bio 0.7.0

data/test/unit/bio/test_sequence.rb

@@ -0,0 +1,386 @@
+#
+# test/unit/bio/tc_sequence.rb - Unit test for Bio::Sequencce
+#
+#   Copyright (C) 2004 Moses Hohman <mmhohman@northwestern.edu>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_sequence.rb,v 1.5 2005/11/26 06:51:45 nakao 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
+
+    def test_to_s_returns_self_as_string
+      s = "abcefghijklmnop"
+      sequence = Sequence.new(s)
+      assert_equal(s, sequence.to_s, "wrong value")
+      assert_instance_of(String, sequence.to_s, "not a String")
+    end
+
+    def test_subseq_returns_nil_blank_sequence_default_end
+      sequence = Sequence.new("")
+      assert_nil(sequence.subseq(5))
+    end
+
+    def test_subseq_returns_nil_start_less_than_one
+      sequence = Sequence.new("blahblah")
+      assert_nil(sequence.subseq(0))
+    end
+    
+    def test_subseq_returns_subsequence
+      sequence = Sequence.new("hahasubhehe")
+      assert_equal("sub", sequence.subseq(5,7))
+    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#to_fasta
+    
+    def test_to_fasta
+      sequence = Sequence.new("agtc"*10)
+      header = "the header"
+      assert_equal(">the header\n" + ("agtc"*5) + "\n" + ("agtc"*5) + "\n", sequence.to_fasta(header, 20))
+    end
+    
+    # Test Sequence#window_wearch
+    
+    def test_window_search_with_width_3_default_step_no_residual
+      sequence = Sequence.new("agtca")
+      windows = []
+      returned_value = sequence.window_search(3) { |window| windows << window }
+      assert_equal(["agt", "gtc", "tca"], windows, "windows wrong")
+      assert_equal("", returned_value, "returned value wrong")
+    end
+    
+    # added
+    def test_window_search_with_width_3_step_two_with_residual
+      sequence = Sequence::NA.new("agtcat")
+      windows = []
+      returned_value = sequence.window_search(3, 2) { |window| windows << window }
+      assert_equal(["agt", "tca"], windows, "windows wrong")
+      assert_equal("t", returned_value, "returned value wrong")
+    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[ag][tc][ac][tg][atg][atc][agc][tgc][gc][at][atgc]/, Sequence::NA.new('atgcrymkdhvbswn').to_re)
+    end
+
+    def test_rna_to_re
+      assert_equal(/augc[ag][uc][ac][ug][aug][auc][agc][ugc][gc][au][augc]/, 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

data/test/unit/bio/test_shell.rb

@@ -0,0 +1,31 @@
+#
+# test/unit/bio/test_shell.rb - Unit test for Bio::Shell
+#
+#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_shell.rb,v 1.4 2005/12/18 17:00:10 k 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 'bioruby'
+
+module Bio
+end

data/test/unit/bio/util/test_color_scheme.rb

@@ -0,0 +1,45 @@
+#
+# test/unit/bio/util/test_color_scheme.rb - Unit test for Bio::ColorScheme
+#
+#   Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_color_scheme.rb,v 1.1 2005/10/23 08:40:41 k Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4 , 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/color_scheme'
+
+module Bio
+  class TestColorScheme < Test::Unit::TestCase
+
+    def test_buried
+      s = Bio::ColorScheme::Buried
+      assert_equal('00DC22', s['A'])
+      assert_equal('00BF3F', s[:c])
+      assert_equal(nil, s[nil])
+      assert_equal('FFFFFF', s['-'])
+      assert_equal('FFFFFF', s[7])
+      assert_equal('FFFFFF', s['junk'])
+      assert_equal('00CC32', s['t'])
+    end
+
+  end
+end