - start
       @validation_report
 
     rescue NotEnoughHitsError
       @validation_report = ValidationReport.new('Not enough evidence', :warning,
                                                 @short_header, @header,
-                                                @description, @approach,
-                                                @explanation, @conclusion)
+                                                @description)
     rescue Exception
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
-                                                @description, @approach,
-                                                @explanation, @conclusion)
+                                                @description)
       @validation_report.errors.push 'Unexpected Error'
     end
   end

data/lib/genevalidator/validation_open_reading_frame.rb

@@ -1,5 +1,10 @@
-require 'genevalidator/validation_report'
 require 'bio'
+require 'forwardable'
+
+require 'genevalidator/exceptions'
+require 'genevalidator/validation_report'
+require 'genevalidator/validation_test'
+
 module GeneValidator
   ##
   # Class that stores the validation output information
@@ -57,24 +62,23 @@ module GeneValidator
   # This class contains the methods necessary for checking whether there is
   # a main Open Reading Frame in the predicted sequence
   class OpenReadingFrameValidation < ValidationTest
-    attr_reader :filename
+    extend Forwardable
+    def_delegators GeneValidator, :config
 
     ##
     # Initilizes the object
     # Params:
-    # +type+: type of the predicted sequence (:nucleotide or :protein)
     # +prediction+: a +Sequence+ object representing the blast query
     # +hits+: a vector of +Sequence+ objects (representing blast hits)
-    # +plot_filename+: name of the input file, used when making plot files
-    def initialize(type, prediction, hits, filename)
+    def initialize(prediction, hits)
       super
-      @short_header = 'ORF'
+      @short_header = 'MainORF'
       @header       = 'Main ORF'
       @description  = 'Check whether there is a single main Open Reading' \
                       ' Frame in the predicted gene. Applicable only for' \
                       ' nucleotide queries.'
       @cli_name     = 'orf'
-      @filename     = filename
+      @type         = config[:type]
     end
 
     ##
@@ -101,15 +105,14 @@ module GeneValidator
       @validation_report = ORFValidationOutput.new(@short_header, @header,
                                                    @description, orfs,
                                                    coverage, longest_orf_frame)
-      @validation_report.running_time = Time.now - start
+      @validation_report.run_time = Time.now - start
 
       @validation_report.plot_files.push(plot1)
       @validation_report
     rescue Exception
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
-                                                @description, @approach,
-                                                @explanation, @conclusion)
+                                                @description)
       @validation_report.errors.push 'Unexpected Error'
     end
 
@@ -157,29 +160,25 @@ module GeneValidator
     # +orfs+: +Hash+ containing the open reading frame
     # +output+: location where the plot will be saved in jped file format
     # +prediction+: Sequence objects
-    def plot_orfs(orfs, translated_length, output = "#{@filename}_orfs.json")
+    def plot_orfs(orfs, translated_length, output = "#{@plot_path}_orfs.json")
       fail QueryError unless orfs.is_a? Hash
 
-      results = []
+      data = []
 
       # Create hashes for the Background
       (-3..3).each do |frame|
         next if frame == 0
-        results << { 'y' => frame, 'start' => 1, 'stop' => translated_length,
+        data << { 'y' => frame, 'start' => 1, 'stop' => translated_length,
                      'color' => 'gray' }
       end
 
       # Create the hashes for the ORFs...
       orfs.each do |_key, h|
-        results << { 'y' => h[:frame], 'start' => h[:orf_start],
+        data << { 'y' => h[:frame], 'start' => h[:orf_start],
                      'stop' => h[:orf_end], 'color' => 'red' }
       end
 
-      f = File.open(output, 'w')
-      f.write((results).to_json)
-      f.close
-
-      Plot.new(output.scan(%r{([^/]+)$})[0][0],
+      Plot.new(data,
                :lines,
                'Open Reading Frames in all 6 Frames',
                'Open Reading Frame (Minimimum Length: 30 amino acids),red',

data/lib/genevalidator/validation_report.rb

@@ -1,6 +1,6 @@
 # Top level module / namespace.
 module GeneValidator
-  Plot = Struct.new(:filename, :type, :title, :footer, :xtitle, :ytitle, :aux1,
+  Plot = Struct.new(:data, :type, :title, :footer, :xtitle, :ytitle, :aux1,
                     :aux2)
 
   ##
@@ -8,7 +8,6 @@ module GeneValidator
   # all validation reports
   class ValidationReport
     attr_reader :message
-    attr_reader :bg_color
     attr_reader :plot_files
     attr_reader :result
     attr_reader :expected
@@ -17,7 +16,7 @@ module GeneValidator
     attr_accessor :short_header
     attr_accessor :header
     attr_accessor :description
-    attr_accessor :running_time
+    attr_accessor :run_time
     attr_accessor :approach
     attr_accessor :explanation
     attr_accessor :conclusion
@@ -31,7 +30,6 @@ module GeneValidator
     # +short_header+: String
     # +header+: String
     # +description+: String
-    # +bg_color+: background color of the table cell for the html output (nil
     # by default)
     def initialize(message = 'Not enough evidence', validation_result = :no,
                    short_header = '', header = '', description = '',
@@ -60,7 +58,6 @@ module GeneValidator
     ##
     # May return "success" or "error"
     def color
-      bg_color unless bg_color.nil?
       if validation == @expected
         'success'
       elsif validation == :error || validation == :unapplicable

data/lib/genevalidator/validation_test.rb

@@ -1,7 +1,11 @@
+require 'forwardable'
+
 module GeneValidator
   # This is an abstract class extended
   # by all validation classes
   class ValidationTest
+    extend Forwardable
+    def_delegators GeneValidator, :config
     attr_accessor :type
     attr_accessor :prediction
     attr_accessor :hits
@@ -10,7 +14,7 @@ module GeneValidator
     attr_accessor :cli_name
     attr_accessor :description
     attr_accessor :validation_report
-    attr_accessor :running_time
+    attr_accessor :run_time
 
     ##
     # Initilizes the object
@@ -19,13 +23,13 @@ module GeneValidator
     # +prediction+: a +Sequence+ object representing the blast query
     # +hits+: a vector of +Sequence+ objects (representing blast hits)
     # +argv+: aditional arguments if needed
-    def initialize(type, prediction, hits = nil, *_argv)
-      @type              = type
+    def initialize(prediction, hits = nil, *_argv)
+      @type              = config[:type]
       @prediction        = prediction
       @hits              = hits
       @short_header      = 'NewVal'
       @header            = 'New Validation'
-      @running_time      = 0
+      @run_time          = 0
       @cli_name          = 'all'
       @description       = 'No description available.'
       @validation_report = ValidationReport.new('Not enough evidence')

data/lib/genevalidator/version.rb

@@ -1,3 +1,3 @@
 module GeneValidator
-  VERSION = '1.6.1'
+  VERSION = '1.6.2'
 end

data/test/test_all_validations.rb

@@ -3,93 +3,79 @@ require 'minitest/autorun'
 require 'yaml'
 require 'fileutils'
 require 'genevalidator'
-require 'genevalidator/blast'
-require 'genevalidator/validation_length_cluster'
-require 'genevalidator/validation_length_rank'
-require 'genevalidator/validation_blast_reading_frame'
-require 'genevalidator/validation_gene_merge'
-require 'genevalidator/validation_duplication'
-require 'genevalidator/validation_open_reading_frame'
-require 'genevalidator/validation_alignment'
 
 module GeneValidator
+  # Test if GV produces the same output with XML and tabular input
   class ValidateOutput < Minitest::Test
-
-    prot_input_fasta_file  = "test/test_files/all_validations_prot/all_validations_prot.fasta"
-    prot_blast_xml_file    = "#{prot_input_fasta_file}.blast_xml"
-    prot_blast_xml_raw_seq = "#{prot_input_fasta_file}.blast_xml.raw_seq"
-
-    prot_blast_tab_file    = "#{prot_input_fasta_file}.blast_tab"
-    prot_blast_tab_raw_seq = "#{prot_input_fasta_file}.blast_tab.raw_seq"
-
-    mrna_input_fasta_file  = "test/test_files/all_validations_mrna/all_validations_mrna.fasta"
-    mrna_blast_xml_file    = "#{mrna_input_fasta_file}.blast_xml"
-    mrna_blast_xml_raw_seq = "#{mrna_input_fasta_file}.blast_xml.raw_seq"
-
-    mrna_blast_tab_file    = "#{mrna_input_fasta_file}.blast_tab"
-    mrna_blast_tab_raw_seq = "#{mrna_input_fasta_file}.blast_tab.raw_seq"
-
-    tab_options            = "qseqid sseqid sacc slen qstart qend sstart send length qframe pident evalue"
-
-    database               = 'swissprot -remote'
-    threads                = '1'
-
-    # Unwanted Output Files 
-    prot_xml_out           = "#{prot_blast_xml_file}.out"
-    prot_tab_out           = "#{mrna_blast_tab_file}.out"
-    mrna_xml_out           = "#{mrna_blast_xml_file}.out"
-    mrna_tab_out           = "#{mrna_blast_tab_file}.out"
-    prot_output_dir        = "#{prot_input_fasta_file}.html"
-    mrna_output_dir        = "#{mrna_input_fasta_file}.html"
-    prot_yaml              = "#{prot_input_fasta_file}.yaml"
-    mrna_yaml              = "#{mrna_input_fasta_file}.yaml"
+    prot_dir    = 'test/test_files/all_validations_prot'
+    prot_input  = File.join(prot_dir, 'prot.fa')
+    prot_xml    = File.join(prot_dir, 'prot.blast_xml')
+    prot_tab    = File.join(prot_dir, 'prot.blast_tab6')
+    prot_raw    = File.join(prot_dir, 'prot.raw_seq')
+
+    mrna_dir    = 'test/test_files/all_validations_mrna'
+    mrna_input  = File.join(mrna_dir, 'mrna.fa')
+    mrna_xml    = File.join(mrna_dir, 'mrna.blast_xml')
+    mrna_tab    = File.join(mrna_dir, 'mrna.blast_tab6')
+    mrna_raw    = File.join(mrna_dir, 'mrna.raw_seq')
+
+    tab_options = 'qseqid sseqid sacc slen qstart qend sstart send length' \
+                  ' qframe pident nident evalue qseq sseq'
+    database    = 'swissprot -remote'
+    threads     = '1'
+
+    # Unwanted Output Files
+    prot_xml_out           = "#{prot_xml}.out"
+    prot_tab_out           = "#{prot_tab}.out"
+    prot_output_dir        = "#{prot_input}.html"
+    mrna_xml_out           = "#{mrna_xml}.out"
+    mrna_tab_out           = "#{mrna_tab}.out"
+    mrna_output_dir        = "#{mrna_input}.html"
 
     describe 'Protein dataset' do
       it 'xml and tabular inputs give the same output' do
-
         original_stdout = $stdout.clone
         $stdout.reopen(prot_xml_out, 'w')
 
-        FileUtils.rm_rf(prot_output_dir) rescue Error
-
+        FileUtils.rm_rf(prot_output_dir) rescue Errno::ENOENT
         opts = {
-          validations: %w(lenc lenr frame merge dup orf),
+          validations: %w(lenc lenr frame merge dup orf align),
           db: database,
           num_threads: threads,
           fast: false,
-          input_fasta_file: prot_input_fasta_file,
-          blast_xml_file: prot_blast_xml_file,
-          raw_sequences: prot_blast_xml_raw_seq,
+          input_fasta_file: prot_input,
+          blast_xml_file: prot_xml,
+          raw_sequences: prot_raw,
           test: true
         }
 
-        (GeneValidator::Validation.new(opts, 1, false)).run
+        GeneValidator.init(opts, 1, false)
+        GeneValidator.run
         $stdout.reopen original_stdout
         $stdout.reopen(prot_tab_out, 'w')
 
-        FileUtils.rm_rf(prot_output_dir) rescue Error
+        FileUtils.rm_rf(prot_output_dir) rescue Errno::ENOENT
 
         opts1 = {
-          validations: %w(lenc lenr frame merge dup orf),
+          validations: %w(lenc lenr frame merge dup orf align),
           db: database,
           num_threads: threads,
           fast: false,
-          input_fasta_file: prot_input_fasta_file,
-          blast_tabular_file: prot_blast_tab_file,
+          input_fasta_file: prot_input,
+          blast_tabular_file: prot_tab,
           blast_tabular_options: tab_options,
-          raw_sequences: prot_blast_tab_raw_seq,
+          raw_sequences: prot_raw,
           test: true
         }
 
-        (GeneValidator::Validation.new(opts1, 1, false)).run
+        GeneValidator.init(opts1, 1, false)
+        GeneValidator.run
         $stdout.reopen original_stdout
 
         diff = FileUtils.compare_file(prot_xml_out, prot_tab_out)
 
         File.delete(prot_xml_out)
         File.delete(prot_tab_out)
-        File.delete(prot_yaml)
-
         FileUtils.rm_rf(prot_output_dir)
 
         assert_equal(true, diff)
@@ -98,50 +84,49 @@ module GeneValidator
 
     describe 'mRNA dataset' do
       it 'xml and tabular inputs give the same output' do
-
         original_stdout = $stdout.clone
         $stdout.reopen(mrna_xml_out, 'w')
 
-        FileUtils.rm_rf(mrna_output_dir) rescue Error
+        FileUtils.rm_rf(mrna_output_dir) rescue Errno::ENOENT
 
         opts = {
           validations: %w(lenc lenr frame merge dup orf align),
           db: database,
           num_threads: threads,
           fast: false,
-          input_fasta_file: mrna_input_fasta_file,
-          blast_xml_file: mrna_blast_xml_file ,
-          raw_sequences: mrna_blast_xml_raw_seq,
+          input_fasta_file: mrna_input,
+          blast_xml_file: mrna_xml,
+          raw_sequences: mrna_raw,
           test: true
         }
 
-        (GeneValidator::Validation.new(opts, 1, false)).run
+        GeneValidator.init(opts, 1, false)
+        GeneValidator.run
         $stdout.reopen original_stdout
         $stdout.reopen(mrna_tab_out, 'w')
 
-        FileUtils.rm_rf(mrna_output_dir) rescue Error
+        FileUtils.rm_rf(mrna_output_dir) rescue Errno::ENOENT
 
         opts1 = {
           validations: %w(lenc lenr frame merge dup orf align),
           db: database,
           num_threads: threads,
           fast: false,
-          input_fasta_file: mrna_input_fasta_file,
-          blast_tabular_file: mrna_blast_tab_file,
+          input_fasta_file: mrna_input,
+          blast_tabular_file: mrna_tab,
           blast_tabular_options: tab_options,
-          raw_sequences: mrna_blast_tab_raw_seq,
+          raw_sequences: mrna_raw,
           test: true
         }
 
-        (GeneValidator::Validation.new(opts1, 1, false)).run
+        GeneValidator.init(opts1, 1, false)
+        GeneValidator.run
         $stdout.reopen original_stdout
 
         diff = FileUtils.compare_file(mrna_xml_out, mrna_tab_out)
 
         File.delete(mrna_xml_out)
         File.delete(mrna_tab_out)
-        File.delete(mrna_yaml)
-
         FileUtils.rm_rf(mrna_output_dir)
 
         assert_equal(true, diff)

data/test/test_blast.rb

@@ -4,8 +4,10 @@ require 'fileutils'
 require 'genevalidator'
 require 'genevalidator/blast'
 require 'genevalidator/tabular_parser'
+require 'genevalidator/validation'
 
 module GeneValidator
+  # Test the BlastUtil Class
   class TestBlastClass < Minitest::Test
     dir = 'test/test_files'
     filename_mrna     = "#{dir}/file_mrna.txt"
@@ -20,9 +22,7 @@ module GeneValidator
     ncbi_mrna_xml20   = "#{dir}/ncbi_mrna.xml.20"
 
     describe 'Test Blast Class' do
-
       it 'should detect nucleotide seq type' do
-
         file_mrna = File.open(filename_mrna, 'w+')
         query_mrna = 'ATGGCTAAATTACAGAGGAAGAGAAGCAAGGCTCTTGGGTCATCTCTAGAGATGT' \
                      'CCCAGATAATGGATGCAGGAACAAACAAAATTAAAAGAAGAATAAGAGATTTAGA' \
@@ -37,7 +37,7 @@ module GeneValidator
         file_mrna.puts(query_mrna)
         file_mrna.close
 
-        FileUtils.rm_rf("#{filename_mrna}.html") rescue Error
+        FileUtils.rm_rf("#{filename_mrna}.html") rescue Errno::ENOENT
 
         default_opt = {
           input_fasta_file: filename_mrna,
@@ -47,11 +47,10 @@ module GeneValidator
           test: true
         }
 
-        val = GeneValidator::Validation.new(default_opt)
-
+        GeneValidator.init(default_opt)
         File.delete(filename_mrna)
         FileUtils.rm_rf("#{filename_mrna}.html")
-        assert_equal(:nucleotide, val.type)
+        assert_equal(:nucleotide, GeneValidator.config[:type])
       end
 
       it 'should detect protein type' do
@@ -72,7 +71,7 @@ module GeneValidator
         file_prot.puts(query_prot)
         file_prot.close
 
-        FileUtils.rm_rf("#{filename_prot}.html") rescue Error
+        FileUtils.rm_rf("#{filename_prot}.html") rescue Errno::ENOENT
 
         default_opt = {
           input_fasta_file: filename_prot,
@@ -82,12 +81,11 @@ module GeneValidator
           test: true
         }
 
-        val = GeneValidator::Validation.new(default_opt)
+        GeneValidator.init(default_opt)
 
         File.delete(filename_prot)
         FileUtils.rm_rf("#{filename_prot}.html")
-        assert_equal(:protein, val.type)
-
+        assert_equal(:protein, GeneValidator.config[:type])
       end
 
       it 'should raise error when input types are mixed in the fasta' do
@@ -96,18 +94,18 @@ module GeneValidator
           original_stderr = $stderr
           $stderr.reopen('/dev/null', 'w')
 
-          FileUtils.rm_rf("#{filename_prot}.html") rescue Error
+          FileUtils.rm_rf("#{filename_prot}.html") rescue Errno::ENOENT
 
           default_opt = {
             input_fasta_file: mixed_fasta,
             validations: ['all'],
             db: 'swissprot -remote',
             num_threads: 1,
-          test: true
+            test: true
           }
 
-          GeneValidator::Validation.new(default_opt)
-        rescue SystemExit => e
+          GeneValidator.init(default_opt)
+        rescue SystemExit
           mixed = true
         end
         $stderr = original_stderr
@@ -126,10 +124,12 @@ module GeneValidator
       end
 
       it 'should parse tabular -6 input with default tabular format' do
-
-        output = File.open(ncbi_mrna_tab20, 'rb').read
-        tabular_headers = 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore'
-        iterator_tab = TabularParser.new(ncbi_mrna_tab20, tabular_headers, :protein)
+        tabular_headers      = 'qseqid sseqid pident length mismatch gapopen' \
+                               ' qstart qend sstart send evalue bitscore'
+        GeneValidator.opt    = { blast_tabular_file: ncbi_mrna_tab20,
+                                 blast_tabular_options: tabular_headers }
+        GeneValidator.config = { type: :protein }
+        iterator_tab = TabularParser.new
         hits = iterator_tab.parse_next
 
         assert_equal(20, hits.length)
@@ -145,9 +145,12 @@ module GeneValidator
       end
 
       it 'should parse tabular -6 input with tabular format as argument' do
-        output = File.open(output_tab6, 'rb').read
-        tabular_headers = 'qseqid sseqid sacc slen qstart qend sstart send pident length qframe evalue'
-        iterator_tab = TabularParser.new(output_tab6, tabular_headers, :protein)
+        tabular_headers      = 'qseqid sseqid sacc slen qstart qend sstart' \
+                               ' send pident length qframe evalue'
+        GeneValidator.opt    = { blast_tabular_file: output_tab6,
+                                 blast_tabular_options: tabular_headers }
+        GeneValidator.config = { type: :protein }
+        iterator_tab = TabularParser.new
         hits = iterator_tab.parse_next
         assert_equal(4, hits.length)
         assert_equal(199, hits[0].length_protein)
@@ -157,9 +160,12 @@ module GeneValidator
       end
 
       it 'should parse tabular -6 input with mixed columns' do
-        output = File.open(output_tab_mixed, 'rb').read
-        tabular_headers = 'qend sstart send pident length qframe evalue qseqid sseqid sacc slen qstart'
-        iterator_tab = TabularParser.new(output_tab_mixed, tabular_headers, :protein)
+        tabular_headers      = 'qend sstart send pident length qframe evalue' \
+                               ' qseqid sseqid sacc slen qstart'
+        GeneValidator.opt    = { blast_tabular_file: output_tab_mixed,
+                                 blast_tabular_options: tabular_headers }
+        GeneValidator.config = { type: :protein }
+        iterator_tab = TabularParser.new
         hits = iterator_tab.parse_next
         assert_equal(4, hits.length)
         assert_equal(199, hits[0].length_protein)
@@ -169,9 +175,12 @@ module GeneValidator
       end
 
       it 'should parse tabular -7 input' do
-        output = File.open(output_tab7, 'rb').read
-        tabular_headers = 'qseqid sseqid sacc slen qstart qend sstart send length qframe evalue'
-        iterator_tab = TabularParser.new(output_tab7, tabular_headers, :protein)
+        tabular_headers = 'qseqid sseqid sacc slen qstart qend sstart send' \
+                          ' length qframe evalue'
+        GeneValidator.opt    = { blast_tabular_file: output_tab7,
+                                 blast_tabular_options: tabular_headers }
+        GeneValidator.config = { type: :protein }
+        iterator_tab = TabularParser.new
         hits = iterator_tab.parse_next
         assert_equal(4, hits.length)
         assert_equal(199, hits[0].length_protein)
@@ -180,10 +189,8 @@ module GeneValidator
         assert_equal(100, hits[0].hsp_list[2].hit_to)
       end
 
-      it 'should remove identical matches among protein sequences' do
-        output = File.open(output_tab6, 'rb').read
-
-        FileUtils.rm_rf("#{filename_fasta}.html") rescue Error
+      it 'should remove identical matches (protein sequences)' do
+        FileUtils.rm_rf("#{filename_fasta}.html") rescue Errno::ENOENT
 
         default_opt = {
           input_fasta_file: filename_fasta,
@@ -193,19 +200,26 @@ module GeneValidator
           test: true
         }
 
-        b = GeneValidator::Validation.new(default_opt) # just use a valida filename to create the object
+        GeneValidator.init(default_opt)
+
         prediction = Sequence.new
         prediction.length_protein = 1808
-        tabular_headers = 'qseqid sseqid sacc slen qstart qend sstart send pident length qframe evalue'
-        iterator_tab = TabularParser.new(output_tab6, tabular_headers, :protein)
+        tabular_headers      = 'qseqid sseqid sacc slen qstart qend sstart' \
+                               ' send pident length qframe evalue'
+        GeneValidator.opt    = { blast_tabular_file: output_tab6,
+                                 blast_tabular_options: tabular_headers }
+        GeneValidator.config = { type: :protein }
+        iterator_tab = TabularParser.new
         iterator_tab.parse_next
         hits = iterator_tab.parse_next
 
-        # before removal
         assert_equal(2, hits.length)
         assert_equal(100, hits[0].hsp_list[0].pidentity)
         assert_in_delta(99.23, hits[0].hsp_list[1].pidentity, 0.01)
         assert_in_delta(90, hits[1].hsp_list[0].pidentity, 0.01)
+
+        # Remove identical hits
+        b = GeneValidator::Validate.new
         hits = b.remove_identical_hits(prediction, hits)
 
         # after removal of identical hits
@@ -214,10 +228,8 @@ module GeneValidator
         FileUtils.rm_rf("#{filename_fasta}.html")
       end
 
-      it 'should remove identical matches among nucleotide sequences with tabular input' do
-        output = File.open(ncbi_mrna_tab20, 'rb').read
-
-        FileUtils.rm_rf("#{filename_fasta}.html") rescue Error
+      it 'should remove identical matches (nucleotide seqs) - tabular input' do
+        FileUtils.rm_rf("#{filename_fasta}.html") rescue Errno::ENOENT
 
         default_opt = {
           input_fasta_file: filename_fasta,
@@ -226,17 +238,22 @@ module GeneValidator
           num_threads: 1,
           test: true
         }
-        tabular_headers = 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore'
 
-        b = GeneValidator::Validation.new(default_opt) # just use a valida filename to create the object
+        GeneValidator.init(default_opt)
 
         prediction = Sequence.new
         prediction.length_protein = 219 / 3
-        iterator_tab = TabularParser.new(ncbi_mrna_tab20, tabular_headers, :nucleotide)
+        tabular_headers      = 'qseqid sseqid pident length mismatch gapopen' \
+                               ' qstart qend sstart send evalue bitscore'
+        GeneValidator.opt    = { blast_tabular_file: ncbi_mrna_tab20,
+                                 blast_tabular_options: tabular_headers }
+        GeneValidator.config = { type: :nucleotide }
+        iterator_tab = TabularParser.new
         hits = iterator_tab.parse_next
 
         assert_equal(20, hits.length)
-
+        # remove identical hits
+        b = GeneValidator::Validate.new
         hits = b.remove_identical_hits(prediction, hits)
 
         assert_equal(13, hits.length)
@@ -244,10 +261,8 @@ module GeneValidator
         FileUtils.rm_rf("#{filename_fasta}.html")
       end
 
-      it 'should remove identical matches among nucleotide sequences with xml input' do
-        output = File.open(ncbi_mrna_xml20, 'rb').read
-
-        FileUtils.rm_rf("#{filename_fasta}.html") rescue Error
+      it 'should remove identical matches (nucleotide seqs) - xml input' do
+        FileUtils.rm_rf("#{filename_fasta}.html") rescue Errno::ENOENT
 
         # just use a valid opts hash to create the object
         default_opt = {
@@ -258,16 +273,17 @@ module GeneValidator
           test: true
         }
 
-        b = GeneValidator::Validation.new(default_opt) 
+        GeneValidator.init(default_opt)
 
         prediction = Sequence.new
         prediction.length_protein = 219 / 3
-
+        output = File.open(ncbi_mrna_xml20, 'rb').read
         iterator = Bio::BlastXMLParser::NokogiriBlastXml.new(output).to_enum
         hits = BlastUtils.parse_next(iterator, :protein)
 
         assert_equal(20, hits.length)
 
+        b = GeneValidator::Validate.new
         hits = b.remove_identical_hits(prediction, hits)
 
         assert_equal(13, hits.length)
@@ -286,8 +302,9 @@ module GeneValidator
             test: true
           }
 
-          (GeneValidator::Validation.new(default_opt)).run
-        rescue SystemExit => error
+          GeneValidator.init(default_opt)
+
+        rescue SystemExit
           error = true
         end
         assert_equal(true, error)