bio 1.4.0 → 1.4.1

data/test/unit/bio/db/kegg/test_genes.rb

@@ -2,6 +2,7 @@
 # test/unit/bio/db/kegg/test_genes.rb - Unit test for Bio::KEGG::GENES
 #
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+#              Copyright (C) 2010 Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
 #  $Id:$
@@ -70,4 +71,283 @@ END
       assert_equal(['15230008', '42572267'], @obj.dblinks['NCBI-GI'])
     end
   end
-end
+
+  class TestBioKEGGGENES_b0529 < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'KEGG/b0529.gene')
+      @obj = Bio::KEGG::GENES.new(File.read(filename))
+    end
+
+    def test_dblinks_as_hash
+      expected = {
+        "NCBI-GI"=>["16128513"],
+        "UniProt"=>["P24186"],
+        "NCBI-GeneID"=>["945221"],
+        "ECOCYC"=>["EG10328"],
+        "EcoGene"=>["EG10328"],
+        "RegulonDB"=>["B0529"]
+      }
+      assert_equal(expected, @obj.dblinks_as_hash)
+    end
+
+    def test_pathways_as_hash
+      expected = {
+        "eco00630" => "Glyoxylate and dicarboxylate metabolism",
+        "eco00670" => "One carbon pool by folate",
+        "eco01100" => "Metabolic pathways"
+      }
+      assert_equal(expected, @obj.pathways_as_hash)
+    end
+
+    def test_orthologs_as_hash
+      expected = { "K01491" => "methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase [EC:1.5.1.5 3.5.4.9]" }
+      assert_equal(expected, @obj.orthologs_as_hash)
+    end
+
+    def test_new
+      assert_instance_of(Bio::KEGG::GENES, @obj)
+    end
+
+    def test_entry
+      expected = {"organism"=>"E.coli", "division"=>"CDS", "id"=>"b0529"}
+      assert_equal(expected, @obj.entry)
+    end
+
+    def test_entry_id
+      assert_equal("b0529", @obj.entry_id)
+    end
+
+    def test_division
+      assert_equal("CDS", @obj.division)
+    end
+
+    def test_organism
+      assert_equal("E.coli", @obj.organism)
+    end
+
+    def test_name
+      assert_equal("folD, ads, ECK0522, JW0518", @obj.name)
+    end
+
+    def test_names_as_array
+      expected = ["folD", "ads", "ECK0522", "JW0518"]
+      assert_equal(expected, @obj.names_as_array)
+      assert_equal(expected, @obj.names)
+    end
+
+    def test_genes
+      expected = ["folD", "ads", "ECK0522", "JW0518"]
+      assert_equal(expected, @obj.genes)
+    end
+
+    def test_gene
+      assert_equal("folD", @obj.gene)
+    end
+
+    def test_definition
+      expected = "bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/5,10-methylene-tetrahydrofolate cyclohydrolase (EC:1.5.1.5 3.5.4.9)"
+      assert_equal(expected, @obj.definition)
+    end
+
+    def test_eclinks
+      assert_equal(["1.5.1.5", "3.5.4.9"], @obj.eclinks)
+    end
+
+    def test_orthologs_as_strings
+      expected = ["K01491  methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase [EC:1.5.1.5 3.5.4.9]"]
+      assert_equal(expected, @obj.orthologs_as_strings)
+    end
+
+    def test_pathway
+      expected = "eco00630 Glyoxylate and dicarboxylate metabolism eco00670 One carbon pool by folate eco01100 Metabolic pathways"
+      assert_equal(expected, @obj.pathway)
+    end
+
+    def test_pathways_as_strings
+      expected = [ "eco00630  Glyoxylate and dicarboxylate metabolism",
+                   "eco00670  One carbon pool by folate",
+                   "eco01100  Metabolic pathways" ]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_position
+      assert_equal("complement(556098..556964)", @obj.position)
+    end
+
+    def test_chromosome
+      assert_equal(nil, @obj.chromosome)
+    end
+
+    def test_gbposition
+      assert_equal("complement(556098..556964)", @obj.gbposition)
+    end
+
+    def test_locations
+      expected = Bio::Locations.new("complement(556098..556964)")
+      assert_equal(expected, @obj.locations)
+    end
+
+    def test_motifs_as_strings
+      expected =
+        [ "Pfam: THF_DHG_CYH_C THF_DHG_CYH Amidohydro_1",
+          "PROSITE: THF_DHG_CYH_1 THF_DHG_CYH_2" ]
+      assert_equal(expected, @obj.motifs_as_strings)
+    end
+
+    def test_motifs_as_hash
+      expected = {
+        "Pfam"    => ["THF_DHG_CYH_C", "THF_DHG_CYH", "Amidohydro_1"],
+        "PROSITE" => ["THF_DHG_CYH_1", "THF_DHG_CYH_2"]
+      }
+      assert_equal(expected, @obj.motifs_as_hash)
+      assert_equal(expected, @obj.motifs)
+      assert_equal(expected, @obj.motif)
+    end
+
+    def test_dblinks_as_strings
+      expected = [ "NCBI-GI: 16128513",
+                   "NCBI-GeneID: 945221",
+                   "RegulonDB: B0529",
+                   "EcoGene: EG10328",
+                   "ECOCYC: EG10328",
+                   "UniProt: P24186" ]
+      assert_equal(expected, @obj.dblinks_as_strings)
+    end
+
+    def test_structure
+      assert_equal(["1B0A"], @obj.structure)
+    end
+
+    def test_codon_usage
+      expected = {
+        "gcg"=>nil,
+        "gtc"=>nil,
+        "cat"=>nil,
+        "ctg"=>nil,
+        "tac"=>nil,
+        "gga"=>nil,
+        "agg"=>nil,
+        "aaa"=>nil,
+        "acc"=>nil,
+        "att"=>nil,
+        "cca"=>nil,
+        "tgt"=>nil,
+        "tta"=>nil,
+        "gag"=>nil,
+        "gct"=>nil,
+        "tcg"=>nil,
+        "ggc"=>nil,
+        "agt"=>nil,
+        "aac"=>nil,
+        "ata"=>nil,
+        "cgg"=>nil,
+        "caa"=>nil,
+        "ccc"=>nil,
+        "ctt"=>nil,
+        "tga"=>nil,
+        "ttc"=>nil,
+        "gat"=>nil,
+        "gtg"=>nil,
+        "tag"=>nil,
+        "gca"=>nil,
+        "aga"=>nil,
+        "acg"=>nil,
+        "atc"=>nil,
+        "cgt"=>nil,
+        "cac"=>nil,
+        "cta"=>nil,
+        "tgc"=>nil,
+        "tct"=>nil,
+        "ggg"=>nil,
+        "gaa"=>nil,
+        "gcc"=>nil,
+        "gtt"=>nil,
+        "agc"=>nil,
+        "aag"=>nil,
+        "act"=>nil,
+        "cga"=>nil,
+        "ccg"=>nil,
+        "ctc"=>nil,
+        "tat"=>nil,
+        "tca"=>nil,
+        "ttg"=>nil,
+        "ggt"=>nil,
+        "gac"=>nil,
+        "gta"=>nil,
+        "aat"=>nil,
+        "aca"=>nil,
+        "atg"=>nil,
+        "cgc"=>nil,
+        "cag"=>nil,
+        "cct"=>nil,
+        "tgg"=>nil,
+        "taa"=>nil,
+        "tcc"=>nil,
+        "ttt"=>nil }
+      assert_equal(expected, @obj.codon_usage)
+    end
+
+    def test_cu_list
+      assert_equal([], @obj.cu_list)
+    end
+
+    def test_aaseq
+      expected = "MAAKIIDGKTIAQQVRSEVAQKVQARIAAGLRAPGLAVVLVGSNPASQIYVASKRKACEEVGFVSRSYDLPETTSEAELLELIDTLNADNTIDGILVQLPLPAGIDNVKVLERIHPDKDVDGFHPYNVGRLCQRAPRLRPCTPRGIVTLLERYNIDTFGLNAVVIGASNIVGRPMSMELLLAGCTTTVTHRFTKNLRHHVENADLLIVAVGKPGFIPGDWIKEGAIVIDVGINRLENGKVVGDVVFEDAAKRASYITPVPGGVGPMTVATLIENTLQACVEYHDPQDE"
+      assert_equal(expected, @obj.aaseq)
+    end
+
+    def test_aalen
+      assert_equal(288, @obj.aalen)
+    end
+
+    def test_ntseq
+      expected = "atggcagcaaagattattgacggtaaaacgattgcgcagcaggtgcgctctgaagttgctcaaaaagttcaggcgcgtattgcagccggactgcgggcaccaggactggccgttgtgctggtgggtagtaaccctgcatcgcaaatttatgtcgcaagcaaacgcaaggcttgtgaagaagtcgggttcgtctcccgctcttatgacctcccggaaaccaccagcgaagcggagctgctggagcttatcgatacgctgaatgccgacaacaccatcgatggcattctggttcaactgccgttaccggcgggtattgataacgtcaaagtgctggaacgtattcatccggacaaagacgtggacggtttccatccttacaacgtcggtcgtctgtgccagcgcgcgccgcgtctgcgtccctgcaccccgcgcggtatcgtcacgctgcttgagcgttacaacattgataccttcggcctcaacgccgtggtgattggcgcatcgaatatcgttggccgcccgatgagcatggaactgctgctggcaggttgcaccactacagtgactcaccgcttcactaaaaatctgcgtcatcacgtagaaaatgccgatctattgatcgttgccgttggcaagccaggctttattcccggtgactggatcaaagaaggcgcaattgtgattgatgtcggcatcaaccgtctggaaaatggcaaagttgtgggcgacgtcgtgtttgaagacgcggctaaacgcgcctcatacattacgcctgttcccggcggcgttggcccgatgacggttgccacgctgattgaaaacacgctacaggcgtgcgttgaatatcatgatccacaggatgagtaa"
+      assert_equal(expected, @obj.ntseq)
+    end
+
+    def test_ntlen
+      assert_equal(867, @obj.ntlen)
+    end
+
+    def test_pathway_after_pathways_as_strings
+      str = "eco00630 Glyoxylate and dicarboxylate metabolism eco00670 One carbon pool by folate eco01100 Metabolic pathways"
+      strary = [ "eco00630  Glyoxylate and dicarboxylate metabolism",
+                 "eco00670  One carbon pool by folate",
+                 "eco01100  Metabolic pathways" ]
+      2.times {
+        assert_equal(str, @obj.pathway)
+        assert_equal(strary, @obj.pathways_as_strings)
+      }
+    end
+
+    def test_pathway_before_pathways_as_strings
+      str = "eco00630 Glyoxylate and dicarboxylate metabolism eco00670 One carbon pool by folate eco01100 Metabolic pathways"
+      strary = [ "eco00630  Glyoxylate and dicarboxylate metabolism",
+                 "eco00670  One carbon pool by folate",
+                 "eco01100  Metabolic pathways" ]
+      2.times {
+        assert_equal(strary, @obj.pathways_as_strings)
+        assert_equal(str, @obj.pathway)
+      }
+    end
+
+    def test_keggclass
+      expected = "Metabolism; Carbohydrate Metabolism; Glyoxylate and dicarboxylate metabolism [PATH:eco00630] Metabolism; Metabolism of Cofactors and Vitamins; One carbon pool by folate [PATH:eco00670]"
+      assert_equal(expected, @obj.keggclass)
+    end
+
+    def test_keggclasses
+      expected =
+        [ "Metabolism; Carbohydrate Metabolism; Glyoxylate and dicarboxylate metabolism",
+          "Metabolism; Metabolism of Cofactors and Vitamins; One carbon pool by folate"
+        ]
+      assert_equal(expected, @obj.keggclasses)
+    end
+
+  end #class TestBioKEGGGENES_b0529
+end #module Bio
+
+
+
+

data/test/unit/bio/db/kegg/test_genome.rb

@@ -0,0 +1,408 @@
+#
+# test/unit/bio/db/kegg/test_genome.rb - Unit test for Bio::KEGG::GENOME
+#
+# Copyright::  Copyright (C) 2010 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/kegg/genome.rb'
+
+module Bio
+  class TestBioKEGGGENOME_T00005 < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'KEGG/T00005.genome')
+      @obj = Bio::KEGG::GENOME.new(File.read(filename))
+    end
+
+    def test_new
+      assert_instance_of(Bio::KEGG::GENOME, @obj)
+    end
+
+    def test_entry_id
+      assert_equal("T00005", @obj.entry_id)
+    end
+
+    def test_name
+      expected = "sce, S.cerevisiae, YEAST, 4932"
+      assert_equal(expected, @obj.name)
+    end
+
+    def test_definition
+      expected = "Saccharomyces cerevisiae S288C"
+      assert_equal(expected, @obj.definition)
+    end
+
+    def test_taxonomy
+      expected = { "lineage"=>
+        "Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces",
+        "taxid"=>"TAX:4932" }
+      assert_equal(expected, @obj.taxonomy)
+    end
+
+    def test_taxid
+      assert_equal("TAX:4932", @obj.taxid)
+    end
+
+    def test_lineage
+      expected = "Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces"
+      assert_equal(expected, @obj.lineage)
+    end
+
+    def test_data_source
+      assert_equal("RefSeq", @obj.data_source)
+    end
+
+    def test_original_db
+      assert_equal("SGD MIPS", @obj.original_db)
+    end
+
+    def test_original_databases
+      assert_equal([ "SGD", "MIPS" ], @obj.original_databases)
+    end
+
+    def test_disease
+      assert_equal("", @obj.disease)
+    end
+
+    def test_comment
+      assert_equal("", @obj.comment)
+    end
+
+    def test_references
+      data =
+        [ { "authors"  => ["Goffeau A", "et al."],
+            "comments" => nil,
+            "journal"  => "Science",
+            "pages"    => "546-67",
+            "pubmed"   => "8849441",
+            "title"    => "Life with 6000 genes.",
+            "volume"   => "274",
+            "year"     => "1996",
+          },
+          { "authors"  => ["Bussey H", "et al."],
+            "comments" => ["(chromosome I)"],
+            "journal"  => "Proc Natl Acad Sci U S A",
+            "pages"    => "3809-13",
+            "pubmed"   => "7731988",
+            "title"    => "The nucleotide sequence of chromosome I from Saccharomyces cerevisiae.",
+            "volume"   => "92",
+            "year"     => "1995",
+          },
+          { "authors"  => ["Feldmann, H.", "et al."],
+            "comments" => ["(chromosome II)"],
+            "journal"  => "EMBO J",
+            "pages"    => "5795-809",
+            "pubmed"   => "7813418",
+            "title"    => "Complete DNA sequence of yeast chromosome II.",
+            "volume"   => "13",
+            "year"     => "1994",
+          },
+          { "authors"  => ["Oliver, S.G.", "et al."],
+            "comments" => ["(chromosome III)"],
+            "journal"  => "Nature",
+            "pages"    => "38-46",
+            "pubmed"   => "1574125",
+            "title"    => "The complete DNA sequence of yeast chromosome III.",
+            "volume"   => "357",
+            "year"     => "1992",
+          },
+          { "authors"  => ["Jacq C", "et al."],
+            "comments" => ["(chromosome IV)"],
+            "journal"  => "Nature",
+            "pages"    => "75-8",
+            "pubmed"   => "9169867",
+            "title"    => "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.",
+            "volume"   => "387(6632 Suppl)",
+            "year"     => "1997",
+          },
+          { "authors"  => ["Dietrich FS", "et al."],
+            "comments" => ["(chromosome V)"],
+            "journal"  => "Nature",
+            "pages"    => "78-81",
+            "pubmed"   => "9169868",
+            "title"    => "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.",
+            "volume"   => "387(6632 Suppl)",
+            "year"     => "1997",
+          },
+          { "authors"  => ["Murakami, Y.", "et al."],
+            "comments" => ["(chromosome VI)"],
+            "journal"  => "Nat Genet",
+            "pages"    => "261-8",
+            "pubmed"   => "7670463",
+            "title"    => "Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae.",
+            "volume"   => "10",
+            "year"     => "1995",
+          },
+          { "authors"  => ["Tettelin H", "et al."],
+            "comments" => ["(chromosome VII)"],
+            "journal"  => "Nature",
+            "pages"    => "81-4",
+            "pubmed"   => "9169869",
+            "title"    => "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.",
+            "volume"   => "387(6632 Suppl)",
+            "year"     => "1997",
+          },
+          { "authors"  => ["Johnston, M.", "et al."],
+            "comments" => ["(chromosome VIII)"],
+            "journal"  => "Science",
+            "pages"    => "2077-82",
+            "pubmed"   => "8091229",
+            "title"    => "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII.",
+            "volume"   => "265",
+            "year"     => "1994",
+          },
+          { "authors"  => ["Churcher C", "et al."],
+            "comments" => ["(chromosome IX)"],
+            "journal"  => "Nature",
+            "pages"    => "84-7",
+            "pubmed"   => "9169870",
+            "title"    => "The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.",
+            "volume"   => "387(6632 Suppl)",
+            "year"     => "1997",
+          },
+          { "authors"  => ["Galibert, F.", "et al."],
+            "comments" => ["(chromosome X)"],
+            "journal"  => "EMBO J",
+            "pages"    => "2031-49",
+            "pubmed"   => "8641269",
+            "title"    => "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.",
+            "volume"   => "15",
+            "year"     => "1996",
+          },
+          { "authors"  => ["Dujon, B.", "et al."],
+            "comments" => ["(chromosome XI)"],
+            "journal"  => "Nature",
+            "pages"    => "371-8",
+            "pubmed"   => "8196765",
+            "title"    => "Complete DNA sequence of yeast chromosome XI.",
+            "volume"   => "369",
+            "year"     => "1994",
+          },
+          { "authors"  => ["Johnston M", "et al."],
+            "comments" => ["(chromosome XII)"],
+            "journal"  => "Nature",
+            "pages"    => "87-90",
+            "pubmed"   => "9169871",
+            "title"    => "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.",
+            "volume"   => "387(6632 Suppl)",
+            "year"     => "1997",
+          },
+          { "authors"  => ["Bowman S", "et al."],
+            "comments" => ["(chromosome XIII)"],
+            "journal"  => "Nature",
+            "pages"    => "90-3",
+            "pubmed"   => "9169872",
+            "title"    => "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.",
+            "volume"   => "387(6632 Suppl)",
+            "year"     => "1997",
+          },
+          { "authors"  => ["Philippsen P", "et al."],
+            "comments" => ["(chromosome XIV)"],
+            "journal"  => "Nature",
+            "pages"    => "93-8",
+            "pubmed"   => "9169873",
+            "title"    => "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications.",
+            "volume"   => "387(6632 Suppl)",
+            "year"     => "1997",
+          },
+          { "authors"  => ["Dujon B", "et al."],
+            "comments" => ["(chromosome XV)"],
+            "journal"  => "Nature",
+            "pages"    => "98-102",
+            "pubmed"   => "9169874",
+            "title"    => "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.",
+            "volume"   => "387(6632 Suppl)",
+            "year"     => "1997",
+          },
+          { "authors"  => ["Bussey H", "et al."],
+            "comments" => ["(chromosome XVI)"],
+            "journal"  => "Nature",
+            "pages"    => "103-5",
+            "pubmed"   => "9169875",
+            "title"    => "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.",
+            "volume"   => "387(6632 Suppl)",
+            "year"     => "1997",
+          }
+        ]
+      expected = data.collect { |h| Bio::Reference.new(h) }
+      #assert_equal(expected, @obj.references)
+      expected.each_with_index do |x, i|
+        assert_equal(x, @obj.references[i])
+      end
+    end
+
+    def test_chromosomes
+      expected =
+        [{"SEQUENCE"=>"RS:NC_001133", "LENGTH"=>"230208", "CHROMOSOME"=>"I"},
+         {"SEQUENCE"=>"RS:NC_001134", "LENGTH"=>"813178", "CHROMOSOME"=>"II"},
+         {"SEQUENCE"=>"RS:NC_001135", "LENGTH"=>"316617", "CHROMOSOME"=>"III"},
+         {"SEQUENCE"=>"RS:NC_001136", "LENGTH"=>"1531919", "CHROMOSOME"=>"IV"},
+         {"SEQUENCE"=>"RS:NC_001137", "LENGTH"=>"576869", "CHROMOSOME"=>"V"},
+         {"SEQUENCE"=>"RS:NC_001138", "LENGTH"=>"270148", "CHROMOSOME"=>"VI"},
+         {"SEQUENCE"=>"RS:NC_001139", "LENGTH"=>"1090947", "CHROMOSOME"=>"VII"},
+         {"SEQUENCE"=>"RS:NC_001140", "LENGTH"=>"562643", "CHROMOSOME"=>"VIII"},
+         {"SEQUENCE"=>"RS:NC_001141", "LENGTH"=>"439885", "CHROMOSOME"=>"IX"},
+         {"SEQUENCE"=>"RS:NC_001142", "LENGTH"=>"745741", "CHROMOSOME"=>"X"},
+         {"SEQUENCE"=>"RS:NC_001143", "LENGTH"=>"666454", "CHROMOSOME"=>"XI"},
+         {"SEQUENCE"=>"RS:NC_001144", "LENGTH"=>"1078175", "CHROMOSOME"=>"XII"},
+         {"SEQUENCE"=>"RS:NC_001145", "LENGTH"=>"924429", "CHROMOSOME"=>"XIII"},
+         {"SEQUENCE"=>"RS:NC_001146", "LENGTH"=>"784333", "CHROMOSOME"=>"XIV"},
+         {"SEQUENCE"=>"RS:NC_001147", "LENGTH"=>"1091289", "CHROMOSOME"=>"XV"},
+         {"SEQUENCE"=>"RS:NC_001148", "LENGTH"=>"948062", "CHROMOSOME"=>"XVI"},
+         {"SEQUENCE"=>"RS:NC_001224",
+           "LENGTH"=>"85779",
+           "CHROMOSOME"=>"MT (mitochondrion); Circular"}
+        ]
+      assert_equal(expected, @obj.chromosomes)
+    end
+
+    def test_plasmids
+      assert_equal([], @obj.plasmids)
+    end
+
+    def test_statistics
+      expected = {"num_rna"=>414, "num_nuc"=>12156676, "num_gene"=>5881}
+      assert_equal(expected, @obj.statistics)
+    end
+
+    def test_nalen
+      assert_equal(12156676, @obj.nalen)
+    end
+
+    def test_num_gene
+      assert_equal(5881, @obj.num_gene)
+    end
+
+    def test_num_rna
+      assert_equal(414, @obj.num_rna)
+    end
+
+  end #class TestBioKEGGGENOME_T00005
+
+  class TestBioKEGGGENOME_T00070 < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'KEGG/T00070.genome')
+      @obj = Bio::KEGG::GENOME.new(File.read(filename))
+    end
+
+    def test_new
+      assert_instance_of(Bio::KEGG::GENOME, @obj)
+    end
+
+    def test_entry_id
+      assert_equal("T00070", @obj.entry_id)
+    end
+
+    def test_name
+      expected = "atu, A.tumefaciens, AGRT5, 176299"
+      assert_equal(expected, @obj.name)
+    end
+
+    def test_definition
+      expected = "Agrobacterium tumefaciens C58"
+      assert_equal(expected, @obj.definition)
+    end
+
+    def test_taxonomy
+      expected = { "lineage"=>
+        "Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium",
+        "taxid" => "TAX:176299" }
+      assert_equal(expected, @obj.taxonomy)
+    end
+
+    def test_taxid
+      assert_equal("TAX:176299", @obj.taxid)
+    end
+
+    def test_lineage
+      expected = "Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium"
+      assert_equal(expected, @obj.lineage)
+    end
+
+    def test_data_source
+      assert_equal("RefSeq", @obj.data_source)
+    end
+
+    def test_original_db
+      assert_equal("UWash", @obj.original_db)
+    end
+
+    def test_original_databases
+      assert_equal([ "UWash" ], @obj.original_databases)
+    end
+
+    def test_disease
+      expected = "Crown gall disease in plants"
+      assert_equal(expected, @obj.disease)
+    end
+
+    def test_comment
+      expected = "Originally called Agrobacterium tumefaciens C58 (U.Washington/Dupont) to distinguish from Agrobacterium tumefaciens C58 (Cereon) [GN:atc]"
+      assert_equal(expected, @obj.comment)
+    end
+
+    def test_references
+      h = {
+        "authors" => [ "Wood DW", "et al." ],
+        "journal" => "Science",
+        "pages"   => "2317-23",
+        "pubmed"  => "11743193",
+        "title"   => "The genome of the natural genetic engineer Agrobacterium tumefaciens C58.",
+        "volume"  => "294",
+        "year"    => "2001"
+      }
+      expected = [ Bio::Reference.new(h) ]
+      assert_equal(expected, @obj.references)
+    end
+
+    def test_chromosomes
+      expected = [ { "SEQUENCE"   => "RS:NC_003062",
+                     "LENGTH"     => "2841580",
+                     "CHROMOSOME" => "Circular"},
+                   { "SEQUENCE"   => "RS:NC_003063",
+                     "LENGTH"     => "2075577",
+                     "CHROMOSOME" => "L (linear chromosome)"} ]
+      assert_equal(expected, @obj.chromosomes)
+    end
+
+    def test_plasmids
+      expected =
+        [ { "SEQUENCE" => "RS:NC_003065",
+            "LENGTH"   => "214233",
+            "PLASMID"  => "Ti; Circular" },
+          { "SEQUENCE" => "RS:NC_003064",
+            "LENGTH"   => "542868",
+            "PLASMID"  => "AT; Circular" }
+        ]
+      assert_equal(expected, @obj.plasmids)
+    end
+
+    def test_statistics
+      expected = {"num_rna"=>74, "num_nuc"=>5674258, "num_gene"=>5355}
+      assert_equal(expected, @obj.statistics)
+    end
+
+    def test_nalen
+      assert_equal(5674258, @obj.nalen)
+    end
+
+    def test_num_gene
+      assert_equal(5355, @obj.num_gene)
+    end
+
+    def test_num_rna
+      assert_equal(74, @obj.num_rna)
+    end
+
+  end #class TestBioKEGGGENOME_T00070
+end #module Bio
+