genevalidator 1.6.12 → 2.1.3

data/test/test_blast.rb

@@ -38,14 +38,16 @@ module GeneValidator
         file_mrna.puts(query_mrna)
         file_mrna.close
 
-        FileUtils.rm_rf("#{filename_mrna}.html") rescue Errno::ENOENT
-
         default_opt = {
           input_fasta_file: filename_mrna,
           validations: ['all'],
           db: 'swissprot -remote',
           num_threads: 1,
-          test: true
+          min_blast_hits: 5,
+          test: true,
+          force_rewrite: true,
+          output_formats: %w[html csv json stdout],
+          output_dir: "#{filename_mrna}.html"
         }
 
         GeneValidator.init(default_opt)
@@ -72,14 +74,16 @@ module GeneValidator
         file_prot.puts(query_prot)
         file_prot.close
 
-        FileUtils.rm_rf("#{filename_prot}.html") rescue Errno::ENOENT
-
         default_opt = {
           input_fasta_file: filename_prot,
           validations: ['all'],
           db: 'swissprot -remote',
           num_threads: 1,
-          test: true
+          min_blast_hits: 5,
+          test: true,
+          force_rewrite: true,
+          output_formats: %w[html csv json stdout],
+          output_dir: "#{filename_prot}.html"
         }
 
         GeneValidator.init(default_opt)
@@ -95,14 +99,16 @@ module GeneValidator
           original_stderr = $stderr
           $stderr.reopen('/dev/null', 'w')
 
-          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
+            min_blast_hits: 5,
+            test: true,
+            force_rewrite: true,
+            output_formats: %w[html csv json stdout],
+            output_dir: "#{mixed_fasta}.html"
           }
 
           GeneValidator.init(default_opt)
@@ -115,8 +121,9 @@ module GeneValidator
 
       it 'should parse xml input' do
         output = File.open(filename_prot_xml, 'rb').read
+        GeneValidator.config = { type: :protein }
         iterator = Bio::BlastXMLParser::NokogiriBlastXml.new(output).to_enum
-        hits = BlastUtils.parse_next(iterator, :protein)
+        hits = BlastUtils.parse_next(iterator)
         assert_equal(500, hits.length)
         assert_equal(870, hits[19].length_protein)
         assert_equal('XP_004524940', hits[19].accession_no)
@@ -136,13 +143,13 @@ module GeneValidator
         assert_equal(20, hits.length)
         assert_equal(1, hits[0].hsp_list.length)
         assert_equal(111, hits[0].hsp_list[0].hit_to)
-        assert(hits[0].hsp_list[0].hit_from.is_a? Fixnum)
+        assert(hits[0].hsp_list[0].hit_from.is_a?(Integer))
 
         assert_equal(100, hits[0].hsp_list[0].pidentity)
-        assert(hits[0].hsp_list[0].pidentity.is_a? Float)
+        assert(hits[0].hsp_list[0].pidentity.is_a?(Float))
 
         assert_equal(2.0e-44, hits[0].hsp_list[0].hsp_evalue)
-        assert(hits[0].hsp_list[0].hsp_evalue.is_a? Float)
+        assert(hits[0].hsp_list[0].hsp_evalue.is_a?(Float))
       end
 
       it 'should parse tabular -6 input with tabular format as argument' do
@@ -191,14 +198,16 @@ module GeneValidator
       end
 
       it 'should remove identical matches (protein sequences)' do
-        FileUtils.rm_rf("#{filename_fasta}.html") rescue Errno::ENOENT
-
         default_opt = {
           input_fasta_file: filename_fasta,
           validations: ['all'],
           db: 'swissprot -remote',
           num_threads: 1,
-          test: true
+          min_blast_hits: 5,
+          test: true,
+          force_rewrite: true,
+          output_formats: %w[html csv json stdout],
+          output_dir: "#{filename_fasta}.html"
         }
 
         GeneValidator.init(default_opt)
@@ -230,14 +239,16 @@ module GeneValidator
       end
 
       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,
           validations: ['all'],
           db: 'swissprot -remote',
           num_threads: 1,
-          test: true
+          min_blast_hits: 5,
+          test: true,
+          force_rewrite: true,
+          output_formats: %w[html csv json stdout],
+          output_dir: "#{filename_fasta}.html"
         }
 
         GeneValidator.init(default_opt)
@@ -263,24 +274,27 @@ module GeneValidator
       end
 
       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 = {
           input_fasta_file: filename_fasta,
           validations: ['all'],
           db: 'swissprot -remote',
           num_threads: 1,
-          test: true
+          min_blast_hits: 5,
+          test: true,
+          force_rewrite: true,
+          output_formats: %w[html csv json stdout],
+          output_dir: "#{filename_fasta}.html"
         }
 
         GeneValidator.init(default_opt)
+        GeneValidator.config = { type: :protein }
 
         prediction = Query.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)
+        hits = BlastUtils.parse_next(iterator)
 
         assert_equal(20, hits.length)
 
@@ -300,11 +314,12 @@ module GeneValidator
             validations: ['all'],
             db: 'swissprot -remote',
             num_threads: 1,
+            min_blast_hits: 5,
+            output_formats: %w[html csv json stdout],
             test: true
           }
 
           GeneValidator.init(default_opt)
-
         rescue SystemExit
           error = true
         end

data/test/test_clusterization_2d.rb

@@ -29,12 +29,12 @@ module GeneValidator
         hc       = HierarchicalClusterization.new(vec3)
         clusters = hc.hierarchical_clusterization_2d(2, 1)
         actual   = clusters[0].objects.map { |elem| elem[0] }
-                   .sort { |a, b| a.x <=> b.x }
-                   .sort { |a, b| a.y <=> b.y }
+                              .sort_by(&:x)
+                              .sort_by(&:y)
         ex_array = [Pair.new(1, 1), Pair.new(1.2, 1), Pair.new(1, 1.5),
                     Pair.new(1.1, 1.3), Pair.new(0.9, 0.9)]
-        expected = ex_array.sort { |a, b| a.x <=> b.x }
-                   .sort { |a, b| a.y <=> b.y }
+        expected = ex_array.sort_by(&:x)
+                           .sort_by(&:y)
         assert_equal(expected, actual)
       end
     end

data/test/test_helper.rb

@@ -1,2 +1,2 @@
-require 'codeclimate-test-reporter'
-CodeClimate::TestReporter.start
+require 'simplecov'
+SimpleCov.start

data/test/test_query.rb

@@ -23,14 +23,10 @@ module GeneValidator
         assert_equal(identifier, seq.identifier)
         assert_equal(accession_no, seq.accession_no)
         assert_equal(slen, seq.length_protein)
-        assert(seq.length_protein.is_a? Fixnum)
+        assert(seq.length_protein.is_a?(Integer))
       end
 
       it 'should initialize hsp tabular attributes' do
-        qseqid = 'sp|Q8GBW6|12S_PROFR'
-        sseqid = 'sp|A5GSN7|ACCD_SYNR3'
-        sacc   = 'A5GSN7'
-        slen   = '291'
         qstart = '49'
         qend   = '217'
         sstart = '65'
@@ -43,10 +39,10 @@ module GeneValidator
         qseq   = 'ERLNNLLDPHSFDEVG---------'
         sseq   = 'ERLRILLDPGSFIPVDGELSPTDPL'
 
-        hash = { 'qseqid' => qseqid,
-                 'sseqid' => sseqid,
-                 'sacc'   => sacc,
-                 'slen'   => slen,
+        hash = { 'qseqid' => 'sp|Q8GBW6|12S_PROFR',
+                 'sseqid' => 'sp|A5GSN7|ACCD_SYNR3',
+                 'sacc'   => 'A5GSN7',
+                 'slen'   => '291',
                  'qstart' => qstart,
                  'qend'   => qend,
                  'sstart' => sstart,
@@ -74,17 +70,17 @@ module GeneValidator
         assert_equal(nident, seq.identity.to_s)
         assert_equal(evalue, seq.hsp_evalue.to_s)
 
-        assert(seq.match_query_from.is_a? Fixnum)
-        assert(seq.match_query_to.is_a? Fixnum)
-        assert(seq.query_reading_frame.is_a? Fixnum)
-        assert(seq.hit_from.is_a? Fixnum)
-        assert(seq.hit_to.is_a? Fixnum)
-        assert(seq.query_alignment.is_a? String)
-        assert(seq.hit_alignment.is_a? String)
-        assert(seq.align_len.is_a? Fixnum)
-        assert(seq.pidentity.is_a? Float)
-        assert(seq.identity.is_a? Float)
-        assert(seq.hsp_evalue.is_a? Float)
+        assert(seq.match_query_from.is_a?(Integer))
+        assert(seq.match_query_to.is_a?(Integer))
+        assert(seq.query_reading_frame.is_a?(Integer))
+        assert(seq.hit_from.is_a?(Integer))
+        assert(seq.hit_to.is_a?(Integer))
+        assert(seq.query_alignment.is_a?(String))
+        assert(seq.hit_alignment.is_a?(String))
+        assert(seq.align_len.is_a?(Integer))
+        assert(seq.pidentity.is_a?(Float))
+        assert(seq.identity.is_a?(Float))
+        assert(seq.hsp_evalue.is_a?(Float))
       end
     end
   end

data/test/test_validation_open_reading_frame.rb

@@ -223,128 +223,128 @@ module GeneValidator
 
         validation = OpenReadingFrameValidation.new(prediction, nil)
         result =
-        { 1 => { frame: 1, orf_start: 1, orf_end: 20, coverage: 4,
-                 translated_length: 1003 },
-          2 => { frame: 1, orf_start: 62, orf_end: 143, coverage: 10,
-                 translated_length: 1003 },
-          3 => { frame: 1, orf_start: 165, orf_end: 187, coverage: 5,
-                 translated_length: 1003 },
-          4 => { frame: 1, orf_start: 244, orf_end: 277, coverage: 6,
-                 translated_length: 1003 },
-          5 => { frame: 1, orf_start: 383, orf_end: 393, coverage: 4,
-                 translated_length: 1003 },
-          6 => { frame: 1, orf_start: 415, orf_end: 443, coverage: 5,
-                 translated_length: 1003 },
-          7 => { frame: 1, orf_start: 477, orf_end: 510, coverage: 6,
-                 translated_length: 1003 },
-          8 => { frame: 1, orf_start: 640, orf_end: 706, coverage: 9,
-                 translated_length: 1003 },
-          9 => { frame: 1, orf_start: 728, orf_end: 757, coverage: 5,
-                 translated_length: 1003 },
-          10 => { frame: 1, orf_start: 786, orf_end: 813, coverage: 5,
-                  translated_length: 1003 },
-          11 => { frame: 2, orf_start: 24, orf_end: 41, coverage: 4,
-                  translated_length: 1003 },
-          12 => { frame: 2, orf_start: 115, orf_end: 129, coverage: 4,
-                  translated_length: 1003 },
-          13 => { frame: 2, orf_start: 151, orf_end: 161, coverage: 4,
-                  translated_length: 1003 },
-          14 => { frame: 2, orf_start: 290, orf_end: 305, coverage: 4,
-                  translated_length: 1003 },
-          15 => { frame: 2, orf_start: 327, orf_end: 339, coverage: 4,
-                  translated_length: 1003 },
-          16 => { frame: 2, orf_start: 391, orf_end: 417, coverage: 5,
-                  translated_length: 1003 },
-          17 => { frame: 2, orf_start: 439, orf_end: 479, coverage: 6,
-                  translated_length: 1003 },
-          18 => { frame: 2, orf_start: 501, orf_end: 557, coverage: 8,
-                  translated_length: 1003 },
-          19 => { frame: 2, orf_start: 660, orf_end: 678, coverage: 4,
-                  translated_length: 1003 },
-          20 => { frame: 2, orf_start: 711, orf_end: 739, coverage: 5,
-                  translated_length: 1003 },
-          21 => { frame: 2, orf_start: 800, orf_end: 809, coverage: 3,
-                  translated_length: 1003 },
-          22 => { frame: 2, orf_start: 832, orf_end: 841, coverage: 3,
-                  translated_length: 1003 },
-          23 => { frame: 2, orf_start: 943, orf_end: 957, coverage: 4,
-                  translated_length: 1003 },
-          24 => { frame: 2, orf_start: 979, orf_end: 1003, coverage: 5,
-                  translated_length: 1003 },
-          25 => { frame: 3, orf_start: 1, orf_end: 720, coverage: 73,
-                  translated_length: 1003 },
-          26 => { frame: 3, orf_start: 749, orf_end: 773, coverage: 5,
-                  translated_length: 1003 },
-          27 => { frame: 3, orf_start: 842, orf_end: 869, coverage: 5,
-                  translated_length: 1003 },
-          28 => { frame: 3, orf_start: 891, orf_end: 904, coverage: 4,
-                  translated_length: 1003 },
-          29 => { frame: 3, orf_start: 982, orf_end: 1003, coverage: 5,
-                  translated_length: 1003 },
-          30 => { frame: -1, orf_start: 69, orf_end: 81, coverage: 4,
-                  translated_length: 1003 },
-          31 => { frame: -1, orf_start: 106, orf_end: 115, coverage: 3,
-                  translated_length: 1003 },
-          32 => { frame: -1, orf_start: 178, orf_end: 219, coverage: 7,
-                  translated_length: 1003 },
-          33 => { frame: -1, orf_start: 299, orf_end: 391, coverage: 12,
-                  translated_length: 1003 },
-          34 => { frame: -1, orf_start: 436, orf_end: 447, coverage: 4,
-                  translated_length: 1003 },
-          35 => { frame: -1, orf_start: 469, orf_end: 540, coverage: 9,
-                  translated_length: 1003 },
-          36 => { frame: -1, orf_start: 562, orf_end: 575, coverage: 4,
-                  translated_length: 1003 },
-          37 => { frame: -1, orf_start: 597, orf_end: 617, coverage: 5,
-                  translated_length: 1003 },
-          38 => { frame: -1, orf_start: 639, orf_end: 655, coverage: 4,
-                  translated_length: 1003 },
-          39 => { frame: -1, orf_start: 728, orf_end: 818, coverage: 11,
-                  translated_length: 1003 },
-          40 => { frame: -1, orf_start: 863, orf_end: 885, coverage: 5,
-                  translated_length: 1003 },
-          41 => { frame: -1, orf_start: 950, orf_end: 963, coverage: 4,
-                  translated_length: 1003 },
-          42 => { frame: -1, orf_start: 985, orf_end: 1003, coverage: 4,
-                  translated_length: 1003 },
-          43 => { frame: -2, orf_start: 79, orf_end: 99, coverage: 5,
-                  translated_length: 1003 },
-          44 => { frame: -2, orf_start: 121, orf_end: 133, coverage: 4,
-                  translated_length: 1003 },
-          45 => { frame: -2, orf_start: 355, orf_end: 599, coverage: 26,
-                  translated_length: 1003 },
-          46 => { frame: -2, orf_start: 652, orf_end: 736, coverage: 11,
-                  translated_length: 1003 },
-          47 => { frame: -2, orf_start: 758, orf_end: 828, coverage: 9,
-                  translated_length: 1003 },
-          48 => { frame: -2, orf_start: 868, orf_end: 887, coverage: 4,
-                  translated_length: 1003 },
-          49 => { frame: -2, orf_start: 952, orf_end: 1003, coverage: 8,
-                  translated_length: 1003 },
-          50 => { frame: -3, orf_start: 1, orf_end: 18, coverage: 4,
-                  translated_length: 1003 },
-          51 => { frame: -3, orf_start: 90, orf_end: 100, coverage: 4,
-                  translated_length: 1003 },
-          52 => { frame: -3, orf_start: 208, orf_end: 220, coverage: 4,
-                  translated_length: 1003 },
-          53 => { frame: -3, orf_start: 279, orf_end: 347, coverage: 9,
-                  translated_length: 1003 },
-          54 => { frame: -3, orf_start: 369, orf_end: 382, coverage: 4,
-                  translated_length: 1003 },
-          55 => { frame: -3, orf_start: 461, orf_end: 511, coverage: 7,
-                  translated_length: 1003 },
-          56 => { frame: -3, orf_start: 533, orf_end: 542, coverage: 3,
-                  translated_length: 1003 },
-          57 => { frame: -3, orf_start: 635, orf_end: 708, coverage: 10,
-                  translated_length: 1003 },
-          58 => { frame: -3, orf_start: 768, orf_end: 801, coverage: 6,
-                  translated_length: 1003 },
-          59 => { frame: -3, orf_start: 830, orf_end: 875, coverage: 7,
-                  translated_length: 1003 },
-          60 => { frame: -3, orf_start: 933, orf_end: 945, coverage: 4,
-                  translated_length: 1003 },
-          61 => { frame: -3, orf_start: 967, orf_end: 980, coverage: 4,
-                  translated_length: 1003 } }
+          { 1 => { frame: 1, orf_start: 1, orf_end: 20, coverage: 4,
+                   translated_length: 1003 },
+            2 => { frame: 1, orf_start: 62, orf_end: 143, coverage: 10,
+                   translated_length: 1003 },
+            3 => { frame: 1, orf_start: 165, orf_end: 187, coverage: 5,
+                   translated_length: 1003 },
+            4 => { frame: 1, orf_start: 244, orf_end: 277, coverage: 6,
+                   translated_length: 1003 },
+            5 => { frame: 1, orf_start: 383, orf_end: 393, coverage: 4,
+                   translated_length: 1003 },
+            6 => { frame: 1, orf_start: 415, orf_end: 443, coverage: 5,
+                   translated_length: 1003 },
+            7 => { frame: 1, orf_start: 477, orf_end: 510, coverage: 6,
+                   translated_length: 1003 },
+            8 => { frame: 1, orf_start: 640, orf_end: 706, coverage: 9,
+                   translated_length: 1003 },
+            9 => { frame: 1, orf_start: 728, orf_end: 757, coverage: 5,
+                   translated_length: 1003 },
+            10 => { frame: 1, orf_start: 786, orf_end: 813, coverage: 5,
+                    translated_length: 1003 },
+            11 => { frame: 2, orf_start: 24, orf_end: 41, coverage: 4,
+                    translated_length: 1003 },
+            12 => { frame: 2, orf_start: 115, orf_end: 129, coverage: 4,
+                    translated_length: 1003 },
+            13 => { frame: 2, orf_start: 151, orf_end: 161, coverage: 4,
+                    translated_length: 1003 },
+            14 => { frame: 2, orf_start: 290, orf_end: 305, coverage: 4,
+                    translated_length: 1003 },
+            15 => { frame: 2, orf_start: 327, orf_end: 339, coverage: 4,
+                    translated_length: 1003 },
+            16 => { frame: 2, orf_start: 391, orf_end: 417, coverage: 5,
+                    translated_length: 1003 },
+            17 => { frame: 2, orf_start: 439, orf_end: 479, coverage: 6,
+                    translated_length: 1003 },
+            18 => { frame: 2, orf_start: 501, orf_end: 557, coverage: 8,
+                    translated_length: 1003 },
+            19 => { frame: 2, orf_start: 660, orf_end: 678, coverage: 4,
+                    translated_length: 1003 },
+            20 => { frame: 2, orf_start: 711, orf_end: 739, coverage: 5,
+                    translated_length: 1003 },
+            21 => { frame: 2, orf_start: 800, orf_end: 809, coverage: 3,
+                    translated_length: 1003 },
+            22 => { frame: 2, orf_start: 832, orf_end: 841, coverage: 3,
+                    translated_length: 1003 },
+            23 => { frame: 2, orf_start: 943, orf_end: 957, coverage: 4,
+                    translated_length: 1003 },
+            24 => { frame: 2, orf_start: 979, orf_end: 1003, coverage: 5,
+                    translated_length: 1003 },
+            25 => { frame: 3, orf_start: 1, orf_end: 720, coverage: 73,
+                    translated_length: 1003 },
+            26 => { frame: 3, orf_start: 749, orf_end: 773, coverage: 5,
+                    translated_length: 1003 },
+            27 => { frame: 3, orf_start: 842, orf_end: 869, coverage: 5,
+                    translated_length: 1003 },
+            28 => { frame: 3, orf_start: 891, orf_end: 904, coverage: 4,
+                    translated_length: 1003 },
+            29 => { frame: 3, orf_start: 982, orf_end: 1003, coverage: 5,
+                    translated_length: 1003 },
+            30 => { frame: -1, orf_start: 69, orf_end: 81, coverage: 4,
+                    translated_length: 1003 },
+            31 => { frame: -1, orf_start: 106, orf_end: 115, coverage: 3,
+                    translated_length: 1003 },
+            32 => { frame: -1, orf_start: 178, orf_end: 219, coverage: 7,
+                    translated_length: 1003 },
+            33 => { frame: -1, orf_start: 299, orf_end: 391, coverage: 12,
+                    translated_length: 1003 },
+            34 => { frame: -1, orf_start: 436, orf_end: 447, coverage: 4,
+                    translated_length: 1003 },
+            35 => { frame: -1, orf_start: 469, orf_end: 540, coverage: 9,
+                    translated_length: 1003 },
+            36 => { frame: -1, orf_start: 562, orf_end: 575, coverage: 4,
+                    translated_length: 1003 },
+            37 => { frame: -1, orf_start: 597, orf_end: 617, coverage: 5,
+                    translated_length: 1003 },
+            38 => { frame: -1, orf_start: 639, orf_end: 655, coverage: 4,
+                    translated_length: 1003 },
+            39 => { frame: -1, orf_start: 728, orf_end: 818, coverage: 11,
+                    translated_length: 1003 },
+            40 => { frame: -1, orf_start: 863, orf_end: 885, coverage: 5,
+                    translated_length: 1003 },
+            41 => { frame: -1, orf_start: 950, orf_end: 963, coverage: 4,
+                    translated_length: 1003 },
+            42 => { frame: -1, orf_start: 985, orf_end: 1003, coverage: 4,
+                    translated_length: 1003 },
+            43 => { frame: -2, orf_start: 79, orf_end: 99, coverage: 5,
+                    translated_length: 1003 },
+            44 => { frame: -2, orf_start: 121, orf_end: 133, coverage: 4,
+                    translated_length: 1003 },
+            45 => { frame: -2, orf_start: 355, orf_end: 599, coverage: 26,
+                    translated_length: 1003 },
+            46 => { frame: -2, orf_start: 652, orf_end: 736, coverage: 11,
+                    translated_length: 1003 },
+            47 => { frame: -2, orf_start: 758, orf_end: 828, coverage: 9,
+                    translated_length: 1003 },
+            48 => { frame: -2, orf_start: 868, orf_end: 887, coverage: 4,
+                    translated_length: 1003 },
+            49 => { frame: -2, orf_start: 952, orf_end: 1003, coverage: 8,
+                    translated_length: 1003 },
+            50 => { frame: -3, orf_start: 1, orf_end: 18, coverage: 4,
+                    translated_length: 1003 },
+            51 => { frame: -3, orf_start: 90, orf_end: 100, coverage: 4,
+                    translated_length: 1003 },
+            52 => { frame: -3, orf_start: 208, orf_end: 220, coverage: 4,
+                    translated_length: 1003 },
+            53 => { frame: -3, orf_start: 279, orf_end: 347, coverage: 9,
+                    translated_length: 1003 },
+            54 => { frame: -3, orf_start: 369, orf_end: 382, coverage: 4,
+                    translated_length: 1003 },
+            55 => { frame: -3, orf_start: 461, orf_end: 511, coverage: 7,
+                    translated_length: 1003 },
+            56 => { frame: -3, orf_start: 533, orf_end: 542, coverage: 3,
+                    translated_length: 1003 },
+            57 => { frame: -3, orf_start: 635, orf_end: 708, coverage: 10,
+                    translated_length: 1003 },
+            58 => { frame: -3, orf_start: 768, orf_end: 801, coverage: 6,
+                    translated_length: 1003 },
+            59 => { frame: -3, orf_start: 830, orf_end: 875, coverage: 7,
+                    translated_length: 1003 },
+            60 => { frame: -3, orf_start: 933, orf_end: 945, coverage: 4,
+                    translated_length: 1003 },
+            61 => { frame: -3, orf_start: 967, orf_end: 980, coverage: 4,
+                    translated_length: 1003 } }
         assert_equal(result, validation.get_orfs)
       end
     end