bio 1.4.0 → 1.4.1

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

@@ -0,0 +1,80 @@
+#
+# test/unit/bio/appl/clustalw/test_report.rb - Unit test for Bio::ClustalW::Report
+#
+# Copyright::  Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl> 
+# License::    The Ruby License
+#
+
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+require 'test/unit'
+require 'bio/appl/clustalw/report'
+
+module Bio
+
+  class TestClustalWReport < Test::Unit::TestCase
+
+    def setup
+      test_data_path = Pathname.new(File.join(BioRubyTestDataPath, 'clustalw')).cleanpath.to_s
+      aln_filename = File.join(test_data_path, 'example1.aln')
+      text = File.read(aln_filename)
+      @aln = Bio::ClustalW::Report.new(text)
+    end
+
+    # CLUSTAL 2.0.9 multiple sequence alignment
+    #
+    #
+    # The alignment reads like:
+    #
+    # query                      -MKNTLLKLGVCVSLLGITPFVSTISSVQAERTVEHKVIKNETGTISISQ
+    # gi|115023|sp|P10425|       MKKNTLLKVGLCVSLLGTTQFVSTISSVQASQKVEQIVIKNETGTISISQ
+    #                                                                          .: :
+    # 
+    # query                      LNKNVWVHTELGYFSG-EAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIE
+    # gi|115023|sp|P10425|       LNKNVWVHTELGYFNG-EAVPSNGLVLNTSKGLVLVDSSWDNKLTKELIE
+    #                                *:   .     .     **. .   ..   ::*:       . * :
+
+    def test_header
+      assert_equal('CLUSTAL 2.0.9 multiple sequence alignment',@aln.header)
+    end
+
+    def test_sequences
+      seq = @aln.get_sequence(0)
+      assert_equal('query',seq.definition)
+      assert_equal("-MKNTLLKLGVCVSLLGITPFVSTISSVQAERTVEHKVIKNETGTISISQLNKNVWVHTELGYFSG-EAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFKKRVTDVIITHAHADRIGGMKTLKERGIKAHSTALTAELAKKNG--------------------YEEPLGDLQSVTNLKFGN----MKVETFYPGKGHTEDNIVVWLPQYQILAGGCLVKSASSKDLGNVADAYVNEWSTSIENVLKRYGNINLVVPGHGEVGDR-----GLLLHTLDLLK---------------------------------------------------------------------",seq.to_s)
+      seq = @aln.get_sequence(1)
+      assert_equal('gi|115023|sp|P10425|',seq.definition)
+      assert_equal("MKKNTLLKVGLCVSLLGTTQFVSTISSVQASQKVEQIVIKNETGTISISQLNKNVWVHTELGYFNG-EAVPSNGLVLNTSKGLVLVDSSWDNKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGITALKERGIKAHSTALTAELAKKSG--------------------YEEPLGDLQTVTNLKFGN----TKVETFYPGKGHTEDNIVVWLPQYQILAGGCLVKSAEAKNLGNVADAYVNEWSTSIENMLKRYRNINLVVPGHGKVGDK-----GLLLHTLDLLK---------------------------------------------------------------------",seq.to_s)
+    end
+
+    def test_alignment
+      assert_equal("???????????SN?????????????D??????????L??????????????????H?H?D",@aln.alignment.consensus[60..120])
+    end
+
+    def test_match_line
+      assert_equal("                                              .: :    *:   .     .     **. .   ..   ::*:       . * : : .        .: .* * *   *   :   * .  :     .     .                       *   :    .: .        .:      .*:  ::***:*  .:* .* :: .           .        ::.:            *              :  .                                                                          " ,@aln.match_line)
+    end
+
+  end # class TestClustalwFormat
+
+  class TestClustalWReportWith2ndArgument < Test::Unit::TestCase
+
+    def setup
+      aln_filename = File.join(BioRubyTestDataPath, 'clustalw',
+                               'example1.aln')
+      text = File.read(aln_filename)
+      @aln = Bio::ClustalW::Report.new(text, "PROTEIN")
+    end
+
+    def test_sequences
+      seq = @aln.get_sequence(0)
+      assert_equal('query',seq.definition)
+      assert_equal("-MKNTLLKLGVCVSLLGITPFVSTISSVQAERTVEHKVIKNETGTISISQLNKNVWVHTELGYFSG-EAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFKKRVTDVIITHAHADRIGGMKTLKERGIKAHSTALTAELAKKNG--------------------YEEPLGDLQSVTNLKFGN----MKVETFYPGKGHTEDNIVVWLPQYQILAGGCLVKSASSKDLGNVADAYVNEWSTSIENVLKRYGNINLVVPGHGEVGDR-----GLLLHTLDLLK---------------------------------------------------------------------",seq.to_s)
+      seq = @aln.get_sequence(1)
+      assert_equal('gi|115023|sp|P10425|',seq.definition)
+      assert_equal("MKKNTLLKVGLCVSLLGTTQFVSTISSVQASQKVEQIVIKNETGTISISQLNKNVWVHTELGYFNG-EAVPSNGLVLNTSKGLVLVDSSWDNKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGITALKERGIKAHSTALTAELAKKSG--------------------YEEPLGDLQTVTNLKFGN----TKVETFYPGKGHTEDNIVVWLPQYQILAGGCLVKSAEAKNLGNVADAYVNEWSTSIENMLKRYRNINLVVPGHGKVGDK-----GLLLHTLDLLK---------------------------------------------------------------------",seq.to_s)
+    end
+
+  end #class TestClustalWReportWith2ndArgument
+end

data/test/unit/bio/appl/paml/codeml/test_rates.rb

@@ -31,15 +31,15 @@ class TestCodemlRates < Test::Unit::TestCase
   end
 
   def test_rates_hundred_and_fiftieth_position
-    assert('GGGG', @example_rates[149][:data])
-    assert(0.828, @example_rates[149][:rate])
-    assert(9, @example_rates[149][:freq])
+    assert_equal('GGGG', @example_rates[150][:data])
+    assert_equal(0.828, @example_rates[150][:rate])
+    assert_equal(8, @example_rates[150][:freq])
   end
   
   def test_rates_last_position
-    assert('PHPP', @example_rates.last[:data])
-    assert(1.752, @example_rates.last[:rate])
-    assert(1, @example_rates.last[:freq])
+    assert_equal('PHPP', @example_rates.last[:data])
+    assert_equal(1.752, @example_rates.last[:rate])
+    assert_equal(1, @example_rates.last[:freq])
   end
 end
 

data/test/unit/bio/appl/paml/codeml/test_report.rb

@@ -1,7 +1,10 @@
 #
-# test/unit/bio/appl/paml/codeml/test_report.rb - Unit test for Bio::PAML::Codeml::Report
+# = test/unit/bio/appl/paml/codeml/test_report.rb - Unit tests for Codeml report parser
+#
+# Copyright::  Copyright (C) 2008-2010
+#              Michael D. Barton <mail@michaelbarton.me.uk>,
+#              Pjotr Prins <pjotr.prins@thebird.nl>
 #
-# Copyright::  Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
 # License::    The Ruby License
 #
 
@@ -14,33 +17,237 @@ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
 require 'test/unit'
 require 'bio/appl/paml/codeml/report'
 
-module Bio; module TestPAMLCodeml
-class TestCodemlReport < Test::Unit::TestCase
+module Bio
+
+  # The test code is copied from the examples of Bio::PAML::Codeml::Report
+  # described in lib/bio/appl/paml/codeml/report.rb.
+  module TestPAMLCodemlReportWithModels
+
+    FILENAME_M0M3 = File.join(BioRubyTestDataPath,
+                             'paml/codeml/models/results0-3.txt')
+
+    class TestCodemlReportM0M3 < Test::Unit::TestCase
+
+      def setup
+        buf = File.read(FILENAME_M0M3)
+        @c = Bio::PAML::Codeml::Report.new(buf)
+      end
+
+      # Invoke Bioruby's PAML codeml parser, after having read the contents
+      # of the codeml result file into _buf_ (for example using File.read)
+      def test_initialize
+        assert_instance_of(Bio::PAML::Codeml::Report, @c)
+      end
+
+      # Do we have two models?
+      def test_models
+        assert_equal(2, @c.models.size)
+        assert_equal("M0", @c.models[0].name)
+        assert_equal("M3", @c.models[1].name)
+      end
+
+      # Check the general information
+      def test_num_sequences
+        assert_equal(6, @c.num_sequences)
+      end
+
+      def test_num_codons
+        assert_equal(134, @c.num_codons)
+      end
+
+      def test_descr
+        assert_equal("M0-3", @c.descr)
+      end
+
+      # Test whether the second model M3 is significant over M0
+      def test_significant
+        assert_equal(true, @c.significant)
+      end
+
+      # Next take the overall posterior analysis
+      def test_nb_sites
+        assert_equal(44, @c.nb_sites.size)
+        assert_equal([17, "I", 0.988, 3.293], @c.nb_sites[0].to_a)
+      end
+
+      # We also provide the raw buffers to adhere to the principle of 
+      # unexpected use. Test the raw buffers for content:
+      def test_header
+        assert_equal(1, @c.header.to_s =~ /seed/)
+      end
+
+      def test_footer
+        assert_equal(16, @c.footer.to_s =~ /Bayes/)
+      end
+
+    end #class TestCodemlReportM0M3
+
+    class TestCodemlModelM0M3 < Test::Unit::TestCase
+
+      # Now fetch the results of the first model M0, and check its values
+      def setup
+        buf = File.read(FILENAME_M0M3)
+        c = Bio::PAML::Codeml::Report.new(buf)
+        @m0 = c.models[0]
+        @m3 = c.models[1]
+      end
+
+      def test_tree_length
+        assert_equal(1.90227, @m0.tree_length)
+      end
+
+      def test_lnL
+        assert_equal(-1125.800375, @m0.lnL)
+      end
+
+      def test_omega
+        assert_equal(0.58589, @m0.omega)
+      end
+
+      def test_dN_dS
+        assert_equal(0.58589, @m0.dN_dS)
+      end
+
+      def test_kappa
+        assert_equal(2.14311, @m0.kappa)
+      end
+
+      def test_alpha
+        assert_equal(nil, @m0.alpha)
+      end
+    
+      # We also have a tree (as a string)
+      def test_tree
+        str = "((((PITG_23265T0: 0.000004, PITG_23253T0: 0.400074): 0.000004, PITG_23257T0: 0.952614): 0.000004, PITG_23264T0: 0.445507): 0.000004, PITG_23267T0: 0.011814, PITG_23293T0: 0.092242);"
+        assert_equal(str, @m0.tree)
+      end
+
+      # Check the M3 and its specific values
+      def test_m3_lnL
+        assert_equal(-1070.964046, @m3.lnL)
+      end
+
+      def test_m3_classes
+        assert_equal(3, @m3.classes.size)
+        assert_equal({:w=>0.00928, :p=>0.56413}, @m3.classes[0])
+      end
+
+      def test_m3_tree
+        str = "((((PITG_23265T0: 0.000004, PITG_23253T0: 0.762597): 0.000004, PITG_23257T0: 2.721710): 0.000004, PITG_23264T0: 0.924326): 0.014562, PITG_23267T0: 0.000004, PITG_23293T0: 0.237433);"
+        assert_equal(str, @m3.tree)
+      end
+
+      def test_to_s
+        assert_equal(3, @m0.to_s =~ /one-ratio/)
+      end
+
+      def test_m3_to_s
+        assert_equal(3, @m3.to_s =~ /discrete/)
+      end
+
+    end #class TestCodemlModelM0M3
+
+    class TestCodemlPositiveSiteM0M3 < Test::Unit::TestCase
+
+      def setup
+        buf = File.read(FILENAME_M0M3)
+        c = Bio::PAML::Codeml::Report.new(buf)
+        @codon = c.nb_sites[0]
+      end
+
+      def test_position
+        assert_equal(17, @codon.position)
+      end
+
+      def test_probability
+        assert_equal(0.988, @codon.probability)
+      end
+
+      def test_dN_dS
+        assert_equal(3.293, @codon.dN_dS)
+      end
+
+      # with aliases
+      def test_p
+        assert_equal(0.988, @codon.p)
+      end
+
+      def test_w
+        assert_equal(3.293, @codon.w)
+      end
+
+    end #class TestCodemlPositiveSiteM0M3
+
+    class TestCodemlPositiveSitesM0M3 < Test::Unit::TestCase
+
+      def setup
+        buf = File.read(FILENAME_M0M3)
+        c = Bio::PAML::Codeml::Report.new(buf)
+        @nb_sites = c.nb_sites
+      end
+  
+      # Now we generate special string 'graph' for positive selection. The 
+      # following returns a string the length of the input alignment and 
+      # shows the locations of positive selection:
+      def test_graph
+        str = "                **    *       * *"
+        assert_equal(str, @nb_sites.graph[0..32])
+      end
+
+      # And with dN/dS (high values are still an asterisk *)
+      def test_graph_omega
+        str = "                3*    6       6 2"
+        assert_equal(str, @nb_sites.graph_omega[0..32])
+      end
+    end #class TestCodemlPositiveSitesM0M3
+
+    # Finally we do a test on an M7+M8 run.
+    FILENAME_M7M8 = File.join(BioRubyTestDataPath,
+                              'paml/codeml/models/results7-8.txt')
+
 
-  TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'paml', 'codeml')).cleanpath.to_s
+    class TestCodemlReportM7M8 < Test::Unit::TestCase
 
-  def setup
-    str = File.read(File.join(TEST_DATA, 'output.txt'))
-    @example_report = Bio::PAML::Codeml::Report.new(str)
-  end
+      def setup
+        buf = File.read(FILENAME_M7M8)
+        @c = Bio::PAML::Codeml::Report.new(buf)
+      end
 
-  def test_tree_log_likelihood
-    assert_equal(-1817.465211, @example_report.tree_log_likelihood)
-  end
+      # Do we have two models?
+      def test_models
+        assert_equal(2, @c.models.size)
+        assert_equal("M7", @c.models[0].name)
+        assert_equal("M8", @c.models[1].name)
+      end
 
-  def test_tree_length
-    assert_equal(0.77902, @example_report.tree_length)
-  end
+      # Assert the results are significant
+      def test_significant
+        assert_equal(true, @c.significant)
+      end
 
-  def test_alpha
-    assert_equal(0.58871, @example_report.alpha)
-  end
+      # Compared to M0/M3 there are some differences. The important ones
+      # are the parameters and the full Bayesian result available for M7/M8.
+      # This is the naive Bayesian result:
+      def test_nb_sites
+        assert_equal(10, @c.nb_sites.size)
+      end
 
-  def test_tree
-    tree = "(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);"
-    assert_equal(tree, @example_report.tree)
-  end
+      # And this is the full Bayesian result:
+      def test_sites
+        assert_equal(30, @c.sites.size)
+        array = [17, "I", 0.672, 2.847]
+        assert_equal(array, @c.sites[0].to_a)
+        str = "                **    *       * *"
+        assert_equal(str, @c.sites.graph[0..32])
+        
+        # Note the differences of omega with earlier M0-M3 naive Bayesian 
+        # analysis:
+        str2 = "                24    3       3 2"
+        assert_equal(str2, @c.sites.graph_omega[0..32])
+        # The locations are the same, but the omega differs.
+      end
+    end #class TestCodemlReportM7M8
 
-end
+  end #module TestPAMLCodemlReportWithModels
+end #module Bio
 
-end; end #module TestPAMLCodeml; module Bio

data/test/unit/bio/appl/paml/codeml/test_report_single.rb

@@ -0,0 +1,46 @@
+#
+# test/unit/bio/appl/paml/codeml/test_report_single.rb - Unit test for Bio::PAML::Codeml::Report
+#
+# Copyright::  Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
+# License::    The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/appl/paml/codeml/report'
+
+module Bio; module TestPAMLCodeml
+class TestCodemlReport < Test::Unit::TestCase
+
+  TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'paml', 'codeml')).cleanpath.to_s
+
+  def setup
+    str = File.read(File.join(TEST_DATA, 'output.txt'))
+    @example_report = Bio::PAML::Codeml::Report.new(str)
+  end
+
+  def test_tree_log_likelihood
+    assert_equal(-1817.465211, @example_report.tree_log_likelihood)
+  end
+
+  def test_tree_length
+    assert_equal(0.77902, @example_report.tree_length)
+  end
+
+  def test_alpha
+    assert_equal(0.58871, @example_report.alpha)
+  end
+
+  def test_tree
+    tree = "(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);"
+    assert_equal(tree, @example_report.tree)
+  end
+
+end
+
+end; end #module TestPAMLCodeml; module Bio

data/test/unit/bio/db/embl/test_sptr.rb

@@ -1660,7 +1660,7 @@ CC   -----------------------------------------------------------------------"
               "     MEEPQSDPSV EPPLSQETFS DLWKLLPENN VLSPLPSQAM DDLMLSPDDI EQWFTEDPGP\n" * 200,
               "//\n"].join
       sp = SPTR.new(data)
-      assert(12000, sp.seq.size)
+      assert_equal(12000, sp.seq.size)
     end
   end
 

data/test/unit/bio/db/fasta/test_defline.rb

@@ -0,0 +1,160 @@
+#
+# test/unit/bio/db/fasta/test_defline.rb - Unit test for Bio::FastaDefline
+#
+# 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/fasta/defline.rb'
+
+module Bio
+  class TestBioFastaDefline < Test::Unit::TestCase
+
+    def setup
+      #test for all the patterns.
+      @rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
+      @ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]") #from an exaple in the class file
+      @sce = Bio::FastaDefline.new(">sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]") #from an exaple in the class file
+      @emb = Bio::FastaDefline.new(">emb:CACDC28 [X80034] C.albicans CDC28 gene") #from an exaple in the class file
+      @abc = Bio::FastaDefline.new(">ABC12345 this is test") #from an exaple in the class file
+      @etc = Bio::FastaDefline.new(">fasta1") # In this case, the defline has only a id like string?
+      #test for the other formats
+    end
+
+    def test_entry_id
+      assert_equal("gi|671595", @rub.entry_id)
+      assert_equal("gi|2495000", @ckr.entry_id)
+      assert_equal("sce:YBR160W", @sce.entry_id)
+      assert_equal("emb:CACDC28", @emb.entry_id)
+      assert_equal("ABC12345", @abc.entry_id)
+      assert_equal("fasta1", @etc.entry_id)
+    end
+
+    def test_to_s
+      assert_equal("gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]", @rub.to_s)
+      assert_equal("gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]", @ckr.to_s)
+      assert_equal("sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]", @sce.to_s)
+      assert_equal("emb:CACDC28 [X80034] C.albicans CDC28 gene", @emb.to_s)
+      assert_equal("ABC12345 this is test", @abc.to_s)
+      assert_equal("fasta1", @etc.to_s)
+    end
+
+    def test_description
+      assert_equal("rubisco large subunit [Perovskia abrotanoides]", @rub.description)
+      assert_equal("CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)", @ckr.description)
+      assert_equal("CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]", @sce.description)
+      assert_equal("[X80034] C.albicans CDC28 gene", @emb.description)
+      assert_equal("this is test", @abc.description)
+      assert_equal("", @etc.description)
+    end
+
+    def test_descriptions
+      assert_equal(["rubisco large subunit [Perovskia abrotanoides]"], @rub.descriptions)
+      assert_equal(["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)", "cholecystokinin A receptor - guinea pig", "cholecystokinin A receptor; CCK-A receptor [Cavia]"], @ckr.descriptions)
+      assert_equal(["CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]"], @sce.descriptions)
+      assert_equal(["[X80034] C.albicans CDC28 gene"], @emb.descriptions)
+      assert_equal("this is test", @abc.description)
+      assert_equal("", @etc.description) #this result that return a string is correct?
+    end
+
+    def test_id_strings
+      assert_equal(["671595", "CAA85678.1"], @rub.id_strings)
+      assert_equal(["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898", "544724", "AAB29504.1", "Cavia"], @ckr.id_strings)
+      assert_equal(["YBR160W", "2.7.1.-", "CC28_YEAST", "CC28_YEAST", "CDC28"], @sce.id_strings)
+      assert_equal(["CACDC28", "X80034", "CDC28", "X80034"] , @emb.id_strings)  #this result that return "X80034" twice is correct?
+      assert_equal(["ABC12345"], @abc.id_strings)
+      assert_equal(["fasta1"], @etc.id_strings)
+    end
+
+    def test_words
+      assert_equal(["abrotanoides", "large", "perovskia", "rubisco", "subunit"], @rub.words)
+      assert_equal(["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig", "receptor", "type"], @ckr.words)
+      assert_equal(["catalytic", "cyclin-dependent", "kinase", "srm5", "subunit"], @sce.words)
+      assert_equal(["albicans"], @emb.words)  #this result that return "X80034" twice is correct?
+      assert_equal(["test"], @abc.words)
+      assert_equal([], @etc.words)
+      assert_equal(["CCK-A", "CCK-AR", "CHOLECYSTOKININ", "Cavia", "RECEPTOR", "TYPE", "cholecystokinin", "guinea", "pig", "receptor"], @ckr.words(true)) #case sensitive
+      #probably, it need not check changes in second and third arguments.
+    end
+    def test_get
+      #get each db from each pattern except the duplicate.
+      assert_equal("671595", @rub.get("gi"))
+      assert_equal("CCKR_CAVPO", @ckr.get("sp"))
+      assert_equal("I51898", @ckr.get("pir"))
+      assert_equal("AAB29504.1", @ckr.get("gb"))
+      assert_equal("YBR160W", @sce.get("sce"))
+      assert_equal("2.7.1.-", @sce.get("EC"))
+      assert_equal("CC28_YEAST", @sce.get("SP"))
+      assert_equal("CACDC28", @emb.get("emb"))
+      #the other dbs
+    end
+    def test_get_by_type
+      #specify each type in each pattern while refering to NSIDs.
+      assert_equal("671595", @rub.get_by_type("gi"))
+      assert_equal("CAA85678.1", @rub.get_by_type("acc_version"))
+      assert_equal(nil, @rub.get_by_type("locus"))
+      assert_equal("Q63931", @ckr.get_by_type("accession"))
+      assert_equal("CCKR_CAVPO", @ckr.get_by_type("entry_id"))
+    end
+    
+    def test_get_all_by_type
+      #specify each type in each pattern while refering to NSIDs.
+      assert_equal(["671595", "CAA85678.1"], @rub.get_all_by_type("gi","acc_version","locus"))
+      assert_equal(["Q63931", "CCKR_CAVPO", "I51898"], @ckr.get_all_by_type("accession","entry_id"))
+    end
+    def test_locus
+      #Any of the examples don't have the locus information ...
+      assert_equal(nil, @rub.locus)
+
+    end
+    def test_gi
+      assert_equal("671595", @rub.gi)
+      assert_equal("2495000", @ckr.gi)
+      assert_equal(nil, @sce.gi) #sce dosen't have "gi" in the type.
+    end
+    def test_acc_version
+       assert_equal("CAA85678.1", @rub.acc_version)
+       assert_equal("AAB29504.1", @ckr.acc_version)
+       assert_equal("CACDC28", @emb.acc_version)
+    end
+
+    def test_accessions
+      assert_equal(["CACDC28"], @emb.accessions)
+      assert_equal(["CAA85678"], @rub.accessions)
+      assert_equal(["Q63931", "AAB29504"], @ckr.accessions)
+      assert_raise(RuntimeError){@sce.accesions} #sce dosen't have "accession" in the type.
+    end
+    def test_accession
+      assert_equal("CACDC28", @emb.accession)
+      assert_equal("CAA85678", @rub.accession)
+      assert_equal("AAB29504", @ckr.accession)
+      assert_raise(RuntimeError){@sce.accesion} #sce dosen't have "accession" in the type.
+
+      # to cover the else statement
+      ckr2 = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)") #from an exaple in the class file
+      assert_equal("Q63931", ckr2.accession)
+
+    end
+
+
+    def test_method_missing
+      #Methods specified with the types are tested only in this test metho.d
+      assert_equal("CCKR_CAVPO", @ckr.sp)
+      assert_equal("I51898", @ckr.pir)
+      assert_equal("AAB29504.1", @ckr.gb)
+      assert_equal("YBR160W", @sce.sce)
+      assert_equal("2.7.1.-", @sce.EC)
+      assert_equal("CC28_YEAST", @sce.SP)
+      assert_equal("CACDC28", @emb.emb)
+    end
+
+  end #class TestBioFastaDefline
+end #module Bio
+