wwood-bioruby 1.2.11

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

@@ -0,0 +1,203 @@
+#
+# test/unit/bio/db/embl/test_embl.rb - Unit test for Bio::EMBL
+#
+# Copyright::  Copyright (C) 2005, 2008
+#                 Mitsuteru Nakao <n@bioruby.org>
+#                 Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::    The Ruby License
+#
+#  $Id:$
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio'
+require 'bio/db/embl/embl'
+
+module Bio
+  class TestEMBLToBioSequence < Test::Unit::TestCase
+    
+    def setup
+      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+      input = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl.rel89')).read
+      embl_object = Bio::EMBL.new(input)
+      embl_object.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
+      @bio_seq = embl_object.to_biosequence
+    end
+
+    def test_entry_id
+      assert_equal('AB090716', @bio_seq.entry_id)
+    end
+    
+    def test_primary_accession
+      assert_equal('AB090716', @bio_seq.primary_accession)
+    end
+    
+    def test_secondary_accessions
+      assert_equal([], @bio_seq.secondary_accessions)
+    end
+    
+    def test_molecule_type
+      assert_equal('genomic DNA', @bio_seq.molecule_type)
+    end
+    
+    def test_definition
+      assert_equal("Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive opsin, partial cds, specimen_voucher:specimen No. HT-9361.", @bio_seq.definition)
+    end
+
+    def test_topology
+      assert_equal('linear', @bio_seq.topology)
+    end
+    
+    def test_date_created
+      # '25-OCT-2002 (Rel. 73, Created)'
+      assert_equal(Date.parse('25-OCT-2002'), @bio_seq.date_created)
+    end
+
+    def test_date_modified
+      # '14-NOV-2006 (Rel. 89, Last updated, Version 3)'
+      assert_equal(Date.parse('14-NOV-2006'), @bio_seq.date_modified)
+    end
+
+    def test_release_created
+      assert_equal('73', @bio_seq.release_created)
+    end
+
+    def test_release_modified
+      assert_equal('89', @bio_seq.release_modified)
+    end
+
+    def test_entry_version
+      assert_equal('3', @bio_seq.entry_version)
+    end
+    
+    def test_division
+      assert_equal('VRT', @bio_seq.division)
+    end
+    
+    def test_sequence_version
+      assert_equal(1, @bio_seq.sequence_version)
+    end
+    
+    def test_keywords
+      assert_equal([], @bio_seq.keywords)
+    end
+    
+    def test_species
+      assert_equal("Haplochromis sp. 'muzu, rukwa'", @bio_seq.species)
+    end
+    
+    def test_classification
+      assert_equal(['Eukaryota','Metazoa','Chordata','Craniata','Vertebrata','Euteleostomi','Actinopterygii','Neopterygii','Teleostei','Euteleostei','Neoteleostei','Acanthomorpha','Acanthopterygii','Percomorpha','Perciformes','Labroidei','Cichlidae','African cichlids','Pseudocrenilabrinae','Haplochromini','Haplochromis'], @bio_seq.classification)
+      
+
+    end
+
+    def test_references
+      assert_equal(2, @bio_seq.references.length)
+      assert_equal(Bio::Reference, @bio_seq.references[0].class)
+    end
+    
+    def test_features
+      assert_equal(3, @bio_seq.features.length)
+      assert_equal(Bio::Feature, @bio_seq.features[0].class)
+    end
+    
+  end
+
+  # To really test the Bio::EMBL to Bio::Sequence conversion, we need to test if
+  # that Bio::Sequence can be made into a valid Bio::EMBL again.
+  class TestEMBLToBioSequenceRoundTrip < Test::Unit::TestCase
+    def setup
+      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+      input = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl.rel89')).read
+      embl_object_1 = Bio::EMBL.new(input)
+      embl_object_1.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
+      @bio_seq_1 = embl_object_1.to_biosequence
+      embl_object_2 = Bio::EMBL.new(@bio_seq_1.output(:embl))
+      @bio_seq_2 = embl_object_2.to_biosequence
+    end
+    
+    def test_entry_id
+      assert_equal('AB090716', @bio_seq_2.entry_id)
+    end
+    
+    def test_primary_accession
+      assert_equal('AB090716', @bio_seq_2.primary_accession)
+    end
+    
+    def test_secondary_accessions
+      assert_equal([], @bio_seq_2.secondary_accessions)
+    end
+    
+    def test_molecule_type
+      assert_equal('genomic DNA', @bio_seq_2.molecule_type)
+    end
+    
+    def test_definition
+      assert_equal("Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive opsin, partial cds, specimen_voucher:specimen No. HT-9361.", @bio_seq_2.definition)
+    end
+
+    def test_topology
+      assert_equal('linear', @bio_seq_2.topology)
+    end
+    
+    def test_date_created
+      # '25-OCT-2002 (Rel. 73, Created)'
+      assert_equal(Date.parse('25-OCT-2002'), @bio_seq_2.date_created)
+    end
+
+    def test_date_modified
+      # '14-NOV-2006 (Rel. 89, Last updated, Version 3)'
+      assert_equal(Date.parse('14-NOV-2006'), @bio_seq_2.date_modified)
+    end
+
+    def test_release_created
+      assert_equal('73', @bio_seq_2.release_created)
+    end
+
+    def test_release_modified
+      assert_equal('89', @bio_seq_2.release_modified)
+    end
+
+    def test_entry_version
+      assert_equal('3', @bio_seq_2.entry_version)
+    end
+    
+    def test_division
+      assert_equal('VRT', @bio_seq_2.division)
+    end
+    
+    def test_sequence_version
+      assert_equal(1, @bio_seq_2.sequence_version)
+    end
+    
+    def test_keywords
+      assert_equal([], @bio_seq_2.keywords)
+    end
+    
+    def test_species
+      assert_equal("Haplochromis sp. 'muzu, rukwa'", @bio_seq_2.species)
+    end
+    
+    def test_classification
+      assert_equal(['Eukaryota','Metazoa','Chordata','Craniata','Vertebrata','Euteleostomi','Actinopterygii','Neopterygii','Teleostei','Euteleostei','Neoteleostei','Acanthomorpha','Acanthopterygii','Percomorpha','Perciformes','Labroidei','Cichlidae','African cichlids','Pseudocrenilabrinae','Haplochromini','Haplochromis'], @bio_seq_2.classification)
+      
+
+    end
+
+    def test_references
+      assert_equal(2, @bio_seq_2.references.length)
+      assert_equal(Bio::Reference, @bio_seq_2.references[0].class)
+    end
+    
+    def test_features
+      assert_equal(3, @bio_seq_2.features.length)
+      assert_equal(Bio::Feature, @bio_seq_2.features[0].class)
+    end
+  end
+end
+

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

@@ -0,0 +1,1812 @@
+#
+# test/unit/bio/db/embl/test_sptr.rb - Unit test for Bio::SPTR
+#
+# Copyright:::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+#  $Id:$
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), 
+                                 ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/db/embl/sptr'
+
+module Bio
+  class TestSPTR < Test::Unit::TestCase
+
+    def setup
+      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), 
+                                            ['..'] * 5)).cleanpath.to_s
+      data = File.open(File.join(bioruby_root, 
+                                 'test', 'data', 'uniprot', 
+                                 'p53_human.uniprot')).read
+      @obj = Bio::SPTR.new(data)
+    end
+
+    def test_id_line
+      assert(@obj.id_line)
+    end
+
+    def test_id_line_entry_name
+      assert_equal('P53_HUMAN', @obj.id_line('ENTRY_NAME'))
+    end   
+
+    def test_id_line_data_class
+      assert_equal('STANDARD', @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(393, @obj.id_line('SEQUENCE_LENGTH'))
+    end
+
+    def test_entry
+      entry = 'P53_HUMAN'
+      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 = 393
+      assert_equal(seqlen, @obj.sequence_length)
+      assert_equal(seqlen, @obj.aalen)
+    end
+
+    def test_ac
+      acs = ["P04637", "Q15086", "Q15087", "Q15088", "Q16535", "Q16807", 
+             "Q16808", "Q16809", "Q16810", "Q16811", "Q16848", "Q86UG1", 
+             "Q8J016", "Q99659", "Q9BTM4", "Q9HAQ8", "Q9NP68", "Q9NPJ2", 
+             "Q9NZD0", "Q9UBI2", "Q9UQ61"]
+      assert_equal(acs, @obj.ac)
+      assert_equal(acs, @obj.accessions)
+    end
+
+    def test_accession
+      assert_equal('P04637', @obj.accession)
+    end
+
+    def test_dr
+      assert_equal(17, @obj.dr.size)
+      assert_equal(27, @obj.dr['GO'].size)
+      assert_equal([["IPR002117", "P53"],
+                    ["IPR011615", "P53_DNA_bd"],
+                    ["IPR012346", "P53_RUNT_DNA_bd"],
+                    ["IPR010991", "p53_tetrameristn"]],
+                   @obj.dr['InterPro'])
+    end
+
+    def test_dr_with_key
+      pfam = [
+              { " "              => "1",
+                "Version"        => "P53",
+                "Accession"      => "PF00870",
+                "Molecular Type" => nil
+              },
+              { " "              => "1",
+                "Version"        => "P53_tetramer",
+                "Accession"      => "PF07710",
+                "Molecular Type" => nil
+              }
+             ]
+      assert_equal(pfam, @obj.dr('Pfam'))
+      embl3 = {
+        " "              => "JOINED",
+        "Version"        => "AAA59987.1",
+        "Accession"      => "M13113",
+        "Molecular Type" => "Genomic_DNA"
+      }
+      assert_equal(embl3, @obj.dr('EMBL')[3])
+    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('13-AUG-1987 (Rel. 05, Created)', @obj.dt('created'))
+    end
+
+    def test_dt_sequence
+      assert_equal('01-MAR-1989 (Rel. 10, Last sequence update)', 
+                   @obj.dt('sequence'))
+    end
+
+    def test_dt_annotation
+      assert_equal('13-SEP-2005 (Rel. 48, Last annotation update)', 
+                   @obj.dt('annotation'))
+    end
+
+    def test_de
+      assert(@obj.de)
+    end
+
+    def test_protein_name
+      assert_equal("Cellular tumor antigen p53", @obj.protein_name)
+    end
+
+    def test_synonyms
+      ary = ["Tumor suppressor p53", "Phosphoprotein p53", "Antigen NY-CO-13"]
+      assert_equal(ary, @obj.synonyms)
+    end
+
+    def test_gn
+      assert_equal([{:orfs=>[], :synonyms=>["P53"], :name=>"TP53", :loci=>[]}], 
+                   @obj.gn)
+    end
+
+    def test_gn_uniprot_parser
+      gn_uniprot_data = ''
+      assert_equal([{:orfs=>[], :loci=>[], :name=>"TP53", :synonyms=>["P53"]}], 
+                   @obj.instance_eval("gn_uniprot_parser"))
+    end
+
+    def test_gn_old_parser
+      gn_old_data = ''
+      assert_equal([["Name=TP53; Synonyms=P53;"]], 
+                   @obj.instance_eval("gn_old_parser"))
+    end
+
+    def test_gene_names
+      assert_equal(["TP53"], @obj.gene_names)
+    end
+
+    def test_gene_name
+      assert_equal('TP53', @obj.gene_name)
+    end
+
+    def test_os
+      assert(@obj.os)
+    end
+
+    def test_os_access
+      assert_equal("Homo sapiens (Human)", @obj.os(0))
+    end
+
+    def test_os_access2
+      assert_equal({"name"=>"(Human)", "os"=>"Homo sapiens"}, @obj.os[0])
+    end
+
+    def test_og_1
+      og = "OG   Plastid; Chloroplast."
+      ary = ['Plastid', 'Chloroplast']
+      @obj.instance_eval("@orig['OG'] = '#{og}'")
+      assert_equal(ary, @obj.og)
+    end
+
+    def test_og_2
+      og = "OG   Mitochondrion."
+      ary = ['Mitochondrion']
+      @obj.instance_eval("@orig['OG'] = '#{og}'")
+      assert_equal(ary, @obj.og)
+    end
+
+    def test_og_3
+      og = "OG   Plasmid sym pNGR234a."
+      ary = ["Plasmid sym pNGR234a"]
+      @obj.instance_eval("@orig['OG'] = '#{og}'")
+      assert_equal(ary, @obj.og)
+    end
+
+    def test_og_4
+      og = "OG   Plastid; Cyanelle."
+      ary = ['Plastid', 'Cyanelle']
+      @obj.instance_eval("@orig['OG'] = '#{og}'")
+      assert_equal(ary, @obj.og)
+    end
+
+    def test_og_5
+      og = "OG   Plasmid pSymA (megaplasmid 1)." 
+      ary = ["Plasmid pSymA (megaplasmid 1)"]
+      @obj.instance_eval("@orig['OG'] = '#{og}'")
+      assert_equal(ary, @obj.og)
+    end
+
+    def test_og_6
+      og = "OG   Plasmid pNRC100, Plasmid pNRC200, and Plasmid pHH1." 
+      ary = ['Plasmid pNRC100', 'Plasmid pNRC200', 'Plasmid pHH1']
+      @obj.instance_eval("@orig['OG'] = '#{og}'")
+      assert_equal(ary, @obj.og)
+    end
+
+    def test_oc
+      assert_equal(["Eukaryota", "Metazoa", "Chordata", "Craniata", 
+                    "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", 
+                    "Euarchontoglires", "Primates", "Catarrhini", "Hominidae", 
+                    "Homo"], 
+                   @obj.oc)
+    end
+
+    def test_ox
+      assert_equal({"NCBI_TaxID"=>["9606"]}, @obj.ox)
+    end
+
+    def test_ref # Bio::SPTR#ref
+      assert_equal(Array, @obj.ref.class)
+    end
+
+    def test_cc
+      assert_equal(Hash, @obj.cc.class)
+    end
+   
+    def test_cc_database
+      db = [{"NAME" => "IARC TP53 mutation database", 
+             "WWW" => "http://www.iarc.fr/p53/", 
+             "FTP" => nil, "NOTE" => "IARC db of somatic p53 mutations"},
+            {"NAME" => "Tokyo p53", 
+             "WWW" => "http://p53.genome.ad.jp/", "FTP" => nil, 
+             "NOTE" => "University of Tokyo db of p53 mutations"},
+            {"NAME" => "p53 web site at the Institut Curie", 
+             "WWW" => "http://p53.curie.fr/", "FTP" => nil, "NOTE" => nil},
+            {"NAME" => "Atlas Genet. Cytogenet. Oncol. Haematol.", 
+             "WWW" => "http://www.infobiogen.fr/services/chromcancer/Genes/P53ID88.html", 
+             "FTP" => nil, "NOTE" => nil}]
+      assert_equal(db, @obj.cc('DATABASE'))
+    end
+
+    def test_cc_alternative_products
+      ap = {"Comment" => "",
+            "Named isoforms" => "2", 
+            "Variants" => [{"IsoId" => ["P04637-1"], 
+                            "Name" => "1", 
+                            "Synonyms" => [], 
+                            "Sequence" => ["Displayed"]},
+                           {"IsoId" => ["P04637-2"], 
+                            "Name" => "2", 
+                            "Synonyms" => ["I9RET"], 
+                            "Sequence" => ["VSP_006535", "VSP_006536"]}],
+            "Event" => ["Alternative splicing"]}
+      assert_equal(ap, @obj.cc('ALTERNATIVE PRODUCTS'))
+    end
+
+    def test_cc_mass_spectrometry
+      assert_equal(nil, @obj.cc('MASS SPECTROMETRY'))
+    end
+
+
+    def test_kw
+      keywords = ["3D-structure", "Acetylation", "Activator", 
+                  "Alternative splicing", "Anti-oncogene", 
+                  "Apoptosis", "Cell cycle", "Disease mutation", "DNA-binding", 
+                  "Glycoprotein", "Li-Fraumeni syndrome", "Metal-binding", 
+                  "Nuclear protein", "Phosphorylation", "Polymorphism", 
+                  "Transcription", "Transcription regulation", "Zinc"]
+      assert_equal(keywords, @obj.kw)
+    end
+    
+    def test_ft
+      assert(@obj.ft)
+      name = 'DNA_BIND'
+      assert_equal([{"FTId"=>"", "From"=>102, "diff"=>[], "To"=>292, 
+                     "Description"=>"", 
+                     "original" => ['DNA_BIND', '102', '292', '', '']}], 
+                   @obj.ft[name])
+    end
+
+    def test_sq
+      assert_equal({"CRC64"=>"AD5C149FD8106131", "aalen"=>393, "MW"=>43653}, 
+                   @obj.sq)
+    end
+
+    def test_sq_crc64
+      assert_equal("AD5C149FD8106131", @obj.sq('CRC64'))
+    end
+
+    def test_sq_mw
+      mw = 43653
+      assert_equal(mw, @obj.sq('mw'))
+      assert_equal(mw, @obj.sq('molecular'))
+      assert_equal(mw, @obj.sq('weight'))
+    end
+
+    def test_sq_len
+      length = 393
+      assert_equal(length, @obj.sq('len'))
+      assert_equal(length, @obj.sq('length'))
+      assert_equal(length, @obj.sq('AA'))
+    end
+
+    def test_seq
+      seq = 'MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD'
+      assert_equal(seq, @obj.seq)
+      assert_equal(seq, @obj.aaseq)
+    end
+
+  end # class TestSPTR
+
+
+
+  class TestSPTRCC < Test::Unit::TestCase
+    def test_allergen
+      # ALLERGEN	Information relevant to allergenic proteins
+      data = 'CC   -!- ALLERGEN: Causes an allergic reaction in human.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(['Causes an allergic reaction in human.'], 
+                   sp.cc['ALLERGEN'])
+      assert_equal(['Causes an allergic reaction in human.'], 
+                   sp.cc('ALLERGEN'))
+    end
+    
+    def test_alternative_products_access_as_hash
+      data = "CC   -!- ALTERNATIVE PRODUCTS:
+CC       Event=Alternative initiation; Named isoforms=2;
+CC       Name=Long;
+CC         IsoId=P68250-1; Sequence=Displayed;
+CC       Name=Short;
+CC         IsoId=P68250-2; Sequence=VSP_018631;
+CC         Note=Contains a N-acetylmethionine at position 1 (By
+CC         similarity);"
+
+      res = ["Event=Alternative initiation; Named isoforms=2; Name=Long; IsoId=P68250-1; Sequence=Displayed; Name=Short; IsoId=P68250-2; Sequence=VSP_018631; Note=Contains a N-acetylmethionine at position 1 (By similarity);"]
+      sp = Bio::SPTR.new(data)
+      assert_equal(res,
+                   sp.cc['ALTERNATIVE PRODUCTS'])
+    end
+
+    def test_alternative_products_ai
+      # ALTERNATIVE PRODUCTS	Description of the existence of related protein sequence(s) produced by alternative splicing of the same gene, alternative promoter usage, ribosomal frameshifting or by the use of alternative initiation codons; see 3.21.15
+      # Alternative promoter usage, Alternative splicing, Alternative initiation, Ribosomal frameshifting
+      data = "CC   -!- ALTERNATIVE PRODUCTS:
+CC       Event=Alternative initiation; Named isoforms=2;
+CC       Name=Long;
+CC         IsoId=P68250-1; Sequence=Displayed;
+CC       Name=Short;
+CC         IsoId=P68250-2; Sequence=VSP_018631;
+CC         Note=Contains a N-acetylmethionine at position 1 (By
+CC         similarity);"
+
+      sp = Bio::SPTR.new(data)
+      assert_equal({"Comment"=>"",
+                    "Named isoforms"=>"2",
+                    "Variants"=>
+                    [{"IsoId"=>["P68250-1"], 
+                      "Name"=>"Long", 
+                      "Synonyms" => [],
+                      "Sequence"=>["Displayed"]},
+                     {"IsoId"=>["P68250-2"], 
+                      "Name"=>"Short", 
+                      "Synonyms" => [],
+                      "Sequence"=>["VSP_018631"]}],
+                    "Event"=>["Alternative initiation"]},
+                   sp.cc('ALTERNATIVE PRODUCTS'))
+    end
+    def test_alternative_products_as
+      data = "CC   -!- ALTERNATIVE PRODUCTS:
+CC       Event=Alternative splicing; Named isoforms=2;
+CC       Name=1;
+CC         IsoId=P04637-1; Sequence=Displayed;
+CC       Name=2; Synonyms=I9RET;
+CC         IsoId=P04637-2; Sequence=VSP_006535, VSP_006536;
+CC         Note=Seems to be non-functional. Expressed in quiescent
+CC         lymphocytes;"
+      sp = Bio::SPTR.new(data)
+      assert_equal({"Comment"=>"",
+                    "Named isoforms"=>"2",
+                    "Variants"=>
+                    [{"Name"=>"1", 
+                      "IsoId"=>["P04637-1"],
+                      "Synonyms"=>[], 
+                      "Sequence"=>["Displayed"]},
+                     {"IsoId"=>["P04637-2"],
+                      "Name"=>"2",
+                      "Synonyms"=>["I9RET"],
+                      "Sequence"=>["VSP_006535", "VSP_006536"]}],
+                    "Event"=>["Alternative splicing"]},
+                   sp.cc('ALTERNATIVE PRODUCTS'))
+    end
+    def test_alternative_products_apu
+      data = "CC   -!- ALTERNATIVE PRODUCTS:
+CC       Event=Alternative promoter usage, Alternative splicing; Named isoforms=5;
+CC         Comment=Additional isoforms (AAT-1L and AAT-1S) may exist;
+CC       Name=1; Synonyms=AAT-1M;
+CC         IsoId=Q7Z4T9-1; Sequence=Displayed;
+CC       Name=2;
+CC         IsoId=Q7Z4T9-2; Sequence=VSP_014910, VSP_014911;
+CC         Note=No experimental confirmation available;
+CC       Name=3;
+CC         IsoId=Q7Z4T9-3; Sequence=VSP_014907, VSP_014912;
+CC       Name=4; Synonyms=AAT1-alpha;
+CC         IsoId=Q7Z4T9-4; Sequence=VSP_014908;
+CC         Note=May be produced by alternative promoter usage;
+CC       Name=5; Synonyms=AAT1-beta, AAT1-gamma;
+CC         IsoId=Q7Z4T9-5; Sequence=VSP_014909;
+CC         Note=May be produced by alternative promoter usage;"
+      sp = Bio::SPTR.new(data)
+      assert_equal({"Comment"=>"Additional isoforms (AAT-1L and AAT-1S) may exist",
+                    "Named isoforms"=>"5",
+                    "Variants"=>
+                    [{"Name"=>"1",
+                      "IsoId"=>["Q7Z4T9-1"],
+                      "Synonyms"=>["AAT-1M"],
+                      "Sequence"=>["Displayed"]},
+                     {"Name"=>"2",
+                      "IsoId"=>["Q7Z4T9-2"],
+                      "Synonyms" => [],
+                      "Sequence"=>["VSP_014910", "VSP_014911"]},
+                     {"Name"=>"3",
+                      "IsoId"=>["Q7Z4T9-3"],
+                      "Synonyms" => [],
+                      "Sequence"=>["VSP_014907", "VSP_014912"]},
+                     {"Name"=>"4",
+                      "IsoId"=>["Q7Z4T9-4"],
+                      "Synonyms"=>["AAT1-alpha"],
+                      "Sequence"=>["VSP_014908"]},
+                     {"Name"=>"5",
+                      "IsoId"=>["Q7Z4T9-5"],
+                      "Synonyms"=>["AAT1-beta", "AAT1-gamma"],
+                      "Sequence"=>["VSP_014909"]}],
+                   "Event"=>["Alternative promoter usage", "Alternative splicing"]},
+                   sp.cc('ALTERNATIVE PRODUCTS'))
+    end
+    def test_alternative_products_rf
+      data = ""
+      sp = Bio::SPTR.new(data)
+      assert_equal({},
+                   sp.cc('ALTERNATIVE PRODUCTS'))
+    end
+    
+    def test_biophysicochemical_properties
+      # BIOPHYSICOCHEMICAL PROPERTIES	Description of the information relevant to biophysical and physicochemical data and information on pH dependence, temperature dependence, kinetic parameters, redox potentials, and maximal absorption; see 3.21.8
+      #
+      data = 'CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
+CC       Kinetic parameters:
+CC         KM=45 uM for AdoMet;
+CC         Vmax=32 uM/h/mg enzyme;
+CC       pH dependence:
+CC         Optimum pH is 8.2;'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Kinetic parameters: KM=45 uM for AdoMet; Vmax=32 uM/h/mg enzyme; pH dependence: Optimum pH is 8.2;"],
+                   sp.cc['BIOPHYSICOCHEMICAL PROPERTIES'])
+      assert_equal({"Redox potential" => "",
+                    "Temperature dependence" => "",
+                    "Kinetic parameters" => {"KM" => "45 uM for AdoMet", 
+                                             "Vmax" => "32 uM/h/mg enzyme"}, 
+                    "Absorption" => {},
+                    "pH dependence" => "Optimum pH is 8.2"},
+                   sp.cc('BIOPHYSICOCHEMICAL PROPERTIES'))
+
+# 3.12.2. Syntax of the topic 'BIOPHYSICOCHEMICAL PROPERTIES'
+      data = "CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
+CC       Absorption:
+CC         Abs(max)=xx nm;
+CC         Note=free_text;
+CC       Kinetic parameters:
+CC         KM=xx unit for substrate [(free_text)];
+CC         Vmax=xx unit enzyme [free_text];
+CC         Note=free_text;
+CC       pH dependence:
+CC         free_text;
+CC       Redox potential:
+CC         free_text;
+CC       Temperature dependence:
+CC         free_text;"
+      sp = Bio::SPTR.new(data)
+      assert_equal({"Redox potential"=>"free_text",
+                    "Temperature dependence"=>"free_text",
+                    "Kinetic parameters"=>
+                    {"KM"=>"xx unit for substrate [(free_text)]",
+                     "Note"=>"free_text",
+                     "Vmax"=>"xx unit enzyme [free_text]"},
+                    "Absorption"=>{"Note"=>"free_text", "Abs(max)"=>"xx nm"},
+                    "pH dependence"=>"free_text"},
+                   sp.cc('BIOPHYSICOCHEMICAL PROPERTIES'))
+    end
+
+
+    def test_biotechnology
+      # BIOTECHNOLOGY	Description of the use of a specific protein in a biotechnological process
+      data = 'CC   -!- BIOTECHNOLOGY: Introduced by genetic manipulation and expressed in
+CC       improved ripening tomato by Monsanto. ACC is the immediate
+CC       precursor of the phytohormone ethylene which is involved in the
+CC       control of ripening. ACC deaminase reduces ethylene biosynthesis
+CC       and thus extends the shelf life of fruits and vegetables.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Introduced by genetic manipulation and expressed in improved ripening tomato by Monsanto. ACC is the immediate precursor of the phytohormone ethylene which is involved in the control of ripening. ACC deaminase reduces ethylene biosynthesis and thus extends the shelf life of fruits and vegetables."],
+                   sp.cc['BIOTECHNOLOGY'])
+    end
+
+    def test_catalytic_activity
+      # CATALYTIC ACTIVITY	Description of the reaction(s) catalyzed by an enzyme [1]
+      data = 'CC   -!- CATALYTIC ACTIVITY: Hydrolysis of alkylated DNA, releasing 3-
+CC       methyladenine, 3-methylguanine, 7-methylguanine and 7-
+CC       methyladenine.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine and 7-methyladenine."],
+                   sp.cc['CATALYTIC ACTIVITY'])
+    end
+
+    def test_caution
+      # CAUTION	Warning about possible errors and/or grounds for confusion
+      data = 'CC   -!- CAUTION: Ref.1 sequence differs from that shown due to a Leu codon
+CC       in position 480 which was translated as a stop codon to shorten
+CC       the sequence.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Ref.1 sequence differs from that shown due to a Leu codon in position 480 which was translated as a stop codon to shorten the sequence."],
+                   sp.cc['CAUTION'])
+      assert_equal("Ref.1 sequence differs from that shown due to a Leu codon in position 480 which was translated as a stop codon to shorten the sequence.",
+                   sp.cc('CAUTION'))
+
+    end
+
+    def test_cofactor
+      # COFACTOR	Description of any non-protein substance required by an enzyme for its catalytic activity
+      data = 'CC   -!- COFACTOR: Cl(-). Is unique in requiring Cl(-) for its activity.
+CC   -!- COFACTOR: Mg(2+).'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Cl(-). Is unique in requiring Cl(-) for its activity.", 
+                    "Mg(2+)."],
+                   sp.cc['COFACTOR'])
+
+      assert_equal(["Cl(-). Is unique in requiring Cl(-) for its activity.", 
+                    "Mg(2+)."],
+                   sp.cc('COFACTOR'))
+    end
+
+    def test_developmental_stage
+      # DEVELOPMENTAL STAGE	Description of the developmentally-specific expression of mRNA or protein
+      data = 'CC   -!- DEVELOPMENTAL STAGE: In females, isoform 1 is expressed at day 35
+CC       with higher levels detected at day 56. Isoform 1 is not detected
+CC       in males of any age.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["In females, isoform 1 is expressed at day 35 with higher levels detected at day 56. Isoform 1 is not detected in males of any age."],
+                   sp.cc['DEVELOPMENTAL STAGE'])
+      assert_equal("In females, isoform 1 is expressed at day 35 with higher levels detected at day 56. Isoform 1 is not detected in males of any age.",
+                   sp.cc('DEVELOPMENTAL STAGE'))
+    end
+
+    def test_disease
+      # DISEASE	Description of the disease(s) associated with a deficiency of a protein
+      data = 'CC   -!- DISEASE: Defects in APP are a cause of hereditary cerebral
+CC       hemorrhage with amyloidosis (HCHWAD) [MIM:609065, 104760]. This
+CC       disorder is characterized by amyloid deposits in cerebral vessels.
+CC       The principal clinical characteristics are recurring cerebral
+CC       hemorrhages, sometimes preceded by migrainous headaches or mental
+CC       cleavage. Various types of HCHWAD are known. They differ in onset
+CC       and aggressiveness of the disease. The Iowa type demonstrated no
+CC       cerebral hemorrhaging but is characterized by progressive
+CC       cognitive decline. Beta-APP40 is the predominant form of
+CC       cerebrovascular amyloid.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Defects in APP are a cause of hereditary cerebral hemorrhage with amyloidosis (HCHWAD) [MIM:609065, 104760]. This disorder is characterized by amyloid deposits in cerebral vessels. The principal clinical characteristics are recurring cerebral hemorrhages, sometimes preceded by migrainous headaches or mental cleavage. Various types of HCHWAD are known. They differ in onset and aggressiveness of the disease. The Iowa type demonstrated no cerebral hemorrhaging but is characterized by progressive cognitive decline. Beta-APP40 is the predominant form of cerebrovascular amyloid."],
+                   sp.cc['DISEASE'])
+      assert_equal("Defects in APP are a cause of hereditary cerebral hemorrhage with amyloidosis (HCHWAD) [MIM:609065, 104760]. This disorder is characterized by amyloid deposits in cerebral vessels. The principal clinical characteristics are recurring cerebral hemorrhages, sometimes preceded by migrainous headaches or mental cleavage. Various types of HCHWAD are known. They differ in onset and aggressiveness of the disease. The Iowa type demonstrated no cerebral hemorrhaging but is characterized by progressive cognitive decline. Beta-APP40 is the predominant form of cerebrovascular amyloid.",
+                   sp.cc('DISEASE'))
+    end
+
+    def test_domain
+      # DOMAIN	Description of the domain structure of a protein
+      data = 'CC   -!- DOMAIN: The basolateral sorting signal (BaSS) is required for
+CC       sorting of membrane proteins to the basolateral surface of
+CC       epithelial cells.
+CC   -!- DOMAIN: The NPXY sequence motif found in many tyrosine-
+CC       phosphorylated proteins is required for the specific binding of
+CC       the PID domain. However, additional amino acids either N- or C-
+CC       terminal to the NPXY motif are often required for complete
+CC       interaction. The PID domain-containing proteins which bind APP
+CC       require the YENPTY motif for full interaction. These interactions
+CC       are independent of phosphorylation on the terminal tyrosine
+CC       residue. The NPXY site is also involved in clathrin-mediated
+CC       endocytosis (By similarity).'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["The basolateral sorting signal (BaSS) is required for sorting of membrane proteins to the basolateral surface of epithelial cells.",
+ "The NPXY sequence motif found in many tyrosine-phosphorylated proteins is required for the specific binding of the PID domain. However, additional amino acids either N-or C-terminal to the NPXY motif are often required for complete interaction. The PID domain-containing proteins which bind APP require the YENPTY motif for full interaction. These interactions are independent of phosphorylation on the terminal tyrosine residue. The NPXY site is also involved in clathrin-mediated endocytosis (By similarity)."],
+                   sp.cc['DOMAIN'])
+      assert_equal(["The basolateral sorting signal (BaSS) is required for sorting of membrane proteins to the basolateral surface of epithelial cells.",
+ "The NPXY sequence motif found in many tyrosine-phosphorylated proteins is required for the specific binding of the PID domain. However, additional amino acids either N-or C-terminal to the NPXY motif are often required for complete interaction. The PID domain-containing proteins which bind APP require the YENPTY motif for full interaction. These interactions are independent of phosphorylation on the terminal tyrosine residue. The NPXY site is also involved in clathrin-mediated endocytosis (By similarity)."],
+                   sp.cc('DOMAIN'))
+    end
+
+    def test_enzyme_regulation
+      # ENZYME REGULATION	Description of an enzyme regulatory mechanism
+      data = 'CC   -!- ENZYME REGULATION: Insensitive to calcium/calmodulin. Stimulated
+CC       by the G protein beta and gamma subunit complex.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Insensitive to calcium/calmodulin. Stimulated by the G protein beta and gamma subunit complex."],
+                   sp.cc['ENZYME REGULATION'])
+      assert_equal("Insensitive to calcium/calmodulin. Stimulated by the G protein beta and gamma subunit complex.",
+                   sp.cc('ENZYME REGULATION'))
+    end
+    
+    def test_function
+      # FUNCTION	General description of the function(s) of a protein
+      data = 'CC   -!- FUNCTION: May play a fundamental role in situations where fine
+CC       interplay between intracellular calcium and cAMP determines the
+CC       cellular function. May be a physiologically relevant docking site
+CC       for calcineurin (By similarity).'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["May play a fundamental role in situations where fine interplay between intracellular calcium and cAMP determines the cellular function. May be a physiologically relevant docking site for calcineurin (By similarity)."],
+                   sp.cc['FUNCTION'])
+      assert_equal("May play a fundamental role in situations where fine interplay between intracellular calcium and cAMP determines the cellular function. May be a physiologically relevant docking site for calcineurin (By similarity).",
+                   sp.cc('FUNCTION'))
+    end
+
+    def test_induction
+      # INDUCTION	Description of the compound(s) or condition(s) that regulate gene expression
+      data = 'CC   -!- INDUCTION: By pheromone (alpha-factor).'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["By pheromone (alpha-factor)."],
+                   sp.cc['INDUCTION'])
+      assert_equal("By pheromone (alpha-factor).",
+                   sp.cc('INDUCTION'))
+    end
+
+    def test_interaction
+      # INTERACTION	Conveys information relevant to binary protein-protein interaction 3.21.12
+      data = 'CC   -!- INTERACTION:
+CC       P62158:CALM1 (xeno); NbExp=1; IntAct=EBI-457011, EBI-397435;
+CC       P62155:calm1 (xeno); NbExp=1; IntAct=EBI-457011, EBI-397568;'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["P62158:CALM1 (xeno); NbExp=1; IntAct=EBI-457011, EBI-397435; P62155:calm1 (xeno); NbExp=1; IntAct=EBI-457011, EBI-397568;"],
+                   sp.cc['INTERACTION'])
+      assert_equal([{'SP_Ac' => 'P62158', 
+                     'identifier' => 'CALM1', 
+                     'optional_identifier' => '(xeno)',
+                     'NbExp' => '1', 
+                     'IntAct' => ['EBI-457011', 'EBI-397435']},
+                    {'SP_Ac' => 'P62155', 
+                     'identifier' => 'calm1', 
+                     'optional_identifier' => '(xeno)',
+                     'NbExp' => '1', 
+                     'IntAct' => ['EBI-457011', 'EBI-397568']}],
+                   sp.cc('INTERACTION'))
+    end
+
+    def test_mass_spectrometry
+      # MASS SPECTROMETRY	Reports the exact molecular weight of a protein or part of a protein as determined by mass spectrometric methods; see 3.21.23
+      data = "CC   -!- MASS SPECTROMETRY: MW=2894.9; MW_ERR=3; METHOD=MALDI; RANGE=1-29;
+CC       NOTE=Ref.1.
+CC   -!- MASS SPECTROMETRY: MW=2892.2; METHOD=Electrospray; RANGE=1-29;
+CC       NOTE=Ref.2."
+      sp = Bio::SPTR.new(data)
+      assert_equal(["MW=2894.9; MW_ERR=3; METHOD=MALDI; RANGE=1-29; NOTE=Ref.1.",
+                    "MW=2892.2; METHOD=Electrospray; RANGE=1-29; NOTE=Ref.2."],
+                   sp.cc['MASS SPECTROMETRY'])
+      assert_equal([{'MW' => '2894.9', 
+                     'MW_ERR' => '3', 
+                     'METHOD' => 'MALDI',  
+                     'RANGE' => '1-29',
+                     'NOTE' => 'Ref.1'},
+                    {'MW' => '2892.2', 
+                     'METHOD' => 'Electrospray',
+                     'MW_ERR' => nil,
+                     'RANGE' => '1-29',
+                     'NOTE' => 'Ref.2'}],
+                   sp.cc('MASS SPECTROMETRY'))
+    end
+
+    def test_miscellaneous
+      # MISCELLANEOUS	Any comment which does not belong to any of the other defined topics
+      data = 'CC   -!- MISCELLANEOUS: There are two isozymes; a cytoplasmic one and a
+CC       mitochondrial one.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["There are two isozymes; a cytoplasmic one and a mitochondrial one."],
+                   sp.cc['MISCELLANEOUS'])
+    end
+
+    def test_pathway
+      # PATHWAY	Description of the metabolic pathway(s) with which a protein is associated
+      data = 'CC   -!- PATHWAY: Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-
+CC       phosphate and glycerone phosphate from D-glucose: step 4.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 4."],
+                   sp.cc['PATHWAY'])
+      assert_equal(["Carbohydrate degradation", 
+                    'glycolysis', 
+                    'D-glyceraldehyde 3-phosphate',
+                    'glycerone phosphate from D-glucose', 
+                    'step 4'],
+                   sp.cc('PATHWAY'))
+    end
+
+    def test_pharmaceutical
+      # PHARMACEUTICAL	Description of the use of a protein as a pharmaceutical drug
+      data = 'CC   -!- PHARMACEUTICAL: Available under the names Factrel (Ayerst Labs),
+CC       Lutrepulse or Lutrelef (Ferring Pharmaceuticals) and Relisorm
+CC       (Serono). Used in evaluating hypothalamic-pituitary gonadotropic
+CC       function.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Available under the names Factrel (Ayerst Labs), Lutrepulse or Lutrelef (Ferring Pharmaceuticals) and Relisorm (Serono). Used in evaluating hypothalamic-pituitary gonadotropic function."],
+                   sp.cc['PHARMACEUTICAL'])
+    end
+
+    def test_polymorphism
+      # POLYMORPHISM	Description of polymorphism(s)
+      data = 'CC   -!- POLYMORPHISM: Position 161 is associated with platelet-specific
+CC       alloantigen Siba. Siba(-) has Thr-161 and Siba(+) has Met-161.
+CC       Siba is involved in neonatal alloimmune thrombocytopenia (NATP).
+CC   -!- POLYMORPHISM: Polymorphisms arise from a variable number of tandem
+CC       13-amino acid repeats of S-E-P-A-P-S-P-T-T-P-E-P-T in the mucin-
+CC       like macroglycopeptide (Pro/Thr-rich) domain. Allele D (shown
+CC       here) contains one repeat starting at position 415, allele C
+CC       contains two repeats, allele B contains three repeats and allele A
+CC       contains four repeats.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Position 161 is associated with platelet-specific alloantigen Siba. Siba(-) has Thr-161 and Siba(+) has Met-161. Siba is involved in neonatal alloimmune thrombocytopenia (NATP).",
+                    "Polymorphisms arise from a variable number of tandem 13-amino acid repeats of S-E-P-A-P-S-P-T-T-P-E-P-T in the mucin-like macroglycopeptide (Pro/Thr-rich) domain. Allele D (shown here) contains one repeat starting at position 415, allele C contains two repeats, allele B contains three repeats and allele A contains four repeats."],
+                   sp.cc['POLYMORPHISM'])
+    end
+
+    def test_ptm
+      # PTM	Description of any chemical alternation of a polypeptide (proteolytic cleavage, amino acid modifications including crosslinks). This topic complements information given in the feature table or indicates polypeptide modifications for which position-specific data is not available.
+      data = 'CC   -!- PTM: N-glycosylated, contains approximately 8 kDa of N-linked
+CC       carbohydrate.
+CC   -!- PTM: Palmitoylated.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["N-glycosylated, contains approximately 8 kDa of N-linked carbohydrate.",
+ "Palmitoylated."],
+                   sp.cc['PTM'])
+    end
+
+    def test_rna_editing
+      # RNA EDITING	Description of any type of RNA editing that leads to one or more amino acid changes
+      data = 'CC   -!- RNA EDITING: Modified_positions=50, 59, 78, 87, 104, 132, 139,
+CC       146, 149, 160, 170, 177, 185, 198, 208, 223, 226, 228, 243, 246,
+CC       252, 260, 264, 277, 285, 295; Note=The nonsense codons at
+CC       positions 50, 78, 104, 260 and 264 are modified to sense codons.'
+
+      data = 'CC   -!- RNA EDITING: Modified_positions=607; Note=Fully edited in the
+CC       brain. Heteromerically expressed edited GLUR2 (R) receptor
+CC       complexes are impermeable to calcium, whereas the unedited (Q)
+CC       forms are highly permeable to divalent ions (By similarity).'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Modified_positions=607; Note=Fully edited in the brain. Heteromerically expressed edited GLUR2 (R) receptor complexes are impermeable to calcium, whereas the unedited (Q) forms are highly permeable to divalent ions (By similarity)."],
+                   sp.cc['RNA EDITING'])
+      assert_equal({"Modified_positions" => ['607'], 
+                    "Note" => "Fully edited in the brain. Heteromerically expressed edited GLUR2 (R) receptor complexes are impermeable to calcium, whereas the unedited (Q) forms are highly permeable to divalent ions (By similarity)."},
+                   sp.cc('RNA EDITING'))
+    end
+
+    def test_similarity
+      # SIMILARITY	Description of the similaritie(s) (sequence or structural) of a protein with other proteins
+      data = 'CC   -!- SIMILARITY: Contains 1 protein kinase domain.
+CC   -!- SIMILARITY: Contains 1 RGS domain.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Contains 1 protein kinase domain.", "Contains 1 RGS domain."],
+                   sp.cc['SIMILARITY'])
+    end
+    
+    def test_subcellular_location
+      # SUBCELLULAR LOCATION	Description of the subcellular location of the mature protein
+
+      data = 'CC   -!- SUBCELLULAR LOCATION: Or: Cytoplasm. Or: Secreted protein. May be
+CC       secreted by a non-classical secretory pathway.'
+
+      data = "CC   -!- SUBCELLULAR LOCATION: Cytoplasmic or may be secreted by a non-
+CC       classical secretory pathway (By similarity)."
+
+      data = "CC   -!- SUBCELLULAR LOCATION: Cytoplasm. In neurons, axonally transported
+CC       to the nerve terminals."
+
+      data = "CC   -!- SUBCELLULAR LOCATION: Cell wall. Probably the external side of the
+CC       cell wall."
+
+      data = "CC   -!- SUBCELLULAR LOCATION: Endosome; late endosome; late endosomal
+CC       membrane; single-pass type I membrane protein. Lysosome; lysosomal
+CC       membrane; single-pass type I membrane protein. Localizes to late
+CC       endocytic compartment. Associates with lysosome membranes."
+
+
+      data = "CC   -!- SUBCELLULAR LOCATION: Plastid; chloroplast; chloroplast membrane;
+CC       peripheral membrane protein. Plastid; chloroplast; chloroplast
+CC       stroma."
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chloroplast stroma."],
+                   sp.cc['SUBCELLULAR LOCATION'])
+      assert_equal([["Plastid",
+                     "chloroplast", 
+                     "chloroplast membrane", 
+                     "peripheral membrane protein"], 
+                    ["Plastid", "chloroplast", 
+                     "chloroplast stroma"]],
+                   sp.cc('SUBCELLULAR LOCATION'))
+    end
+
+    def test_subunit
+      # SUBUNIT	Description of the quaternary structure of a protein and any kind of interactions with other proteins or protein complexes; except for receptor-ligand interactions, which are described in the topic FUNCTION.
+
+      data = 'CC   -!- SUBUNIT: Interacts with BTK. Interacts with all isoforms of MAPK8,
+CC       MAPK9, MAPK10 and MAPK12.'
+
+      data = 'CC   -!- SUBUNIT: Homotetramer.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Homotetramer."],
+                   sp.cc['SUBUNIT'])
+    end
+
+    def test_tissue_specificity
+      # TISSUE SPECIFICITY	Description of the tissue-specific expression of mRNA or protein
+      data = "CC   -!- TISSUE SPECIFICITY: Heart, brain and liver mitochondria."
+
+      data = "CC   -!- TISSUE SPECIFICITY: Widely expressed with highest expression in
+CC       thymus, testis, embryo and proliferating blood lymphocytes."
+
+      data = "CC   -!- TISSUE SPECIFICITY: Isoform 2 is highly expressed in the brain,
+CC       heart, spleen, kidney and blood. Isoform 2 is expressed (at
+CC       protein level) in the spleen, skeletal muscle and gastrointestinal
+CC       epithelia."
+      sp = Bio::SPTR.new(data)
+      assert_equal(["Isoform 2 is highly expressed in the brain, heart, spleen, kidney and blood. Isoform 2 is expressed (at protein level) in the spleen, skeletal muscle and gastrointestinal epithelia."],
+                   sp.cc['TISSUE SPECIFICITY'])
+    end
+
+    def test_toxic_dose
+      # TOXIC DOSE	Description of the lethal dose (LD), paralytic dose (PD) or effective dose of a protein
+      data = 'CC   -!- TOXIC DOSE: LD(50) is 12 mg/kg by intraperitoneal injection.'
+      sp = Bio::SPTR.new(data)
+      assert_equal(["LD(50) is 12 mg/kg by intraperitoneal injection."],
+                   sp.cc['TOXIC DOSE'])
+    end
+
+    def test_web_resource
+      # WEB RESOURCE	Description of a cross-reference to a network database/resource for a specific protein; see 3.21.34
+      data = 'CC   -!- WEB RESOURCE: NAME=Inherited peripheral neuropathies mutation db;
+CC       URL="http://www.molgen.ua.ac.be/CMTMutations/".
+CC   -!- WEB RESOURCE: NAME=Connexin-deafness homepage;
+CC       URL="http://www.crg.es/deafness/".
+CC   -!- WEB RESOURCE: NAME=GeneReviews;
+CC       URL="http://www.genetests.org/query?gene=GJB1".'
+            sp = Bio::SPTR.new(data)
+      assert_equal(['NAME=Inherited peripheral neuropathies mutation db; URL="http://www.molgen.ua.ac.be/CMTMutations/".',
+                    '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}],
+                   sp.cc('WEB RESOURCE'))
+
+    end
+
+  end # class TestSPTRCC
+
+  # http://br.expasy.org/sprot/userman.html#Ref_line
+  class TestSPTRRef < Test::Unit::TestCase
+
+    def setup
+      data = 'RN   [1]
+RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND C), FUNCTION, INTERACTION
+RP   WITH PKC-3, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL
+RP   STAGE, AND MUTAGENESIS OF PHE-175 AND PHE-221.
+RC   STRAIN=Bristol N2;
+RX   PubMed=11134024; DOI=10.1074/jbc.M008990200;
+RG   The mouse genome sequencing consortium;
+RA   Galinier A., Bleicher F., Negre D., Perriere G., Duclos B.,
+RA   Cozzone A.J., Cortay J.-C.;
+RT   "A novel adapter protein employs a phosphotyrosine binding domain and
+RT   exceptionally basic N-terminal domains to capture and localize an
+RT   atypical protein kinase C: characterization of Caenorhabditis elegans
+RT   C kinase adapter 1, a protein that avidly binds protein kinase C3.";
+RL   J. Biol. Chem. 276:10463-10475(2001).'
+      @obj = SPTR.new(data)
+    end
+
+    def test_ref
+      res = {"RT" => "A novel adapter protein employs a phosphotyrosine binding domain and exceptionally basic N-terminal domains to capture and localize an atypical protein kinase C: characterization of Caenorhabditis elegans C kinase adapter 1, a protein that avidly binds protein kinase C3.",
+             "RL" => "J. Biol. Chem. 276:10463-10475(2001).",
+             "RA" => "Galinier A., Bleicher F., Negre D., Perriere G., Duclos B., Cozzone A.J., Cortay J.-C.",
+             "RX" => {"MEDLINE" => nil, 
+                      "DOI" => "10.1074/jbc.M008990200", 
+                      "PubMed" => "11134024"}, 
+             "RC" => [{"Text" => "Bristol N2", "Token" => "STRAIN"}], 
+             "RN" => "[1]", 
+             "RP" =>  ["NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND C)",
+                       "FUNCTION",
+                       "INTERACTION WITH PKC-3",
+                       "SUBCELLULAR LOCATION",
+                       "TISSUE SPECIFICITY", 
+                       "DEVELOPMENTAL STAGE",
+                       "MUTAGENESIS OF PHE-175 AND PHE-221"],
+             "RG" => ["The mouse genome sequencing consortium"]}
+      assert_equal(res, @obj.ref.first)
+    end
+
+    def test_RN
+      assert_equal("[1]", @obj.ref.first['RN'])
+    end
+      
+    def test_RP
+      assert_equal(["NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND C)",
+                    "FUNCTION", "INTERACTION WITH PKC-3",
+                    "SUBCELLULAR LOCATION",
+                    "TISSUE SPECIFICITY",
+                    "DEVELOPMENTAL STAGE",
+                    "MUTAGENESIS OF PHE-175 AND PHE-221"],
+                   @obj.ref.first['RP'])
+    end
+
+    def test_RC
+      assert_equal([{"Text"=>"Bristol N2", "Token"=>"STRAIN"}],
+                   @obj.ref.first['RC'])
+    end
+
+    def test_RX
+      assert_equal({'MEDLINE' => nil,
+                    'PubMed' => '11134024', 
+                    'DOI' => '10.1074/jbc.M008990200'},
+                   @obj.ref.first['RX'])
+    end
+
+    def test_RG
+      assert_equal(["The mouse genome sequencing consortium"],
+                   @obj.ref.first['RG'])
+    end
+
+    def test_RA
+      assert_equal("Galinier A., Bleicher F., Negre D., Perriere G., Duclos B., Cozzone A.J., Cortay J.-C.",
+                   @obj.ref.first['RA'])
+    end
+
+    def test_RT
+      assert_equal("A novel adapter protein employs a phosphotyrosine binding domain and exceptionally basic N-terminal domains to capture and localize an atypical protein kinase C: characterization of Caenorhabditis elegans C kinase adapter 1, a protein that avidly binds protein kinase C3.",
+                   @obj.ref.first['RT'])
+    end
+
+    def test_RL
+      assert_equal("J. Biol. Chem. 276:10463-10475(2001).",
+                   @obj.ref.first['RL'])
+    end
+    
+  end # class TestSPTRReferences
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel41.0
+  class TestSPTRSwissProtRel41_0 < Test::Unit::TestCase
+    # Progress in the conversion of Swiss-Prot to mixed-case characters
+
+    # Multiple RP lines
+    def test_multiple_RP_lines
+      data = "RN    [1]
+RP   SEQUENCE FROM N.A., SEQUENCE OF 23-42 AND 351-365, AND
+RP   CHARACTERIZATION."
+      sp = SPTR.new(data)
+      assert_equal(['SEQUENCE FROM N.A.', 
+                    'SEQUENCE OF 23-42 AND 351-365',
+                    'CHARACTERIZATION'],
+                   sp.ref.first['RP'])
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel41.1
+  class TestSPTRSwissProtRel41_1 < Test::Unit::TestCase
+    # New syntax of the CC line topic ALTERNATIVE PRODUCTS
+    def test_alternative_products
+      data = "ID   TEST_ENTRY      STANDARD;      PRT;   393 AA.
+CC   -!- ALTERNATIVE PRODUCTS:
+CC       Event=Alternative promoter;
+CC         Comment=Free text;
+CC       Event=Alternative splicing; Named isoforms=2;
+CC         Comment=Optional free text;
+CC       Name=Isoform_1; Synonyms=Synonym_1;
+CC         IsoId=Isoform_identifier_1;
+CC         Sequence=Displayed;
+CC         Note=Free text;
+CC       Name=Isoform_2; Synonyms=Synonym_1, Synonym_2;
+CC         IsoId=Isoform_identifier_1, Isoform_identifer_2; 
+CC         Sequence=VSP_identifier_1, VSP_identifier_2;
+CC         Note=Free text;
+CC       Event=Alternative initiation;
+CC         Comment=Free text;"
+      sp = SPTR.new(data)
+      res = {"Comment" => "Free text",
+             "Named isoforms" => "2", 
+             "Variants" => [{"Name" => "Isoform_1",
+                             "Synonyms" => ["Synonym_1"],
+                             "IsoId" => ["Isoform_identifier_1"],
+                             "Sequence" => ["Displayed"]   },
+                            {"Name" => "Isoform_2",
+                             "Synonyms" => ["Synonym_1", "Synonym_2"],
+                             "IsoId" => ["Isoform_identifier_1", "Isoform_identifer_2"],
+                             "Sequence" => ["VSP_identifier_1", "VSP_identifier_2"]}],
+             "Event" => ["Alternative promoter"]}
+      assert_equal(res,
+                   sp.cc('ALTERNATIVE PRODUCTS'))
+    end
+
+    def test_alternative_products_with_ft
+data = "ID   TEST_ENTRY      STANDARD;      PRT;   393 AA.
+CC   -!- ALTERNATIVE PRODUCTS:
+CC       Event=Alternative splicing; Named isoforms=6;
+CC       Name=1;
+CC         IsoId=Q15746-4; Sequence=Displayed;
+CC       Name=2;
+CC         IsoId=Q15746-5; Sequence=VSP_000040;
+CC       Name=3A;
+CC         IsoId=Q15746-6; Sequence=VSP_000041, VSP_000043; 
+CC       Name=3B;
+CC         IsoId=Q15746-7; Sequence=VSP_000040, VSP_000041, VSP_000042;
+CC       Name=4;
+CC         IsoId=Q15746-8; Sequence=VSP_000041, VSP_000042;
+CC       Name=del-1790;
+CC         IsoId=Q15746-9; Sequence=VSP_000044;
+FT   VARSPLIC    437    506       VSGIPKPEVAWFLEGTPVRRQEGSIEVYEDAGSHYLCLLKA
+FT                                RTRDSGTYSCTASNAQGQVSCSWTLQVER -> G (in
+FT                                isoform 2 and isoform 3B).
+FT                                /FTId=VSP_004791.
+FT   VARSPLIC   1433   1439       DEVEVSD -> MKWRCQT (in isoform 3A,
+FT                                isoform 3B and isoform 4).
+FT                                /FTId=VSP_004792.
+FT   VARSPLIC   1473   1545       Missing (in isoform 4).
+FT                                /FTId=VSP_004793.
+FT   VARSPLIC   1655   1705       Missing (in isoform 3A and isoform 3B).
+FT                                /FTId=VSP_004794.
+FT   VARSPLIC   1790   1790       Missing (in isoform Del-1790).
+FT                                /FTId=VSP_004795."
+      sp = SPTR.new(data)
+      
+      assert_equal({"Comment" => "",
+                    "Named isoforms" => "6",
+                    "Variants" => [{"IsoId"=>["Q15746-4"],
+                                    "Name"=>"1",
+                                    "Synonyms"=>[], 
+                                    "Sequence"=>["Displayed"]},
+                                   {"IsoId"=>["Q15746-5"],
+                                    "Name"=>"2",
+                                    "Synonyms"=>[],
+                                    "Sequence"=>["VSP_000040"]},
+                                   {"IsoId"=>["Q15746-6"],
+                                    "Name"=>"3A",
+                                    "Synonyms"=>[],
+                                    "Sequence"=>["VSP_000041", "VSP_000043"]}, 
+                                   {"IsoId"=>["Q15746-7"],  
+                                    "Name"=>"3B",  
+                                    "Synonyms"=>[], 
+                                    "Sequence"=>["VSP_000040", "VSP_000041", "VSP_000042"]},
+                                   {"IsoId"=>["Q15746-8"],  
+                                    "Name"=>"4", 
+                                    "Synonyms"=>[], 
+                                    "Sequence"=>["VSP_000041", "VSP_000042"]},
+                                   {"IsoId"=>["Q15746-9"],
+                                    "Name"=>"del-1790", 
+                                    "Synonyms"=>[], 
+                                    "Sequence"=>["VSP_000044"]}], 
+                    "Event"=>["Alternative splicing"]},
+                   sp.cc('ALTERNATIVE PRODUCTS'))
+      assert_equal([{"FTId"=>"VSP_004791",
+                     "From"=>437,
+                     "To"=>506,  
+                    "Description"=>"VSGIPKPEVAWFLEGTPVRRQEGSIEVYEDAGSHYLCLLKA RTRDSGTYSCTASNAQGQVSCSWTLQVER -> G (in isoform 2 and isoform 3B).",
+                     "diff"=> ["VSGIPKPEVAWFLEGTPVRRQEGSIEVYEDAGSHYLCLLKARTRDSGTYSCTASNAQGQVSCSWTLQVER",    "G"],  
+                    "original"=> ["VARSPLIC", "437", "506", "VSGIPKPEVAWFLEGTPVRRQEGSIEVYEDAGSHYLCLLKA RTRDSGTYSCTASNAQGQVSCSWTLQVER -> G (in isoform 2 and isoform 3B).", "/FTId=VSP_004791."]},
+                   {"FTId"=>"VSP_004792",
+                    "From"=>1433,
+                    "diff"=>["DEVEVSD", "MKWRCQT"],
+                    "To"=>1439,
+                    "original"=> ["VARSPLIC", "1433", "1439", "DEVEVSD -> MKWRCQT (in isoform 3A, isoform 3B and isoform 4).", "/FTId=VSP_004792."], 
+                    "Description"=>"DEVEVSD -> MKWRCQT (in isoform 3A, isoform 3B and isoform 4)."},
+                   {"FTId"=>"VSP_004793",
+                    "From"=>1473,
+                    "diff"=>[nil, nil],
+                    "To"=>1545, 
+                    "original"=> ["VARSPLIC", "1473", "1545", "Missing (in isoform 4).", "/FTId=VSP_004793."], "Description"=>"Missing (in isoform 4)."}, 
+                   {"FTId"=>"VSP_004794",
+                    "From"=>1655,
+                    "diff"=>[nil, nil], 
+                    "To"=>1705, 
+                    "original"=> ["VARSPLIC", "1655", "1705", "Missing (in isoform 3A and isoform 3B).", "/FTId=VSP_004794."],
+                    "Description"=>"Missing (in isoform 3A and isoform 3B)."}, 
+                   {"FTId"=>"VSP_004795",
+                    "From"=>1790,
+                    "diff"=>[nil, nil],
+                    "To"=>1790, 
+                    "original"=>["VARSPLIC", "1790", "1790", "Missing (in isoform Del-1790).", "/FTId=VSP_004795."],
+                    "Description"=>"Missing (in isoform Del-1790)."}],
+                   sp.ft['VARSPLIC'])
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel41.10
+  class TestSPTRSwissProtRel41_10 < Test::Unit::TestCase
+    # Reference Comment (RC) line topics may span lines
+    def test_RC_lines
+      data = "RN    [1]
+RC   STRAIN=AZ.026, DC.005, GA.039, GA2181, IL.014, IN.018, KY.172, KY2.37,
+RC   LA.013, MN.001, MNb027, MS.040, NY.016, OH.036, TN.173, TN2.38,
+RC   UT.002, AL.012, AZ.180, MI.035, VA.015, and IL2.17;"
+      sp = SPTR.new(data)
+      assert_equal([{"Text"=>"AZ.026", "Token"=>"STRAIN"}, 
+                    {"Text"=>"DC.005", "Token"=>"STRAIN"},
+                    {"Text"=>"GA.039", "Token"=>"STRAIN"},
+                    {"Text"=>"GA2181", "Token"=>"STRAIN"}, 
+                    {"Text"=>"IL.014", "Token"=>"STRAIN"}, 
+                    {"Text"=>"IN.018", "Token"=>"STRAIN"}, 
+                    {"Text"=>"KY.172", "Token"=>"STRAIN"}, 
+                    {"Text"=>"KY2.37", "Token"=>"STRAIN"}, 
+                    {"Text"=>"LA.013", "Token"=>"STRAIN"}, 
+                    {"Text"=>"MN.001", "Token"=>"STRAIN"}, 
+                    {"Text"=>"MNb027", "Token"=>"STRAIN"}, 
+                    {"Text"=>"MS.040", "Token"=>"STRAIN"}, 
+                    {"Text"=>"NY.016", "Token"=>"STRAIN"}, 
+                    {"Text"=>"OH.036", "Token"=>"STRAIN"}, 
+                    {"Text"=>"TN.173", "Token"=>"STRAIN"}, 
+                    {"Text"=>"TN2.38", "Token"=>"STRAIN"}, 
+                    {"Text"=>"UT.002", "Token"=>"STRAIN"},
+                    {"Text"=>"AL.012", "Token"=>"STRAIN"}, 
+                    {"Text"=>"AZ.180", "Token"=>"STRAIN"}, 
+                    {"Text"=>"MI.035", "Token"=>"STRAIN"}, 
+                    {"Text"=>"VA.015", "Token"=>"STRAIN"},
+                    {"Text"=>"IL2.17", "Token"=>"STRAIN"}],
+                   sp.ref.first['RC'])
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel41.20
+  class TestSPTRSwissProtRel41_20 < Test::Unit::TestCase
+    # Case and wording change for submissions to Swiss-Prot in reference location (RL) lines
+    def test_RL_lines
+      data = "RL   Submitted (MAY-2002) to the SWISS-PROT data bank."
+      sp = SPTR.new(data)
+      assert_equal('',
+                    sp.ref.first['RL'])
+    end
+
+    # New comment line (CC) topic ALLERGEN
+    def test_CC_allergen
+      data = "CC   -!- ALLERGEN: Causes an allergic reaction in human. Binds IgE. It is a
+CC       partially heat-labile allergen that may cause both respiratory and
+CC       food-allergy symptoms in patients with the bird-egg syndrome."
+      sp = SPTR.new(data)
+      assert_equal(["Causes an allergic reaction in human. Binds IgE. It is a partially heat-labile allergen that may cause both respiratory and food-allergy symptoms in patients with the bird-egg syndrome."],
+                   sp.cc("ALLERGEN"))
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel42.6
+  class TestSPTRSwissProtRel42_6 < Test::Unit::TestCase
+    # New comment line (CC) topic RNA EDITING
+    def test_CC_rna_editing
+      data = "CC   -!- RNA EDITING: Modified_positions=393, 431, 452, 495."
+      sp = SPTR.new(data)
+      assert_equal({"Note"=>"", 
+                    "Modified_positions"=>['393', '431', '452', '495']},
+                   sp.cc("RNA EDITING"))
+
+      data = "CC   -!- RNA EDITING: Modified_positions=59, 78, 94, 98, 102, 121; Note=The
+CC       stop codon at position 121 is created by RNA editing. The nonsense
+CC       codon at position 59 is modified to a sense codon."
+      sp = SPTR.new(data)
+      assert_equal({"Note"=>"The stop codon at position 121 is created by RNA editing. The nonsense codon at position 59 is modified to a sense codon.", 
+                    "Modified_positions"=>['59', '78', '94', '98', '102', '121']},
+                   sp.cc("RNA EDITING"))
+
+      data = "CC   -!- RNA EDITING: Modified_positions=Not_applicable; Note=Some
+CC       positions are modified by RNA editing via nucleotide insertion or
+CC       deletion. The initiator methionine is created by RNA editing."
+      sp = SPTR.new(data)
+      assert_equal({'Modified_positions' => ['Not_applicable'],
+                    'Note' => "Some positions are modified by RNA editing via nucleotide insertion or deletion. The initiator methionine is created by RNA editing."},
+                   sp.cc("RNA EDITING"))
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel1_12
+  class TestSPTRUniProtRel1_12 < Test::Unit::TestCase
+    # Digital Object Identifier (DOI) in the RX line
+    def test_DOI_in_RX_line
+      # RX   [MEDLINE=Medline_identifier; ][PubMed=Pubmed_identifier; ][DOI=Digital_object_identifier;]
+      data = "
+RN   [1]
+RX   MEDLINE=97291283; PubMed=9145897; DOI=10.1007/s00248-002-2038-4;"
+      sp = SPTR.new(data)
+      assert_equal({'MEDLINE' => '97291283', 
+                    'PubMed' => '9145897', 
+                     'DOI' => '10.1007/s00248-002-2038-4'},
+                   sp.ref.first['RX'])
+    end
+
+    # New line type: RG (Reference Group)
+    def test_RG_line
+      data = "
+RN   [1]
+RG   The C. elegans sequencing consortium;
+RG   The Brazilian network for HIV isolation and characterization;"
+      sp = SPTR.new(data)
+      assert_equal(['The C. elegans sequencing consortium', 
+                    'The Brazilian network for HIV isolation and characterization'],
+                   sp.ref.first['RG'])
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel2_0
+  class TestSPTRUniProtRel2_0 < Test::Unit::TestCase
+    # New format for the GN (Gene Name) line
+    # GN   Name=<name>; Synonyms=<name1>[, <name2>...]; OrderedLocusNames=<name1>[, <name2>...];
+    # xsGN   ORFNames=<name1>[, <name2>...];
+    def test_GN_line
+      data = "GN   Name=atpG; Synonyms=uncG, papC;
+GN   OrderedLocusNames=b3733, c4659, z5231, ECs4675, SF3813, S3955;"
+      sp = SPTR.new(data)
+      assert_equal([{:orfs => [],
+                     :loci => ["b3733", "c4659", "z5231", "ECs4675", "SF3813", "S3955"],
+                     :name => "atpG",
+                     :synonyms => ["uncG", "papC"]}],
+                   sp.gn)
+
+      data = "GN   ORFNames=SPAC1834.11c;"
+      sp = SPTR.new(data)
+      assert_equal([{:orfs => ['SPAC1834.11c'], 
+                     :loci => [], 
+                     :name => '', 
+                     :synonyms => []}],
+                   sp.gn)
+
+      data = "GN   Name=cysA1; Synonyms=cysA; OrderedLocusNames=Rv3117, MT3199;
+GN   ORFNames=MTCY164.27;
+GN   and
+GN   Name=cysA2; OrderedLocusNames=Rv0815c, MT0837; ORFNames=MTV043.07c;"
+      sp = SPTR.new(data)
+      assert_equal([{:orfs => ["MTCY164.27"],
+                     :loci => ["Rv3117", "MT3199"],
+                     :name => "cysA1", 
+                     :synonyms => ["cysA"]},
+                    {:orfs => ["MTV043.07c"],
+                     :loci => ["Rv0815c", "MT0837"], 
+                     :name => "cysA2",
+                     :synonyms => []}],
+                   sp.gn)
+    end
+  end
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel2_1
+  class TestSPTRUniProtRel2_1 < Test::Unit::TestCase
+    # Format change in the comment line (CC) topic: MASS SPECTROMETRY
+    def test_CC_mass_spectrometry
+      data = "CC   -!- MASS SPECTROMETRY: MW=32875.93; METHOD=MALDI;
+CC       RANGE=1-284 (Isoform 3); NOTE=Ref.6."
+      sp = SPTR.new(data)
+      assert_equal([{"RANGE"=>"1-284",
+                     "METHOD"=>"MALDI",
+                     "MW_ERR"=>nil,
+                     "NOTE"=>"Ref.6",
+                     "MW"=>"32875.93"}],
+                   sp.cc("MASS SPECTROMETRY"))
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel2_3
+  class TestSPTRUniProtRel2_3 < Test::Unit::TestCase
+    # New RL line structure for electronic publications
+    def test_RL_line
+      data = "RL   Submitted (XXX-YYYY) to the HIV data bank."
+      sp = SPTR.new(data)
+      assert_equal('',
+                   sp.ref.first['RL'])
+    end
+
+    # Format change in the cross-reference to PDB
+    def test_DR_PDB
+      data = "DR   PDB; 1NB3; X-ray; A/B/C/D=116-335, P/R/S/T=98-105."
+      sp = SPTR.new(data)
+      assert_equal([["1NB3", "X-ray", "A/B/C/D=116-335, P/R/S/T=98-105"]],
+                   sp.dr['PDB'])
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel3_4
+  class TestSPTRUniProtRel3_4 < Test::Unit::TestCase
+    # Changes in the RP (Reference Position) line
+    def test_RP_line
+      data = "
+RN   [1]
+RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), PROTEIN SEQUENCE 
+RP   OF 108-131; 220-231 AND 349-393, CHARACTERIZATION, AND MUTAGENESIS OF 
+RP   ARG-336."
+      sp = SPTR.new(data)
+      assert_equal(['NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1)', 
+                    'PROTEIN SEQUENCE OF 108-131; 220-231 AND 349-393', 
+                    'CHARACTERIZATION', 
+                    'MUTAGENESIS OF ARG-336'],
+                   sp.ref.first['RP'])
+
+      data = "
+RN   [1]
+RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA]."
+      sp = SPTR.new(data)
+      assert_equal(['NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA]'],
+                   sp.ref.first['RP'])
+    end
+
+
+    # New comment line (CC) topic: BIOPHYSICOCHEMICAL PROPERTIES
+    def test_CC_biophysiochemical_properties
+      data = "CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
+CC       Absorption:
+CC         Abs(max)=395 nm;
+CC         Note=Exhibits a smaller absorbance peak at 470 nm. The
+CC         fluorescence emission spectrum peaks at 509 nm with a shoulder
+CC         at 540 nm;"
+      sp = SPTR.new(data)
+      assert_equal({"Redox potential" => "", 
+                    "Temperature dependence" => "", 
+                    "Kinetic parameters" => {}, 
+                    "Absorption" => {"Note" => "Exhibits a smaller absorbance peak at 470 nm. The fluorescence emission spectrum peaks at 509 nm with a shoulder at 540 nm", 
+                                     "Abs(max)" => "395 nm"}, 
+                    "pH dependence" => ""},
+                   sp.cc("BIOPHYSICOCHEMICAL PROPERTIES"))
+
+data = "CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
+CC       Kinetic parameters:
+CC         KM=62 mM for glucose;
+CC         KM=90 mM for maltose;
+CC         Vmax=0.20 mmol/min/mg enzyme with glucose as substrate;
+CC         Vmax=0.11 mmol/min/mg enzyme with maltose as substrate;
+CC         Note=Acetylates glucose, maltose, mannose, galactose, and
+CC         fructose with a decreasing relative rate of 1, 0.55, 0.20, 0.07,
+CC         0.04;"
+      sp = SPTR.new(data)
+      assert_equal({"Redox potential" => "", 
+                    "Temperature dependence" => "", 
+                    "Kinetic parameters" => {"KM" => "62 mM for glucose; KM=90 mM for maltose",  
+                                             "Note" => "Acetylates glucose, maltose, mannose, galactose, and fructose with a decreasing relative rate of 1, 0.55, 0.20, 0.07, 0.04",   
+                                             "Vmax" => "0.20 mmol/min/mg enzyme with glucose as substrate"},
+                    "Absorption" => {},
+                    "pH dependence" => ""},
+                   sp.cc("BIOPHYSICOCHEMICAL PROPERTIES"))
+
+data = "CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
+CC       Kinetic parameters:
+CC         KM=1.76 uM for chlorophyll;
+CC       pH dependence:
+CC         Optimum pH is 7.5. Active from pH 5.0 to 9.0;
+CC       Temperature dependence:
+CC         Optimum temperature is 45 degrees Celsius. Active from 30 to 60
+CC         degrees Celsius;"
+      sp = SPTR.new(data)
+      assert_equal({"Redox potential" => "", 
+                    "Temperature dependence" => "Optimum temperature is 45 degrees Celsius. Active from 30 to 60 degrees Celsius", 
+                    "Kinetic parameters" => {},
+                    "Absorption" => {},
+                    "pH dependence" => "Optimum pH is 7.5. Active from pH 5.0 to 9.0"},
+                   sp.cc("BIOPHYSICOCHEMICAL PROPERTIES"))
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel3_5
+  class TestSPTRUniProtRel3_5 < Test::Unit::TestCase
+    # Extension of the Swiss-Prot entry name format
+    def test_entry_name_format
+      # TBD
+    end
+  end
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel4_0
+  class TestSPTRUniProtRel4_0 < Test::Unit::TestCase
+    # Extension of the TrEMBL entry name format
+
+    # Change of the entry name in many Swiss-Prot entries
+
+    # New comment line (CC) topic: INTERACTION
+    def test_CC_interaction
+      data = "CC   -!- INTERACTION:
+CC       P11450:fcp3c; NbExp=1; IntAct=EBI-126914, EBI-159556;"
+      sp = SPTR.new(data)
+      assert_equal([{"SP_Ac" => "P11450",
+                     "identifier" => "fcp3c",
+                     "optional_identifier" => nil,
+                     "NbExp" => "1",
+                     "IntAct" => ["EBI-126914", "EBI-159556"]}],
+                   sp.cc("INTERACTION"))
+    end
+
+    def test_CC_interaction_isoform
+      data = "CC   -!- INTERACTION:
+CC       Q9W1K5-1:cg11299; NbExp=1; IntAct=EBI-133844, EBI-212772;"
+      sp = SPTR.new(data)
+      assert_equal([{"SP_Ac" => 'Q9W1K5-1',
+                     "identifier" => 'cg11299',
+                     "optional_identifier" => nil,
+                     "NbExp" => "1",
+                     "IntAct" => ["EBI-133844", "EBI-212772"]}],
+                   sp.cc("INTERACTION"))
+    end
+
+    def test_CC_interaction_no_gene_name
+      data = "CC   -!- INTERACTION:
+CC       Q8NI08:-; NbExp=1; IntAct=EBI-80809, EBI-80799;"
+      sp = SPTR.new(data)
+      assert_equal([{"SP_Ac" => 'Q8NI08',
+                     "identifier" => '-',
+                     "optional_identifier" => nil,
+                     "NbExp" => "1",
+                     "IntAct" => ["EBI-80809", "EBI-80799"]}],
+                   sp.cc("INTERACTION"))
+    end
+
+    def test_CC_interaction_self_association
+      data = "ID   TEST_ENTRY      STANDARD;      PRT;   393 AA.
+CC   -!- INTERACTION:
+CC       Self; NbExp=1; IntAct=EBI-123485, EBI-123485;"
+      sp = SPTR.new(data)
+      assert_equal([{"SP_Ac" => 'TEST_ENTRY',
+                     "identifier" => 'TEST_ENTRY',
+                     "optional_identifier" => nil,
+                     "NbExp" => "1",
+                     "IntAct" => ["EBI-123485", "EBI-123485"]}],
+                   sp.cc("INTERACTION"))
+    end
+
+    def test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different
+      data = "CC   -!- INTERACTION:
+CC       Q8C1S0:2410018m14rik (xeno); NbExp=1; IntAct=EBI-394562, EBI-398761;"
+      sp = SPTR.new(data)
+      assert_equal([{"SP_Ac" => 'Q8C1S0', 
+                     "identifier" => '2410018m14rik',
+                     "optional_identifier" => '(xeno)',  
+                     "NbExp" => "1", 
+                     "IntAct" => ["EBI-394562", "EBI-398761"]}],
+                   sp.cc("INTERACTION"))
+    end
+
+    def test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein
+      data = "CC   -!- INTERACTION:
+CC       P51617:irak1; NbExp=1; IntAct=EBI-448466, EBI-358664;
+CC       P51617:irak1; NbExp=1; IntAct=EBI-448472, EBI-358664;"
+      sp = SPTR.new(data)
+      assert_equal([{"SP_Ac" => "P51617", 
+                     "identifier" => "irak1",
+                     "optional_identifier" => nil,
+                     "NbExp" => "1",
+                     "IntAct" => ["EBI-448466", "EBI-358664"]}, 
+                    {"SP_Ac" => "P51617",
+                     "identifier" => "irak1",
+                     "optional_identifier" => nil,
+                     "NbExp" => "1",  
+                     "IntAct" => ["EBI-448472", "EBI-358664"]}],
+                   sp.cc("INTERACTION"))
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel5_0
+  class TestSPTRUniProtRel5_0 < Test::Unit::TestCase
+    # Format change in the DR line
+    # DR   DATABASE_IDENTIFIER; PRIMARY_IDENTIFIER; SECONDARY_IDENTIFIER[; TERTIARY_IDENTIFIER][; QUATERNARY_IDENTIFIER].
+    def test_DR_line
+      data = "
+DR   EMBL; M68939; AAA26107.1; -; Genomic_DNA.
+DR   EMBL; U56386; AAB72034.1; -; mRNA."
+
+      sp = SPTR.new(data)
+      assert_equal([["M68939", "AAA26107.1", "-", "Genomic_DNA"],
+                    ["U56386", "AAB72034.1", "-", "mRNA"]],
+                   sp.dr['EMBL'])
+      
+      assert_equal([{" "=>"-",  
+                     "Version"=>"AAA26107.1",  
+                     "Accession"=>"M68939",  
+                     "Molecular Type"=>"Genomic_DNA"}, 
+                    {" "=>"-", 
+                     "Version"=>"AAB72034.1",
+                     "Accession"=>"U56386", 
+                     "Molecular Type"=>"mRNA"}],
+                   sp.dr('EMBL'))
+                   
+    end
+    # New feature (FT) keys and redefinition of existing FT keys
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel5_4
+  class TestSPTRUniProtRel5_4 < Test::Unit::TestCase
+    # Multiple comment line (CC) topics COFACTOR
+    def test_multiple_cofactors
+      data = "CC   -!- COFACTOR: Binds 1 2Fe-2S cluster per subunit (By similarity).
+CC   -!- COFACTOR: Binds 1 Fe(2+) ion per subunit (By similarity)."
+      sp = SPTR.new(data)
+      assert_equal(["Binds 1 2Fe-2S cluster per subunit (By similarity).", 
+                    "Binds 1 Fe(2+) ion per subunit (By similarity)."],
+                   sp.cc['COFACTOR'])
+      assert_equal(["Binds 1 2Fe-2S cluster per subunit (By similarity).", 
+                    "Binds 1 Fe(2+) ion per subunit (By similarity)."],
+                   sp.cc('COFACTOR'))
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel6_0
+  class TestSPTRUniProtRel6_0 < Test::Unit::TestCase
+    # Changes in the OG (OrGanelle) line
+    def test_OG_line
+      data = "OG   Plastid."
+      sp = SPTR.new(data)
+      assert_equal(['Plastid'], sp.og)
+
+      data = "OG   Plastid; Apicoplast."
+      sp = SPTR.new(data)
+      assert_equal(['Plastid', 'Apicoplast'], sp.og)
+
+      data = "OG   Plastid; Chloroplast."
+      sp = SPTR.new(data)
+      assert_equal(['Plastid', 'Chloroplast'], sp.og)
+
+      data = "OG   Plastid; Cyanelle."
+      sp = SPTR.new(data)
+      assert_equal(['Plastid', 'Cyanelle'], sp.og)
+
+      data = "OG   Plastid; Non-photosynthetic plastid."
+      sp = SPTR.new(data)
+      assert_equal(['Plastid', 'Non-photosynthetic plastid'], sp.og)
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel6_1
+  class TestSPTRUniProtRel6_1 < Test::Unit::TestCase
+    # Annotation changes concerning the feature key METAL
+    def test_FT_metal
+      old_data = "FT   METAL        61     61       Copper and zinc."
+      sp = SPTR.new(old_data)
+      assert_equal([{'From' => 61,
+                     'To' => 61,
+                     'Description' => 'Copper and zinc.',
+                     'FTId' =>'',
+                     'diff' => [],
+                     'original' => ["METAL", "61", "61", "Copper and zinc.", ""]}],
+                   sp.ft['METAL'])
+
+      new_data = "FT   METAL        61     61       Copper.
+FT   METAL        61     61       Zinc."
+      sp = SPTR.new(new_data)
+      assert_equal([{"From" => 61, 
+                     "To" => 61, 
+                     "Description" => "Copper.",
+                     "FTId" => "",  
+                     "diff" => [], 
+                     "original" => ["METAL", "61", "61", "Copper.", ""]},
+                    {"From" => 61, 
+                     "To" => 61, 
+                     "Description" => "Zinc.",
+                     "FTId" => "",  
+                     "diff" => [], 
+                     "original" => ["METAL", "61", "61", "Zinc.", ""]}],
+                   sp.ft['METAL'])
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel6_5
+  class TestSPTRUniProtRel6_5 < Test::Unit::TestCase
+    # Changes in the keywlist.txt file
+    # * Modification of the HI line format:
+    def test_HI_line
+      # HI   Category: Keyword_1; ...; Keyword_n; Described_Keyword.
+      # The first term listed in an HI line is a category. It is followed by a hierarchical list of keywords of that category and ends with the described keyword. There can be more than one HI line of the same category in one keyword entry.
+      data = "HI   Molecular function: Ionic channel; Calcium channel.
+HI   Biological process: Transport; Ion transport; Calcium transport; Calcium channel.
+HI   Ligand: Calcium; Calcium channel."
+      sp = SPTR.new(data)
+      assert_equal([{'Category' => 'Molecular function', 
+                     'Keywords' => ['Ionic channel'], 
+                     'Keyword' => 'Calcium channel'},
+                    {'Category' => 'Biological process',
+                     'Keywords' =>  ['Transport', 'Ion transport', 'Calcium transport'],
+                     'Keyword' =>  'Calcium channel'},
+                    {'Category' => 'Ligand',
+                     'Keywords' => ['Calcium'],
+                     'Keyword' => 'Calcium channel'}],
+                   sp.hi)
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel7.0
+  class TestSPTRUniProtRel7_0 < Test::Unit::TestCase
+    # Changes concerning dates and versions numbers (DT lines)
+    def test_DT_line
+      up_sp_data = "DT   01-JAN-1998, integrated into UniProtKB/Swiss-Prot.
+DT   15-OCT-2001, sequence version 3.
+DT   01-APR-2004, entry version 14."
+      sp = SPTR.new(up_sp_data)
+      assert_equal({"sequence" => "15-OCT-2001, sequence version 3.", 
+                    "annotation" => "01-APR-2004, entry version 14.", 
+                    "created" => "01-JAN-1998, integrated into UniProtKB/Swiss-Prot."},
+                   sp.dt)
+
+      up_tr_data = "DT   01-FEB-1999, integrated into UniProtKB/TrEMBL.
+DT   15-OCT-2000, sequence version 2.
+DT   15-DEC-2004, entry version 5."
+      sp = SPTR.new(up_tr_data)
+      assert_equal({"sequence" => "15-OCT-2000, sequence version 2.", 
+                    "annotation" => "15-DEC-2004, entry version 5.",
+                    "created" => "01-FEB-1999, integrated into UniProtKB/TrEMBL."},
+                   sp.dt)
+    end
+
+    # Addition of a feature (FT) key CHAIN over the whole sequence length
+
+    # Changes concerning the copyright statement
+    def test_CC_copyright_statement
+      data = "CC   -----------------------------------------------------------------------
+CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
+CC   Distributed under the Creative Commons Attribution-NoDerivs License
+CC   -----------------------------------------------------------------------"
+      sp = SPTR.new(data)
+      assert_equal({}, sp.cc)
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel7.6
+  class TestSPTRUniProtRel7_6 < Test::Unit::TestCase
+    # Sequences with over 10000 amino acids in UniProtKB/Swiss-Prot
+    def test_10000aa
+      entry_id = 'Q09165'
+      data = ["SQ   SEQUENCE   393 AA;  43653 MW;  AD5C149FD8106131 CRC64;\n",
+              "     MEEPQSDPSV EPPLSQETFS DLWKLLPENN VLSPLPSQAM DDLMLSPDDI EQWFTEDPGP\n" * 200,
+              "//\n"].join
+      sp = SPTR.new(data)
+      assert(12000, sp.seq.size)
+    end
+  end
+
+
+  # Changes in http://br.expasy.org/sprot/relnotes/sp_news.html#rel8.0
+  class TestSPTRUniProtRel8_0 < Test::Unit::TestCase
+    # Replacement of the feature key VARSPLIC by VAR_SEQ
+    def test_FT_VER_SEQ
+      data = "FT   VAR_SEQ       1     34       Missing (in isoform 3).
+FT                                /FTId=VSP_004099."
+      sp = SPTR.new(data)
+      res = [{'From' => 1, 
+              'To' => 34, 
+              'Description' => 'Missing (in isoform 3).', 
+              'diff' => ['', nil], 
+              'FTId' => 'VSP_004099',
+              'original' =>   ["VAR_SEQ", "1", "34", "Missing (in isoform 3).", 
+                               "/FTId=VSP_004099."]}]
+      assert_equal(res, sp.ft('VAR_SEQ'))
+    end
+
+                 
+    # Syntax modification of the comment line (CC) topic ALTERNATIVE PRODUCTS
+    def test_CC_alternative_products
+#  CC   -!- ALTERNATIVE PRODUCTS:
+#  CC       Event=Event(, Event)*; Named isoforms=Number_of_isoforms;
+# (CC         Comment=Free_text;)?
+# (CC       Name=Isoform_name;( Synonyms=Synonym(, Synonym)*;)?
+#  CC         IsoId=Isoform_identifier(, Isoform_identifer)*;
+#  CC         Sequence=(Displayed|External|Not described|Feature_identifier(, Feature_identifier)*);
+# (CC         Note=Free_text;)?)+
+# Note: Variable values are represented in italics. Perl-style multipliers indicate whether a pattern (as delimited by parentheses) is optional (?), may occur 0 or more times (*), or 1 or more times (+). Alternative values are separated by a pipe symbol (|).
+
+      data = "CC   -!- ALTERNATIVE PRODUCTS:
+CC       Event=Alternative splicing, Alternative initiation; Named isoforms=3;
+CC         Comment=Isoform 1 and isoform 2 arise due to the use of two
+CC         alternative first exons joined to a common exon 2 at the same
+CC         acceptor site but in different reading frames, resulting in two
+CC         completely different isoforms;
+CC       Name=1; Synonyms=p16INK4a;
+CC         IsoId=O77617-1; Sequence=Displayed;
+CC       Name=3;
+CC         IsoId=O77617-2; Sequence=VSP_004099;
+CC         Note=Produced by alternative initiation at Met-35 of isoform 1;
+CC       Name=2; Synonyms=p19ARF;
+CC         IsoId=O77618-1; Sequence=External;
+FT   VAR_SEQ       1     34       Missing (in isoform 3).
+FT                                /FTId=VSP_004099."
+      sp = SPTR.new(data)
+      assert_equal({"Comment" => "Isoform 1 and isoform 2 arise due to the use of two alternative first exons joined to a common exon 2 at the same acceptor site but in different reading frames, resulting in two completely different isoforms", 
+                     "Named isoforms" => "3",
+                     "Variants" =>  [{"IsoId" => ["O77617-1"], 
+                                      "Name" => "1",
+                                      "Synonyms" => ["p16INK4a"],
+                                      "Sequence" => ["Displayed"]},
+                                     {"IsoId" => ["O77617-2"], 
+                                      "Name" => "3",
+                                      "Synonyms" => [],
+                                      "Sequence" => ["VSP_004099"]},
+                                     {"IsoId" => ["O77618-1"],
+                                      "Name" => "2",
+                                      "Synonyms" => ["p19ARF"],
+                                      "Sequence" => ["External"]}],
+                     "Event" => ["Alternative splicing", "Alternative initiation"]},
+                   sp.cc("ALTERNATIVE PRODUCTS"))
+      assert_equal([{"From" => 1,  
+                      "To" => 34,
+                      "Description"=>"Missing (in isoform 3).",
+                      "FTId" => "VSP_004099",
+                      "diff" => ["", nil],
+                      "original"=> ["VAR_SEQ", "1", "34", 
+                                    "Missing (in isoform 3).", "/FTId=VSP_004099."]}],
+                   sp.ft("VAR_SEQ"))
+    end
+
+
+    # Replacement of the comment line (CC) topic DATABASE by WEB RESOURCE
+    def test_CC_web_resource
+      # CC   -!- DATABASE: NAME=ResourceName[; NOTE=FreeText][; WWW=WWWAddress][; FTP=FTPAddress].
+      # CC   -!- WEB RESOURCE: NAME=ResourceName[; NOTE=FreeText]; URL=WWWAddress.
+      # The length of these lines may exceed 75 characters because long URL addresses are not wrapped into multiple lines.
+      assert(true)
+    end
+
+    # Introduction of the new line type OH (Organism Host) for viral hosts
+    def test_OH_lines
+      data = 'OS   Tomato black ring virus (strain E) (TBRV).
+OC   Viruses; ssRNA positive-strand viruses, no DNA stage; Comoviridae;
+OC   Nepovirus; Subgroup B.
+OX   NCBI_TaxID=12277;
+OH   NCBI_TaxID=4681; Allium porrum (Leek).
+OH   NCBI_TaxID=4045; Apium graveolens (Celery).
+OH   NCBI_TaxID=161934; Beta vulgaris (Sugar beet).
+OH   NCBI_TaxID=38871; Fraxinus (ash trees).
+OH   NCBI_TaxID=4236; Lactuca sativa (Garden lettuce).
+OH   NCBI_TaxID=4081; Lycopersicon esculentum (Tomato).
+OH   NCBI_TaxID=39639; Narcissus pseudonarcissus (Daffodil).
+OH   NCBI_TaxID=3885; Phaseolus vulgaris (Kidney bean) (French bean).
+OH   NCBI_TaxID=35938; Robinia pseudoacacia (Black locust).
+OH   NCBI_TaxID=23216; Rubus (bramble).
+OH   NCBI_TaxID=4113; Solanum tuberosum (Potato).
+OH   NCBI_TaxID=13305; Tulipa.
+OH   NCBI_TaxID=3603; Vitis.'
+
+      res = [{'NCBI_TaxID' => '4681',  'HostName' => 'Allium porrum (Leek)'},
+             {'NCBI_TaxID' => '4045',  'HostName' => 'Apium graveolens (Celery)'},
+             {'NCBI_TaxID' => '161934', 'HostName' => 'Beta vulgaris (Sugar beet)'},
+             {'NCBI_TaxID' => '38871', 'HostName' => 'Fraxinus (ash trees)'},
+             {'NCBI_TaxID' => '4236', 'HostName' => 'Lactuca sativa (Garden lettuce)'},
+             {'NCBI_TaxID' => '4081', 'HostName' =>  'Lycopersicon esculentum (Tomato)'},
+             {'NCBI_TaxID' => '39639', 'HostName' => 'Narcissus pseudonarcissus (Daffodil)'},
+             {'NCBI_TaxID' => '3885', 
+               'HostName' => 'Phaseolus vulgaris (Kidney bean) (French bean)'},
+             {'NCBI_TaxID' => '35938', 'HostName' => 'Robinia pseudoacacia (Black locust)'},
+             {'NCBI_TaxID' => '23216', 'HostName' =>  'Rubus (bramble)'},
+             {'NCBI_TaxID' => '4113', 'HostName' => 'Solanum tuberosum (Potato)'},
+             {'NCBI_TaxID' => '13305', 'HostName' => 'Tulipa'},
+             {'NCBI_TaxID' => '3603', 'HostName' => 'Vitis'}]
+      sp = SPTR.new(data)
+      assert_equal(res, sp.oh)
+    end
+
+    def test_OH_line_exception
+      data = "ID   TEST_ENTRY      STANDARD;      PRT;   393 AA.
+OH   NCBI_TaxID=23216x: Rubus (bramble)."
+      sp = SPTR.new(data)
+      assert_raise(ArgumentError) { sp.oh }
+    end
+
+  end
+
+  class TestOSLine < Test::Unit::TestCase
+    def test_uncapitalized_letter_Q32725_9POAL
+      data = "OS   unknown cyperaceous sp.\n"
+      sp = SPTR.new(data)
+      assert_equal('unknown cyperaceous sp.', sp.os.first['os'])
+    end
+
+    def test_period_trancation_O63147
+      data = "OS   Hippotis sp. Clark and Watts 825.\n"
+      sp = SPTR.new(data)
+      assert_equal('Hippotis sp. Clark and Watts 825.', sp.os.first['os'])
+    end
+  end
+
+end # module Bio
+