bio 2.0.5 → 2.0.6

data/lib/bio/appl/clustalw/report.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/appl/clustalw/report.rb - CLUSTAL W format data (*.aln) class
 #
@@ -138,7 +139,7 @@ module Bio
         a = @raw.split(/\r?\n\r?\n/)
         @header = a.shift.to_s
         xalign = Bio::Alignment.new
-        @match_line = ''
+        @match_line = String.new
         if a.size > 0 then
           a[0].gsub!(/\A(\r?\n)+/, '')
           a.collect! { |x| x.split(/\r?\n/) }
@@ -151,7 +152,7 @@ module Bio
             @match_line << x.pop.to_s[@tagsize..-1]
           end
           a[0].each do |y|
-            xalign.store(y[0, @tagsize].sub(/\s+\z/, ''), '')
+            xalign.store(y[0, @tagsize].sub(/\s+\z/, ''), String.new)
           end
           a.each do |x|
             x.each do |y|

data/lib/bio/appl/iprscan/report.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/appl/iprscan/report.rb - a class for iprscan output.
 #
@@ -69,7 +70,7 @@ module Bio
       #  end
       #
       def self.parse_raw(io)
-        entry = ''
+        entry = String.new
         while line = io.gets
           if entry != '' and entry.split("\t").first == line.split("\t").first
             entry << line

data/lib/bio/appl/meme/mast.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/appl/meme/mast.rb - Wrapper for running MAST program
 #
@@ -113,7 +114,7 @@ module Meme
 
     def config(options)
       @options = DEFAULT_OPTIONS.merge(options)
-      mfile, opts, flags = "", "", ""
+      mfile, opts, flags = String.new, String.new, String.new
       @options.each_pair do |opt, val|
         if val.nil? or val == false
           next

data/lib/bio/appl/paml/common.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/appl/paml/common.rb - Basic wrapper class common to PAML programs
 #
@@ -270,7 +271,7 @@ module PAML
     def dump_parameters
       keyorder = DEFAULT_PARAMETERS_ORDER
       keys = parameters.keys
-      str = ''
+      str = String.new
       keys.sort do |x, y|
         (keyorder.index(x) || (keyorder.size + keys.index(x))) <=>
           (keyorder.index(y) || (keyorder.size + keys.index(y)))

data/lib/bio/db/embl/common.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/db/embl.rb - Common methods for EMBL style database classes
 #
@@ -243,8 +244,10 @@ module Common
     unless @data['R']
       ary = Array.new
       get('R').split(/\nRN   /).each do |str|
-        raw = {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '', 
-               'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}
+        raw = {'RN' => String.new, 'RC' => String.new,
+               'RP' => String.new, 'RX' => String.new,
+               'RA' => String.new, 'RT' => String.new,
+               'RL' => String.new, 'RG' => String.new}
         str = 'RN   ' + str unless /^RN   / =~ str
         str.split("\n").each do |line|
           if /^(R[NPXARLCTG])   (.+)/ =~ line

data/lib/bio/db/fastq.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/db/fastq.rb - FASTQ format parser class
 #
@@ -349,7 +350,7 @@ class Fastq
       return self
     end
     if defined? @definition2 then
-      @quality_string ||= ''
+      @quality_string ||= String.new
       if line[0, 1] == "@" and
           @quality_string.size >= @sequence_string.size then
         return false
@@ -358,7 +359,7 @@ class Fastq
         return self
       end
     else
-      @sequence_string ||= ''
+      @sequence_string ||= String.new
       if line[0, 1] == '+' then
         @definition2 = line[1..-1]
       else

data/lib/bio/db/gff.rb

@@ -1,4 +1,5 @@
 # coding: US-ASCII
+# frozen_string_literal: true
 #
 # = bio/db/gff.rb - GFF format class
 #
@@ -137,13 +138,13 @@ module Bio
 
         sc = StringScanner.new(attributes)
         attrs = []
-        token = ''
+        token = String.new
         while !sc.eos?
           if sc.scan(/[^\\\;\"]+/) then
             token.concat sc.matched
           elsif sc.scan(/\;/) then
             attrs.push token unless token.empty?
-            token = ''
+            token = String.new
           elsif sc.scan(/\"/) then
             origtext = sc.matched
             while !sc.eos?
@@ -690,22 +691,22 @@ module Bio
           sc = StringScanner.new(str)
           attr_pairs = []
           tokens = []
-          cur_token = ''
+          cur_token = String.new
           while !sc.eos?
             if sc.scan(/[^\\\;\"\s]+/) then
               cur_token.concat sc.matched
             elsif sc.scan(/\s+/) then
               tokens.push cur_token unless cur_token.empty?
-              cur_token = ''
+              cur_token = String.new
             elsif sc.scan(/\;/) then
               tokens.push cur_token unless cur_token.empty?
-              cur_token = ''
+              cur_token = String.new
               attr_pairs.push tokens
               tokens = []
             elsif sc.scan(/\"/) then
               tokens.push cur_token unless cur_token.empty?
-              cur_token = ''
-              freetext = ''
+              cur_token = String.new
+              freetext = String.new
               while !sc.eos?
                 if sc.scan(/[^\\\"]+/) then
                   freetext.concat sc.matched
@@ -999,10 +1000,15 @@ module Bio
           str.empty? ? '.' : str
         end
 
-        if URI.const_defined?(:Parser) then
+        if URI.const_defined?(:RFC2396_Parser) then
+          # (private) URI::Parser object for escape/unescape GFF3 columns
+          URI_PARSER = URI::RFC2396_Parser.new
+        elsif URI.const_defined?(:Parser) then
           # (private) URI::Parser object for escape/unescape GFF3 columns
           URI_PARSER = URI::Parser.new
+        end
 
+        if const_defined?(:URI_PARSER) then
           # (private) the same as URI::Parser#escape(str, unsafe)
           def _escape(str, unsafe)
             URI_PARSER.escape(str, unsafe)

data/lib/bio/db/newick.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/db/newick.rb - Newick Standard phylogenetic tree parser / formatter
 #
@@ -150,7 +151,7 @@ module Bio
             # Molphy-style boostrap values
             # let molphy mode if nothing determined
             @options[:original_format] ||= :molphy
-            bstr = ''
+            bstr = String.new
             while t = btokens.shift and t != :']'
               bstr.concat t.to_s
             end
@@ -162,7 +163,7 @@ module Bio
       if !btokens and !leaf_tokens.empty? then
         # syntax error?
       end
-      node.name ||= '' # compatibility for older BioRuby
+      node.name ||= String.new # compatibility for older BioRuby
 
       # returns true
       true
@@ -242,7 +243,7 @@ module Bio
 
         elsif ss.scan(/\'/) then
           # quoted_label
-          t = ''
+          t = String.new
           while true
             if ss.scan(/([^\']*)\'/) then
               t.concat ss[1]
@@ -317,7 +318,7 @@ module Bio
           if previous_token == :',' or previous_token == :'(' then
             # there is a leaf whose name is empty.
             ary.unshift(token)
-            ary.unshift('')
+            ary.unshift(String.new)
             token = nil
           end
         when :'('
@@ -330,7 +331,7 @@ module Bio
           if previous_token == :',' or previous_token == :'(' then
             # there is a leaf whose name is empty.
             ary.unshift(token)
-            ary.unshift('')
+            ary.unshift(String.new)
             token = nil
           else
             edge = Edge.new

data/lib/bio/db/pdb/chain.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/db/pdb/chain.rb - chain class for PDB
 #
@@ -180,7 +181,7 @@ module Bio
       # gets an amino acid sequence of this chain from ATOM records
       def aaseq
         unless defined? @aaseq
-          string = ""
+          string = String.new
           last_residue_num = nil
           @residues.each do |residue|
             if last_residue_num and 

data/lib/bio/db/pdb/pdb.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/db/pdb/pdb.rb - PDB database class for PDB file format
 #
@@ -1645,7 +1646,7 @@ module Bio
     # Returns a string of Bio::PDB::Models. This propogates down the heirarchy
     # till you get to Bio::PDB::Record::ATOM which are outputed in PDB format
     def to_s
-      string = ""
+      string = String.new
       @models.each{ |model| string << model.to_s }
       string << "END\n"
       return string

data/lib/bio/db/prosite.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/db/prosite.rb - PROSITE database class
 #
@@ -465,6 +466,7 @@ class PROSITE < EMBLDB
   # translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val
   #
   def self.pa2re(pattern)
+    pattern = pattern.dup
     pattern.gsub!(/\s/, '')	# remove white spaces
     pattern.sub!(/\.$/, '')	# (1) remove trailing '.'
     pattern.sub!(/^</, '^')	# (2) restricted to the N-terminal : `<'

data/lib/bio/db.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/db.rb - common API for database parsers
 #
@@ -192,19 +193,19 @@ class DB
   # Returns a String with successive white spaces are replaced by one
   # space and stripeed.
   def truncate(str)
-    str ||= ""
+    str ||= String.new
     return str.gsub(/\s+/, ' ').strip
   end
 
   # Returns a tag name of the field as a String.
   def tag_get(str)
-    str ||= ""
+    str ||= String.new
     return str[0,@tagsize].strip
   end
 
   # Returns a String of the field without a tag name.
   def tag_cut(str)
-    str ||= ""
+    str ||= String.new
     str[0,@tagsize] = ''
     return str
   end
@@ -313,7 +314,7 @@ class EMBLDB < DB
 
   # Returns the contents of the entry as a Hash.
   def entry2hash(entry)
-    hash = Hash.new { |h,k| h[k] = '' }
+    hash = Hash.new { |h,k| h[k] = String.new }
     entry.each_line do |line|
       tag = tag_get(line)
       next if tag == 'XX'

data/lib/bio/io/flatfile/buffer.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/io/flatfile/buffer.rb - Input stream buffer for FlatFile
 #
@@ -24,7 +25,7 @@ module Bio
         @io = io
         @path = path
         # initialize prefetch buffer
-        @buffer = ''
+        @buffer = String.new
       end
 
       # Creates a new input stream wrapper from the given IO object.

data/lib/bio/io/flatfile/splitter.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/io/flatfile/splitter.rb - input data splitter for FlatFile
 #
@@ -157,7 +158,7 @@ module Bio
         # Otherwise, returns nil.
         def skip_leader
           if @header then
-            data = ''
+            data = String.new
             while s = stream.gets(@header)
               data << s
               if data.split(/[\r\n]+/)[-1] == @header then

data/lib/bio/pathway.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/pathway.rb - Binary relations and Graph algorithms
 #
@@ -307,7 +308,7 @@ class Pathway
     end
     # end workaround removing depencency to order of Hash#each
 
-    list = ""
+    list = String.new
     enum.each do |from, hash|
       list << "#{from} => "
       # begin workaround removing depencency to order of Hash#each

data/lib/bio/sequence/common.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/sequence/common.rb - common methods for biological sequence
 #
@@ -286,7 +287,7 @@ module Common
     unless position.is_a?(Locations) then
       position = Locations.new(position)
     end
-    s = ''
+    s = String.new
     position.each do |location|
       if location.sequence
         s << location.sequence

data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # bio/util/restriction_enzyme/range/sequence_range/fragment.rb - 
 #
@@ -27,8 +28,8 @@ class Fragment
 
   def for_display(p_str=nil, c_str=nil)
     df = DisplayFragment.new
-    df.primary = ''
-    df.complement = ''
+    df.primary = String.new
+    df.complement = String.new
 
     both_bins = @primary_bin + @complement_bin
     both_bins.each do |item|

data/lib/bio/util/sirna.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = bio/util/sirna.rb - Class for designing small inhibitory RNAs
 #
@@ -202,7 +203,7 @@ module Bio
 
       # human readable report
       def report
-        report =  "### siRNA\n"
+        report =  "### siRNA\n".dup
         report << 'Start: ' + @start.to_s + "\n"
         report << 'Stop:  ' + @stop.to_s  + "\n"
         report << 'Rule:  ' + @rule.to_s  + "\n"
@@ -280,7 +281,7 @@ module Bio
       def report
         # raise NomethodError for compatibility
         raise NoMethodError if !defined?(@top_strand) || !@top_strand
-        report = "### shRNA\n"
+        report = "### shRNA\n".dup
         report << "Top strand shRNA (#{@top_strand.length} nt):\n"
         report << "  5'-#{@top_strand.upcase}-3'\n"
         report << "Bottom strand shRNA (#{@bottom_strand.length} nt):\n"

data/lib/bio/version.rb

@@ -10,7 +10,7 @@
 module Bio
 
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [2, 0, 5].extend(Comparable).freeze
+  BIORUBY_VERSION = [2, 0, 6].extend(Comparable).freeze
 
   # Extra version specifier (String or nil).
   # Existance of the value indicates development version.

data/test/network/bio/db/kegg/test_genes_hsa7422.rb

@@ -38,7 +38,6 @@ module Bio
                   "H01457  Diabetic retinopathy",
                   "H01459  Diabetic neuropathy",
                   "H01529  Avascular necrosis of femoral head",
-                  "H01709  Glucocorticoid-induced osteonecrosis",
                   "H02559  Microvascular complications of diabetes"]
 
       assert_equal(expected, @obj.diseases_as_strings)
@@ -49,7 +48,6 @@ module Bio
                   "H01457"=>"Diabetic retinopathy",
                   "H01459"=>"Diabetic neuropathy",
                   "H01529"=>"Avascular necrosis of femoral head",
-                  "H01709"=>"Glucocorticoid-induced osteonecrosis",
                   "H02559"=>"Microvascular complications of diabetes"}
       assert_equal(expected, @obj.diseases_as_hash)
     end
@@ -64,6 +62,7 @@ module Bio
                   "Dilpacimab: D11642",
                   "Emvododstat: D11890",
                   "Faricimab: D11516<JP/US>",
+                  "Ivonescimab: D12808",
                   "Navicixizumab: D11126",
                   "Pegaptanib: D05386",
                   "Ranibizumab: D05697<JP/US>",
@@ -74,29 +73,28 @@ module Bio
     end
 
     def test_networks_as_strings
-      expected = ["nt06124  Chemokine signaling (viruses)",
-                  "nt06164  Kaposi sarcoma-associated herpesvirus (KSHV)",
-                  "nt06219  JAK-STAT signaling",
-                  "nt06224  CXCR signaling",
-                  "nt06225  HIF-1 signaling",
-                  "nt06227  Nuclear receptor signaling",
+      expected = ["nt06219  JAK-STAT signaling (cancer)",
+                  "nt06225  HIF-1 signaling (cancer)",
+                  "nt06227  Nuclear receptor signaling (cancer)",
                   "nt06262  Pancreatic cancer",
                   "nt06264  Renal cell carcinoma",
                   "nt06360  Cushing syndrome",
                   "nt06526  MAPK signaling",
                   "nt06528  Calcium signaling",
                   "nt06530  PI3K signaling",
+                  "nt06542  HIF signaling",
                   "N00079  HIF-1 signaling pathway",
                   "N00080  Loss of VHL to HIF-1 signaling pathway",
                   "N00081  Mutation-inactivated VHL to HIF-1 signaling pathway",
                   "N00095  ERBB2-overexpression to EGF-Jak-STAT signaling pathway",
-                  "N00157  KSHV vGPCR to GNB/G-ERK signaling pathway",
                   "N00317  AhR signaling pathway",
                   "N01412  Metals to HTF-1 signaling pathway",
                   "N01592  GF-RTK-RAS-ERK signaling pathway",
                   "N01641  RTK-PLCG-ITPR signaling pathway",
                   "N01656  GF-RTK-PI3K signaling pathway",
-                  "N01658  GF-RTK-RAS-PI3K signaling pathway"]
+                  "N01658  GF-RTK-RAS-PI3K signaling pathway",
+                  "N01870  HIF-2A signaling pathway",
+                  "N01873  VHL mutation to HIF-2 signaling pathway"]
       assert_equal(expected, @obj.networks_as_strings)
     end
 

data/test/unit/bio/appl/iprscan/test_report.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # test/unit/bio/appl/iprscan/test_report.rb - Unit test for Bio::InterProScan::Report
 #
@@ -211,14 +212,14 @@ END
   class TestIprscanRawReport < Test::Unit::TestCase
     def setup
       test_raw = Bio::TestIprscanData.raw_format
-      entry = ''
+      entry = String.new
       @obj = []
       while line = test_raw.gets
         if entry.split("\t").first == line.split("\t").first
           entry << line
         elsif entry != '' and entry.split("\t").first != line.split("\t").first
           @obj << Bio::Iprscan::Report.parse_raw_entry(entry)
-          entry = ''
+          entry = String.new
         else
           entry << line
         end

data/test/unit/bio/io/flatfile/test_splitter.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = test/unit/bio/io/flatfile/test_splitter.rb - unit test for Bio::FlatFile::Splitter
 #
@@ -37,7 +38,7 @@ module Bio::TestFlatFileSplitter
     end
   end #class TestDataClass
 
-  TestData01 = <<__END_OF_TESTDATA__
+  testdata01 = <<__END_OF_TESTDATA__
 
         # This is test
 
@@ -54,10 +55,12 @@ tttttttttttttttttttttttt
 >test3
 atatatatatatatatatatatat
 __END_OF_TESTDATA__
-  TestData01.chomp!
-  # workaround for Windows
-  TestData01.gsub!(/\r\n/, "\n")
 
+  testdata01 = testdata01.chomp
+  # workaround for Windows
+  testdata01.gsub!(/\r\n/, "\n")
+  TestData01 = testdata01
+  
   class TestTemplate < Test::Unit::TestCase
     def setup
       @stream = Bio::FlatFile::BufferedInputStream.new(StringIO.new(TestData01), 'TestData01')

data/test/unit/bio/sequence/test_common.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # test/unit/bio/sequence/test_common.rb - Unit test for Bio::Sequencce::Common
 #
@@ -155,7 +156,7 @@ module Bio; module TestSequenceCommon
 
       rseqs = (0..2).collect do |i|
         newcomposition = Hash.new(0)
-        newseq = ''
+        newseq = String.new
         ret = @seq.randomize do |c|
           assert_kind_of(TSequence, c)
           newcomposition[c] += 1
@@ -215,7 +216,7 @@ module Bio; module TestSequenceCommon
 
       rseqs = (0..2).collect do |i|
         newcomposition = Hash.new(0)
-        newseq = ''
+        newseq = String.new
         ret = @seq.randomize(hash) do |c|
           #assert_kind_of(TSequence, c)
           assert_kind_of(String, c)

data/test/unit/bio/test_alignment.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # test/unit/bio/test_alignment.rb - Unit test for Bio::Alignment
 #
@@ -436,29 +437,29 @@ module Bio
 
     def test_convert_match
       a = A[
-        'aaaa',
-        'accc',
-        'acac',
-        'actc'
+        'aaaa'.dup,
+        'accc'.dup,
+        'acac'.dup,
+        'actc'.dup
       ]
       a.convert_match
       assert_equal(A[ 'aaaa', '.ccc', '.c.c', '.ctc' ], a)
     end
 
     def test_convert_unmatch
-      a = A[ 'aaaa', '.ccc', '.c.c', '.ctc' ]
+      a = A[ 'aaaa'.dup, '.ccc'.dup, '.c.c'.dup, '.ctc'.dup ]
       a.convert_unmatch
       assert_equal(A[ 'aaaa', 'accc', 'acac', 'actc' ], a)
     end
 
     def test_alignment_normalize!
-      a = A[ 'a', 'atg', 'atgc', '' ]
+      a = A[ 'a'.dup, 'atg'.dup, 'atgc'.dup, ''.dup ]
       a.alignment_normalize!
       assert_equal(A[ 'a---', 'atg-', 'atgc', '----'], a)
     end
 
     def test_alignment_rstrip!
-      a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
+      a = A[ '--aaa--'.dup, '--t-t--'.dup, '---g---'.dup, '--t'.dup ]
       assert(a.alignment_rstrip!)
       assert_equal(A[ '--aaa', '--t-t', '---g-', '--t' ], a)
     end
@@ -470,7 +471,7 @@ module Bio
     end
 
     def test_alignment_lstrip!
-      a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
+      a = A[ '--aaa--'.dup, '--t-t--'.dup, '---g---'.dup, '--t'.dup ]
       assert(a.alignment_lstrip!)
       assert_equal(A[ 'aaa--', 't-t--', '-g---', 't' ], a)
     end
@@ -482,7 +483,7 @@ module Bio
     end
 
     def test_alignment_strip!
-      a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
+      a = A[ '--aaa--'.dup, '--t-t--'.dup, '---g---'.dup, '--t'.dup ]
       assert(a.alignment_strip!)
       assert_equal(A[ 'aaa', 't-t', '-g-', 't' ], a)
     end
@@ -494,7 +495,7 @@ module Bio
     end
 
     def test_remove_all_gaps!
-      a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
+      a = A[ '--aaa--'.dup, '--t-t--'.dup, '---g---'.dup, '--t'.dup ]
       assert(a.remove_all_gaps!)
       assert_equal(A[ 'aaa', 'tt', 'g', 't' ], a)
     end
@@ -525,7 +526,7 @@ module Bio
     end
 
     def test_alignment_concat
-      a = A[ 'aaa',  'c', 'gg', 't' ]
+      a = A[ 'aaa'.dup,  'c'.dup, 'gg'.dup, 't'.dup ]
       a.alignment_concat(A[ 'ttt', 'gg', 'aa', 'cc', 'aa' ])
       assert_equal(A[ 'aaattt', 'cgg', 'ggaa', 'tcc' ], a)
       a.alignment_concat([ 'c', 't' ])
@@ -702,7 +703,7 @@ module Bio
     end
 
     def test_add_seq_using_seq_with_seq_method
-      seq = "agtc"
+      seq = "agtc".dup
       class <<seq
         def seq
           Sequence::NA.new(self)
@@ -716,7 +717,7 @@ module Bio
     end
 
     def test_add_seq_using_seq_with_naseq_method
-      seq = "agtc"
+      seq = "agtc".dup
       class <<seq
 	def naseq
           Sequence::NA.new(self)
@@ -730,7 +731,7 @@ module Bio
     end
 
     def test_add_seq_using_seq_with_aaseq_method
-      seq = "AVGR"
+      seq = "AVGR".dup
       class <<seq
 	def aaseq
           Sequence::AA.new(self)
@@ -744,7 +745,7 @@ module Bio
     end
 
     def test_add_seq_using_seq_with_definition_method
-      seq = "atgc"
+      seq = "atgc".dup
       class <<seq
 	def definition
           "this is the key"
@@ -757,7 +758,7 @@ module Bio
     end
 
     def test_add_seq_using_seq_with_entry_id_method
-      seq = "atgc"
+      seq = "atgc".dup
       class <<seq
 	def entry_id
           271828