wwood-bioruby 1.2.11

data/test/unit/bio/test_reference.rb

@@ -0,0 +1,252 @@
+#
+# = test/bio/tc_pathway.rb - Unit test for Bio::Pathway
+#
+# Copyright::  Copyright (C) 2006 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+# $Id: test_reference.rb,v 1.3.2.2 2008/06/17 12:24:41 ngoto Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 3, "lib")).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/reference'
+require 'bio/compat/references'
+
+
+module Bio
+  class TestReference < Test::Unit::TestCase
+    
+    def setup
+      hash = {'authors' => [ "Hoge, J.P.", "Fuga, F.B." ], 'title' => "Title of the study.",
+              'journal' => "Theor. J. Hoge", 'volume' => 12, 'issue' => 3, 'pages' => "123-145",
+              'year' => 2001, 'pubmed' => 12345678, 'medline' => 98765432, 'abstract' => "Hoge fuga. hoge fuga.",
+              'url' => "http://example.com", 'mesh' => ['Hoge'], 'affiliations' => ['Tokyo']}
+      @obj = Bio::Reference.new(hash)
+    end
+
+    def test_authors
+      ary = [ "Hoge, J.P.", "Fuga, F.B." ]
+      assert_equal(ary, @obj.authors)
+    end
+
+    def test_journal
+      str = 'Theor. J. Hoge'
+      assert_equal(str, @obj.journal)      
+    end
+    
+    def test_volume
+      str = 12
+      assert_equal(str, @obj.volume)      
+    end
+
+    def test_issue
+      str = 3
+      assert_equal(str, @obj.issue)      
+    end
+
+    def test_pages
+      str = '123-145'
+      assert_equal(str, @obj.pages)
+    end
+
+    def test_year
+      str = 2001
+      assert_equal(str, @obj.year)
+    end
+    
+    def test_pubmed
+      str = 12345678
+      assert_equal(str, @obj.pubmed)
+    end
+
+    def test_abstract
+      str = 'Hoge fuga. hoge fuga.'
+      assert_equal(str, @obj.abstract)
+    end
+
+    def test_url
+      str = 'http://example.com'
+      assert_equal(str, @obj.url)
+    end
+
+    def test_mesh
+      str = ['Hoge']
+      assert_equal(str, @obj.mesh)
+    end
+
+    def test_affiliations
+      str = ['Tokyo']
+      assert_equal(str, @obj.affiliations)
+    end
+
+    def test_format_general
+      str = 'Hoge, J.P., Fuga, F.B. (2001). "Title of the study." Theor. J. Hoge 12:123-145.'
+      assert_equal(str, @obj.format)
+      assert_equal(str, @obj.format('general'))
+      assert_equal(str, @obj.general)
+    end
+
+    def test_format_endnote
+      str = "%0 Journal Article\n%A Hoge, J.P.\n%A Fuga, F.B.\n%D 2001\n%T Title of the study.\n%J Theor. J. Hoge\n%V 12\n%N 3\n%P 123-145\n%M 12345678\n%U http://example.com\n%X Hoge fuga. hoge fuga.\n%K Hoge\n%+ Tokyo"
+      assert_equal(str, @obj.format('endnote'))
+      assert_equal(str, @obj.endnote)
+    end
+
+    def test_format_bibitem
+      str = "\\bibitem{PMID:12345678}\nHoge, J.P., Fuga, F.B.\nTitle of the study.,\n{\\em Theor. J. Hoge}, 12(3):123--145, 2001."
+      assert_equal(str, @obj.format('bibitem'))
+      assert_equal(str, @obj.bibitem)
+    end
+
+    def test_format_bibtex
+      str =<<__END__
+@article{PMID:12345678,
+  author       = {Hoge, J.P. and Fuga, F.B.},
+  title        = {Title of the study.},
+  journal      = {Theor. J. Hoge},
+  year         = {2001},
+  volume       = {12},
+  number       = {3},
+  pages        = {123--145},
+  url          = {http://example.com},
+}
+__END__
+      assert_equal(str, @obj.format('bibtex'))
+      assert_equal(str, @obj.bibtex)
+    end
+
+    def test_format_bibtex_with_arguments
+      str =<<__END__
+@inproceedings{YourArticle,
+  author       = {Hoge, J.P. and Fuga, F.B.},
+  title        = {Title of the study.},
+  year         = {2001},
+  volume       = {12},
+  number       = {3},
+  pages        = {123--145},
+  booktitle    = {Theor. J. Hoge},
+  month        = {December},
+}
+__END__
+      assert_equal(str, @obj.format('bibtex', 'inproceedings', 'YourArticle',
+                                    { 'journal'   => false,
+                                      'url' => false,
+                                      'booktitle' => @obj.journal,
+                                      'month' => 'December'}))
+      assert_equal(str, @obj.bibtex('inproceedings', 'YourArticle',
+                                    { 'journal'   => false,
+                                      'url' => false,
+                                      'booktitle' => @obj.journal,
+                                      'month' => 'December'}))
+    end
+
+    def test_format_rd
+      str = "== Title of the study.\n\n* Hoge, J.P. and Fuga, F.B.\n\n* Theor. J. Hoge 2001 12:123-145 [PMID:12345678]\n\nHoge fuga. hoge fuga."
+      assert_equal(str, @obj.format('rd'))
+      assert_equal(str, @obj.rd)
+    end
+
+    def test_format_nature
+      str = 'Hoge, J.P. & Fuga, F.B. Title of the study. Theor. J. Hoge 12, 123-145 (2001).'
+      assert_equal(str, @obj.format('Nature'))
+      assert_equal(str, @obj.format('nature'))
+      assert_equal(str, @obj.nature)
+    end
+
+    def test_format_science
+      str = 'J.P. Hoge, F.B. Fuga, Theor. J. Hoge 12 123 (2001).'
+      assert_equal(str, @obj.format('Science'))
+      assert_equal(str, @obj.format('science'))
+      assert_equal(str, @obj.science)
+    end
+
+    def test_format_genome_biol
+      str = 'Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.'
+      assert_equal(str, @obj.format('genome biol'))
+      assert_equal(str, @obj.genome_biol)
+    end
+
+    def test_format_genome_res
+      str = "Hoge, J.P. and Fuga, F.B. 2001.\n  Title of the study. Theor. J. Hoge 12: 123-145."
+      assert_equal(str, @obj.format('genome res'))
+      assert_equal(str, @obj.genome_res)
+    end
+
+    def test_format_nar
+      str = 'Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge, 12, 123-145.'
+      assert_equal(str, @obj.format('nar'))
+      assert_equal(str, @obj.nar)
+    end
+
+    def test_format_current
+      str = 'Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.'
+      assert_equal(str, @obj.format('current biology'))
+    end
+
+    def test_format_trends
+      str = 'Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge 12, 123-145'
+      assert_equal(str, @obj.trends)
+    end
+
+    def test_format_cell
+      str = 'Hoge, J.P. and Fuga, F.B. (2001). Title of the study. Theor. J. Hoge 12, 123-145.'
+      assert_equal(str, @obj.format('cell'))
+    end
+
+  end
+
+  class NullStderr
+    def initialize
+      @log = []
+    end
+
+    def write(*arg)
+      #p arg
+      @log.push([ :write, *arg ])
+      nil
+    end
+
+    def method_missing(*arg)
+      #p arg
+      @log.push arg
+      nil
+    end
+  end
+
+  class TestReferences < Test::Unit::TestCase
+
+    def setup
+      # To suppress warning messages, $stderr is replaced by dummy object.
+      @stderr_orig = $stderr
+      $stderr = NullStderr.new
+
+      hash = {}
+      ary = [Bio::Reference.new(hash),
+             Bio::Reference.new(hash)]
+      @obj = Bio::References.new(ary)
+    end
+
+    def teardown
+      # bring back $stderr
+      $stderr = @stderr_orig
+    end
+
+    def test_append
+      hash = {}
+      ref = Bio::Reference.new(hash)
+      assert(@obj.append(ref))
+    end
+
+    def test_each
+      @obj.each do |ref|
+        assert(ref)
+      end
+    end
+
+  end
+
+end

data/test/unit/bio/test_sequence.rb

@@ -0,0 +1,329 @@
+#
+# test/unit/bio/test_sequence.rb - Unit test for Bio::Sequencce
+#
+# Copyright::  Copyright (C) 2004
+#              Moses Hohman <mmhohman@northwestern.edu>
+#              2006 Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id: test_sequence.rb,v 1.9 2007/04/05 23:35:42 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/sequence'
+
+module Bio
+  class TestSequence < Test::Unit::TestCase
+
+    def setup
+      @na  = Sequence::NA.new('atgcatgcatgcatgcaaaa')
+      @rna = Sequence::NA.new('augcaugcaugcaugcaaaa')
+      @aa  = Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')
+    end
+
+
+    # "main" method tests translated into unit tests
+    
+    # Test Sequence::NA.new
+    
+    def test_DNA_new_blank_sequence
+      sequence = Sequence::NA.new('')
+      assert_equal(0, sequence.size)
+    end
+    
+    def test_DNA_new_sequence_downcases_symbols
+      string = 'atgcatgcATGCATGCAAAA'
+      sequence = Sequence::NA.new(string)
+      assert_equal(string.downcase, sequence.to_s)
+    end
+    
+    def test_RNA_new_sequence
+      string = 'augcaugcaugcaugcaaaa'
+      sequence = Sequence::NA.new(string)
+      assert_equal(string, sequence.to_s)
+    end
+    
+    # added
+    
+    def test_DNA_new_sequence_removes_whitespace
+      sequence = Sequence::NA.new("a g\tc\nt\ra")
+      assert_equal("agcta", sequence)
+    end
+
+    # Test Sequence::AA.new
+    
+    def test_AA_new_blank_sequence
+      sequence = Sequence::AA.new('')
+      assert_equal(0, sequence.size)
+    end
+
+    def test_AA_new_sequence_all_legal_symbols
+      string = 'ACDEFGHIKLMNPQRSTVWYU'
+      sequence = Sequence::AA.new(string)
+      assert_equal(string, sequence.to_s)
+    end
+
+    # added
+    
+    def test_AA_new_sequence_upcases_symbols
+      string = 'upcase'
+      sequence = Sequence::AA.new(string)
+      assert_equal(string.upcase, sequence.to_s)
+    end
+
+    def test_AA_new_sequence_removes_whitespace
+      sequence = Sequence::AA.new("S T\tR\nI\rP")
+      assert_equal("STRIP", sequence)
+    end
+
+    # test element indexing
+    
+    def test_element_reference_operator_with_two_arguments
+      sequence = Sequence::NA.new("atggggggtc")
+      assert_equal("gggggg", sequence[2,6])
+    end
+    
+    # added
+    def test_element_reference_operator_with_one_argument
+      sequence = Sequence::NA.new("atggggggtc")
+      assert_equal(?t, sequence[1])
+    end
+    
+    
+    # Test Sequence#total
+    
+    def test_total
+      sequence = Sequence::NA.new("catccagtccctggt")
+      assert_equal(2346, sequence.total({'a'=>1000, 'g'=>100, 't'=>10, 'c'=>1}))
+    end
+
+    # Test Sequence#composition
+    
+    def test_dna_composition
+      sequence = Sequence::NA.new("aggtttcccc")
+      expected = {'a'=>1,'g'=>2,'t'=>3,'c'=>4}
+      expected.default = 0
+      assert_equal(expected, sequence.composition)
+    end
+
+    def test_rna_composition
+      sequence = Sequence::NA.new("agguuucccc")
+      expected = {'a'=>1,'g'=>2,'u'=>3,'c'=>4}
+      expected.default = 0
+      assert_equal(expected, sequence.composition)
+    end
+
+    # I don't get splicing
+
+    # Test Sequence::NA#complement
+
+    def test_dna_sequence_complement
+      assert_equal('ttttgcatgcatgcatgcat', @na.complement)
+    end
+
+    def test_rna_sequence_complement
+      assert_equal('uuuugcaugcaugcaugcau', @rna.complement)
+    end
+    
+    def test_ambiguous_dna_sequence_complement
+      assert_equal("nwsbvhdkmyrcgta", Sequence::NA.new('tacgyrkmhdbvswn').complement)
+    end
+
+    def test_ambiguous_rna_sequence_complement
+      assert_equal("nwsbvhdkmyrcgua", Sequence::NA.new('uacgyrkmhdbvswn').complement)
+    end
+
+    # Test Sequence::NA#translate
+
+    def test_dna_sequence_translate
+      assert_equal("MHACMQ", @na.translate)
+    end
+
+    def test_rna_sequence_translate
+      assert_equal("MHACMQ", @rna.translate)
+    end
+
+    # Test Sequence::NA#gc_percent
+
+    def test_dna_gc_percent
+      assert_equal(40, @na.gc_percent)
+    end
+
+    def test_rna_gc_percent
+      assert_equal(40, @rna.gc_percent)
+    end
+
+    # Test Sequence::NA#illegal_bases
+
+    def test_valid_dna_sequence_illegal_bases
+      assert_equal([], @na.illegal_bases)
+    end
+
+    def test_invalid_nucleic_acid_illegal_bases
+      string = 'tacgyrkmhdbvswn'
+      expected = []
+      string[4..-1].each_byte { |val| expected << val.chr }
+      assert_equal(expected.sort, Sequence::NA.new(string).illegal_bases)
+    end
+
+    def test_invalid_nucleic_acid_illegal_bases_more
+      string = ('abcdefghijklmnopqrstuvwxyz-!%#$@')
+      expected = []
+      'bdefhijklmnopqrsvwxyz-!%#$@'.each_byte { |val| expected << val.chr }
+      assert_equal(expected.sort, Sequence::NA.new(string).illegal_bases)
+    end
+
+    # Test Sequence::NA#molecular_weight
+
+    def test_dna_molecular_weight
+      assert_in_delta(6174.3974, @na.molecular_weight, 1e-5)
+    end
+    
+    def test_rna_molecular_weight
+      assert_in_delta(6438.2774, @rna.molecular_weight, 1e-5)
+    end
+
+    # Test Sequence::NA#to_re
+
+    def test_dna_to_re
+      assert_equal(/atgc[agr][tcy][acm][tgk][atgrwkd][atcwmyh][agcmrsv][tgcyskb][gcw][atw][atgcyrwskmbdhvn]/, Sequence::NA.new('atgcrymkdhvbswn').to_re)
+    end
+
+    def test_rna_to_re
+      assert_equal(/augc[agr][ucy][acm][ugk][augrwkd][aucwmyh][agcmrsv][ugcyskb][gcw][auw][augcyrwskmbdhvn]/, Sequence::NA.new('augcrymkdhvbswn').to_re)
+    end
+
+    # Test Sequence::NA#names
+
+    def test_nucleic_acid_names
+      # It is a Bio::NucleicAcid feature.
+      #      assert_equal(["adenine", "cytosine", "guanine", "thymine", "uracil"], Sequence::NA.new('acgtu').names)
+      assert(Sequence::NA.new('acgtu').names)
+    end
+
+    # Test Sequence::NA#pikachu
+
+    def test_dna_pikachu
+      assert_equal("pika", Sequence::NA.new('atgc').pikachu)
+    end
+
+    def test_rna_pikachu
+      assert_equal("pika", Sequence::NA.new('augc').pikachu)
+    end
+
+    # Test Sequence::NA#randomize
+
+    def test_randomize_dna_retains_composition
+      assert_equal(@na.composition, @na.randomize.composition)
+    end
+
+    # this test has a neglibly small chance of failure
+    def test_two_consecutive_dna_randomizations_not_equal
+      assert_not_equal(@na.randomize, @na.randomize)
+    end
+
+    def test_randomize_dna_can_be_chained
+      assert_equal(@na.composition, @na.randomize.randomize.composition)
+    end
+
+    def test_randomize_dna_with_block
+      appended = ""
+      @na.randomize {|x| appended << x}
+      assert_equal(@na.composition, Sequence::NA.new(appended).composition)
+    end
+
+    # Test Sequence::NA.randomize(counts)
+
+    def test_NA_randomize_with_counts
+      counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
+      counts.default = 0
+      assert_equal(counts, Sequence::NA.randomize(counts).composition)
+    end
+
+    def test_NA_randomize_with_counts_and_block
+      appended = ""
+      counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
+      counts.default = 0
+      Sequence::NA.randomize(counts) {|x| appended << x}
+      assert_equal(counts, Sequence::NA.new(appended).composition)
+    end
+
+    # Test Sequence::AA#codes
+
+    def test_amino_acid_codes
+      assert_equal(["Ala", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile", "Lys", 
+                    "Leu", "Met", "Asn", "Pro", "Gln", "Arg", "Ser", "Thr", "Val", "Trp", 
+                    "Tyr", "Sec"], @aa.codes)
+    end
+
+    # Test Sequence::AA#names
+
+    def test_amino_acid_names
+      assert_equal(["alanine", "cysteine", "aspartic acid", "glutamic acid", "phenylalanine",
+                    "glycine", "histidine", "isoleucine", "lysine", "leucine", "methionine",
+                    "asparagine", "proline", "glutamine", "arginine", "serine", "threonine",
+                    "valine", "tryptophan", "tyrosine", "selenocysteine"], @aa.names)
+    end
+
+    # Test Sequence::AA#molecular_weight
+
+    def test_amino_acid_molecular_weight
+      assert_in_delta(2395.725, @aa.subseq(1,20).molecular_weight, 0.0001)
+    end
+
+    #Test Sequence::AA#randomize
+
+    def test_amino_acid_randomize_has_same_composition
+      aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
+      s = Sequence::AA.new(aaseq)
+      assert_equal(s.composition, s.randomize.composition)
+    end
+
+    # this test has a neglibly small chance of failure
+    def test_consecutive_amino_acid_randomizes_are_not_equal
+      aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
+      s = Sequence::AA.new(aaseq)
+      assert_not_equal(s.randomize, s.randomize)
+    end
+
+    def test_amino_acid_randomize_can_be_chained
+      aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
+      s = Sequence::AA.new(aaseq)
+      assert_equal(s.randomize.composition, s.randomize.randomize.composition)
+    end
+  end
+
+
+  class TestNATranslate < Test::Unit::TestCase
+    def setup
+      @obj = Bio::Sequence::NA.new("AAA")
+    end
+
+    def test_translate
+      assert_equal("K", @obj.translate)
+    end
+    def test_translate_1
+      assert_equal("K", @obj.translate(1))
+    end
+    def test_translate_2
+      assert_equal("", @obj.translate(2))
+    end
+    def test_translate_3
+      assert_equal("", @obj.translate(3))
+    end
+    def test_translate_4
+      assert_equal("F", @obj.translate(4))
+    end
+    def test_translate_5
+      assert_equal("", @obj.translate(5))
+    end
+    def test_translate_5
+      assert_equal("", @obj.translate(6))
+    end
+  end
+
+end