bio 2.0.4 → 2.0.6

data/test/unit/bio/db/embl/test_uniprotkb_P49144.rb

@@ -0,0 +1,359 @@
+# frozen_string_literal: true
+#
+# test/unit/bio/db/embl/test_uniprotkb_P49144.rb - Unit tests for Bio::UniProtKB
+#
+# Copyright:::  Copyright (C) 2022 BioRuby Project <staff@bioruby.org>
+# License::     The Ruby License
+# Contributor:: 2005 Mitsuteru Nakao <n@bioruby.org>
+#               2022 Naohisa Goto <ng@bioruby.org>
+#
+
+# 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/uniprotkb'
+
+module Bio
+  class TestUniProtKB_P49144 < Test::Unit::TestCase
+
+    def setup
+      data = File.read(File.join(BioRubyTestDataPath, 
+                                 'uniprot', 'P49144.uniprot'))
+      @obj = Bio::UniProtKB.new(data)
+    end
+
+    def test_id_line
+      assert(@obj.id_line)
+    end
+
+    def test_id_line_entry_name
+      assert_equal('5HT1B_RABIT', @obj.id_line('ENTRY_NAME'))
+    end   
+
+    def test_id_line_data_class
+      assert_equal('Reviewed', @obj.id_line('DATA_CLASS'))
+    end
+
+    #def test_id_line_molecule_type
+    #  assert_equal('PRT', @obj.id_line('MOLECULE_TYPE'))
+    #end
+
+    def test_id_line_sequence_length
+      assert_equal(390, @obj.id_line('SEQUENCE_LENGTH'))
+    end
+
+    def test_entry
+      entry = '5HT1B_RABIT'
+      assert_equal(entry, @obj.entry)
+      assert_equal(entry, @obj.entry_name)
+      assert_equal(entry, @obj.entry_id)
+    end
+
+    #def test_molecule
+    #  assert_equal('PRT', @obj.molecule)
+    #  assert_equal('PRT', @obj.molecule_type)
+    #end
+
+    def test_sequence_length
+      seqlen = 390
+      assert_equal(seqlen, @obj.sequence_length)
+      assert_equal(seqlen, @obj.aalen)
+    end
+
+    def test_ac
+      acs = ["P49144"].freeze
+      assert_equal(acs, @obj.ac)
+      assert_equal(acs, @obj.accessions)
+    end
+
+    def test_accession
+      assert_equal('P49144', @obj.accession)
+    end
+
+    def test_dr
+      assert_equal(28, @obj.dr.size)
+      assert_equal(12, @obj.dr['GO'].size)
+      assert_equal([["IPR002147", "5HT1B_rcpt"],
+                    ["IPR002231", "5HT_rcpt"],
+                    ["IPR000276", "GPCR_Rhodpsn"],
+                    ["IPR017452", "GPCR_Rhodpsn_7TM"]],
+                   @obj.dr['InterPro'])
+    end
+
+    def test_dr_with_key
+      pfam = [{"Accession"      => "PF00001",
+               "Version"        => "7tm_1",
+               " "              => "1",
+               "Molecular Type" => nil}
+             ].freeze
+      assert_equal(pfam, @obj.dr('Pfam'))
+      embl = [{"Accession"      => "Z50163",
+               "Version"        => "CAA90531.1",
+               " "              => "-",
+               "Molecular Type" => "Genomic_DNA"},
+              {"Accession"      => "X89731",
+               "Version"        => "CAA61883.1",
+               " "              => "-",
+               "Molecular Type" => "mRNA"},
+              {"Accession"      => "U60826",
+               "Version"        => "AAB58467.1",
+               " "              => "-",
+               "Molecular Type" => "Genomic_DNA"}
+             ].freeze
+      assert_equal(embl, @obj.dr('EMBL'))
+    end
+
+    def test_dr_with_key_empty
+      assert_equal([], @obj.dr('NOT_A_DATABASE'))
+    end
+
+    def test_dt
+      assert(@obj.dt)
+    end
+
+    def test_dt_created
+      assert_equal('01-FEB-1996, integrated into UniProtKB/Swiss-Prot.',
+                   @obj.dt('created'))
+    end
+
+    def test_dt_sequence
+      assert_equal('01-FEB-1996, sequence version 1.', 
+                   @obj.dt('sequence'))
+    end
+
+    def test_dt_annotation
+      assert_equal('22-FEB-2023, entry version 127.',
+                   @obj.dt('annotation'))
+    end
+
+    def test_de
+      assert(@obj.de)
+    end
+
+    def test_protein_name
+      assert_equal("5-hydroxytryptamine receptor 1B",
+                   @obj.protein_name)
+    end
+
+    def test_synonyms
+      ary = [
+        "5-HT-1B",
+        "5-HT1B",
+        "Serotonin 1D beta receptor",
+        "5-HT-1D-beta",
+        "Serotonin receptor 1B"
+      ].freeze
+      assert_equal(ary, @obj.synonyms)
+    end
+
+    def test_protein_name_after_calling_de
+      assert(@obj.de)
+      assert_equal("5-hydroxytryptamine receptor 1B",
+                   @obj.protein_name)
+    end
+
+    def test_synonyms_after_calling_de
+      assert(@obj.de)
+      assert_equal(5, @obj.synonyms.size)
+    end
+
+    def test_gn
+      assert_equal([{:orfs=>[], :synonyms=>[], :name=>"HTR1B", :loci=>[]}], 
+                   @obj.gn)
+    end
+
+    def test_gn_uniprot_parser
+      assert_equal([{:orfs=>[], :loci=>[], :name=>"HTR1B", :synonyms=>[]}], 
+                   @obj.instance_eval("gn_uniprot_parser"))
+    end
+
+    def test_gn_old_parser
+      assert_equal([["Name=HTR1B;"]], 
+                   @obj.instance_eval("gn_old_parser"))
+    end
+
+    def test_gene_names
+      assert_equal(["HTR1B"], @obj.gene_names)
+    end
+
+    def test_gene_name
+      assert_equal('HTR1B', @obj.gene_name)
+    end
+
+    def test_os
+      assert(@obj.os)
+    end
+
+    def test_os_access
+      assert_equal("Oryctolagus cuniculus (Rabbit)", @obj.os(0))
+    end
+
+    def test_os_access2
+      assert_equal({"name"=>"(Rabbit)", "os"=>"Oryctolagus cuniculus"},
+                   @obj.os[0])
+    end
+
+    def test_oc
+      assert_equal(["Eukaryota", "Metazoa", "Chordata", "Craniata",
+                    "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria",
+                    "Euarchontoglires", "Glires", "Lagomorpha",
+                    "Leporidae", "Oryctolagus"],
+                   @obj.oc)
+    end
+
+    def test_ox
+      assert_equal({"NCBI_TaxID"=>["9986"]}, @obj.ox)
+    end
+
+    def test_ref # Bio::UniProtKB#ref
+      assert_equal(Array, @obj.ref.class)
+    end
+
+    def test_cc
+      assert_equal(Hash, @obj.cc.class)
+    end
+   
+    def test_cc_database
+      assert_equal(nil, @obj.cc('DATABASE'))
+    end
+
+    def test_cc_alternative_products
+      assert_equal(nil, @obj.cc('ALTERNATIVE PRODUCTS'))
+    end
+
+    def test_cc_mass_spectrometry
+      assert_equal(nil, @obj.cc('MASS SPECTROMETRY'))
+    end
+
+
+    def test_kw
+      keywords = [ "Behavior", "Cell membrane", "Disulfide bond",
+                   "G-protein coupled receptor", "Glycoprotein",
+                   "Lipoprotein", "Membrane", "Palmitate",
+                   "Phosphoprotein", "Receptor", "Reference proteome",
+                   "Transducer", "Transmembrane", "Transmembrane helix" ]
+      assert_equal(keywords, @obj.kw)
+    end
+    
+    def test_ft
+      assert(@obj.ft)
+      name = 'TOPO_DOM'
+      data = [{"From"=>1,
+               "To"=>49,
+               "diff"=>[],
+               "original"=>
+               ["TOPO_DOM",
+                "1",
+                "49",
+                [["note", "Extracellular"], ["evidence", "ECO:0000250"]]],
+               "note"=>"Extracellular",
+               "evidence"=>"ECO:0000250"},
+              {"From"=>76,
+               "To"=>84,
+               "diff"=>[],
+               "original"=>
+               ["TOPO_DOM",
+                "76",
+                "84",
+                [["note", "Cytoplasmic"], ["evidence", "ECO:0000250"]]],
+               "note"=>"Cytoplasmic",
+               "evidence"=>"ECO:0000250"},
+              {"From"=>111,
+               "To"=>123,
+               "diff"=>[],
+               "original"=>
+               ["TOPO_DOM",
+                "111",
+                "123",
+                [["note", "Extracellular"], ["evidence", "ECO:0000250"]]],
+               "note"=>"Extracellular",
+               "evidence"=>"ECO:0000250"},
+              {"From"=>146,
+               "To"=>165,
+               "diff"=>[],
+               "original"=>
+               ["TOPO_DOM",
+                "146",
+                "165",
+                [["note", "Cytoplasmic"], ["evidence", "ECO:0000250"]]],
+               "note"=>"Cytoplasmic",
+               "evidence"=>"ECO:0000250"},
+              {"From"=>188,
+               "To"=>205,
+               "diff"=>[],
+               "original"=>
+               ["TOPO_DOM",
+                "188",
+                "205",
+                [["note", "Extracellular"], ["evidence", "ECO:0000250"]]],
+               "note"=>"Extracellular",
+               "evidence"=>"ECO:0000250"},
+              {"From"=>229,
+               "To"=>315,
+               "diff"=>[],
+               "original"=>
+               ["TOPO_DOM",
+                "229",
+                "315",
+                [["note", "Cytoplasmic"], ["evidence", "ECO:0000250"]]],
+               "note"=>"Cytoplasmic",
+               "evidence"=>"ECO:0000250"},
+              {"From"=>337,
+               "To"=>349,
+               "diff"=>[],
+               "original"=>
+               ["TOPO_DOM",
+                "337",
+                "349",
+                [["note", "Extracellular"], ["evidence", "ECO:0000250"]]],
+               "note"=>"Extracellular",
+               "evidence"=>"ECO:0000250"},
+              {"From"=>372,
+               "To"=>390,
+               "diff"=>[],
+               "original"=>
+               ["TOPO_DOM",
+                "372",
+                "390",
+                [["note", "Cytoplasmic"], ["evidence", "ECO:0000250"]]],
+               "note"=>"Cytoplasmic",
+               "evidence"=>"ECO:0000250"}].freeze
+      assert_equal(data, @obj.ft[name])
+    end
+
+    def test_sq
+      assert_equal({"CRC64"=>"C22EBC077C6C897D", "aalen"=>390, "MW"=>43496}, 
+                   @obj.sq)
+    end
+
+    def test_sq_crc64
+      assert_equal("C22EBC077C6C897D", @obj.sq('CRC64'))
+    end
+
+    def test_sq_mw
+      mw = 43496
+      assert_equal(mw, @obj.sq('mw'))
+      assert_equal(mw, @obj.sq('molecular'))
+      assert_equal(mw, @obj.sq('weight'))
+    end
+
+    def test_sq_len
+      length = 390
+      assert_equal(length, @obj.sq('len'))
+      assert_equal(length, @obj.sq('length'))
+      assert_equal(length, @obj.sq('AA'))
+    end
+
+    def test_seq
+      seq = "MEEPGAQCAPPLAAGSQIAVPQANLSAAHSHNCSAEGYIYQDSIALPWKVLLVLLLALFTLATTLSNAFVVATVYRTRKLHTPANYLIASLAVTDLLVSILVMPISTMYTVTGRWTLGQVVCDLWLSSDITCCTASIMHLCVIALDRYWAITDAVEYSAKRTPKRAAIMIRLVWVFSICISLPPFFWRQAKAEEEVSECLVNTDHVLYTVYSTVGAFYLPTLLLIALYGRIYVEARSRILKQTPNRTGKRLTRAQLITDSPGSTTSVTSINSRAPDVPSESGSPVYVNQVKVRVSDALLEKKKLMAARERKATKTLGIILGVFIVCWLPFFIISLVMPICKDACWFHQAIFDFFTWLGYVNSLINPIIYTMSNEDFKQAFHKLIRFKCTS"
+      assert_equal(seq, @obj.seq)
+      assert_equal(seq, @obj.aaseq)
+    end
+
+  end # class TestUniProtKB_P49144
+end # module Bio
+

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

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # = test/unit/bio/io/flatfile/test_splitter.rb - unit test for Bio::FlatFile::Splitter
 #
@@ -37,7 +38,7 @@ module Bio::TestFlatFileSplitter
     end
   end #class TestDataClass
 
-  TestData01 = <<__END_OF_TESTDATA__
+  testdata01 = <<__END_OF_TESTDATA__
 
         # This is test
 
@@ -54,10 +55,12 @@ tttttttttttttttttttttttt
 >test3
 atatatatatatatatatatatat
 __END_OF_TESTDATA__
-  TestData01.chomp!
-  # workaround for Windows
-  TestData01.gsub!(/\r\n/, "\n")
 
+  testdata01 = testdata01.chomp
+  # workaround for Windows
+  testdata01.gsub!(/\r\n/, "\n")
+  TestData01 = testdata01
+  
   class TestTemplate < Test::Unit::TestCase
     def setup
       @stream = Bio::FlatFile::BufferedInputStream.new(StringIO.new(TestData01), 'TestData01')

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

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # test/unit/bio/sequence/test_common.rb - Unit test for Bio::Sequencce::Common
 #
@@ -155,7 +156,7 @@ module Bio; module TestSequenceCommon
 
       rseqs = (0..2).collect do |i|
         newcomposition = Hash.new(0)
-        newseq = ''
+        newseq = String.new
         ret = @seq.randomize do |c|
           assert_kind_of(TSequence, c)
           newcomposition[c] += 1
@@ -215,7 +216,7 @@ module Bio; module TestSequenceCommon
 
       rseqs = (0..2).collect do |i|
         newcomposition = Hash.new(0)
-        newseq = ''
+        newseq = String.new
         ret = @seq.randomize(hash) do |c|
           #assert_kind_of(TSequence, c)
           assert_kind_of(String, c)

data/test/unit/bio/test_alignment.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # test/unit/bio/test_alignment.rb - Unit test for Bio::Alignment
 #
@@ -436,29 +437,29 @@ module Bio
 
     def test_convert_match
       a = A[
-        'aaaa',
-        'accc',
-        'acac',
-        'actc'
+        'aaaa'.dup,
+        'accc'.dup,
+        'acac'.dup,
+        'actc'.dup
       ]
       a.convert_match
       assert_equal(A[ 'aaaa', '.ccc', '.c.c', '.ctc' ], a)
     end
 
     def test_convert_unmatch
-      a = A[ 'aaaa', '.ccc', '.c.c', '.ctc' ]
+      a = A[ 'aaaa'.dup, '.ccc'.dup, '.c.c'.dup, '.ctc'.dup ]
       a.convert_unmatch
       assert_equal(A[ 'aaaa', 'accc', 'acac', 'actc' ], a)
     end
 
     def test_alignment_normalize!
-      a = A[ 'a', 'atg', 'atgc', '' ]
+      a = A[ 'a'.dup, 'atg'.dup, 'atgc'.dup, ''.dup ]
       a.alignment_normalize!
       assert_equal(A[ 'a---', 'atg-', 'atgc', '----'], a)
     end
 
     def test_alignment_rstrip!
-      a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
+      a = A[ '--aaa--'.dup, '--t-t--'.dup, '---g---'.dup, '--t'.dup ]
       assert(a.alignment_rstrip!)
       assert_equal(A[ '--aaa', '--t-t', '---g-', '--t' ], a)
     end
@@ -470,7 +471,7 @@ module Bio
     end
 
     def test_alignment_lstrip!
-      a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
+      a = A[ '--aaa--'.dup, '--t-t--'.dup, '---g---'.dup, '--t'.dup ]
       assert(a.alignment_lstrip!)
       assert_equal(A[ 'aaa--', 't-t--', '-g---', 't' ], a)
     end
@@ -482,7 +483,7 @@ module Bio
     end
 
     def test_alignment_strip!
-      a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
+      a = A[ '--aaa--'.dup, '--t-t--'.dup, '---g---'.dup, '--t'.dup ]
       assert(a.alignment_strip!)
       assert_equal(A[ 'aaa', 't-t', '-g-', 't' ], a)
     end
@@ -494,7 +495,7 @@ module Bio
     end
 
     def test_remove_all_gaps!
-      a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
+      a = A[ '--aaa--'.dup, '--t-t--'.dup, '---g---'.dup, '--t'.dup ]
       assert(a.remove_all_gaps!)
       assert_equal(A[ 'aaa', 'tt', 'g', 't' ], a)
     end
@@ -525,7 +526,7 @@ module Bio
     end
 
     def test_alignment_concat
-      a = A[ 'aaa',  'c', 'gg', 't' ]
+      a = A[ 'aaa'.dup,  'c'.dup, 'gg'.dup, 't'.dup ]
       a.alignment_concat(A[ 'ttt', 'gg', 'aa', 'cc', 'aa' ])
       assert_equal(A[ 'aaattt', 'cgg', 'ggaa', 'tcc' ], a)
       a.alignment_concat([ 'c', 't' ])
@@ -702,7 +703,7 @@ module Bio
     end
 
     def test_add_seq_using_seq_with_seq_method
-      seq = "agtc"
+      seq = "agtc".dup
       class <<seq
         def seq
           Sequence::NA.new(self)
@@ -716,7 +717,7 @@ module Bio
     end
 
     def test_add_seq_using_seq_with_naseq_method
-      seq = "agtc"
+      seq = "agtc".dup
       class <<seq
 	def naseq
           Sequence::NA.new(self)
@@ -730,7 +731,7 @@ module Bio
     end
 
     def test_add_seq_using_seq_with_aaseq_method
-      seq = "AVGR"
+      seq = "AVGR".dup
       class <<seq
 	def aaseq
           Sequence::AA.new(self)
@@ -744,7 +745,7 @@ module Bio
     end
 
     def test_add_seq_using_seq_with_definition_method
-      seq = "atgc"
+      seq = "atgc".dup
       class <<seq
 	def definition
           "this is the key"
@@ -757,7 +758,7 @@ module Bio
     end
 
     def test_add_seq_using_seq_with_entry_id_method
-      seq = "atgc"
+      seq = "atgc".dup
       class <<seq
 	def entry_id
           271828

data/test/unit/bio/test_sequence.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 #
 # test/unit/bio/test_sequence.rb - Unit test for Bio::Sequencce
 #
@@ -233,7 +234,7 @@ module Bio
     end
 
     def test_randomize_dna_with_block
-      appended = ""
+      appended = String.new
       @na.randomize {|x| appended << x}
       assert_equal(@na.composition, Sequence::NA.new(appended).composition)
     end
@@ -247,7 +248,7 @@ module Bio
     end
 
     def test_NA_randomize_with_counts_and_block
-      appended = ""
+      appended = String.new
       counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
       counts.default = 0
       Sequence::NA.randomize(counts) {|x| appended << x}

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: bio
 version: !ruby/object:Gem::Version
-  version: 2.0.4
+  version: 2.0.6
 platform: ruby
 authors:
 - BioRuby project
-autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-09-13 00:00:00.000000000 Z
+date: 2025-03-07 00:00:00.000000000 Z
 dependencies: []
 description: BioRuby is a library for bioinformatics (biology + information science).
 email: staff@bioruby.org
@@ -26,7 +25,8 @@ extra_rdoc_files:
 - doc/RELEASE_NOTES-1.4.3.rdoc
 - doc/RELEASE_NOTES-1.5.0.rdoc
 files:
-- ".travis.yml"
+- ".github/workflows/ruby.yml"
+- ".gitignore"
 - BSDL
 - COPYING
 - COPYING.ja
@@ -54,20 +54,14 @@ files:
 - doc/RELEASE_NOTES-1.4.2.rdoc
 - doc/RELEASE_NOTES-1.4.3.rdoc
 - doc/RELEASE_NOTES-1.5.0.rdoc
+- doc/Tutorial.md
 - doc/Tutorial.rd
 - doc/Tutorial.rd.html
 - doc/Tutorial.rd.ja
 - doc/Tutorial.rd.ja.html
+- doc/Tutorial_ja.md
 - doc/bioruby.css
 - etc/bioinformatics/seqdatabase.ini
-- gemfiles/Gemfile.travis-jruby1.8
-- gemfiles/Gemfile.travis-jruby1.9
-- gemfiles/Gemfile.travis-rbx
-- gemfiles/Gemfile.travis-ruby1.8
-- gemfiles/Gemfile.travis-ruby1.9
-- gemfiles/Gemfile.windows
-- gemfiles/modify-Gemfile.rb
-- gemfiles/prepare-gemspec.rb
 - lib/bio.rb
 - lib/bio/alignment.rb
 - lib/bio/appl/bl2seq/report.rb
@@ -465,7 +459,9 @@ files:
 - test/data/sim4/simple2-A4.sim4
 - test/data/soft/GDS100_partial.soft
 - test/data/soft/GSE3457_family_partial.soft
+- test/data/uniprot/P03589.uniprot
 - test/data/uniprot/P28907.uniprot
+- test/data/uniprot/P49144.uniprot
 - test/data/uniprot/p53_human.uniprot
 - test/functional/bio/sequence/test_output_embl.rb
 - test/functional/bio/test_command.rb
@@ -510,7 +506,9 @@ files:
 - test/unit/bio/db/embl/test_embl_to_bioseq.rb
 - test/unit/bio/db/embl/test_uniprot.rb
 - test/unit/bio/db/embl/test_uniprotkb.rb
+- test/unit/bio/db/embl/test_uniprotkb_P03589.rb
 - test/unit/bio/db/embl/test_uniprotkb_P28907.rb
+- test/unit/bio/db/embl/test_uniprotkb_P49144.rb
 - test/unit/bio/db/embl/test_uniprotkb_new_part.rb
 - test/unit/bio/db/fasta/test_defline.rb
 - test/unit/bio/db/fasta/test_defline_misc.rb
@@ -596,7 +594,6 @@ homepage: http://bioruby.org/
 licenses:
 - Ruby
 metadata: {}
-post_install_message: 
 rdoc_options:
 - "--main"
 - README.rdoc
@@ -619,8 +616,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.6
-signing_key: 
+rubygems_version: 3.6.2
 specification_version: 4
 summary: Bioinformatics library
 test_files: []