bio 1.4.2 → 1.4.3

data/test/unit/bio/db/sanger_chromatogram/test_abif.rb

@@ -21,7 +21,8 @@ module Bio
     DataPath = Pathname.new(File.join(BioRubyTestDataPath,
                                       'sanger_chromatogram')).cleanpath.to_s
     def self.abif
-      File.read(File.join(DataPath, 'test_chromatogram_abif.ab1'))
+      fn = File.join(DataPath, 'test_chromatogram_abif.ab1')
+      File.open(fn, 'rb') { |f| f.read }
     end
   end #module TestAbifData
 

data/test/unit/bio/db/sanger_chromatogram/test_scf.rb

@@ -20,10 +20,12 @@ module Bio
     DataPath = Pathname.new(File.join(BioRubyTestDataPath,
                                       'sanger_chromatogram')).cleanpath.to_s
     def self.scf_version_2
-      File.read(File.join(DataPath, 'test_chromatogram_scf_v2.scf'))
+      fn = File.join(DataPath, 'test_chromatogram_scf_v2.scf')
+      File.open(fn, "rb") { |f| f.read }
     end
     def self.scf_version_3
-      File.read(File.join(DataPath, 'test_chromatogram_scf_v3.scf'))
+      fn = File.join(DataPath, 'test_chromatogram_scf_v3.scf')
+      File.open(fn, "rb") { |f| f.read }
     end
   end #module TestScfData
 

data/test/unit/bio/db/test_newick.rb

@@ -57,7 +57,9 @@ module Bio
 
     def test_reparse
       tree = @newick.tree
+      tree_text = tree.output(:newick)
       assert_equal(@newick, @newick.reparse)
+      assert_equal(tree_text, @newick.tree.output(:newick))
     end
 
     def test_reparse_before_lazy_parsing

data/test/unit/bio/db/test_phyloxml.rb

@@ -83,6 +83,20 @@ end #end module TestPhyloXMLData
       assert_instance_of(Bio::PhyloXML::Parser,
                          phyloxml = Bio::PhyloXML::Parser.open(filename))
       common_test_next_tree(phyloxml)
+      phyloxml.close
+    end
+
+    def test_open_with_block
+      filename = TestPhyloXMLData.example_xml
+      phyloxml_bak = nil
+      ret = Bio::PhyloXML::Parser.open(filename) do |phyloxml|
+        assert_instance_of(Bio::PhyloXML::Parser, phyloxml)
+        common_test_next_tree(phyloxml)
+        phyloxml_bak = phyloxml
+        "ok"
+      end
+      assert_equal("ok", ret)
+      assert_equal(true, phyloxml_bak.closed?)
     end
 
     def test_new
@@ -192,8 +206,8 @@ end #end module TestPhyloXMLData
 
 
   class TestPhyloXML_close < Test::Unit::TestCase
-    def phyloxml_open
-      Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml)
+    def phyloxml_open(&block)
+      Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml, &block)
     end
     private :phyloxml_open
 
@@ -203,6 +217,25 @@ end #end module TestPhyloXMLData
       assert_nil(phyloxml.close)
     end
 
+    def test_closed?
+      phyloxml = phyloxml_open
+      assert_equal(false, phyloxml.closed?)
+      phyloxml.next_tree
+      assert_equal(false, phyloxml.closed?)
+      phyloxml.close
+      assert_equal(true, phyloxml.closed?)
+    end
+
+    def test_closed_with_block
+      ret = phyloxml_open do |phyloxml|
+        assert_equal(false, phyloxml.closed?)
+        phyloxml.next_tree
+        assert_equal(false, phyloxml.closed?)
+        phyloxml
+      end
+      assert_equal(true, ret.closed?)
+    end
+
     def test_close_after_close
       phyloxml = phyloxml_open
       phyloxml.close
@@ -215,6 +248,25 @@ end #end module TestPhyloXMLData
       assert_raise(LibXML::XML::Error) { phyloxml.next_tree }
     end
 
+    def test_next_tree_after_open_with_block
+      phyloxml = phyloxml_open { |arg| arg }
+      assert_raise(LibXML::XML::Error) { phyloxml.next_tree }
+    end
+
+    def test_close_after_open_with_block
+      phyloxml = phyloxml_open { |arg| arg }
+      assert_raise(LibXML::XML::Error) { phyloxml.close }
+    end
+
+    def test_close_in_open_with_block
+      phyloxml = phyloxml_open do |arg|
+        ret = arg
+        assert_nil(arg.close)
+        ret
+      end
+      assert_raise(LibXML::XML::Error) { phyloxml.close }
+    end
+
     def test_close_does_not_affect_io
       io = File.open(TestPhyloXMLData.example_xml)
       phyloxml = Bio::PhyloXML::Parser.for_io(io)

data/test/unit/bio/db/test_phyloxml_writer.rb

@@ -116,12 +116,12 @@ module Bio
       filename = @writeto.file("test2.xml")
       writer = Bio::PhyloXML::Writer.new(filename)
       
-      tree = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.mollusca_short_xml).next_tree
+      tree = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.mollusca_short_xml) { |px| px.next_tree }
       
       writer.write(tree)
 
       assert_nothing_thrown do
-        Bio::PhyloXML::Parser.open(filename)
+        Bio::PhyloXML::Parser.open(filename) { |px| true }
       end
 
       #File.delete(filename)
@@ -145,7 +145,7 @@ module Bio
       tree.add_edge(root_node, node2)
       writer.write(tree)
       
-      lines = File.open(filename).readlines()
+      lines = File.readlines(filename)
       assert_equal("<phyloxml xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd\" xmlns=\"http://www.phyloxml.org\">",
                     lines[1].chomp)
       assert_equal("  <phylogeny rooted=\"true\">", lines[2].chomp)
@@ -164,7 +164,7 @@ module Bio
     end
 
     def test_phyloxml_examples_tree1
-      tree = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml).next_tree
+      tree = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml) { |px| px.next_tree }
 
       filename = @writeto.file('example_tree1.xml')
       writer = Bio::PhyloXML::Writer.new(filename)
@@ -172,7 +172,7 @@ module Bio
       writer.write(tree)
 
       assert_nothing_thrown do
-        tree2  = Bio::PhyloXML::Parser.open(filename)
+        tree2  = Bio::PhyloXML::Parser.open(filename) { |px| true }
       end
 
       #File.delete(filename)
@@ -185,13 +185,14 @@ module Bio
       2.times do
         @tree = phyloxml.next_tree
       end
+      phyloxml.close
       
       filename = @writeto.file('example_tree2.xml')
       writer = Bio::PhyloXML::Writer.new(filename)
       writer.write(@tree)
 
       assert_nothing_thrown do
-        tree2  = Bio::PhyloXML::Parser.open(filename)
+        tree2  = Bio::PhyloXML::Parser.open(filename) { |px| true }
       end
       
       #File.delete(filename)
@@ -202,12 +203,13 @@ module Bio
       4.times do
         @tree = phyloxml.next_tree
       end
+      phyloxml.close
       #@todo tree = phyloxml[4]
       filename = @writeto.file('example_tree4.xml')
       writer = Bio::PhyloXML::Writer.new(filename)
       writer.write(@tree)
       assert_nothing_thrown do
-        @tree2 = Bio::PhyloXML::Parser.open(filename).next_tree
+        @tree2 = Bio::PhyloXML::Parser.open(filename) { |px| px.next_tree }
       end
       assert_equal(@tree.name, @tree2.name)
       assert_equal(@tree.get_node_by_name('A').taxonomies[0].scientific_name, @tree2.get_node_by_name('A').taxonomies[0].scientific_name)
@@ -224,6 +226,7 @@ module Bio
       phyloxml.each do |tree|
         writer.write(tree)
       end
+      phyloxml.close
 
       assert_nothing_thrown do
         @phyloxml_test = Bio::PhyloXML::Parser.open(filename)
@@ -233,6 +236,8 @@ module Bio
         @tree = @phyloxml_test.next_tree
       end
 
+      @phyloxml_test.close
+
       assert_equal("x", @tree.sequence_relations[0].id_ref_0)
       assert_equal("z", @tree.sequence_relations[1].id_ref_1)
       assert_equal(nil, @tree.sequence_relations[2].distance)
@@ -285,7 +290,7 @@ module Bio
       Bio::PhyloXML::Writer.new(filename).write(tree)
 
       assert_nothing_thrown do
-        Bio::PhyloXML::Parser.open(filename).next_tree
+        Bio::PhyloXML::Parser.open(filename) { |px| px.next_tree }
       end
 
       #File.delete(filename)
@@ -302,7 +307,7 @@ module Bio
       writer.write_other(phyloxml.other)
 
       assert_nothing_thrown do
-        Bio::PhyloXML::Parser.open(filename)
+        Bio::PhyloXML::Parser.open(filename) { |px| true }
       end
       # The output file is not deleted since it might be used in the phyloxml
       # parser test. But since the order of tests can't be assumed, I can't
@@ -319,6 +324,7 @@ module Bio
       phyloxml.each do |tree|
         writer.write(tree)
       end      
+      phyloxml.close
     end
 
   end

data/test/unit/bio/db/test_soft.rb

@@ -90,7 +90,7 @@ module Bio #:nodoc:
       assert_equal( @obj_dataset.database[:institute], 'NCBI NLM NIH')
 
       assert_equal( @obj_dataset.subsets.size, 8)
-      assert_equal( @obj_dataset.subsets.keys, ["GDS100_1",
+      assert_equal( @obj_dataset.subsets.keys.sort, ["GDS100_1",
        "GDS100_2",
        "GDS100_3",
        "GDS100_4",

data/test/unit/bio/io/flatfile/test_autodetection.rb

@@ -347,6 +347,12 @@ __END_OF_TEXT__
 #    def test_sim4
 #    end
 
+    def test_fastq
+      fn = File.join(TestDataPath, 'fastq', 'longreads_original_sanger.fastq')
+      text = File.read(fn, length=300)
+      assert_equal(Bio::Fastq, @ad.autodetect(text))
+    end
+
     def test_fastaformat
       fn = File.join(TestDataPath, 'fasta', 'example1.txt')
       text = File.read(fn)

data/test/unit/bio/io/flatfile/test_buffer.rb

@@ -23,6 +23,145 @@ module Bio::TestFlatFileBufferedInputStream
   TestDataPath = BioRubyTestDataPath
   TestDataFastaFormat01 = File.join(TestDataPath, 'fasta', 'example1.txt')
 
+  class TestBufferedInputStreamParseFileOpenArg < Test::Unit::TestCase
+
+    K = Bio::FlatFile::BufferedInputStream
+
+    def _parse_file_open_mode(mode)
+      K.module_eval { _parse_file_open_mode(mode) }
+    end
+    private :_parse_file_open_mode
+
+    def _parse_file_open_arg(*arg)
+      K.module_eval { _parse_file_open_arg(*arg) }
+    end
+    private :_parse_file_open_arg
+
+    def test_parse_file_open_mode_nil
+      assert_equal(nil, _parse_file_open_mode(nil))
+    end
+
+    def test_parse_file_open_mode_integer
+      assert_equal({ :fmode_integer => 127 },
+                   _parse_file_open_mode(127))
+    end
+
+    def test_parse_file_open_mode_str
+      assert_equal({ :fmode_string => "r+b" },
+                   _parse_file_open_mode("r+b"))
+    end
+
+    def test_parse_file_open_mode_str_with_ext_enc
+      assert_equal({ :fmode_string => "r+t",
+                     :external_encoding => "UTF-8" },
+                   _parse_file_open_mode("r+t:UTF-8"))
+    end
+
+    def test_parse_file_open_mode_str_with_enc
+      assert_equal({ :fmode_string => "rb",
+                     :external_encoding => "EUC-JP",
+                     :internal_encoding => "UTF-8" },
+                   _parse_file_open_mode("rb:EUC-JP:UTF-8"))
+    end
+
+    def test_parse_file_open_arg_nil
+      assert_equal({}, _parse_file_open_arg(nil))
+    end
+
+    def test_parse_file_open_arg_integer
+      assert_equal({ :fmode_integer => 127 },
+                   _parse_file_open_arg(127))
+    end
+
+    def test_parse_file_open_arg_str
+      assert_equal({ :fmode_string => "r+b" },
+                   _parse_file_open_arg("r+b"))
+    end
+
+    def test_parse_file_open_arg_str_with_ext_enc
+      assert_equal({ :fmode_string => "r+t",
+                     :external_encoding => "UTF-8" },
+                   _parse_file_open_arg("r+t:UTF-8"))
+    end
+
+    def test_parse_file_open_arg_str_with_enc
+      assert_equal({ :fmode_string => "rb",
+                     :external_encoding => "EUC-JP",
+                     :internal_encoding => "UTF-8" },
+                   _parse_file_open_arg("rb:EUC-JP:UTF-8"))
+    end
+
+    def test_parse_file_open_arg_str_perm
+      assert_equal({ :fmode_string => "r+b",
+                     :perm => 0644 },
+                   _parse_file_open_arg("r+b", 0644))
+    end
+
+    def test_parse_file_open_arg_int_perm
+      assert_equal({ :fmode_integer => 255,
+                     :perm => 0755 },
+                   _parse_file_open_arg(255, 0755))
+    end
+
+    def test_parse_file_open_arg_int_perm_opt
+      assert_equal({ :fmode_integer => 191,
+                     :perm => 0600,
+                     :textmode => true,
+                     :internal_encoding => "EUC-JP" },
+                   _parse_file_open_arg(191, 0600,
+                                        :textmode => true,
+                                        :internal_encoding => "EUC-JP"))
+    end
+
+    def test_parse_file_open_arg_int_opt
+      assert_equal({ :fmode_integer => 191,
+                     :textmode => true,
+                     :internal_encoding => "EUC-JP" },
+                   _parse_file_open_arg(191, 
+                                        :textmode => true,
+                                        :internal_encoding => "EUC-JP"))
+    end
+
+    def test_parse_file_open_arg_str_perm_opt
+      assert_equal({ :fmode_string => "a",
+                     :perm => 0644,
+                     :binmode => true,
+                     :external_encoding => "UTF-8" },
+                   _parse_file_open_arg("a", 0644,
+                                        :binmode => true,
+                                        :external_encoding => "UTF-8"))
+    end
+
+    def test_parse_file_open_arg_str_opt
+      assert_equal({ :fmode_string => "a",
+                     :binmode => true,
+                     :external_encoding => "UTF-8" },
+                   _parse_file_open_arg("a",
+                                        :binmode => true,
+                                        :external_encoding => "UTF-8"))
+    end
+
+    def test_parse_file_open_arg_opt
+      assert_equal({ :fmode_string => "r",
+                     :binmode => true,
+                     :external_encoding => "UTF-8" },
+                   _parse_file_open_arg(:mode => "r",
+                                        :binmode => true,
+                                        :external_encoding => "UTF-8"))
+    end
+
+    def test_parse_file_open_arg_opt_with_integer_mode
+      assert_equal({ :fmode_integer => 123,
+                     :perm => 0600,
+                     :textmode => true,
+                     :external_encoding => "EUC-JP" },
+                   _parse_file_open_arg(:mode => 123,
+                                        :perm => 0600,
+                                        :textmode => true,
+                                        :external_encoding => "EUC-JP"))
+    end
+  end #class TestBufferedInputStreamParseFileOpenArg
+
   class TestBufferedInputStreamClassMethod < Test::Unit::TestCase
 
     def test_self_for_io
@@ -52,6 +191,7 @@ module Bio::TestFlatFileBufferedInputStream
   class TestBufferedInputStream < Test::Unit::TestCase
     def setup
       io = File.open(TestDataFastaFormat01)
+      io.binmode
       path = TestDataFastaFormat01
       @obj = Bio::FlatFile::BufferedInputStream.new(io, path)
     end
@@ -80,6 +220,7 @@ module Bio::TestFlatFileBufferedInputStream
     def test_pos=()
       str = @obj.gets
       assert_equal(0, @obj.pos = 0)
+      assert_equal(str, @obj.gets)
     end
       
     def test_eof_false_first

data/test/unit/bio/sequence/test_common.rb

@@ -239,6 +239,10 @@ module Bio; module TestSequenceCommon
       assert(rseqs[1] != rseqs[2])
     end
 
+  end #class TestSequenceCommonRandomize
+
+  class TestSequenceCommonRandomizeChi2 < Test::Unit::TestCase
+
     def chi2(hist, f, k)
       chi2 = 0
       (0...k).each do |i|
@@ -250,7 +254,7 @@ module Bio; module TestSequenceCommon
 
     # chi-square test for distribution of chi2 values from
     # distribution of index('a')
-    def randomize_equiprobability
+    def randomize_equiprobability_chi2
       # Reference: http://www.geocities.jp/m_hiroi/light/pystat04.html
       seq = TSequence.new('ccccgggtta') # length must be 10
       k = 10
@@ -280,10 +284,38 @@ module Bio; module TestSequenceCommon
       chi2_chi2 = chi2(chi2_hist, chi2_f, k)
       #$stderr.puts chi2_chi2
 
+      chi2_chi2
+    end
+    private :randomize_equiprobability_chi2
+
+    def randomize_equiprobability(&block)
       ## chi-square test, freedom 9, significance level 5%
-      #assert_operator(16.919, :>, chi2_chi2, "test of chi2 < 16.919 failed (#{chi2_chi2})")
+      #critical_value = 16.919
+      #significance_level_message = "5%"
+      #
       # chi-square test, freedom 9, significance level 1%
-      assert_operator(21.666, :>, chi2_chi2, "test of chi2 < 21.666 failed (#{chi2_chi2})")
+      critical_value = 21.666
+      significance_level_message = "1%"
+
+      # max trial times till the test sucess
+      max_trial = 10
+
+      values =[]
+      max_trial.times do |i|
+        chi2_chi2 = randomize_equiprobability_chi2(&block)
+        values.push chi2_chi2
+        # immediately breaks if the test succeeds
+        break if chi2_chi2 < critical_value
+        $stderr.print "Bio::Sequence::Common#randomize test of chi2 (=#{chi2_chi2}) < #{critical_value} failed (expected #{significance_level_message} by chance)"
+        if values.size < max_trial then
+          $stderr.puts ", retrying."
+        else
+          $stderr.puts " #{values.size} consecutive times!"
+        end
+      end
+
+      assert_operator(values[-1], :<, critical_value,
+                      "test of chi2 < #{critical_value} failed #{values.size} times consecutively (#{values.inspect})")
     end
     private :randomize_equiprobability
 
@@ -319,7 +351,7 @@ module Bio; module TestSequenceCommon
     #  end
     #end
 
-  end
+  end #class TestSequenceCommonRandomizeChi2
 
 
   class TestSequenceCommonSubseq < Test::Unit::TestCase