wwood-bioruby 1.2.11

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

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+#
+# test/unit/bio/appl/mafft/test_report.rb - Unit test for Bio::Alignment::MultiFastaFormat
+#
+# Copyright::  Copyright (C) 2007
+#              2005 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id: test_report.rb,v 1.1 2007/07/16 12:21:39 ngoto Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+
+require 'bio'
+
+module Bio
+  class TestAlignmentMultiFastaFormat < Test::Unit::TestCase
+    def setup
+      @na = Bio::Alignment::MultiFastaFormat.new <<__END_OF_NASEQS__
+>naseq1
+TAGATTTCGAATTTCTAGnGAACCGAACCGkACAGCCTTACATyATTCAGACCAATGTGT
+TACCAATTCGAGTATACAAGAACAGTGATAAGGTACCAAACAACGACTTCTTCCCGAACC
+>naseq2
+TAGATTTCGAATCTAGGGAATCCGATACGGACAGCCTTACATTATTCAGACCAATGTGTA
+TACCAATTCGAGAATACAAGAACGTGATAAGGTACCCAAACAACGACTTCTTCCCGAACC
+>naseq3
+TAGATTTCGAATCTAGGGAATCCGATACCGGACAGCCTTACATTATTCAGACCAATGTGT
+TACCAATTCGAGAATACAAGAACGTGATAAGGTACCCAAACAACGACTTCTTCCCGAACC
+__END_OF_NASEQS__
+
+      @aa = Bio::Alignment::MultiFastaFormat.new <<__END_OF_AASEQS__
+>aaseq1
+MVHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLT
+>aaseq2
+MLTAEEKAAVTGFWGKVKVDEVGAEALGRLLVVYPWTQRFFEHFGDLSSADAVMNNAKVKAHGKKVLDSF
+>aaseq3
+MVHLTDAEKSAVSCLWAKVNPDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIT
+>aaseq4
+MVHLTDAEKAAVNGLWGKVNPDDVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIN
+__END_OF_AASEQS__
+    end #def setup
+
+    def test_alignment
+      assert_equal(120, @na.alignment.alignment_length)
+      assert_equal(70, @aa.alignment.alignment_length)
+    end
+
+    def test_entries
+      assert_equal(3, @na.entries.size)
+      assert_equal(4, @aa.entries.size)
+    end
+
+    def test_determine_seq_method
+      @na.alignment
+      assert_equal(:naseq, @na.instance_eval { @seq_method })
+      @aa.alignment
+      assert_equal(:aaseq, @aa.instance_eval { @seq_method })
+    end
+  end #class TestAlignmentMultiFastaFormat
+end #module Bio

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

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+#
+# test/unit/bio/appl/paml/codeml/test_rates.rb - Unit test for Bio::PAML::Codeml::Rates
+#
+# Copyright::  Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
+# License::    The Ruby License
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/paml/codeml/rates'
+
+module Bio; module TestPAMLCodeml
+class TestCodemlRates < Test::Unit::TestCase
+
+  bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6)).cleanpath.to_s
+  TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
+
+  def setup
+    str = File.read(File.join(TEST_DATA, 'rates'))
+    @example_rates = Bio::PAML::Codeml::Rates.new(str)
+  end
+
+  def test_rates_first_position
+    assert_equal('***M', @example_rates.first[:data])
+    assert_equal(1, @example_rates.first[:rate])
+    assert_equal(1, @example_rates.first[:freq])
+  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])
+  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])
+  end
+end
+
+end; end #module TestPAMLCodeml; module Bio

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

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+#
+# test/unit/bio/appl/paml/codeml/test_report.rb - Unit test for Bio::PAML::Codeml::Report
+#
+# Copyright::  Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
+# License::    The Ruby License
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/paml/codeml/report'
+
+module Bio; module TestPAMLCodeml
+class TestCodemlReport < Test::Unit::TestCase
+
+  bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6)).cleanpath.to_s
+  TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', '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/appl/paml/test_codeml.rb

@@ -0,0 +1,174 @@
+#
+# test/unit/bio/appl/paml/test_codeml.rb - Unit test for Bio::PAML::Codeml
+#
+# Copyright::  Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
+# License::    The Ruby License
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/paml/codeml'
+
+module Bio; module TestPAMLCodeml
+  module TestCodemlData
+
+    bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+    TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
+
+    def self.example_control
+      File.join TEST_DATA, 'control_file.txt'
+    end
+
+  end #module TestCodemlData
+
+  class TestCodemlInitialize < Test::Unit::TestCase
+
+    def test_new_with_one_argument
+      factory = Bio::PAML::Codeml.new('echo')
+      assert_instance_of(Bio::PAML::Codeml, factory)
+      assert_equal('echo', factory.instance_eval { @program })
+    end
+
+    def test_new_with_two_argument
+      factory = Bio::PAML::Codeml.new('echo', { :test => 'value' })
+      assert_instance_of(Bio::PAML::Codeml, factory)
+      assert_equal('echo', factory.instance_eval { @program })
+      assert_equal('value', factory.parameters[:test])
+    end
+
+    def test_new_with_parameters
+      factory = Bio::PAML::Codeml.new(nil, { :test => 'value' })
+      assert_instance_of(Bio::PAML::Codeml, factory)
+      assert_equal('codeml', factory.instance_eval { @program })
+      assert_equal('value', factory.parameters[:test])
+    end
+
+    def test_new_without_argument
+      factory = Bio::PAML::Codeml.new
+      assert_instance_of(Bio::PAML::Codeml, factory)
+      assert_equal('codeml', factory.instance_eval { @program })
+    end
+
+  end #class TestCodemlInitialize
+
+  class TestCodeml < Test::Unit::TestCase
+    def setup
+      @codeml = Bio::PAML::Codeml.new
+    end
+
+    def test_parameters
+      params = { :verbose => 1 }
+      @codeml.parameters = params
+      assert_equal(params, @codeml.parameters)
+    end
+
+    def test_load_parameters
+      str = " seqfile = test.aa \n verbose = 1 \n"
+      params = { :seqfile => 'test.aa', :verbose => '1' }
+      assert_equal(params, @codeml.load_parameters(str))
+    end
+
+    def test_set_default_parameters
+      assert_equal(Bio::PAML::Codeml::DEFAULT_PARAMETERS,
+                   @codeml.set_default_parameters)
+      # modifying parameters should not affect DEFAULT_PARAMETERS
+      @codeml.parameters[:only_for_test] = 'this is test'
+      assert_not_equal(Bio::PAML::Codeml::DEFAULT_PARAMETERS,
+                       @codeml.parameters)
+    end
+
+    def test_dump_parameters
+      params = { :seqfile => 'test.aa', :verbose => '1' }
+      @codeml.parameters = params
+      assert_equal("seqfile = test.aa\nverbose = 1\n",
+                   @codeml.dump_parameters)
+    end
+
+  end #class TestCodeml
+
+  class TestCodemlControlGeneration < Test::Unit::TestCase
+
+    TEST_DATA = TestCodemlData::TEST_DATA
+
+    def generate_control_file
+      @tempfile_control = Tempfile.new('codeml_control')
+      @tempfile_control.close(false)
+      @tempfile_outfile = Tempfile.new('codeml_test')
+      @tempfile_outfile.close(false)
+
+      test_control = @tempfile_control.path
+      Bio::PAML::Codeml.create_control_file({
+        :model       => 1,
+        :fix_kappa   => 1,
+        :aaRatefile  => File.join(TEST_DATA, 'wag.dat'),
+        :seqfile     => File.join(TEST_DATA, 'abglobin.aa'),
+        :treefile    => File.join(TEST_DATA, 'abglobin.trees'),
+        :outfile     => @tempfile_outfile.path,
+      }, test_control)
+      test_control
+    end
+    private :generate_control_file
+
+    def setup
+      @example_control = generate_control_file
+    end
+
+    def teardown
+      @tempfile_control.close(true)
+      @tempfile_outfile.close(true)
+    end
+
+    def test_control_file_generated
+      assert_not_nil(File.size?(@example_control))
+    end
+
+    def test_expected_parameters_set_in_control_file
+      produced_control = File.open(@example_control) do |f|
+        f.inject(Hash.new) do |hash,line|
+          hash.store(*line.strip.split(' = '))
+          hash
+        end
+      end
+      assert_equal(File.join(TEST_DATA, 'abglobin.aa'),
+                   produced_control['seqfile'])
+      assert_equal('1', produced_control['fix_kappa'])
+      assert_equal('1', produced_control['model'])
+    end
+  end #class TestCodemlControlGeneration
+
+  class TestControlFileUsage < Test::Unit::TestCase
+    
+    def setup
+      @codeml = Bio::PAML::Codeml.new
+      @codeml.load_parameters(File.read(TestCodemlData.example_control))
+    end
+
+    def test_parameters_should_be_loaded_from_control
+      assert_not_nil(@codeml.parameters)
+    end
+
+    def test_correct_parameters_should_be_loaded
+      assert_equal('abglobin.aa', @codeml.parameters[:seqfile])
+      assert_equal('1', @codeml.parameters[:fix_kappa])
+      assert_equal('1', @codeml.parameters[:model])
+    end
+
+  end #class TestControlFileUsage
+
+  class TestExpectedErrorsThrown < Test::Unit::TestCase
+  
+    def test_error_thrown_if_seqfile_does_not_specified
+      codeml = Bio::PAML::Codeml.new('echo')
+      codeml.load_parameters(File.read(TestCodemlData.example_control))
+      codeml.parameters[:seqfile] = nil
+      assert_raises RuntimeError do
+        codeml.query_by_string()
+      end
+    end
+  
+  end #class TestExpectedErrorsThrown
+
+end; end #module TestPAMLCodeml; module Bio

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

@@ -0,0 +1,81 @@
+#
+# test/unit/bio/appl/sosui/test_report.rb - Unit test for Bio::SOSUI::Report
+#
+# Copyright::   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+#  $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/sosui/report'
+
+
+module Bio
+
+  bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+  test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'SOSUI')).cleanpath.to_s
+  SOSUIReport = File.open(File.join(test_data, 'sample.report')).read
+
+
+  class TestSOSUIReportConst  < Test::Unit::TestCase
+
+    def test_delimiter
+      assert_equal("\n>", Bio::SOSUI::Report::DELIMITER)
+    end
+
+    def test_rs
+      assert_equal("\n>", Bio::SOSUI::Report::RS)
+    end
+
+  end
+
+
+  class TestSOSUIReport < Test::Unit::TestCase
+
+    def setup
+      @obj = Bio::SOSUI::Report.new(SOSUIReport)
+    end
+
+    def test_entry_id
+      assert_equal('Q9HC19', @obj.entry_id)
+    end
+
+    def test_prediction
+      assert_equal('MEMBRANE PROTEIN', @obj.prediction)
+    end
+
+    def test_tmhs
+      assert_equal(Array, @obj.tmhs.class)
+      assert_equal(Bio::SOSUI::Report::TMH, @obj.tmhs[0].class)
+    end
+
+    def test_tmh
+      assert_equal(7, @obj.tmhs.size)
+    end
+
+  end # class TestSOSUIReport
+
+  class TestSOSUITMH < Test::Unit::TestCase
+    def setup
+      @obj = Bio::SOSUI::Report.new(SOSUIReport).tmhs.first
+    end
+
+    def test_range
+      assert_equal(31..53, @obj.range)
+    end
+
+    def test_grade
+      assert_equal('SECONDARY', @obj.grade)
+    end
+    
+    def test_sequence
+      assert_equal('HIRMTFLRKVYSILSLQVLLTTV', @obj.sequence)
+    end
+
+  end # class TestSOSUITMH
+end

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

@@ -0,0 +1,146 @@
+#
+# test/unit/bio/appl/targetp/test_report.rb - Unit test for Bio::TargetP::Report
+#
+# Copyright:  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::   The Ruby License
+#
+#  $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/targetp/report'
+
+
+module Bio
+
+  TargetPReport_plant =<<HOGE
+ 
+### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
+ 
+# Number of input sequences:  1
+# Cleavage site predictions not included.
+# Using PLANT networks.
+ 
+#                        Name   Length	  cTP   mTP    SP other  Loc.  RC
+#----------------------------------------------------------------------------------
+                   MGI_2141503	  640	0.031 0.161 0.271 0.844   _     3
+#----------------------------------------------------------------------------------
+# cutoff                                 0.00  0.00  0.00  0.00
+
+
+HOGE
+
+TargetPReport_plant_c =<<HOGE
+ 
+### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
+ 
+# Number of input sequences:  1
+# Cleavage site predictions included.
+# Using PLANT networks.
+ 
+#                        Name   Length	  cTP   mTP    SP other  Loc.  RC     TPlen
+#----------------------------------------------------------------------------------
+                   MGI_2141503	  640	0.031 0.161 0.271 0.844   _     3	  -
+#----------------------------------------------------------------------------------
+# cutoff                                 0.00  0.00  0.00  0.00
+
+
+
+HOGE
+
+TargetPReport_non_plant_c =<<HOGE
+ 
+### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
+ 
+# Number of input sequences:  1
+# Cleavage site predictions included.
+# Using NON-PLANT networks.
+ 
+#                        Name   Length    mTP   SP  other  Loc.  RC   TPlen
+#--------------------------------------------------------------------------
+                     MGI_96083	 2187	0.292 0.053 0.746   _     3	  -
+#--------------------------------------------------------------------------
+# cutoff                                 0.00  0.00  0.00
+
+
+
+HOGE
+
+
+  class TestTargetPReportConst  < Test::Unit::TestCase
+
+    def test_delimiter
+      assert_equal("\n \n", Bio::TargetP::Report::DELIMITER)
+    end
+
+    def test_rs
+      assert_equal("\n \n", Bio::TargetP::Report::RS)
+    end
+
+  end # class TestTargetPReportConst
+
+
+  class TestTargetPReport < Test::Unit::TestCase
+
+    def setup
+      @obj = Bio::TargetP::Report.new(TargetPReport_plant)
+    end
+
+    def test_version
+      assert_equal('1.0', @obj.version)
+    end
+
+    def test_query_sequences
+      assert_equal(0, @obj.query_sequences)
+    end
+
+    def test_cleavage_site_prediction
+      assert_equal('not included', @obj.cleavage_site_prediction)
+    end
+
+    def test_networks
+      assert_equal('PLANT', @obj.networks)
+    end
+
+    def test_prediction
+      hash = {"Name"=>"MGI_2141503", "Loc."=>"_", "RC"=>3, "SP"=>0.271,
+              "other"=>0.844, "mTP"=>0.161, "cTP"=>0.031, "Length"=>640}
+      assert_equal(hash, @obj.pred)
+      assert_equal(hash, @obj.prediction)
+    end
+
+    def test_cutoff
+      hash = {"SP"=>0.0, "other"=>0.0, "mTP"=>0.0, "cTP"=>0.0}
+      assert_equal(hash, @obj.cutoff)
+    end
+
+
+    def test_entry_id
+      assert_equal('MGI_2141503', @obj.entry_id)
+    end
+
+    def test_name
+      assert_equal('MGI_2141503', @obj.name)
+    end
+
+    def test_query_len
+      assert_equal(640, @obj.query_len)
+    end
+
+    def test_length
+      assert_equal(640, @obj.length)
+    end
+
+    def test_loc
+      assert_equal('_', @obj.loc)
+    end
+
+    def test_rc
+      assert_equal(3, @obj.rc)
+    end
+  end # class TestTargetPReport
+end