bio 1.4.1 → 1.4.2

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

@@ -140,6 +140,40 @@ END
       assert_equal(data, @obj.entry)
     end
 
+    def test_entry_overrun
+      data =<<END
+>gi|55416190|gb|AAV50057.1| NADH dehydrogenase subunit 2 [Dasyurus hallucatus]
+MSPYVLMILTLSLFIGTCLTIFSNHWFTAWMGLEINTLAIIPLMTAPNNPRSTEAATKYFLTQATASMLMMFAIIYNAWS
+TNQWALPQLSDDWISLLMTVALAIKLGLAPFHFWVPEVTQGIPLLTGMILLTWQKIAPTAILFQIAPYLNMKFLVILAIL
+STLVGGWGGLNQTHLRKILAYSSIAHMGWMIIIVQINPTLSIFTLTIYVMATLTTFLTLNLSNSTKIKSLGNLWNKSATA
+TIIIFLTLLSLGGLPPLTGFMPKWLILQELINNGNIITATMMALSALLNLFFYMRLIYASSLTMFPSINNSKMQWYNNSM
+KTTTLIPTATVISSLLLPLTPLFVTLY
+END
+      assert_equal(data, @obj.entry_overrun)
+    end
+
+    class DummyFactory
+      def query(str)
+        @query_str = str
+        "DummyFactoryResult#{str.length}"
+      end
+      attr_reader :query_str
+    end #class DummyFactory
+
+    def test_query
+      data =<<END
+>gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]
+MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT
+IALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF
+TLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI
+LFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL
+END
+
+      factory = DummyFactory.new
+      assert_equal("DummyFactoryResult401", @obj.query(factory))
+      assert_equal(data, factory.query_str)
+    end
+
     def test_entry_id
       assert_equal('gi|55416189', @obj.entry_id)
     end
@@ -194,16 +228,4 @@ END
 
   end # class TestFastaFormat
 
-
-
-
-  class TestFastaDefinition < Test::Unit::TestCase
-
-    def setup
-    end
-
-    def test_defline
-    end
-  end # class TestFastaDefinition
-
 end

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

@@ -278,6 +278,20 @@ _9_
         end
       end
 
+      def test_to_s
+        ids = IDLINES.dup
+        seqs = SEQS.dup
+        qstrs = QUALITY_STRINGS.dup
+        ent = []
+        while !ids.empty?
+          ent.push "@#{ids.shift}\n#{seqs.shift}\n+\n#{qstrs.shift}\n"
+        end
+        @ff.each do |e|
+          assert_equal(ent.shift, e.to_s)
+        end
+        assert(ent.empty?)
+      end
+
       def test_definition
         ids = IDLINES.dup
         @ff.each do |e|
@@ -369,6 +383,18 @@ _9_
         end
       end
 
+      def test_to_biosequence_and_output
+        @ff.each_with_index do |e, i|
+          id_line = IDLINES[i]
+          seq_line = SEQS[i]
+          qual_line = QUALITY_STRINGS[i]
+          # Changed default width to nil (no wrapping)
+          expected = "@#{id_line}\n#{seq_line}\n+\n#{qual_line}\n"
+          actual = e.to_biosequence.output(:fastq_sanger)
+          assert_equal(expected, actual)
+        end
+      end
+
       def test_roundtrip
         @ff.each_with_index do |e, i|
           str_orig = @ff.entry_raw

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

@@ -0,0 +1,95 @@
+#
+# test/unit/bio/db/litdb.rb - Unit test for Bio::LITDB
+#
+# Copyright::  Copyright (C) 2010 Kazuhiro Hayashi <k.hayashi.info@gmail.com>
+# License::    The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/litdb'
+require 'bio/reference'
+
+module Bio
+  class TestBioLITDB < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'litdb', '1717226.litdb')
+      @obj = Bio::LITDB.new(File.read(filename))
+    end
+
+    # it return the reference infromation formatted as part of a Bio::Reference object.
+    def test_reference
+      expected = 
+ {:authors=>
+  ["Boyd, L.A.",
+   "Adam, L.",
+   "Pelcher, L.E.",
+   "McHughen, A.",
+   "Hirji, R.",
+   " Selvaraj, G."],
+
+ :issue=>"1",
+ :journal=>"Gene",
+ :pages=>"45-52",
+ :title=>
+  "Characterization of an Escherichia coli gene encoding betaine aldehyde dehydrogenase (BADH). Structural similarity to mammalian ALDHs and a plant BADH.",
+ :volume=>"103",
+ :year=>"(1991)"}
+     litdb_ref = @obj.reference
+       actual = {:authors=>litdb_ref.authors,
+         :journal=> litdb_ref.journal,
+         :pages=> litdb_ref.pages,
+         :volume=>litdb_ref.volume,
+         :year=>litdb_ref.year,
+         :issue=>litdb_ref.issue,
+         :title=>litdb_ref.title
+       }
+      assert_equal(expected, actual)
+    end
+
+    #access to the each field with field_fetch method.
+   #most methods are the same as values of Bio::Refence object.
+    def test_entry_id
+      assert_equal("1717226", @obj.entry_id)
+    end
+
+    def test_title
+      expected = "Characterization of an Escherichia coli gene encoding betaine aldehyde dehydrogenase (BADH). Structural similarity to mammalian ALDHs and a plant BADH."
+      assert_equal(expected, @obj.title)
+    end
+
+    def test_field
+      assert_equal("q (sequence analysis)", @obj.field)
+    end
+
+    def test_journal
+      assert_equal("Gene", @obj.journal)
+    end
+
+    def test_volume
+      assert_equal("Vol.103, No.1, 45-52 (1991)", @obj.volume)
+    end
+
+    def test_keyword
+      expected = ["*Betaine Aldehyde Dehydrogenase",
+ "*betB Gene;E.coli",
+ "Seq Determination;1854bp;491AAs",
+ "Hydropathy Plot;*EC1.2.1.8",
+ "Seq Comparison"]
+      assert_equal(expected, @obj.keyword)
+    end
+
+    def test_author
+      expected = "Boyd,L.A.;Adam,L.;Pelcher,L.E.;McHughen,A.;Hirji,R.; Selvaraj,G."
+      assert_equal(expected, @obj.author)
+    end
+
+  end #class TestBioLITDB
+end #module Bio
+

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

@@ -41,6 +41,7 @@ module Bio
         'volume' => "11",
         'year' => "2010",
         'pubmed' => "20146148",
+        'doi' => "10.1080/15389580903471126",
         'mesh' =>
         [ "Accidents, Traffic/mortality/*statistics & numerical data",
           "Adult",

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

@@ -0,0 +1,82 @@
+#
+# test/unit/bio/db/test_nbrf.rb - Unit test for Bio::NBRF
+#
+# Copyright::  Copyright (C) 2010 Kazuhiro Hayashi <k.hayashi.info@gmail.com>
+# License::    The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/nbrf'
+
+#some condition is not covered with it. This unit test need a nucleotide acid sequence.
+#I can't find a nucleic acid sequence in PIR format 
+module Bio
+  class TestBioNBRF < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'pir', 'CRAB_ANAPL.pir')
+      @obj = Bio::NBRF.new(File.read(filename))
+    end
+
+
+    def test_entry
+      expected = <<END_OF_EXPECTED_ENTRY
+>P1;CRAB_ANAPL
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR 
+  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH 
+  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ 
+  SDVPERSIPI TREEKPAIAG AQRK*
+END_OF_EXPECTED_ENTRY
+      assert_equal(expected, @obj.entry)
+    end
+
+    def test_seq_class
+      assert_equal(Bio::Sequence::AA, @obj.seq_class)
+    end
+
+    def test_seq
+      expected = "MDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELLPASPSLSPFLMRSPIFRMPSWLETGLSEMRLEKDKFSVNLDVKHFSPEELKVKVLGDMVEIHGKHEERQDEHGFIAREFNRKYRIPADVDPLTITSSLSLDGVLTVSAPRKQSDVPERSIPITREEKPAIAGAQRK"
+      assert_equal(expected, @obj.seq)
+    end
+
+    def test_length
+      assert_equal(174, @obj.length)
+    end
+
+    def test_naseq
+      assert_raise(RuntimeError){ @obj.naseq} #@obj is a protein sequence. the method must output error.
+    end
+
+    def test_nalen
+      assert_raise(RuntimeError){ @obj.nalen} #@obj is a protein sequence. the method must output error.
+    end
+
+    def test_aaseq
+      expected = "MDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELLPASPSLSPFLMRSPIFRMPSWLETGLSEMRLEKDKFSVNLDVKHFSPEELKVKVLGDMVEIHGKHEERQDEHGFIAREFNRKYRIPADVDPLTITSSLSLDGVLTVSAPRKQSDVPERSIPITREEKPAIAGAQRK"
+      assert_equal(expected, @obj.aaseq)
+    end
+
+    def test_aalen
+      assert_equal(174, @obj.aalen)
+    end
+
+    def test_to_nbrf
+      expected =<<EOS
+>aaa;ABCD
+this is a fake entry.
+atgc*
+EOS
+      nbrf = {:seq_type=>"aaa", :seq=>"atgc", :width=>7, :entry_id=>"ABCD", :definition=>"this is a fake entry."}
+      assert_equal(expected, Bio::NBRF.to_nbrf(nbrf))
+    end
+
+  end #class TestBioNBRF
+end #module Bio
+

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

@@ -39,9 +39,12 @@ module Bio
     )[0.1250];
     END_OF_TREE_STRING
 
+    def setup
+      @newick = Bio::Newick.new(TREE_STRING)
+    end
+
     def test_string_tree
-      newick = Bio::Newick.new(TREE_STRING)
-      tree = newick.tree
+      tree = @newick.tree
       assert_equal(3, tree.children(tree.root).size)
       assert_equal(9, tree.descendents(tree.root).size)
       assert_equal(6, tree.leaves.size)
@@ -52,6 +55,18 @@ module Bio
       assert_equal("HexFLZ83", leaf.name)
     end
 
+    def test_reparse
+      tree = @newick.tree
+      assert_equal(@newick, @newick.reparse)
+    end
+
+    def test_reparse_before_lazy_parsing
+      # not to use @newick to guarantee that the Newick object
+      # is before lazy parsing.
+      newick = Bio::Newick.new(TREE_STRING)
+      assert_equal(newick, newick.reparse)
+    end
+
   end #class TestNewick
 
   class TestNewick2 < Test::Unit::TestCase
@@ -72,9 +87,12 @@ module Bio
     )root;
     END_OF_TREE_STRING
 
+    def setup
+      @newick = Bio::Newick.new(TREE_STRING)
+    end
+
     def test_string_tree
-      newick = Bio::Newick.new(TREE_STRING)
-      tree = newick.tree
+      tree = @newick.tree
       assert_equal('root', tree.root.name)
       assert_equal([ 
                     "this is test",

data/test/unit/bio/test_reference.rb

@@ -85,6 +85,11 @@ module Bio
       assert_equal(str, @obj.affiliations)
     end
 
+    def test_pubmed_url
+      assert_equal("http://www.ncbi.nlm.nih.gov/pubmed/12345678",
+                   @obj.pubmed_url)
+    end
+
     def test_format_general
       str = 'Hoge, J.P., Fuga, F.B. (2001). "Title of the study." Theor. J. Hoge 12:123-145.'
       assert_equal(str, @obj.format)
@@ -201,6 +206,36 @@ __END__
 
   end
 
+  class TestReference_noURL < Test::Unit::TestCase
+    def setup
+      hash = {
+        'authors' => [ "Hoge, J.P.", "Fuga, F.B." ],
+        'title' => "Title of the study.",
+        'journal' => "Theor. J. Hoge",
+        'volume' => 12,
+        'issue' => 3,
+        'pages' => "123-145",
+        'year' => 2001,
+        'pubmed' => 12345678,
+        'medline' => 98765432,
+        'abstract' => "Hoge fuga. hoge fuga.",
+        'mesh' => ['Hoge'],
+        'affiliations' => ['Tokyo']
+      }
+      @obj = Bio::Reference.new(hash)
+    end
+
+    def test_url
+      assert_equal(nil, @obj.url)
+    end
+
+    def test_format_endnote
+      str = "%0 Journal Article\n%A Hoge, J.P.\n%A Fuga, F.B.\n%D 2001\n%T Title of the study.\n%J Theor. J. Hoge\n%V 12\n%N 3\n%P 123-145\n%M 12345678\n%U http://www.ncbi.nlm.nih.gov/pubmed/12345678\n%X Hoge fuga. hoge fuga.\n%K Hoge\n%+ Tokyo"
+      assert_equal(str, @obj.format('endnote'))
+      assert_equal(str, @obj.endnote)
+    end
+  end #class TestReference_noURL
+
   class TestReferences < Test::Unit::TestCase
 
     class NullStderr

data/test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb

@@ -0,0 +1,201 @@
+#
+# test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb - Unit test for Bio::RestrictionEnzyme::DenseIntArray
+#
+# Copyright::   Copyright (C) 2011
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/util/restriction_enzyme'
+require 'bio/util/restriction_enzyme/dense_int_array'
+
+module Bio
+module TestRestrictionEnzyme
+
+  class TestDenseIntArray < Test::Unit::TestCase
+
+    def setup
+      @klass = Bio::RestrictionEnzyme::DenseIntArray
+      @obj = @klass[ -1, 11, 12, 13, 14, 15, 50, 60 ]
+    end
+
+    def test_self_bracket
+      assert_equal([ -1, 11, 12, 13, 14, 15, 50, 60 ], @obj.to_a)
+    end
+
+    def test_self_new
+      a = @klass.new
+      assert_instance_of(Bio::RestrictionEnzyme::DenseIntArray, a)
+    end
+
+    def test_dup
+      assert_equal(@obj.to_a, @obj.dup.to_a)
+      d_obj = @obj.instance_eval { internal_data }
+      d_dup = @obj.dup.instance_eval { internal_data }
+      assert(d_obj == d_dup)
+      assert_not_equal(d_obj.__id__, d_dup.__id__)
+    end
+
+    def test_internal_data
+      d = @obj.instance_eval { internal_data }
+      r = @klass::MutableRange
+      expected = [ r.new(-1, -1), r.new(11, 15),
+                   r.new(50, 50), r.new(60, 60) ]
+      assert_equal(expected, d)
+    end
+
+    def test_internal_data_eq
+      r = @klass::MutableRange
+      d = [ r.new(-2, -2), r.new(50, 50), r.new(65, 70) ]
+      @obj.instance_eval { self.internal_data = d }
+      assert_equal(70, @obj.last)
+      assert_equal([-2, 50, 65, 66, 67, 68, 69, 70], @obj.to_a)
+    end
+
+    def test_bracket
+      assert_equal(-1, @obj[0])
+      assert_equal(13, @obj[3])
+      assert_equal(60, @obj[-1])
+      assert_equal([-1, 11, 12], @obj[0..2])
+      assert_equal([14, 15, 50], @obj[4,3])
+    end
+
+    def test_bracket_eq
+      assert_raise(NotImplementedError) {
+        @obj[3] = 999
+      }
+    end
+
+    def test_each
+      expected_values = [ -1, 11, 12, 13, 14, 15, 50, 60 ]
+      @obj.each do |i|
+        assert_equal(expected_values.shift, i)
+      end
+    end
+
+    def test_reverse_each
+      expected_values = [ -1, 11, 12, 13, 14, 15, 50, 60 ]
+      @obj.reverse_each do |i|
+        assert_equal(expected_values.pop, i)
+      end
+    end
+
+    def test_plus
+      obj2 = @klass[ 9, 10, 11, 12, 30 ]
+      assert_equal([ -1, 9, 10, 11, 12, 13, 14, 15, 30, 50, 60 ],
+                   (@obj + obj2).to_a)
+    end
+
+    def test_plus_error
+      assert_raise(TypeError) {
+        @obj + 2
+      }
+    end
+
+    def test_eqeq
+      obj2 = @klass[ -1, 11, 12, 13, 14, 15, 50, 60 ]
+      assert_equal(true, @obj == obj2)
+    end
+
+    def test_eqeq_self
+      assert_equal(true, @obj == @obj)
+    end
+
+    def test_eqeq_false
+      obj2 = @klass[ 2, 3, 14, 15 ]
+      assert_equal(false, @obj == obj2)
+    end
+
+    def test_eqeq_other
+      obj2 = 'test'
+      assert_equal(false, @obj == obj2)
+    end
+
+    def test_concat
+      ary = [ 61, 62, -2, 14, 15 ]
+      expected = [ -1, 11, 12, 13, 14, 15, 50, 60, 61, 62, -2, 14, 15 ]
+      # checks if the method returns self
+      assert_equal(@obj, @obj.concat(ary))
+      # checks the value
+      assert_equal(expected, @obj.to_a)
+    end
+
+    def test_push
+      expected = [ -1, 11, 12, 13, 14, 15, 50, 60, 61, 62, -2, 14, 15 ]
+      # checks if the method returns self
+      assert_equal(@obj, @obj.push(61, 62, -2, 14, 15))
+      # checks the value
+      assert_equal(expected, @obj.to_a)
+    end
+
+    def test_unshift
+      assert_raise(NotImplementedError) { @obj.unshift(-5, -2) }
+    end
+
+    def test_ltlt
+      expected = [ -1, 11, 12, 13, 14, 15, 50, 60, 61 ]
+      # checks if the method returns self
+      assert_equal(@obj, @obj << 61)
+      # checks the value
+      assert_equal(expected, @obj.to_a)
+    end
+
+    def test_ltlt_larger
+      expected = [ -1, 11, 12, 13, 14, 15, 50, 60, 70 ]
+      # checks if the method returns self
+      assert_equal(@obj, @obj << 70)
+      # checks the value
+      assert_equal(expected, @obj.to_a)
+    end
+
+    def test_ltlt_middle
+      expected = [ -1, 11, 12, 13, 14, 15, 50, 60, 30 ]
+      # checks if the method returns self
+      assert_equal(@obj, @obj << 30)
+      # checks the value
+      assert_equal(expected, @obj.to_a)
+    end
+
+    def test_include?
+      assert_equal(true, @obj.include?(13))
+      assert_equal(false, @obj.include?(999))
+    end
+
+    def test_size
+      assert_equal(8, @obj.size)
+    end
+
+    def test_length
+      assert_equal(8, @obj.length)
+    end
+
+    def test_delete
+      assert_raise(NotImplementedError) { @obj.delete(11) }
+    end
+
+    def test_sort!
+      assert_equal(@obj, @obj.sort!)
+    end
+
+    def test_uniq!
+      assert_equal(@obj, @obj.uniq!)
+    end
+
+    def test_to_a
+      expected = [ -1, 11, 12, 13, 14, 15, 50, 60 ]
+      assert_equal(expected, @obj.to_a)
+    end
+
+  end #class TestDenseIntArray
+
+end #module TestRestrictionEnzyme
+end #module Bio
+
+