bio 1.2.1 → 1.3.0

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/test_blast.rb

@@ -4,7 +4,7 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_blast.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -81,6 +81,12 @@ module Bio
       assert_equal('-m 7 -p T', @blast.option) 
     end
 
+    def test_option_set_m0
+      @blast.option = '-m 0'
+      assert_equal('-m 0', @blast.option) 
+    end
+
+
     def test_server
       assert_equal(@server, @blast.server) 
     end
@@ -121,10 +127,135 @@ module Bio
        # to be tested in test/functional/bio/test_blast.rb
      end
 
-     def test_blast_reports
-       Bio::Blast.reports(TestBlastData.output) do |report|
-         assert(report)
+     def test_blast_reports_xml
+       ret = Bio::Blast.reports_xml(TestBlastData.output)
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_xml_with_block
+       count = 0
+       Bio::Blast.reports_xml(TestBlastData.output) do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format0
+       ret = Bio::Blast.reports(TestBlastData.output('0'))
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Default::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format7
+       ret = Bio::Blast.reports(TestBlastData.output('7'))
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format8
+       ret = Bio::Blast.reports(TestBlastData.output('8'))
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_kind_of(Bio::Blast::Report, report)
        end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format0_with_block
+       count = 0
+       Bio::Blast.reports(TestBlastData.output('0')) do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Default::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format7_with_block
+       count = 0
+       Bio::Blast.reports(TestBlastData.output('7')) do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format8_with_block
+       count = 0
+       Bio::Blast.reports(TestBlastData.output('8')) do |report|
+         count += 1
+         assert_kind_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+     
+     def test_blast_reports_format7_with_parser
+       ret = Bio::Blast.reports(TestBlastData.output('7'), :rexml)
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format8_with_parser
+       ret = Bio::Blast.reports(TestBlastData.output('8'), :tab)
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_kind_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format7_with_parser_with_block
+       count = 0
+       Bio::Blast.reports(TestBlastData.output('7'), :rexml) do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format8_with_parser_with_block
+       count = 0
+       Bio::Blast.reports(TestBlastData.output('8'), :tab) do |report|
+         count += 1
+         assert_kind_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_make_command_line
+       @blast = Bio::Blast.new(@program, @db, '-m 7 -F F')
+       assert_equal(["blastall", "-p", "blastp", "-d", "test", "-m", "7", "-F", "F"], 
+                    @blast.instance_eval { make_command_line })
+     end
+     def test_make_command_line_2
+       @blast = Bio::Blast.new(@program, @db, '-m 0 -F F')
+       assert_equal(["blastall", "-p", "blastp", "-d", "test", "-m", "0", "-F",  "F"], 
+                    @blast.instance_eval { make_command_line })
      end
 
      def test_parse_result

data/test/unit/bio/appl/test_fasta.rb

@@ -5,7 +5,7 @@
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-#  $Id: test_fasta.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -94,7 +94,7 @@ module Bio
     end
     
     def test_option
-      option = ['-M'].to_s
+      option = ['-M'].join(' ')
       assert(@obj.option = option)
       assert_equal(option, @obj.option)
     end

data/test/unit/bio/appl/test_pts1.rb

@@ -5,7 +5,7 @@
 #               Mitsuteru Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: test_pts1.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
+# $Id:$
 #
 
 require 'pathname'
@@ -46,12 +46,6 @@ module Bio
   class TestPTS1 < Test::Unit::TestCase
 
     def setup
-      @seq =<<END
->AB000464
-MRTGGDNAGPSHSHIKRLPTSGLSTWLQGTQTCVLHLPTGTRPPAHHPLLGYSSRRSYRL
-LENPAAGCWARFSFCQGAAWDWDLEGVQWLRALAGGVSTAPSAPPGNLVFLSVSIFLCGS
-LLLETCPAYFSSLDPD*
-END
       @serv = Bio::PTS1.new
     end
 
@@ -79,62 +73,5 @@ END
       @serv.function(3)
       assert_equal("GENERAL", @serv.function)
     end
-
-
-    def test_exec
-      report = @serv.exec(@seq)
-      assert_equal(Bio::PTS1::Report, report.class)
-    end
-
-    def test_exec_with_faa
-      report = @serv.exec(Bio::FastaFormat.new(@seq))
-      assert_equal(Bio::PTS1::Report, report.class)
-    end
-
-  end
-
-  class TestPTS1Report < Test::Unit::TestCase
-    def setup
-      serv = Bio::PTS1.new
-      seq = ">hoge\nAVSFLSMRRARL\n"
-      @report = serv.exec(seq)
-    end
-    
-
-    def test_output_size
-      assert_equal(1634, @report.output.size)
-    end
-
-    def test_entry_id
-      assert_equal("hoge", @report.entry_id)
-    end
-
-    def test_prediction
-      assert_equal("Targeted", @report.prediction)
-    end
-    
-    def test_cterm
-      assert_equal("AVSFLSMRRARL", @report.cterm)
-    end
-    
-    def test_score
-      assert_equal("7.559", @report.score)
-    end
-
-    def test_fp
-      assert_equal("2.5e-04", @report.fp)
-    end
-    
-    def test_sppta
-      assert_equal("-5.833", @report.sppta)
-    end
-    
-    def test_spptna
-      assert_equal("-1.698", @report.spptna)
-    end
-
-    def test_profile
-      assert_equal("15.091", @report.profile)
-    end
   end
 end

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

@@ -4,7 +4,7 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_common.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -30,59 +30,59 @@ module Bio
     end
 
     def test_ac
-      assert(@obj.instance_methods.find {|x| x ==  'ac' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'ac' })
     end
 
     def test_accessions
-      assert(@obj.instance_methods.find {|x| x ==  'accessions' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'accessions' })
     end
     
     def test_accession
-      assert(@obj.instance_methods.find {|x| x ==  'accession' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'accession' })
     end
 
     def test_de
-      assert(@obj.instance_methods.find {|x| x ==  'de' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'de' })
     end
     
     def test_description
-      assert(@obj.instance_methods.find {|x| x ==  'description' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'description' })
     end
 
     def test_definition
-      assert(@obj.instance_methods.find {|x| x ==  'definition' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'definition' })
     end
 
     def test_os
-      assert(@obj.instance_methods.find {|x| x ==  'os' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'os' })
     end
 
     def test_og
-      assert(@obj.instance_methods.find {|x| x ==  'og' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'og' })
     end
     
     def test_oc
-      assert(@obj.instance_methods.find {|x| x ==  'oc' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'oc' })
     end
     
     def test_kw
-      assert(@obj.instance_methods.find {|x| x ==  'kw' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'kw' })
     end
 
     def test_keywords
-      assert(@obj.instance_methods.find {|x| x ==  'keywords' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'keywords' })
     end
 
     def test_ref
-      assert(@obj.instance_methods.find {|x| x ==  'ref' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'ref' })
     end
 
     def test_references
-      assert(@obj.instance_methods.find {|x| x ==  'references' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'references' })
     end
 
     def test_dr
-      assert(@obj.instance_methods.find {|x| x ==  'dr' })
+      assert(@obj.instance_methods.find {|x| x.to_s ==  'dr' })
     end
   end