bio 1.4.3.0001 → 1.5.0

data/test/unit/bio/db/embl/{test_uniprot_new_part.rb → test_uniprotkb_new_part.rb}

@@ -1,5 +1,5 @@
 #
-# test/unit/bio/db/embl/test_uniprot_new_part.rb - Unit test for Bio::UniProt for new file formats using part of psudo entries
+# test/unit/bio/db/embl/test_uniprotkb_new_part.rb - Unit test for Bio::UniProtKB for new file formats using part of psudo entries
 #
 # Copyright::  Copyright (C) 2011 Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
@@ -12,14 +12,14 @@ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
 
 # libraries needed for the tests
 require 'test/unit'
-require 'bio/db/embl/uniprot'
+require 'bio/db/embl/uniprotkb'
 
 module Bio
-  class TestUniProt_ID_since_rel9_0 < Test::Unit::TestCase
+  class TestUniProtKB_ID_since_rel9_0 < Test::Unit::TestCase
 
     def setup
       text = "ID   ABC_DEFGH               Reviewed;         256 AA.\n"
-      @obj = Bio::UniProt.new(text)
+      @obj = Bio::UniProtKB.new(text)
     end
 
     def test_id_line
@@ -55,9 +55,9 @@ module Bio
     def test_molecule
       assert_nil(@obj.molecule)
     end
-  end #class TestUniProt_ID_since_rel9_0
+  end #class TestUniProtKB_ID_since_rel9_0
 
-  class TestUniProt_DE_since_rel14_0 < Test::Unit::TestCase
+  class TestUniProtKB_DE_since_rel14_0 < Test::Unit::TestCase
 
     def setup
       text = <<the_end_of_the_text
@@ -87,7 +87,7 @@ DE              Short=CPAC;
 DE   Flags: Precursor; Fragment;
 the_end_of_the_text
 
-      @obj = Bio::UniProt.new(text)
+      @obj = Bio::UniProtKB.new(text)
     end
 
     def test_private_parse_DE_line_rel14
@@ -165,9 +165,9 @@ the_end_of_the_text
       assert_equal(expected, @obj.synonyms)
     end
 
-  end #class TestUniProt_DE_since_rel14_0
+  end #class TestUniProtKB_DE_since_rel14_0
 
-  class TestUniProt_CC_WEB_RESOURCE_since_rel12_2 < Test::Unit::TestCase
+  class TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2 < Test::Unit::TestCase
 
     def setup
       text = <<the_end_of_the_text
@@ -182,7 +182,7 @@ CC   -!- WEB RESOURCE: Name=BioRuby Wiki site;
 CC       URL="http://bioruby.open-bio.org/wiki/";
 the_end_of_the_text
 
-      @obj = Bio::UniProt.new(text)
+      @obj = Bio::UniProtKB.new(text)
     end
 
     def test_cc_web_resource
@@ -203,6 +203,6 @@ the_end_of_the_text
 
       assert_equal(expected, @obj.cc('WEB RESOURCE'))
     end
-  end #class TestUniProt_CC_WEB_RESOURCE_since_rel12_2
+  end #class TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2
 
 end #module Bio

data/test/unit/bio/db/genbank/test_genbank.rb

@@ -202,7 +202,7 @@ module Bio
  "Saccharomycetaceae",
  "Saccharomyces"]
       assert_equal(expected, @obj.classification)
-    end
+   end
 
     def test_strandedness
       assert_equal(nil, @obj.strandedness)
@@ -222,10 +222,10 @@ module Bio
       expected_topology = "linear"
       expected_strandedness = nil
       expected_keywords = []
-      expected_sequence_version = "1"
-      expected_date_modified = "2010-03-23"
+      expected_sequence_version = 1
+      expected_date_modified = Date.parse("2010-03-23")
       expected_definition = "Saccharomyces cerevisiae TCP1-beta gene, partial cds; and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds."
-      expected_species = []
+      expected_species = 'Saccharomyces cerevisiae'
       expected_classification= ["Eukaryota", "Fungi", "Dikarya", "Ascomycota", "Saccharomyceta", "Saccharomycotina", "Saccharomycetes", "Saccharomycetales", "Saccharomycetaceae", "Saccharomyces"]
       expected_comments = ""
       expected_references = [{
@@ -353,9 +353,15 @@ module Bio
       seqids = seq.other_seqids.first
       actual_other_seqids = [seqids.id, seqids.database, seqids.secondary_ids]
       assert_equal(expected_other_seqids, actual_other_seqids)
+      assert_equal(expected_molecule_type, seq.molecule_type)
       assert_equal(expected_division, seq.division)
+      assert_equal(expected_topology, seq.topology)
       assert_equal(expected_strandedness, seq.strandedness)
       assert_equal(expected_keywords, seq.keywords)
+      assert_equal(expected_sequence_version, seq.sequence_version)
+      assert_equal(expected_date_modified, seq.date_modified)
+      assert_equal(expected_definition, seq.definition)
+      assert_equal(expected_species, seq.species)
       assert_equal(expected_classification, seq.classification)
       assert_equal(expected_comments, seq.comments)
       refs = seq.references

data/test/unit/bio/db/pdb/test_pdb.rb

@@ -6,7 +6,6 @@
 #
 # License:: The Ruby License
 #
-#  $Id:$
 #
 
 # loading helper routine for testing bioruby
@@ -2517,7 +2516,8 @@ EOS
   # test of Bio::PDB::Record::ATOM
   class TestResidue < Test::Unit::TestCase
     def setup
-      @res = Bio::PDB::Residue.new(resName="ALA",resSeq = 7, iCode = "", chain = nil)
+      # resName="ALA",resSeq = 7, iCode = "", chain = nil
+      @res = Bio::PDB::Residue.new("ALA", 7, "", nil)
       @res.addAtom(Bio::PDB::Record::ATOM.new.initialize_from_string("ATOM      1  N   ALA A   7      23.484 -35.866  44.510  1.00 28.52           N"))
       @res.addAtom(Bio::PDB::Record::ATOM.new.initialize_from_string("ATOM      2  CA  ALA A   7      23.849 -34.509  44.904  1.00 27.89           C"))
       @res.addAtom(Bio::PDB::Record::ATOM.new.initialize_from_string("ATOM      3  C   ALA A   7      23.102 -34.082  46.159  1.00 26.68           C"))
@@ -2615,14 +2615,16 @@ expected = [{:serial=>1, :name=>"N", :altLoc=>" ", :resName=>"ALA", :chainID=>"A
       assert_equal(expected,actual)
     end
     def test_update_resudue_id
-      res = Bio::PDB::Residue.new(resName="ALA", resSeq = nil, iCode = nil, chain = nil)
+      # resName="ALA", resSeq = nil, iCode = nil, chain = nil
+      res = Bio::PDB::Residue.new("ALA", nil, nil, nil)
       assert_equal(nil, res.residue_id)
     end
   end
   
   class TestHeterogen < Test::Unit::TestCase
     def setup
-      @res = Bio::PDB::Heterogen.new(resName="EDO",resSeq = 701, iCode = "", chain = nil)
+      # resName="EDO",resSeq = 701, iCode = "", chain = nil
+      @res = Bio::PDB::Heterogen.new("EDO", 701, "", nil)
       @res.addAtom(Bio::PDB::Record::HETATM.new.initialize_from_string("HETATM30583  O1  EDO A 701      -1.516 -26.859  49.587  1.00 35.20           O"))
       @res.addAtom(Bio::PDB::Record::HETATM.new.initialize_from_string("HETATM30584  C2  EDO A 701      -0.275 -28.124  51.219  1.00 34.49           C"))
       @res.addAtom(Bio::PDB::Record::HETATM.new.initialize_from_string("HETATM30585  O2  EDO A 701      -1.442 -28.941  51.167  1.00 33.95           O"))
@@ -2716,7 +2718,8 @@ expected = [{:z=>49.587, :resName=>"EDO", :altLoc=>" ", :resSeq=>701, :occupancy
       assert_equal(expected,actual)
     end
     def test_update_resudue_id
-      res = Bio::PDB::Heterogen.new(resName="EDD", resSeq = nil, iCode = nil, chain = nil)
+      # resName="EDD", resSeq = nil, iCode = nil, chain = nil
+      res = Bio::PDB::Heterogen.new("EDD", nil, nil, nil)
       assert_equal(nil, res.residue_id)
     end
   end
@@ -2770,13 +2773,15 @@ expected = [{:z=>49.587, :resName=>"EDO", :altLoc=>" ", :resSeq=>701, :occupancy
         assert_equal(expected, actual)
       end
       def test_addResidue
-        assert_nothing_raised{ @chain.addResidue(Bio::PDB::Residue.new(resName="ALA",resSeq = 9, iCode = 1, chain = @chain))}
+        # resName="ALA",resSeq = 9, iCode = 1, chain = @chain
+        assert_nothing_raised{ @chain.addResidue(Bio::PDB::Residue.new("ALA", 9, 1, @chain))}
       end
       def test_aaseq
         assert_equal("AAA", @chain.aaseq)
       end
       def test_addLigand
-         assert_nothing_raised{ @chain.addLigand(Bio::PDB::Heterogen.new(resName="EDD",resSeq = 10, iCode = 2, chain = @chain)) }
+         # resName="EDD",resSeq = 10, iCode = 2, chain = @chain
+         assert_nothing_raised{ @chain.addLigand(Bio::PDB::Heterogen.new("EDD", 10, 2, @chain)) }
       end
       def test_atom_seq
         assert_equal("AAA", @chain.atom_seq)
@@ -2940,7 +2945,8 @@ expected = [{:z=>49.587, :resName=>"EDO", :altLoc=>" ", :resSeq=>701, :occupancy
   #this class tests Bio::PDB::Utils with Bio::PDB::Residue class witch is generated directly
   class TestUtils < Test::Unit::TestCase
     def setup
-      @res = Bio::PDB::Residue.new(resName="ALA",resSeq = 7, iCode = "", chain = nil)
+      # resName="ALA",resSeq = 7, iCode = "", chain = nil
+      @res = Bio::PDB::Residue.new("ALA", 7, "", nil)
       @res.addAtom(Bio::PDB::Record::ATOM.new.initialize_from_string("ATOM      1  N   ALA A   7      23.484 -35.866  44.510  1.00 28.52           N"))
       @res.addAtom(Bio::PDB::Record::ATOM.new.initialize_from_string("ATOM      2  CA  ALA A   7      23.849 -34.509  44.904  1.00 27.89           C"))
       @res.addAtom(Bio::PDB::Record::ATOM.new.initialize_from_string("ATOM      3  C   ALA A   7      23.102 -34.082  46.159  1.00 26.68           C"))

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

@@ -95,7 +95,7 @@ END
     def test_entry_id
       assert_equal('sce:YBR160W', @obj.entry_id)
     end
-
+    
     def test_acc_version
       assert_equal(nil, @obj.acc_version)
     end
@@ -109,6 +109,10 @@ END
       data = "sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]"
       assert_equal(data, @obj.definition)
     end
+    
+    def test_first_name
+      assert_equal('sce:YBR160W', @obj.first_name)
+    end
 
     def test_data
       data = "\nMSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG\nVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME\nGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL\nKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC\nIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP\nQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES\n"
@@ -225,7 +229,43 @@ END
     def test_acc_version
       assert_equal('AAV50056.1', @obj.acc_version)
     end
+    
+    def test_first_name
+      assert_equal('gi|55416189|gb|AAV50056.1|', @obj.first_name)
+    end
 
   end # class TestFastaFormat
 
+
+  class TestFastaFirstName < Test::Unit::TestCase
+    def test_first_name1
+      data = ">abc def\nATGC"
+      assert_equal 'abc', Bio::FastaFormat.new(data).first_name
+    end
+    
+    def test_first_name_multi_identifier
+      data = ">gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c] #=> 'gi|398365175|ref|NP_009718.3|\nATGCTG"
+      assert_equal 'gi|398365175|ref|NP_009718.3|', Bio::FastaFormat.new(data).first_name
+    end
+    
+    def test_first_name_single_worded_defintion
+      data = ">abc\nATGC"
+      assert_equal 'abc', Bio::FastaFormat.new(data).first_name
+    end
+    
+    def test_no_definition
+      data = ">\nATGC"
+      assert_equal '', Bio::FastaFormat.new(data).first_name
+    end
+    
+    def test_tabbed_defintion
+      data = ">gabc\tdef\nATGC"
+      assert_equal 'gabc', Bio::FastaFormat.new(data).first_name
+    end
+    
+    def test_space_before_first_name
+      data = "> gabcds\tdef\nATGC"
+      assert_equal 'gabcds', Bio::FastaFormat.new(data).first_name
+    end
+  end
 end

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

@@ -795,7 +795,7 @@ _9_
       ERRORS = [ Bio::Fastq::Error::Long_qual.new ]
     end #class TestFastq_error_short_qual
 
-    class TestFastq_error_spaces < Test::Unit::TestCase
+    module TemplateTestFastq_error_spaces
       include TestFastq_error
 
       FILENAME = 'error_spaces.fastq'
@@ -821,22 +821,32 @@ _9_
           end
         end
       end
+    end #module TemplateTestFastq_error_spaces
+
+    class TestFastq_error_spaces < Test::Unit::TestCase
+      include TemplateTestFastq_error_spaces
     end #class TestFastq_error_spaces
 
-    class TestFastq_error_tabs < TestFastq_error_spaces
+    class TestFastq_error_tabs < Test::Unit::TestCase
+      include TemplateTestFastq_error_spaces
       FILENAME = 'error_tabs.fastq'
     end #class TestFastq_error_tabs
 
-    class TestFastq_error_trunc_at_plus < Test::Unit::TestCase
+    module TemplateTestFastq_error_trunc_at_plus
       include TestFastq_error
 
       FILENAME = 'error_trunc_at_plus.fastq'
       PRE_SKIP = 4
       POST_SKIP = 0
       ERRORS = [ Bio::Fastq::Error::No_qual.new ]
+    end #module TemplateTestFastq_error_trunc_at_plus
+
+    class TestFastq_error_trunc_at_plus < Test::Unit::TestCase
+      include TemplateTestFastq_error_trunc_at_plus
     end #class TestFastq_error_trunc_at_plus
 
-    class TestFastq_error_trunc_at_qual < TestFastq_error_trunc_at_plus
+    class TestFastq_error_trunc_at_qual < Test::Unit::TestCase
+      include TemplateTestFastq_error_trunc_at_plus
       FILENAME = 'error_trunc_at_qual.fastq'
     end #class TestFastq_error_trunc_at_qual
 

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

@@ -268,7 +268,7 @@ END_OF_DATA
       assert_equal(val_Target, @obj.attribute('Target'))
       assert_equal('0.0003', @obj.attribute('E_value'))
       val_Align0 = Bio::GFF::GFF2::Record::Value.new(['101', '11'])
-      val_Align1 = Bio::GFF::GFF2::Record::Value.new(['179', '36'])
+      #val_Align1 = Bio::GFF::GFF2::Record::Value.new(['179', '36'])
       assert_equal(val_Align0, @obj.attribute('Align'))
       val_Comment = Bio::GFF::GFF2::Record::Value.new(["Please ignore this \"Comment\" attribute; Escape \x1a\037 and \\\t\r\n\f\b\a\e\v; This is test.", "123", "4.56e-34", "Test for freetext"])
       assert_equal(val_Comment, @obj.attribute('Comment'))
@@ -285,7 +285,7 @@ END_OF_DATA
       assert_equal(val_Target, @obj.get_attribute('Target'))
       assert_equal('0.0003', @obj.get_attribute('E_value'))
       val_Align0 = Bio::GFF::GFF2::Record::Value.new(['101', '11'])
-      val_Align1 = Bio::GFF::GFF2::Record::Value.new(['179', '36'])
+      #val_Align1 = Bio::GFF::GFF2::Record::Value.new(['179', '36'])
       assert_equal(val_Align0, @obj.get_attribute('Align'))
       val_Comment = Bio::GFF::GFF2::Record::Value.new(["Please ignore this \"Comment\" attribute; Escape \x1a\037 and \\\t\r\n\f\b\a\e\v; This is test.", "123", "4.56e-34", "Test for freetext"])
       assert_equal(val_Comment, @obj.get_attribute('Comment'))

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

@@ -36,43 +36,43 @@ module Bio
 
   module TestPhyloXMLData
 
-  PHYLOXML_TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'phyloxml')).cleanpath.to_s
+    PHYLOXML_TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'phyloxml')).cleanpath.to_s
 
-  def self.example_xml
-    File.join PHYLOXML_TEST_DATA, 'phyloxml_examples.xml'
-    #If you want to test the output of writer, then do this:
-    #File.join PHYLOXML_TEST_DATA, 'phyloxml_examples_test.xml'
-    # But make sure you run ruby test/unit/bio/db/test_phyloxml_writer.rb before
-  end
+    def self.example_xml
+      File.join PHYLOXML_TEST_DATA, 'phyloxml_examples.xml'
+      #If you want to test the output of writer, then do this:
+      #File.join PHYLOXML_TEST_DATA, 'phyloxml_examples_test.xml'
+      # But make sure you run ruby test/unit/bio/db/test_phyloxml_writer.rb before
+    end
 
-  def self.made_up_xml
-    File.join PHYLOXML_TEST_DATA, 'made_up.xml'
-    #If you want to test the output of writer, then do this:
-    #File.join PHYLOXML_TEST_DATA, 'made_up_test.xml'
-    # But make sure you run ruby test/unit/bio/db/test_phyloxml_writer.rb before
-  end
+    def self.made_up_xml
+      File.join PHYLOXML_TEST_DATA, 'made_up.xml'
+      #If you want to test the output of writer, then do this:
+      #File.join PHYLOXML_TEST_DATA, 'made_up_test.xml'
+      # But make sure you run ruby test/unit/bio/db/test_phyloxml_writer.rb before
+    end
 
-  def self.metazoa_xml
-    File.join PHYLOXML_TEST_DATA, 'ncbi_taxonomy_metazoa.xml'
-  end
+    def self.metazoa_xml
+      File.join PHYLOXML_TEST_DATA, 'ncbi_taxonomy_metazoa.xml'
+    end
 
-  def self.mollusca_xml
-    File.join PHYLOXML_TEST_DATA, 'ncbi_taxonomy_mollusca.xml'
-  end
+    def self.mollusca_xml
+      File.join PHYLOXML_TEST_DATA, 'ncbi_taxonomy_mollusca.xml'
+    end
 
-  def self.life_xml
-    File.join PHYLOXML_TEST_DATA, 'tol_life_on_earth_1.xml'
-  end
+    def self.life_xml
+      File.join PHYLOXML_TEST_DATA, 'tol_life_on_earth_1.xml'
+    end
 
-  def self.dollo_xml
-    File.join PHYLOXML_TEST_DATA, 'o_tol_332_d_dollo.xml'
-  end
+    def self.dollo_xml
+      File.join PHYLOXML_TEST_DATA, 'o_tol_332_d_dollo.xml'
+    end
 
-  def self.mollusca_short_xml
-    File.join PHYLOXML_TEST_DATA, 'ncbi_taxonomy_mollusca_short.xml'
-  end
+    def self.mollusca_short_xml
+      File.join PHYLOXML_TEST_DATA, 'ncbi_taxonomy_mollusca_short.xml'
+    end
 
-end #end module TestPhyloXMLData
+  end #end module TestPhyloXMLData
 
   
 
@@ -100,7 +100,7 @@ end #end module TestPhyloXMLData
     end
 
     def test_new
-      str = File.read(TestPhyloXMLData.example_xml)
+      str = File.open(TestPhyloXMLData.example_xml, "rb") { |f| f.read }
       assert_instance_of(Bio::PhyloXML::Parser,
                          phyloxml = Bio::PhyloXML::Parser.new(str))
       common_test_next_tree(phyloxml)

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

@@ -172,7 +172,7 @@ module Bio
       writer.write(tree)
 
       assert_nothing_thrown do
-        tree2  = Bio::PhyloXML::Parser.open(filename) { |px| true }
+        Bio::PhyloXML::Parser.open(filename) { |px| true }
       end
 
       #File.delete(filename)
@@ -192,7 +192,7 @@ module Bio
       writer.write(@tree)
 
       assert_nothing_thrown do
-        tree2  = Bio::PhyloXML::Parser.open(filename) { |px| true }
+        Bio::PhyloXML::Parser.open(filename) { |px| true }
       end
       
       #File.delete(filename)

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

@@ -5,7 +5,6 @@
 #
 # License:: The Ruby License
 #
-#  $Id:$
 #
 
 # loading helper routine for testing bioruby
@@ -349,7 +348,7 @@ __END_OF_TEXT__
 
     def test_fastq
       fn = File.join(TestDataPath, 'fastq', 'longreads_original_sanger.fastq')
-      text = File.read(fn, length=300)
+      text = File.read(fn, 300)
       assert_equal(Bio::Fastq, @ad.autodetect(text))
     end
 

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

@@ -184,7 +184,13 @@ module Bio::TestFlatFileBufferedInputStream
         assert_equal(TestDataFastaFormat01, obj.path)
         obj2 = obj
       end
-      assert_raise(IOError) { obj2.close }
+      # Since Ruby 2.3.0, calling IO#close to closed IO object is allowed
+      # without error.
+      if RUBY_VERSION >= "2.3.0"
+        assert_nothing_raised { obj2.close }
+      else
+        assert_raise(IOError) { obj2.close }
+      end
     end
   end #class TestBufferedInputStreamClassMethod
 

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

@@ -251,7 +251,7 @@ __END_OF_DATA__
             flag_header = add_header_line(line)
           end
           unless flag_header then
-            r = add_line(line)
+            add_line(line)
           end
         end
       end