bio 1.4.1 → 1.4.2

data/test/unit/bio/db/genbank/test_genbank.rb

@@ -0,0 +1,401 @@
+#
+# test/unit/bio/db/genbank/test_genbank.rb - Unit test for Bio::GenBank
+#
+# Copyright::  Copyright (C) 2010 Kazuhiro Hayashi <k.hayashi.info@gmail.com>
+# 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/sequence'
+require 'bio/reference'
+require 'bio/feature'
+require 'bio/compat/features'
+require 'bio/compat/references'
+require 'bio/db/genbank/genbank'
+require 'bio/db/genbank/genbank_to_biosequence'
+
+
+module Bio
+  class TestBioGenBank < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'genbank', 'SCU49845.gb')
+      @obj = Bio::GenBank.new(File.read(filename))
+    end
+
+    def test_locus_class
+      expected = Bio::GenBank::Locus
+      assert_equal(expected, @obj.locus.class)
+      locus_rel126 = "LOCUS       AB000383     5423 bp    DNA   circular  VRL       05-FEB-1999"#another type of LOCUS line.(release 126)
+      obj_rel126 = Bio::GenBank.new(locus_rel126)
+      assert_equal(Bio::GenBank::Locus, obj_rel126.locus.class)
+    end
+    def test_locus_circular
+       expected = "linear"
+       assert_equal(expected, @obj.locus.circular)
+       locus_rel126 = "LOCUS       AB000383     5423 bp    DNA   circular  VRL       05-FEB-1999"
+       obj_rel126 = Bio::GenBank.new(locus_rel126)
+       assert_equal("circular", obj_rel126.locus.circular)
+    end
+    def test_locus_date
+       expected = "23-MAR-2010"
+       assert_equal(expected, @obj.locus.date)
+       locus_rel126 = "LOCUS       AB000383     5423 bp    DNA   circular  VRL       05-FEB-1999"
+       obj_rel126 = Bio::GenBank.new(locus_rel126)
+       assert_equal("05-FEB-1999", obj_rel126.locus.date)
+    end
+    def test_locus_division
+       expected = "PLN"
+       assert_equal(expected, @obj.locus.division)
+       locus_rel126 = "LOCUS       AB000383     5423 bp    DNA   circular  VRL       05-FEB-1999"
+       obj_rel126 = Bio::GenBank.new(locus_rel126)
+       assert_equal("VRL", obj_rel126.locus.division)
+    end
+    def test_locus_entry_id
+       expected = "SCU49845"
+       assert_equal(expected, @obj.locus.entry_id)
+       locus_rel126 = "LOCUS       AB000383     5423 bp    DNA   circular  VRL       05-FEB-1999"
+       obj_rel126 = Bio::GenBank.new(locus_rel126)
+       assert_equal("AB000383", obj_rel126.locus.entry_id)
+    end
+    def test_locus_length
+       expected = 5028
+       assert_equal(expected, @obj.locus.length)
+       locus_rel126 = "LOCUS       AB000383     5423 bp    DNA   circular  VRL       05-FEB-1999"
+       obj_rel126 = Bio::GenBank.new(locus_rel126)
+       assert_equal(5423, obj_rel126.locus.length)
+    end
+    def test_locus_natype
+       expected = "DNA"
+       assert_equal(expected, @obj.locus.natype)
+       locus_rel126 = "LOCUS       AB000383     5423 bp    DNA   circular  VRL       05-FEB-1999"
+       obj_rel126 = Bio::GenBank.new(locus_rel126)
+       assert_equal("DNA", obj_rel126.locus.natype)
+    end
+    def test_locus_strand
+       expected = ""
+       assert_equal(expected, @obj.locus.strand)
+       locus_rel126 = "LOCUS       AB000383     5423 bp    DNA   circular  VRL       05-FEB-1999"
+       obj_rel126 = Bio::GenBank.new(locus_rel126)
+       assert_equal("", obj_rel126.locus.strand)
+    end
+    def test_entry_id
+      assert_equal("SCU49845", @obj.entry_id)
+    end
+
+    def test_length
+      assert_equal(5028, @obj.length)
+    end
+
+    def test_circular
+      assert_equal("linear", @obj.circular)
+    end
+
+    def test_division
+      assert_equal("PLN", @obj.division)
+    end
+
+    def test_date
+      assert_equal("23-MAR-2010", @obj.date)
+    end
+
+    def test_strand
+      assert_equal("", @obj.strand)
+    end
+
+    def test_natype
+      assert_equal("DNA", @obj.natype)
+    end
+
+    def test_each_cds_feature
+      @obj.each_cds do |feature|
+        assert_equal("CDS", feature.feature)
+      end
+    end
+=begin
+    def test_each_cds_qualifiers
+      @obj.each_cds do |feature|
+        feature.qualifiers do |qualifier|
+          assert_equal(Bio::Feature::Qualifier, qualifier.class)
+        end
+      end
+    end
+=end
+    def test_each_cds_qualifiers
+      expected = [[["codon_start", 3],
+                ["product", "TCP1-beta"],
+                ["protein_id", "AAA98665.1"],
+                ["db_xref", "GI:1293614"],
+                ["translation", "SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEAAEVLLRVDNIIRARPRTANRQHM"]],
+                [["gene", "AXL2"],
+                ["note", "plasma membrane glycoprotein"],
+                ["codon_start", 1],
+                ["product", "Axl2p"],
+                ["protein_id", "AAA98666.1"],
+                ["db_xref", "GI:1293615"],
+                ["translation", "MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESFTFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFNVILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNEVFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPETSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYVYLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYGDVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQDHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSANATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIACGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLNNPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQSQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDSYGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTKHRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRLVDFSNKSNVNVGQVKDIHGRIPEML"]],
+               [["gene", "REV7"],
+                ["codon_start", 1],
+                ["product", "Rev7p"],
+                ["protein_id", "AAA98667.1"],
+                ["db_xref", "GI:1293616"],
+["translation", "MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQFVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVDKDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNRRVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEKLISGDDKILNGVYSQYEEGESIFGSLF"]]]
+      actual = []
+      @obj.each_cds do |feature|
+        tmp = []
+        feature.qualifiers.each{|qualifier| 
+          tmp << [qualifier.qualifier, qualifier.value]
+        }
+        actual << tmp
+      end
+      assert_equal(expected, actual)
+    end
+    def test_each_gene
+      expected_position = ["<687..>3158", "complement(<3300..>4037)"]
+      expected_gene = [["gene","AXL2"], ["gene","REV7"]]
+      actual_position = []
+      actual_gene = []
+      @obj.each_gene do |gene| 
+        assert_equal("gene", gene.feature)
+        actual_position << gene.position
+        gene.qualifiers.each do |qualifier| 
+          actual_gene << [qualifier.qualifier, qualifier.value]
+        end
+      end
+      assert_equal(expected_position,actual_position)
+      assert_equal(expected_gene, actual_gene)
+    end
+
+    def test_basecount
+      assert_equal({}, @obj.basecount)
+    end
+
+    def test_seq
+      expected = "gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgtaacatatttaggatatacctcgaaaataataaaccgccacactgtcattattataattagaaacagaacgcaaaaattatccactatataattcaaagacgcgaaaaaaaaagaacaacgcgtcatagaacttttggcaattcgcgtcacaaataaattttggcaacttatgtttcctcttcgagcagtactcgagccctgtctcaagaatgtaataatacccatcgtaggtatggttaaagatagcatctccacaacctcaaagctccttgccgagagtcgccctcctttgtcgagtaattttcacttttcatatgagaacttattttcttattctttactctcacatcctgtagtgattgacactgcaacagccaccatcactagaagaacagaacaattacttaatagaaaaattatatcttcctcgaaacgatttcctgcttccaacatctacgtatatcaagaagcattcacttaccatgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtgattatacgcaacgatattttgcttaattttattttcctgttttattttttattagtggtttacagataccctatattttatttagtttttatacttagagacatttaattttaattccattcttcaaatttcatttttgcacttaaaacaaagatccaaaaatgctctcgccctcttcatattgagaatacactccattcaaaattttgtcgtcaccgctgattaatttttcactaaactgatgaataatcaaaggccccacgtcagaaccgactaaagaagtgagttttattttaggaggttgaaaaccattattgtctggtaaattttcatcttcttgacatttaacccagtttgaatccctttcaatttctgctttttcctccaaactatcgaccctcctgtttctgtccaacttatgtcctagttccaattcgatcgcattaataactgcttcaaatgttattgtgtcatcgttgactttaggtaatttctccaaatgcataatcaaactatttaaggaagatcggaattcgtcgaacacttcagtttccgtaatgatctgatcgtctttatccacatgttgtaattcactaaaatctaaaacgtatttttcaatgcataaatcgttctttttattaataatgcagatggaaaatctgtaaacgtgcgttaatttagaaagaacatccagtataagttcttctatatagtcaattaaagcaggatgcctattaatgggaacgaactgcggcaagttgaatgactggtaagtagtgtagtcgaatgactgaggtgggtatacatttctataaaataaaatcaaattaatgtagcattttaagtataccctcagccacttctctacccatctattcataaagctgacgcaacgattactattttttttttcttcttggatctcagtcgtcgcaaaaacgtataccttctttttccgaccttttttttagctttctggaaaagtttatattagttaaacagggtctagtcttagtgtgaaagctagtggtttcgattgactgatattaagaaagtggaaattaaattagtagtgtagacgtatatgcatatgtatttctcgcctgtttatgtttctacgtacttttgatttatagcaaggggaaaagaaatacatactattttttggtaaaggtgaaagcataatgtaaaagctagaataaaatggacgaaataaagagaggcttagttcatcttttttccaaaaagcacccaatgataataactaaaatgaaaaggatttgccatctgtcagcaacatcagttgtgtgagcaataataaaatcatcacctccgttgcctttagcgcgtttgtcgtttgtatcttccgtaattttagtcttatcaatgggaatcataaattttccaatgaattagcaatttcgtccaattctttttgagcttcttcatatttgctttggaattcttcgcacttcttttcccattcatctctttcttcttccaaagcaacgatccttctacccatttgctcagagttcaaatcggcctctttcagtttatccattgcttccttcagtttggcttcactgtcttctagctgttgttctagatcctggtttttcttggtgtagttctcattattagatctcaagttattggagtcttcagccaattgctttgtatcagacaattgactctctaacttctccacttcactgtcgagttgctcgtttttagcggacaaagatttaatctcgttttctttttcagtgttagattgctctaattctttgagctgttctctcagctcctcatatttttcttgccatgactcagattctaattttaagctattcaatttctctttgatc"
+      assert_equal(expected, @obj.seq)
+    end
+
+    def test_seq_len
+      assert_equal(5028, @obj.seq_len)
+    end
+
+    def test_date_modified
+      assert_equal(Date, @obj.date_modified.class)
+      assert_equal('2010-03-23', @obj.date_modified.to_s)
+    end
+ 
+   def test_classification
+      expected = ["Eukaryota",
+ "Fungi",
+ "Dikarya",
+ "Ascomycota",
+ "Saccharomyceta",
+ "Saccharomycotina",
+ "Saccharomycetes",
+ "Saccharomycetales",
+ "Saccharomycetaceae",
+ "Saccharomyces"]
+      assert_equal(expected, @obj.classification)
+    end
+
+    def test_strandedness
+      assert_equal(nil, @obj.strandedness)
+    end
+
+    #test for bio_to_sequence
+    def test_to_biosequence
+      seq = @obj.to_biosequence
+      expected_seq = "gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgtaacatatttaggatatacctcgaaaataataaaccgccacactgtcattattataattagaaacagaacgcaaaaattatccactatataattcaaagacgcgaaaaaaaaagaacaacgcgtcatagaacttttggcaattcgcgtcacaaataaattttggcaacttatgtttcctcttcgagcagtactcgagccctgtctcaagaatgtaataatacccatcgtaggtatggttaaagatagcatctccacaacctcaaagctccttgccgagagtcgccctcctttgtcgagtaattttcacttttcatatgagaacttattttcttattctttactctcacatcctgtagtgattgacactgcaacagccaccatcactagaagaacagaacaattacttaatagaaaaattatatcttcctcgaaacgatttcctgcttccaacatctacgtatatcaagaagcattcacttaccatgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtgattatacgcaacgatattttgcttaattttattttcctgttttattttttattagtggtttacagataccctatattttatttagtttttatacttagagacatttaattttaattccattcttcaaatttcatttttgcacttaaaacaaagatccaaaaatgctctcgccctcttcatattgagaatacactccattcaaaattttgtcgtcaccgctgattaatttttcactaaactgatgaataatcaaaggccccacgtcagaaccgactaaagaagtgagttttattttaggaggttgaaaaccattattgtctggtaaattttcatcttcttgacatttaacccagtttgaatccctttcaatttctgctttttcctccaaactatcgaccctcctgtttctgtccaacttatgtcctagttccaattcgatcgcattaataactgcttcaaatgttattgtgtcatcgttgactttaggtaatttctccaaatgcataatcaaactatttaaggaagatcggaattcgtcgaacacttcagtttccgtaatgatctgatcgtctttatccacatgttgtaattcactaaaatctaaaacgtatttttcaatgcataaatcgttctttttattaataatgcagatggaaaatctgtaaacgtgcgttaatttagaaagaacatccagtataagttcttctatatagtcaattaaagcaggatgcctattaatgggaacgaactgcggcaagttgaatgactggtaagtagtgtagtcgaatgactgaggtgggtatacatttctataaaataaaatcaaattaatgtagcattttaagtataccctcagccacttctctacccatctattcataaagctgacgcaacgattactattttttttttcttcttggatctcagtcgtcgcaaaaacgtataccttctttttccgaccttttttttagctttctggaaaagtttatattagttaaacagggtctagtcttagtgtgaaagctagtggtttcgattgactgatattaagaaagtggaaattaaattagtagtgtagacgtatatgcatatgtatttctcgcctgtttatgtttctacgtacttttgatttatagcaaggggaaaagaaatacatactattttttggtaaaggtgaaagcataatgtaaaagctagaataaaatggacgaaataaagagaggcttagttcatcttttttccaaaaagcacccaatgataataactaaaatgaaaaggatttgccatctgtcagcaacatcagttgtgtgagcaataataaaatcatcacctccgttgcctttagcgcgtttgtcgtttgtatcttccgtaattttagtcttatcaatgggaatcataaattttccaatgaattagcaatttcgtccaattctttttgagcttcttcatatttgctttggaattcttcgcacttcttttcccattcatctctttcttcttccaaagcaacgatccttctacccatttgctcagagttcaaatcggcctctttcagtttatccattgcttccttcagtttggcttcactgtcttctagctgttgttctagatcctggtttttcttggtgtagttctcattattagatctcaagttattggagtcttcagccaattgctttgtatcagacaattgactctctaacttctccacttcactgtcgagttgctcgtttttagcggacaaagatttaatctcgttttctttttcagtgttagattgctctaattctttgagctgttctctcagctcctcatatttttcttgccatgactcagattctaattttaagctattcaatttctctttgatc"
+      expected_id_namespace = "GenBank"
+      expected_entry_id = "SCU49845"
+      expected_primary_accession = "U49845"
+      expected_secondary_accessions = []
+      expected_other_seqids = ["1293613", "GI", []]
+      expected_molecule_type = "DNA"
+      expected_division = "PLN"
+      expected_topology = "linear"
+      expected_strandedness = nil
+      expected_keywords = []
+      expected_sequence_version = "1"
+      expected_date_modified = "2010-03-23"
+      expected_definition = "Saccharomyces cerevisiae TCP1-beta gene, partial cds; and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds."
+      expected_species = []
+      expected_classification= ["Eukaryota", "Fungi", "Dikarya", "Ascomycota", "Saccharomyceta", "Saccharomycotina", "Saccharomycetes", "Saccharomycetales", "Saccharomycetaceae", "Saccharomyces"]
+      expected_comments = ""
+      expected_references = [{
+  :abstract=>"",
+  :affiliations=>[],
+  :authors=>["Roemer, T.", "Madden, K.", "Chang, J.", "Snyder, M."],
+  :comments=>nil,
+  :doi=>nil,
+  :embl_gb_record_number=>1,
+  :issue=>"7",
+  :journal=>"Genes Dev.",
+  :medline=>"",
+  :mesh=>[],
+  :pages=>"777-793",
+  :pubmed=>"8846915",
+  :sequence_position=>"1-5028",
+  :title=>
+   "Selection of axial growth sites in yeast requires Axl2p, a novel plasma membrane glycoprotein",
+  :url=>nil,
+  :volume=>"10",
+  :year=>"1996"},
+
+  {:abstract=>"",
+  :affiliations=>[],
+  :authors=>["Roemer, T."],
+  :comments=>nil,
+  :doi=>nil,
+  :embl_gb_record_number=>2,
+  :issue=>"",
+  :journal=>
+   "Submitted (22-FEB-1996) Biology, Yale University, New Haven, CT 06520, USA",
+  :medline=>"",
+  :mesh=>[],
+  :pages=>"",
+  :pubmed=>"",
+  :sequence_position=>"1-5028",
+  :title=>"Direct Submission",
+  :url=>nil,
+  :volume=>"",
+  :year=>""}]
+
+      expected_features = [
+ {:feature=>"source",
+  :position=>"1..5028",
+  :qualifiers=>
+   [{:qualifier=>"organism",
+     :value=>"Saccharomyces cerevisiae"},
+    {:qualifier=>"mol_type",
+     :value=>"genomic DNA"},
+    {:qualifier=>"db_xref",
+     :value=>"taxon:4932"},
+    {:qualifier=>"chromosome",
+      :value=>"IX"}]},
+  {:feature=>"mRNA",
+   :position=>"<1..>206",
+   :qualifiers=>
+   [{   
+     :qualifier=>"product",
+     :value=>"TCP1-beta"}]},
+  {:feature=>"CDS",
+   :position=>"<1..206",
+   :qualifiers=>   [{:qualifier=>"codon_start", :value=>3},    {:qualifier=>"product",     :value=>"TCP1-beta"},
+    {:qualifier=>"protein_id",
+     :value=>"AAA98665.1"},
+    {:qualifier=>"db_xref",
+     :value=>"GI:1293614"},
+    {:qualifier=>"translation",
+     :value=>
+      "SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEAAEVLLRVDNIIRARPRTANRQHM"}]},
+  {:feature=>"gene",
+   :position=>"<687..>3158",
+   :qualifiers=>
+   [{:qualifier=>"gene", :value=>"AXL2"}]},
+  {:feature=>"mRNA",
+   :position=>"<687..>3158",
+   :qualifiers=>
+   [{:qualifier=>"gene", :value=>"AXL2"},
+   {:qualifier=>"product",
+    :value=>"Axl2p"}]},
+  {:feature=>"CDS",
+   :position=>"687..3158",
+   :qualifiers=>
+   [{:qualifier=>"gene", :value=>"AXL2"},
+   {:qualifier=>"note",
+    :value=>"plasma membrane glycoprotein"},
+   {:qualifier=>"codon_start", :value=>1},   {:qualifier=>"product",
+     :value=>"Axl2p"},
+   {:qualifier=>"protein_id",
+    :value=>"AAA98666.1"},
+   {:qualifier=>"db_xref",
+    :value=>"GI:1293615"},
+   {:qualifier=>"translation",
+    :value=>
+      "MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESFTFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFNVILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNEVFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPETSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYVYLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYGDVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQDHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSANATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIACGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLNNPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQSQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDSYGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTKHRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRLVDFSNKSNVNVGQVKDIHGRIPEML"}]},
+  {:feature=>"gene",
+   :position=>"complement(<3300..>4037)",
+   :qualifiers=>
+  [{:qualifier=>"gene", :value=>"REV7"}]},
+  {:feature=>"mRNA",
+   :position=>"complement(<3300..>4037)",
+   :qualifiers=>
+     [{:qualifier=>"gene", :value=>"REV7"},
+     {:qualifier=>"product",
+     :value=>"Rev7p"}]},
+  {:feature=>"CDS",
+   :position=>"complement(3300..4037)",
+   :qualifiers=>
+   [{:qualifier=>"gene", :value=>"REV7"},
+    {:qualifier=>"codon_start", :value=>1},
+    {:qualifier=>"product",
+     :value=>"Rev7p"},
+    {:qualifier=>"protein_id",
+     :value=>"AAA98667.1"},
+    {:qualifier=>"db_xref",
+     :value=>"GI:1293616"},
+    {:qualifier=>"translation",
+     :value=>
+      "MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQFVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVDKDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNRRVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEKLISGDDKILNGVYSQYEEGESIFGSLF"}]}]
+
+      assert_equal(expected_seq, seq.seq)
+      assert_equal(expected_id_namespace, seq.id_namespace)
+      assert_equal(expected_entry_id, seq.entry_id)
+      assert_equal(expected_primary_accession, seq.primary_accession)
+      assert_equal(expected_secondary_accessions, seq.secondary_accessions)
+      seqids = seq.other_seqids.first
+      actual_other_seqids = [seqids.id, seqids.database, seqids.secondary_ids]
+      assert_equal(expected_other_seqids, actual_other_seqids)
+      assert_equal(expected_division, seq.division)
+      assert_equal(expected_strandedness, seq.strandedness)
+      assert_equal(expected_keywords, seq.keywords)
+      assert_equal(expected_classification, seq.classification)
+      assert_equal(expected_comments, seq.comments)
+      refs = seq.references
+      actual_references = []
+      refs.each do |ref|
+       actual_references << {:abstract => ref.abstract,
+                             :affiliations => ref.affiliations,
+                             :authors => ref.authors,
+                             :comments => ref.comments,
+                             :doi => ref.doi,
+                             :embl_gb_record_number => ref.embl_gb_record_number,
+                             :issue => ref.issue,
+                             :journal =>  ref.journal,
+                             :medline => ref.medline,
+                             :mesh => ref.mesh,
+                             :pages => ref.pages,
+                             :pubmed => ref.pubmed,
+                             :sequence_position => ref.sequence_position,
+                             :title => ref.title,
+                             :url => ref.url,
+                             :volume => ref.volume,
+                             :year => ref.year}
+      end
+      assert_equal(expected_references, actual_references)
+      fets = seq.features
+      actual_features = []
+      fets.each do |fet|
+        feature = fet.feature
+        position = fet.position
+        quals = []
+        fet.qualifiers.each do |qual|
+          quals << {:qualifier => qual.qualifier, :value => qual.value}
+        end
+      actual_features << {:feature => feature, :position => position, :qualifiers => quals}
+      end
+      assert_equal(expected_features, actual_features) # skip
+      
+
+    end
+
+  end #class TestBioGenBank
+end #module Bio
+

data/test/unit/bio/db/genbank/test_genpept.rb

@@ -0,0 +1,81 @@
+#
+# test/unit/bio/db/genbank/test_genpept.rb - Unit test for Bio::GenPept
+#
+# Copyright::  Copyright (C) 2010 Kazuhiro Hayashi <k.hayashi.info@gmail.com>
+# 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/genbank/genpept.rb'
+
+#The coverage of this class is 100%
+#It tests only the methods descripbed in the soruce class.(It dosen't test the inherited methods from NCBIDB)
+module Bio
+  class TestBioGenPept < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'genbank', 'CAA35997.gp')
+      @obj = Bio::GenPept.new(File.read(filename))
+    end
+
+    def test_locus
+      expected =
+        {:circular=>"linear",
+          :date=>"12-SEP-1993",
+          :division=>"MAM",
+          :entry_id=>"CAA35997",
+          :length=>100}
+      locus  = @obj.locus
+      actual =
+        {:entry_id=>locus.entry_id,
+          :circular=>locus.circular,
+          :date=>locus.date,
+          :division=>locus.division,
+          :length=>locus.length}
+        
+      assert_equal(expected, actual)
+    end
+
+    def test_entry_id
+      assert_equal("CAA35997", @obj.entry_id)
+    end
+
+    def test_length
+      assert_equal(100, @obj.length)
+    end
+
+    def test_circular
+      assert_equal("linear", @obj.circular)
+    end
+
+    def test_division
+      assert_equal("MAM", @obj.division)
+    end
+
+    def test_date
+      assert_equal("12-SEP-1993", @obj.date)
+    end
+
+    def test_seq
+      expected = "MRTPMLLALLALATLCLAGRADAKPGDAESGKGAAFVSKQEGSEVVKRLRRYLDHWLGAPAPYPDPLEPKREVCELNPDCDELADHIGFQEAYRRFYGPV"
+      assert_equal(expected, @obj.seq)
+    end
+
+    def test_seq_len
+      assert_equal(100, @obj.seq_len)
+    end
+
+    def test_dbsource
+      expected = "DBSOURCE    embl accession X51700.1\n"
+      assert_equal(expected, @obj.dbsource)
+    end
+
+  end #class TestBioGenPept
+end #module Bio
+