bio 1.4.1 → 1.4.2

data/test/functional/bio/test_command.rb

@@ -96,9 +96,9 @@ module Bio
         @sort = "sort"
         @data = @data.join("\r\n") + "\r\n"
       else
-        @sort = "/usr/bin/sort"
-        unless FileTest.executable?(@sort) then
-          raise "Unsupported environment: /usr/bin/sort not found"
+        @sort = `which sort`.chomp
+        if @sort.empty? or !FileTest.executable?(@sort) then
+          raise "Unsupported environment: sort not found in PATH"
         end
         @data = @data.join("\n") + "\n"
       end

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

@@ -864,12 +864,12 @@ CC       URL="http://www.genetests.org/query?gene=GJB1".'
                     'NAME=Connexin-deafness homepage; URL="http://www.crg.es/deafness/".',
                     'NAME=GeneReviews; URL="http://www.genetests.org/query?gene=GJB1".'],
                    sp.cc['WEB RESOURCE'])
-      assert_equal([{'NAME' => "Inherited peripheral neuropathies mutation db", 
-                     'URL' => 'http://www.molgen.ua.ac.be/CMTMutations/', 'NOTE' => nil},
-                    {'NAME' => "Connexin-deafness homepage", 
-                     'URL' => 'http://www.crg.es/deafness/', 'NOTE' => nil},
-                    {'NAME' => "GeneReviews", 
-                     'URL' => 'http://www.genetests.org/query?gene=GJB1', 'NOTE' => nil}],
+      assert_equal([{'Name' => "Inherited peripheral neuropathies mutation db", 
+                     'URL' => 'http://www.molgen.ua.ac.be/CMTMutations/', 'Note' => nil},
+                    {'Name' => "Connexin-deafness homepage", 
+                     'URL' => 'http://www.crg.es/deafness/', 'Note' => nil},
+                    {'Name' => "GeneReviews", 
+                     'URL' => 'http://www.genetests.org/query?gene=GJB1', 'Note' => nil}],
                    sp.cc('WEB RESOURCE'))
 
     end

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

@@ -0,0 +1,208 @@
+#
+# test/unit/bio/db/embl/test_uniprot_new_part.rb - Unit test for Bio::UniProt for new file formats using part of psudo entries
+#
+# 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/db/embl/uniprot'
+
+module Bio
+  class TestUniProt_ID_since_rel9_0 < Test::Unit::TestCase
+
+    def setup
+      text = "ID   ABC_DEFGH               Reviewed;         256 AA.\n"
+      @obj = Bio::UniProt.new(text)
+    end
+
+    def test_id_line
+      expected = {
+        "ENTRY_NAME" => "ABC_DEFGH",
+        "DATA_CLASS" => "Reviewed",
+        "SEQUENCE_LENGTH" => 256,
+        "MOLECULE_TYPE" => nil
+      }
+      assert_equal(expected, @obj.id_line)
+    end
+
+    def test_entry_id
+      assert_equal("ABC_DEFGH", @obj.entry_id)
+    end
+
+    def test_entry_name
+      assert_equal("ABC_DEFGH", @obj.entry_name)
+    end
+
+    def test_entry
+      assert_equal("ABC_DEFGH", @obj.entry)
+    end
+
+    def test_sequence_length
+      assert_equal(256, @obj.sequence_length)
+    end
+
+    def test_aalen
+      assert_equal(256, @obj.aalen)
+    end
+
+    def test_molecule
+      assert_nil(@obj.molecule)
+    end
+  end #class TestUniProt_ID_since_rel9_0
+
+  class TestUniProt_DE_since_rel14_0 < Test::Unit::TestCase
+
+    def setup
+      text = <<the_end_of_the_text
+ID   ABC_DEFGH               Unreviewed;       256 AA.
+DE   RecName: Full=Aaa Bbbb Ccccc-Dddddd Eeeeeee factor;
+DE            Short=ABC-DEF;
+DE            Short=A-DF;
+DE            EC=9.8.0.1;
+DE   AltName: Full=Bbbb-Aaa Eeeeeee Ccccc;
+DE            Short=Bbbb-Aaa;
+DE            EC=9.8.0.-;
+DE   AltName: Allergen=Bet v 1-B;
+DE   AltName: Biotech=this is fake entry;
+DE   AltName: CD_antigen=CD42c;
+DE   AltName: INN=Pseudo;
+DE   SubName: Full=submitter named this ABC_DEFGH;
+DE            EC=9.8.2.1;
+DE   Includes:
+DE     RecName: Full=Included protein example;
+DE              Short=IPE;
+DE              EC=9.9.9.9;
+DE     AltName: Full=Inclided protein altname;
+DE              Short=IPA;
+DE   Contains:
+DE     RecName: Full=Contained protein alpha chain;
+DE              Short=CPAC;
+DE   Flags: Precursor; Fragment;
+the_end_of_the_text
+
+      @obj = Bio::UniProt.new(text)
+    end
+
+    def test_private_parse_DE_line_rel14
+      expected =
+        [ [ "RecName",
+            ["Full", "Aaa Bbbb Ccccc-Dddddd Eeeeeee factor"],
+            ["Short", "ABC-DEF"],
+            ["Short", "A-DF"],
+            ["EC", "9.8.0.1"]
+          ],
+          [ "AltName",
+            ["Full", "Bbbb-Aaa Eeeeeee Ccccc"],
+            ["Short", "Bbbb-Aaa"],
+            ["EC", "9.8.0.-"]
+          ],
+          [ "AltName",
+            ["Allergen", "Bet v 1-B"]
+          ],
+          [ "AltName",
+            ["Biotech", "this is fake entry"]
+          ],
+          [ "AltName",
+            ["CD_antigen", "CD42c"]
+          ],
+          [ "AltName",
+            ["INN", "Pseudo"]
+          ],
+          [ "SubName",
+            ["Full", "submitter named this ABC_DEFGH"],
+            ["EC", "9.8.2.1"]
+          ],
+          [ "Includes" ],
+          [ "RecName",
+            ["Full", "Included protein example"],
+            ["Short", "IPE"],
+            ["EC", "9.9.9.9"]
+          ],
+          ["AltName",
+           ["Full", "Inclided protein altname"],
+           ["Short", "IPA"]
+          ],
+          [ "Contains" ],
+          [ "RecName",
+            ["Full", "Contained protein alpha chain"],
+            ["Short", "CPAC"]
+          ],
+          [ "Flags",
+            ["Precursor", "Fragment"]
+          ]
+        ]
+      @obj.protein_name
+      ary = @obj.instance_eval { @data['DE'] }
+      assert_equal(expected, ary)
+    end
+
+    def test_protein_name
+      assert_equal('Aaa Bbbb Ccccc-Dddddd Eeeeeee factor',
+                   @obj.protein_name)
+    end
+
+    def test_synonyms
+      expected = [ 'ABC-DEF',
+                   'A-DF',
+                   'EC 9.8.0.1',
+                   'Bbbb-Aaa Eeeeeee Ccccc',
+                   'Bbbb-Aaa',
+                   'EC 9.8.0.-',
+                   'Allergen=Bet v 1-B',
+                   'this is fake entry',
+                   'CD_antigen=CD42c',
+                   'Pseudo',
+                   'submitter named this ABC_DEFGH',
+                   'EC 9.8.2.1'
+                 ]
+      assert_equal(expected, @obj.synonyms)
+    end
+
+  end #class TestUniProt_DE_since_rel14_0
+
+  class TestUniProt_CC_WEB_RESOURCE_since_rel12_2 < Test::Unit::TestCase
+
+    def setup
+      text = <<the_end_of_the_text
+ID   ABC_DEFGH               Unreviewed;       256 AA.
+CC   -!- WEB RESOURCE: Name=BioRuby web site; Note=BioRuby main web site
+CC       located in Tokyo, Japan;
+CC       URL="http://bioruby.org";
+CC   -!- WEB RESOURCE: Name=official mirror of BioRuby web site hosted in
+CC       the Open Bioinformatics Foundation;
+CC       URL="http://bioruby.open-bio.org/";
+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)
+    end
+
+    def test_cc_web_resource
+      expected =
+        [ { "Name" => "BioRuby web site",
+            "Note" => "BioRuby main web site located in Tokyo, Japan",
+            "URL"  => "http://bioruby.org"
+          },
+          { "Name" => "official mirror of BioRuby web site hosted in the Open Bioinformatics Foundation",
+            "Note" => nil,
+            "URL"  => "http://bioruby.open-bio.org/"
+          },
+          { "Name" => "BioRuby Wiki site",
+            "Note" => nil,
+            "URL"  => "http://bioruby.open-bio.org/wiki/"
+          }
+        ]
+
+      assert_equal(expected, @obj.cc('WEB RESOURCE'))
+    end
+  end #class TestUniProt_CC_WEB_RESOURCE_since_rel12_2
+
+end #module Bio

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

@@ -0,0 +1,274 @@
+#
+# test/unit/bio/db/genbank/test_common.rb - Unit test for Bio::NCBIDB::Common
+#
+# 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__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/genbank/common'
+require 'bio/reference'
+require 'bio/compat/references' #  Bio::References in this file seems to be obsolete, but Bio::NCBIDB::Common should require it.
+require 'bio/feature'
+require 'bio/compat/features'    #  Bio::Features in this file seems to be obsolete, but Bio::NCBIDB::Common should require it.
+
+
+# - This class has low coverage, because a sample entry used in it lacks a lot of fields.
+# - There are all the methods for test.
+module Bio
+  class NCBIDB
+    class TestCommon < Test::Unit::TestCase
+
+      #Mock Class including the target module.
+      #BioNCBIDBCommon is used for the test.
+      class BioNCBIDBCommon < Bio::NCBIDB
+        include Bio::NCBIDB::Common
+      end
+
+      #a sample entry is a part of data/genbank/SCU49845.gb
+      def setup
+entry =<<EOF
+LOCUS       SCU49845                5028 bp    DNA     linear   PLN 23-MAR-2010
+DEFINITION  Saccharomyces cerevisiae TCP1-beta gene, partial cds; and Axl2p
+            (AXL2) and Rev7p (REV7) genes, complete cds.
+ACCESSION   U49845
+VERSION     U49845.1  GI:1293613
+KEYWORDS    .
+SOURCE      Saccharomyces cerevisiae (baker's yeast)
+  ORGANISM  Saccharomyces cerevisiae
+            Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomyceta;
+            Saccharomycotina; Saccharomycetes; Saccharomycetales;
+            Saccharomycetaceae; Saccharomyces.
+EOF
+        @obj = BioNCBIDBCommon.new(entry)
+      end
+
+      def test_locus
+        #Since locus method is supposed to be overloaded in a child class, it may not be neccesary to test the method here.
+      end
+      
+      def test_definition
+        expected = "Saccharomyces cerevisiae TCP1-beta gene, partial cds; and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds."
+        assert_equal(expected, @obj.definition)
+      end
+
+      def test_accessions
+         expected = ["U49845"]
+        assert_equal(expected, @obj.accessions)
+      end
+
+      def test_accession
+         expected = "U49845"
+        assert_equal(expected, @obj.accession)
+      end
+
+      def test_versions
+         expected = ["U49845.1", "GI:1293613"]
+        assert_equal(expected, @obj.versions)
+      end
+
+      def test_version
+         expected = 1 
+        assert_equal(expected, @obj.version)
+      end
+
+      def test_acc_version
+         expected = "U49845.1"
+        assert_equal(expected, @obj.acc_version)
+      end
+
+      def test_gi
+         expected = "GI:1293613"
+        assert_equal(expected, @obj.gi)
+      end
+
+      def test_nid
+         expected = ""
+        assert_equal(expected, @obj.nid)
+      end
+
+      def test_keywords
+         expected = []
+        assert_equal(expected, @obj.keywords)
+      end
+
+      def test_segment
+         expected = ""
+        assert_equal(expected, @obj.segment)
+      end
+
+      def test_source
+         expected = {"organism"=>"Saccharomyces cerevisiae",
+                           "common_name"=>"Saccharomyces cerevisiae (baker's yeast)",
+                           "taxonomy"=>
+                                "Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces."}
+        assert_equal(expected, @obj.source)
+
+        #another pattern to pass line 103-105
+        source_pattern2 =<<EOS
+SOURCE      Saccharomyces cerevisiae (baker's yeast)
+  ORGANISM  Saccharomyces cerevisiae
+            Saccharomyces.
+EOS
+        obj2 = BioNCBIDBCommon.new(source_pattern2)
+          expected2 = {"organism"=>"Saccharomyces cerevisiae",
+                       "common_name"=>"Saccharomyces cerevisiae (baker's yeast)",
+                       "taxonomy"=>"Saccharomyces."}
+        assert_equal(expected2, obj2.source)
+
+        #the other pattern to pass line 106-109
+        source_pattern3 =<<EOS
+SOURCE      Saccharomyces cerevisiae (baker's yeast)
+  ORGANISM  Saccharomyces cerevisiae
+EOS
+        obj3 = BioNCBIDBCommon.new(source_pattern3)
+          expected3 = {"organism"=>"Saccharomyces cerevisiae",
+                       "common_name"=>"Saccharomyces cerevisiae (baker's yeast)",
+                       "taxonomy"=>""}
+        assert_equal(expected3, obj3.source)
+      end
+
+      def test_common_name
+         expected = "Saccharomyces cerevisiae (baker's yeast)"
+        assert_equal(expected, @obj.common_name)
+      end
+
+      def test_organism
+         expected = "Saccharomyces cerevisiae"
+        assert_equal(expected, @obj.organism)
+      end
+
+      def test_taxonomy
+         expected = "Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces."
+        assert_equal(expected, @obj.taxonomy)
+      end
+
+      def test_references
+        str=<<EOS
+REFERENCE   2  (bases 1 to 2264)
+  AUTHORS   Zhao,X., Brade,T., Cunningham,T.J. and Duester,G.
+  TITLE     Retinoic acid controls expression of tissue remodeling genes Hmgn1
+            and Fgf18 at the digit-interdigit junction
+  JOURNAL   Dev. Dyn. 239 (2), 665-671 (2010)
+   PUBMED   20034106
+  REMARK    GeneRIF: limited to the digit-interdigit junction rather than being
+            expressed throughout the interdigital zone
+EOS
+        com = BioNCBIDBCommon.new(str)
+        obj = com.references
+         expected = 
+           {:mesh=>[],
+            :volume=>"239",
+            :doi=>nil,
+            :pages=>"665-671",
+            :embl_gb_record_number=>2,
+            :pubmed=>"20034106",
+            :abstract=>"",
+            :issue=>"2",
+            :year=>"2010",
+            :sequence_position=>"1-2264",
+            :affiliations=>[],
+            :journal=>"Dev. Dyn.",
+            :title=>
+             "Retinoic acid controls expression of tissue remodeling genes Hmgn1 and Fgf18 at the digit-interdigit junction",
+            :authors=>["Zhao, X.", "Brade, T.", "Cunningham, T.J.", "Duester, G."],
+            :medline=>"",
+            :url=>nil,
+            :comments=>
+             ["GeneRIF: limited to the digit-interdigit junction rather than being expressed throughout the interdigital zone"]}  
+        actual            = {:abstract => obj[0].abstract,
+                             :affiliations => obj[0].affiliations,
+                             :authors => obj[0].authors,
+                             :comments => obj[0].comments,
+                             :doi => obj[0].doi,
+                             :embl_gb_record_number => obj[0].embl_gb_record_number,
+                             :issue => obj[0].issue,
+                             :journal =>  obj[0].journal,
+                             :medline => obj[0].medline,
+                             :mesh => obj[0].mesh,
+                             :pages => obj[0].pages,
+                             :pubmed => obj[0].pubmed,
+                             :sequence_position => obj[0].sequence_position,
+                             :title => obj[0].title,
+                             :url => obj[0].url,
+                             :volume => obj[0].volume,
+                             :year => obj[0].year}
+      assert_equal(expected, actual)
+        actual2 = ""
+      com.references do |reference|
+        actual2 = reference.authors
+        break
+      end
+      assert_equal(["Zhao, X.", "Brade, T.", "Cunningham, T.J.", "Duester, G."],actual2) 
+
+      
+      #the other pattern where a journal doesn't match the regexp.
+      ref=<<EOS
+REFERENCE   2  (bases 1 to 2264)
+  JOURNAL   testcase
+EOS
+      obj2 = BioNCBIDBCommon.new(ref)
+      actual3 = obj2.references[0].journal
+      assert_equal("testcase",actual3)
+      end
+
+      def test_comment
+         expected = ""
+        assert_equal(expected, @obj.comment)
+      end
+
+      def test_features
+        expected =
+        {:feature=>"CDS",
+         :position=>"<1..206",
+         :qualifiers=>
+          [{:qualifier=>"product",
+           :value=>"TCP1-beta"},
+           {:value=>3, :qualifier=>"codon_start"},
+           {:qualifier=>"translation",
+            :value=>
+             "SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEAAEVLLRVDNIIRARPRTANRQHM"}]}
+        fet =<<EOS
+FEATURES             Location/Qualifiers
+     CDS             <1..206
+                     /product="TCP1-beta"
+                     /codon_start=3
+                     /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA
+                     AEVLLRVDNIIRARPRTANRQHM"
+EOS
+        obj = BioNCBIDBCommon.new(fet)
+        actual =
+        {:feature=>obj.features[0].feature,
+         :position=>obj.features[0].position,
+         :qualifiers=>
+           [{:qualifier=>obj.features[0].qualifiers[0].qualifier,
+             :value=>obj.features[0].qualifiers[0].value},
+            {:qualifier=>obj.features[0].qualifiers[1].qualifier,
+             :value=>
+              obj.features[0].qualifiers[1].value},
+            {:qualifier=>obj.features[0].qualifiers[2].qualifier,
+             :value=>
+              obj.features[0].qualifiers[2].value}]}
+        assert_equal(expected, actual)
+          actual2 = ""
+        obj.features do |feature|
+          actual2 = feature.feature
+        end
+          
+          assert_equal("CDS", actual2)
+      end
+
+      def test_origin
+         expected = ""
+        assert_equal(expected, @obj.origin)
+      end
+
+    end
+  end
+end