bio 1.5.2 → 1.6.0.pre.20181210

data/gemfiles/Gemfile.travis-jruby1.8

@@ -1,8 +1,6 @@
 source "https://rubygems.org"
 
-gem "rake"
-gem "rdoc"
-
-## disabled because of build error on Travis
-#gem "libxml-ruby"
+gem "rake", "~>10.4"
+# rdoc 4.3.0 requires Ruby >= 1.9.3
+gem "rdoc", "~>4.2.0"
 

data/gemfiles/Gemfile.travis-jruby1.9

@@ -3,6 +3,3 @@ source "https://rubygems.org"
 gem "rake"
 gem "rdoc"
 
-## disabled because of build error on Travis
-#gem "libxml-ruby"
-

data/gemfiles/Gemfile.travis-rbx

@@ -4,7 +4,6 @@ gem "rake"
 gem "rdoc"
 
 gem "xmlparser"
-gem "libxml-ruby"
 
 platforms :rbx do
   gem 'racc'

data/gemfiles/Gemfile.travis-ruby1.8

@@ -1,8 +1,8 @@
 source "https://rubygems.org"
 
-gem "rake"
-gem "rdoc"
+gem "rake", "~>10.4"
+# rdoc 4.3.0 requires Ruby >= 1.9.3
+gem "rdoc", "~>4.2.0"
 
-gem "xmlparser"
-gem "libxml-ruby"
+gem "xmlparser", "~>0.7.2"
 

data/gemfiles/Gemfile.travis-ruby1.9

@@ -4,5 +4,4 @@ gem "rake"
 gem "rdoc"
 
 gem "xmlparser"
-gem "libxml-ruby"
 

data/gemfiles/prepare-gemspec.rb

@@ -15,6 +15,10 @@ else
   exit(0)
 end
 
+# update bundler to avoid Bundler's bug fixed in the latest version
+$stderr.puts "gem update bundler"
+system("gem update bundler")
+
 $stderr.puts "cd #{gem_dir}"
 Dir.chdir(gem_dir)
 

data/lib/bio.rb

@@ -142,20 +142,10 @@ module Bio
   autoload :Newick,         'bio/db/newick'
   autoload :Nexus,          'bio/db/nexus'
 
-  autoload :PhyloXML,       'bio/db/phyloxml/phyloxml_elements'
-  # Bio::Taxonomy will be moved to other file
-  autoload :Taxonomy,       'bio/db/phyloxml/phyloxml_elements'
-  ## below are described in bio/db/phyloxml/phyloxml_elements.rb
-  #module PhyloXML
-  #  autoload :Parser,       'bio/db/phyloxml/phyloxml_parser'
-  #  autoload :Writer,       'bio/db/phyloxml/phyloxml_writer'
-  #end
-
   ### IO interface modules
 
   autoload :Registry,       'bio/io/registry'
   autoload :Fetch,          'bio/io/fetch'
-  autoload :SQL,            'bio/io/sql'
   autoload :FlatFile,       'bio/io/flatfile'
   autoload :FlatFileIndex,  'bio/io/flatfile/index' # chage to FlatFile::Index ?
   ## below are described in bio/io/flatfile/index.rb

data/lib/bio/data/codontable.rb

@@ -51,10 +51,15 @@ class CodonTable
   def self.[](i)
     hash = TABLES[i]
     raise "ERROR: Unknown codon table No.#{i}" unless hash
+    if AMBIGUITY_CODON_TABLES != nil
+      atable = AMBIGUITY_CODON_TABLES[i]
+    else
+      atable = nil
+    end
     definition = DEFINITIONS[i]
     start = STARTS[i]
     stop = STOPS[i]
-    self.new(hash, definition, start, stop)
+    self.new(hash, definition, start, stop, atable)
   end
 
   # Similar to Bio::CodonTable[num] but returns a copied codon table.
@@ -70,8 +75,13 @@ class CodonTable
   #
   # Two Arrays 'start' and 'stop' can be specified which contains a list of
   # start and stop codons used by 'start_codon?' and 'stop_codon?' methods.
-  def initialize(hash, definition = nil, start = [], stop = [])
+  def initialize(hash, definition = nil, start = [], stop = [], atable = nil)
     @table = hash
+    if atable == nil
+      @atable = gen_ambiguity_map(hash)
+    else
+      @atable = atable
+    end
     @definition = definition
     @start = start
     @stop = stop.empty? ? generate_stop : stop
@@ -87,10 +97,55 @@ class CodonTable
   # codons respectively.
   attr_accessor :start, :stop
 
+  # Compute possible ambiguity nucleotide code to amino acid conversion
+  # the codon is defined when all decomposed codon translates to the
+  # same amino acid / stop codon
+  def gen_ambiguity_map(hash)
+    nucleotide_sets={
+      'a'       => ['a'],
+      't'       => ['t'],
+      'g'       => ['g'],
+      'c'       => ['c'],
+
+      'y'       => ['t','c'],
+      'r'       => ['a','g'],
+      'w'       => ['a','t'],
+      's'       => ['g','c'],
+      'k'       => ['t','g'],
+      'm'       => ['a','c'],
+
+      'b'       => ['t','g','c'],
+      'd'       => ['a','t','g'],
+      'h'       => ['a','t','c'],
+      'v'       => ['a','g','c'],
+
+      'n'       => ['a','t','g','c'],
+    }
+    atable=Hash.new
+    nucleotide_sets.keys.each{|n1|
+      nucleotide_sets.keys.each{|n2|
+        nucleotide_sets.keys.each{|n3|
+          a = Array.new
+          nucleotide_sets[n1].each{|c1|
+            nucleotide_sets[n2].each{|c2|
+              nucleotide_sets[n3].each{|c3|
+                a << hash["#{c1}#{c2}#{c3}"]
+              }
+            }
+          }
+          a.uniq!
+          atable["#{n1}#{n2}#{n3}"] = a.to_a[0] if a.size== 1
+        }
+      }
+    }
+    atable
+  end
+
   # Translate a codon into a relevant amino acid.  This method is used for
   # translating a DNA sequence into amino acid sequence.
   def [](codon)
-    @table[codon]
+    @atable=gen_ambiguity_map(@table) if @atable == nil
+    @atable[codon]
   end
 
   # Modify the codon table.  Use with caution as it may break hard coded
@@ -107,6 +162,7 @@ class CodonTable
   #
   def []=(codon, aa)
     @table[codon] = aa
+    @atable = nil
   end
 
   # Iterates on codon table hash.
@@ -625,3 +681,43 @@ end # CodonTable
 
 end # module Bio
 
+module Bio
+class CodonTable
+AMBIGUITY_CODON_TABLES = {
+1 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+2 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"M", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atr"=>"M", "aga"=>"*", "agt"=>"S", "agg"=>"*", "agc"=>"S", "agy"=>"S", "agr"=>"*", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L"}, 
+3 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"M", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atr"=>"M", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"T", "ctt"=>"T", "ctg"=>"T", "ctc"=>"T", "cty"=>"T", "ctr"=>"T", "ctw"=>"T", "cts"=>"T", "ctk"=>"T", "ctm"=>"T", "ctb"=>"T", "ctd"=>"T", "cth"=>"T", "ctv"=>"T", "ctn"=>"T", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+4 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+5 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"M", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atr"=>"M", "aga"=>"S", "agt"=>"S", "agg"=>"S", "agc"=>"S", "agy"=>"S", "agr"=>"S", "agw"=>"S", "ags"=>"S", "agk"=>"S", "agm"=>"S", "agb"=>"S", "agd"=>"S", "agh"=>"S", "agv"=>"S", "agn"=>"S", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L"}, 
+6 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"Q", "tat"=>"Y", "tag"=>"Q", "tac"=>"Y", "tay"=>"Y", "tar"=>"Q", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yaa"=>"Q", "yag"=>"Q", "yar"=>"Q", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+9 =>
+{"aaa"=>"N", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aaw"=>"N", "aam"=>"N", "aah"=>"N", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"S", "agt"=>"S", "agg"=>"S", "agc"=>"S", "agy"=>"S", "agr"=>"S", "agw"=>"S", "ags"=>"S", "agk"=>"S", "agm"=>"S", "agb"=>"S", "agd"=>"S", "agh"=>"S", "agv"=>"S", "agn"=>"S", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L"}, 
+10 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"C", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgw"=>"C", "tgm"=>"C", "tgh"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+11 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+12 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"S", "ctc"=>"L", "cty"=>"L", "ctw"=>"L", "ctm"=>"L", "cth"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+13 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"M", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atr"=>"M", "aga"=>"G", "agt"=>"S", "agg"=>"G", "agc"=>"S", "agy"=>"S", "agr"=>"G", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "rga"=>"G", "rgg"=>"G", "rgr"=>"G"}, 
+14 =>
+{"aaa"=>"N", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aaw"=>"N", "aam"=>"N", "aah"=>"N", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"S", "agt"=>"S", "agg"=>"S", "agc"=>"S", "agy"=>"S", "agr"=>"S", "agw"=>"S", "ags"=>"S", "agk"=>"S", "agm"=>"S", "agb"=>"S", "agd"=>"S", "agh"=>"S", "agv"=>"S", "agn"=>"S", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"Y", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "taw"=>"Y", "tam"=>"Y", "tah"=>"Y", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L"}, 
+15 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"Q", "tac"=>"Y", "tay"=>"Y", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yag"=>"Q", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+16 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"L", "tac"=>"Y", "tay"=>"Y", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "twg"=>"L", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+21 =>
+{"aaa"=>"N", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aaw"=>"N", "aam"=>"N", "aah"=>"N", "ata"=>"M", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atr"=>"M", "aga"=>"S", "agt"=>"S", "agg"=>"S", "agc"=>"S", "agy"=>"S", "agr"=>"S", "agw"=>"S", "ags"=>"S", "agk"=>"S", "agm"=>"S", "agb"=>"S", "agd"=>"S", "agh"=>"S", "agv"=>"S", "agn"=>"S", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L"}, 
+22 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"L", "tac"=>"Y", "tay"=>"Y", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"*", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcs"=>"S", "tck"=>"S", "tcb"=>"S", "tra"=>"*", "twg"=>"L", "tsa"=>"*", "tma"=>"*", "tva"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+23 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"*", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "twa"=>"*", "tka"=>"*", "tda"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "ytg"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+}
+end #CodonTable
+end #Bio

data/lib/bio/io/togows.rb

@@ -107,14 +107,14 @@ module Bio
     # 
     # For light users, class methods can be used.
     #
-    #   print Bio::TogoWS::REST.entry('genbank', 'AF237819')
+    #   print Bio::TogoWS::REST.entry('ncbi-nucleotide', 'AF237819')
     #   print Bio::TogoWS::REST.search('uniprot', 'lung cancer')
     #
     # For heavy users, an instance of the REST class can be created, and
     # using the instance is more efficient than using class methods.
     #
     #   t = Bio::TogoWS::REST.new
-    #   print t.entry('genbank', 'AF237819')
+    #   print t.entry('ncbi-nucleotide', 'AF237819')
     #   print t.search('uniprot', 'lung cancer')
     #
     # == References
@@ -222,9 +222,9 @@ module Bio
       #
       # Example:
       #   t = Bio::TogoWS::REST.new
-      #   kuma = t.entry('genbank', 'AF237819')
+      #   kuma = t.entry('ncbi-nucleotide', 'AF237819')
       #   # multiple IDs at a time
-      #   misc = t.entry('genbank', [ 'AF237819', 'AF237820' ])
+      #   misc = t.entry('ncbi-nucleotide', [ 'AF237819', 'AF237820' ])
       #   # with format change
       #   p53 = t.entry('uniprot', 'P53_HUMAN', 'fasta')
       #
@@ -366,7 +366,7 @@ module Bio
       # Access to the TogoWS by using GET method.
       #
       # Example 1:
-      #   get('entry', 'genbank', AF209156')
+      #   get('entry', 'ncbi-nucleotide', AF209156')
       # Example 2:
       #   get('search', 'uniprot', 'lung cancer')
       #

data/lib/bio/version.rb

@@ -10,19 +10,17 @@
 module Bio
 
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [1, 5, 2].extend(Comparable).freeze
+  BIORUBY_VERSION = [1, 6, 0].extend(Comparable).freeze
 
   # Extra version specifier (String or nil).
   # Existance of the value indicates development version.
   #
-  # nil                 :: Release version.
-  # "-dev"              :: Development version (with YYYYMMDD digits).
-  # ".20150630"         :: Development version (specify the date digits).
+  # nil             :: Release version.
+  # ".pre           :: Pre-release version.
   #
-  # By default, if the third digit (teeny) of BIORUBY_VERSION is 0,
-  # the version is regarded as a development version.
-  BIORUBY_EXTRA_VERSION =
-    nil #"-dev" #(BIORUBY_VERSION[2] == 0) ? "-dev" : nil
+  # References: https://guides.rubygems.org/patterns/#prerelease-gems
+  BIORUBY_EXTRA_VERSION = #nil
+    ".pre"
 
   # Version identifier, including extra version string (String)
   # Unlike BIORUBY_VERSION, it is not comparable.

data/sample/test_restriction_enzyme_long.rb

@@ -14,7 +14,7 @@ require 'test/unit'
 require 'benchmark'
 require 'bio'
 
-entry = Bio::TogoWS::REST.entry('genbank', 'BA000007.2')
+entry = Bio::TogoWS::REST.entry('ncbi-nucleotide', 'BA000007.2')
 EcoliO157H7Seq = Bio::GenBank.new(entry).naseq.freeze
 
 module TestRestrictionEnzymeAnalysisCutLong

data/test/unit/bio/data/test_codontable.rb

@@ -71,6 +71,9 @@ module Bio
 
     def test_accessor #[]
       assert_equal('M', @ct['atg'])
+      assert_equal('*', @ct['tag'])
+      assert_equal('*', @ct['tra'])
+      assert_equal('*', @ct['tar'])
     end
 
     def test_set_accessor #[]=

metadata

@@ -1,23 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: bio
 version: !ruby/object:Gem::Version
-  version: 1.5.2
+  version: 1.6.0.pre.20181210
 platform: ruby
 authors:
 - BioRuby project
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-09-20 00:00:00.000000000 Z
+date: 2018-12-11 00:00:00.000000000 Z
 dependencies: []
 description: BioRuby is a library for bioinformatics (biology + information science).
 email: staff@bioruby.org
-executables:
-- bioruby
-- br_biofetch.rb
-- br_bioflat.rb
-- br_biogetseq.rb
-- br_pmfetch.rb
+executables: []
 extensions: []
 extra_rdoc_files:
 - KNOWN_ISSUES.rdoc
@@ -29,6 +24,7 @@ extra_rdoc_files:
 - doc/RELEASE_NOTES-1.4.1.rdoc
 - doc/RELEASE_NOTES-1.4.2.rdoc
 - doc/RELEASE_NOTES-1.4.3.rdoc
+- doc/RELEASE_NOTES-1.5.0.rdoc
 files:
 - ".travis.yml"
 - BSDL
@@ -36,6 +32,7 @@ files:
 - COPYING.ja
 - ChangeLog
 - GPL
+- Gemfile
 - KNOWN_ISSUES.rdoc
 - LEGAL
 - LGPL
@@ -43,14 +40,11 @@ files:
 - README_DEV.rdoc
 - RELEASE_NOTES.rdoc
 - Rakefile
-- bin/bioruby
-- bin/br_biofetch.rb
-- bin/br_bioflat.rb
-- bin/br_biogetseq.rb
-- bin/br_pmfetch.rb
+- appveyor.yml
 - bioruby.gemspec
 - bioruby.gemspec.erb
 - doc/ChangeLog-1.4.3
+- doc/ChangeLog-1.5.0
 - doc/ChangeLog-before-1.3.1
 - doc/ChangeLog-before-1.4.2
 - doc/Changes-0.7.rd
@@ -59,6 +53,7 @@ files:
 - doc/RELEASE_NOTES-1.4.1.rdoc
 - doc/RELEASE_NOTES-1.4.2.rdoc
 - doc/RELEASE_NOTES-1.4.3.rdoc
+- doc/RELEASE_NOTES-1.5.0.rdoc
 - doc/Tutorial.rd
 - doc/Tutorial.rd.html
 - doc/Tutorial.rd.ja
@@ -70,7 +65,6 @@ files:
 - gemfiles/Gemfile.travis-rbx
 - gemfiles/Gemfile.travis-ruby1.8
 - gemfiles/Gemfile.travis-ruby1.9
-- gemfiles/Gemfile.travis-ruby2.2
 - gemfiles/modify-Gemfile.rb
 - gemfiles/prepare-gemspec.rb
 - lib/bio.rb
@@ -135,8 +129,6 @@ files:
 - lib/bio/data/na.rb
 - lib/bio/db.rb
 - lib/bio/db/aaindex.rb
-- lib/bio/db/biosql/biosql_to_biosequence.rb
-- lib/bio/db/biosql/sequence.rb
 - lib/bio/db/embl/common.rb
 - lib/bio/db/embl/embl.rb
 - lib/bio/db/embl/embl_to_biosequence.rb
@@ -195,10 +187,6 @@ files:
 - lib/bio/db/pdb/pdb.rb
 - lib/bio/db/pdb/residue.rb
 - lib/bio/db/pdb/utils.rb
-- lib/bio/db/phyloxml/phyloxml.xsd
-- lib/bio/db/phyloxml/phyloxml_elements.rb
-- lib/bio/db/phyloxml/phyloxml_parser.rb
-- lib/bio/db/phyloxml/phyloxml_writer.rb
 - lib/bio/db/prosite.rb
 - lib/bio/db/rebase.rb
 - lib/bio/db/sanger_chromatogram/abif.rb
@@ -208,9 +196,6 @@ files:
 - lib/bio/db/soft.rb
 - lib/bio/db/transfac.rb
 - lib/bio/feature.rb
-- lib/bio/io/biosql/ar-biosql.rb
-- lib/bio/io/biosql/biosql.rb
-- lib/bio/io/biosql/config/database.yml
 - lib/bio/io/das.rb
 - lib/bio/io/fastacmd.rb
 - lib/bio/io/fetch.rb
@@ -225,7 +210,6 @@ files:
 - lib/bio/io/ncbirest.rb
 - lib/bio/io/pubmed.rb
 - lib/bio/io/registry.rb
-- lib/bio/io/sql.rb
 - lib/bio/io/togows.rb
 - lib/bio/location.rb
 - lib/bio/map.rb
@@ -243,44 +227,6 @@ files:
 - lib/bio/sequence/na.rb
 - lib/bio/sequence/quality_score.rb
 - lib/bio/sequence/sequence_masker.rb
-- lib/bio/shell.rb
-- lib/bio/shell/core.rb
-- lib/bio/shell/demo.rb
-- lib/bio/shell/interface.rb
-- lib/bio/shell/irb.rb
-- lib/bio/shell/object.rb
-- lib/bio/shell/plugin/blast.rb
-- lib/bio/shell/plugin/codon.rb
-- lib/bio/shell/plugin/das.rb
-- lib/bio/shell/plugin/emboss.rb
-- lib/bio/shell/plugin/entry.rb
-- lib/bio/shell/plugin/flatfile.rb
-- lib/bio/shell/plugin/midi.rb
-- lib/bio/shell/plugin/ncbirest.rb
-- lib/bio/shell/plugin/obda.rb
-- lib/bio/shell/plugin/psort.rb
-- lib/bio/shell/plugin/seq.rb
-- lib/bio/shell/plugin/togows.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
-- lib/bio/shell/script.rb
-- lib/bio/shell/setup.rb
-- lib/bio/shell/web.rb
 - lib/bio/tree.rb
 - lib/bio/tree/output.rb
 - lib/bio/util/color_scheme.rb
@@ -378,7 +324,6 @@ files:
 - sample/seqdatabase.ini
 - sample/ssearch2tab.rb
 - sample/tdiary.rb
-- sample/test_phyloxml_big.rb
 - sample/test_restriction_enzyme_long.rb
 - sample/tfastx2tab.rb
 - sample/vs-genes.rb
@@ -500,11 +445,6 @@ files:
 - test/data/paml/codeml/models/results7-8.txt
 - test/data/paml/codeml/output.txt
 - test/data/paml/codeml/rates
-- test/data/phyloxml/apaf.xml
-- test/data/phyloxml/bcl_2.xml
-- test/data/phyloxml/made_up.xml
-- test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml
-- test/data/phyloxml/phyloxml_examples.xml
 - test/data/pir/CRAB_ANAPL.pir
 - test/data/prosite/prosite.dat
 - test/data/refseq/nm_126355.entret
@@ -554,8 +494,6 @@ files:
 - test/unit/bio/data/test_aa.rb
 - test/unit/bio/data/test_codontable.rb
 - test/unit/bio/data/test_na.rb
-- test/unit/bio/db/biosql/tc_biosql.rb
-- test/unit/bio/db/biosql/ts_suite_biosql.rb
 - test/unit/bio/db/embl/test_common.rb
 - test/unit/bio/db/embl/test_embl.rb
 - test/unit/bio/db/embl/test_embl_rel89.rb
@@ -594,8 +532,6 @@ files:
 - test/unit/bio/db/test_nbrf.rb
 - test/unit/bio/db/test_newick.rb
 - test/unit/bio/db/test_nexus.rb
-- test/unit/bio/db/test_phyloxml.rb
-- test/unit/bio/db/test_phyloxml_writer.rb
 - test/unit/bio/db/test_prosite.rb
 - test/unit/bio/db/test_qual.rb
 - test/unit/bio/db/test_rebase.rb
@@ -613,7 +549,6 @@ files:
 - test/unit/bio/sequence/test_na.rb
 - test/unit/bio/sequence/test_quality_score.rb
 - test/unit/bio/sequence/test_sequence_masker.rb
-- test/unit/bio/shell/plugin/test_seq.rb
 - test/unit/bio/test_alignment.rb
 - test/unit/bio/test_command.rb
 - test/unit/bio/test_db.rb
@@ -623,7 +558,6 @@ files:
 - test/unit/bio/test_pathway.rb
 - test/unit/bio/test_reference.rb
 - test/unit/bio/test_sequence.rb
-- test/unit/bio/test_shell.rb
 - test/unit/bio/test_tree.rb
 - test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb
 - test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb
@@ -669,12 +603,12 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.5.2.1
+rubygems_version: 2.7.6
 signing_key: 
 specification_version: 4
 summary: Bioinformatics library