bio 1.4.1 → 1.4.2

data/test/data/fasta/EFTU_BACSU.fasta

@@ -0,0 +1,8 @@
+>sp|P33166|EFTU_BACSU Elongation factor Tu;
+MAKEKFDRSKSHANIGTIGHVDHGKTTLTAAITTVLHKKSGKGTAMAYDQIDGAPEERER
+GITISTAHVEYETETRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREH
+ILLSKNVGVPYIVVFLNKCDMVDDEELLELVEMEVRDLLSEYDFPGDDVPVVKGSALKAL
+EGDAEWEAKIFELMDAVDEYIPTPERDTEKPFMMPVEDVFSITGRGTVATGRVERGQVKV
+GDEVEIIGLQEENKKTTVTGVEMFRKLLDYAEAGDNIGALLRGVSREEIQRGQVLAKPGT
+ITPHSKFKAEVYVLSKEEGGRHTPFFSNYRPQFYFRTTDVTGIIHLPEGVEMVMPGDNTE
+MNVELISTIAIEEGTRFSIREGGRTVGSGVVSTITE

data/test/data/genbank/CAA35997.gp

@@ -0,0 +1,48 @@
+LOCUS       CAA35997                 100 aa            linear   MAM 12-SEP-1993
+DEFINITION  unnamed protein product [Bos taurus].
+ACCESSION   CAA35997
+VERSION     CAA35997.1  GI:8
+DBSOURCE    embl accession X51700.1
+KEYWORDS    .
+SOURCE      Bos taurus (cattle)
+  ORGANISM  Bos taurus
+            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
+            Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia;
+            Pecora; Bovidae; Bovinae; Bos.
+REFERENCE   1  (residues 1 to 100)
+  AUTHORS   Kiefer,M.C., Saphire,A.C.S., Bauer,D.M. and Barr,P.J.
+  JOURNAL   Unpublished
+REFERENCE   2  (residues 1 to 100)
+  AUTHORS   Kiefer,M.C.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (30-JAN-1990) Kiefer M.C., Chiron Corporation, 4560
+            Hortom St, Emeryville CA 94608-2916, U S A
+COMMENT     See <X15699> for Human sequence.
+            Data kindly reviewed (08-MAY-1990) by Kiefer M.C.
+FEATURES             Location/Qualifiers
+     source          1..100
+                     /organism="Bos taurus"
+                     /db_xref="taxon:9913"
+                     /clone="bBGP-3"
+                     /tissue_type="bone matrix"
+                     /clone_lib="Zap-bb"
+     Protein         1..100
+                     /name="unnamed protein product"
+     Region          33..97
+                     /region_name="Gla"
+                     /note="Vitamin K-dependent
+                     carboxylation/gamma-carboxyglutamic (GLA) domain; cl02449"
+                     /db_xref="CDD:141428"
+     CDS             1..100
+                     /coded_by="X51700.1:28..330"
+                     /note="bone Gla precursor (100 AA)"
+                     /db_xref="GOA:P02820"
+                     /db_xref="InterPro:IPR000294"
+                     /db_xref="InterPro:IPR002384"
+                     /db_xref="PDB:1Q3M"
+                     /db_xref="UniProtKB/Swiss-Prot:P02820"
+ORIGIN      
+        1 mrtpmllall alatlclagr adakpgdaes gkgaafvskq egsevvkrlr ryldhwlgap
+       61 apypdplepk revcelnpdc deladhigfq eayrrfygpv
+//
+

data/test/data/genbank/SCU49845.gb

@@ -0,0 +1,167 @@
+LOCUS       SCU49845                5028 bp    DNA     linear   PLN 23-MAR-2010
+DEFINITION  Saccharomyces cerevisiae TCP1-beta gene, partial cds; and Axl2p
+            (AXL2) and Rev7p (REV7) genes, complete cds.
+ACCESSION   U49845
+VERSION     U49845.1  GI:1293613
+KEYWORDS    .
+SOURCE      Saccharomyces cerevisiae (baker's yeast)
+  ORGANISM  Saccharomyces cerevisiae
+            Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomyceta;
+            Saccharomycotina; Saccharomycetes; Saccharomycetales;
+            Saccharomycetaceae; Saccharomyces.
+REFERENCE   1  (bases 1 to 5028)
+  AUTHORS   Roemer,T., Madden,K., Chang,J. and Snyder,M.
+  TITLE     Selection of axial growth sites in yeast requires Axl2p, a novel
+            plasma membrane glycoprotein
+  JOURNAL   Genes Dev. 10 (7), 777-793 (1996)
+   PUBMED   8846915
+REFERENCE   2  (bases 1 to 5028)
+  AUTHORS   Roemer,T.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (22-FEB-1996) Biology, Yale University, New Haven, CT
+            06520, USA
+FEATURES             Location/Qualifiers
+     source          1..5028
+                     /organism="Saccharomyces cerevisiae"
+                     /mol_type="genomic DNA"
+                     /db_xref="taxon:4932"
+                     /chromosome="IX"
+     mRNA            <1..>206
+                     /product="TCP1-beta"
+     CDS             <1..206
+                     /codon_start=3
+                     /product="TCP1-beta"
+                     /protein_id="AAA98665.1"
+                     /db_xref="GI:1293614"
+                     /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA
+                     AEVLLRVDNIIRARPRTANRQHM"
+     gene            <687..>3158
+                     /gene="AXL2"
+     mRNA            <687..>3158
+                     /gene="AXL2"
+                     /product="Axl2p"
+     CDS             687..3158
+                     /gene="AXL2"
+                     /note="plasma membrane glycoprotein"
+                     /codon_start=1
+                     /product="Axl2p"
+                     /protein_id="AAA98666.1"
+                     /db_xref="GI:1293615"
+                     /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF
+                     TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN
+                     VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE
+                     VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE
+                     TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV
+                     YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG
+                     DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ
+                     DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA
+                     NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA
+                     CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN
+                     NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ
+                     SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS
+                     YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK
+                     HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL
+                     VDFSNKSNVNVGQVKDIHGRIPEML"
+     gene            complement(<3300..>4037)
+                     /gene="REV7"
+     mRNA            complement(<3300..>4037)
+                     /gene="REV7"
+                     /product="Rev7p"
+     CDS             complement(3300..4037)
+                     /gene="REV7"
+                     /codon_start=1
+                     /product="Rev7p"
+                     /protein_id="AAA98667.1"
+                     /db_xref="GI:1293616"
+                     /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ
+                     FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD
+                     KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR
+                     RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK
+                     LISGDDKILNGVYSQYEEGESIFGSLF"
+ORIGIN      
+        1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg
+       61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct
+      121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa
+      181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg
+      241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa
+      301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa
+      361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat
+      421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga
+      481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc
+      541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga
+      601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta
+      661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag
+      721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa
+      781 aacaataccc cccagtggca agagtcaatg aatcgtttac atttcaaatt tccaatgata
+      841 cctataaatc gtctgtagac aagacagctc aaataacata caattgcttc gacttaccga
+      901 gctggctttc gtttgactct agttctagaa cgttctcagg tgaaccttct tctgacttac
+      961 tatctgatgc gaacaccacg ttgtatttca atgtaatact cgagggtacg gactctgccg
+     1021 acagcacgtc tttgaacaat acataccaat ttgttgttac aaaccgtcca tccatctcgc
+     1081 tatcgtcaga tttcaatcta ttggcgttgt taaaaaacta tggttatact aacggcaaaa
+     1141 acgctctgaa actagatcct aatgaagtct tcaacgtgac ttttgaccgt tcaatgttca
+     1201 ctaacgaaga atccattgtg tcgtattacg gacgttctca gttgtataat gcgccgttac
+     1261 ccaattggct gttcttcgat tctggcgagt tgaagtttac tgggacggca ccggtgataa
+     1321 actcggcgat tgctccagaa acaagctaca gttttgtcat catcgctaca gacattgaag
+     1381 gattttctgc cgttgaggta gaattcgaat tagtcatcgg ggctcaccag ttaactacct
+     1441 ctattcaaaa tagtttgata atcaacgtta ctgacacagg taacgtttca tatgacttac
+     1501 ctctaaacta tgtttatctc gatgacgatc ctatttcttc tgataaattg ggttctataa
+     1561 acttattgga tgctccagac tgggtggcat tagataatgc taccatttcc gggtctgtcc
+     1621 cagatgaatt actcggtaag aactccaatc ctgccaattt ttctgtgtcc atttatgata
+     1681 cttatggtga tgtgatttat ttcaacttcg aagttgtctc cacaacggat ttgtttgcca
+     1741 ttagttctct tcccaatatt aacgctacaa ggggtgaatg gttctcctac tattttttgc
+     1801 cttctcagtt tacagactac gtgaatacaa acgtttcatt agagtttact aattcaagcc
+     1861 aagaccatga ctgggtgaaa ttccaatcat ctaatttaac attagctgga gaagtgccca
+     1921 agaatttcga caagctttca ttaggtttga aagcgaacca aggttcacaa tctcaagagc
+     1981 tatattttaa catcattggc atggattcaa agataactca ctcaaaccac agtgcgaatg
+     2041 caacgtccac aagaagttct caccactcca cctcaacaag ttcttacaca tcttctactt
+     2101 acactgcaaa aatttcttct acctccgctg ctgctacttc ttctgctcca gcagcgctgc
+     2161 cagcagccaa taaaacttca tctcacaata aaaaagcagt agcaattgcg tgcggtgttg
+     2221 ctatcccatt aggcgttatc ctagtagctc tcatttgctt cctaatattc tggagacgca
+     2281 gaagggaaaa tccagacgat gaaaacttac cgcatgctat tagtggacct gatttgaata
+     2341 atcctgcaaa taaaccaaat caagaaaacg ctacaccttt gaacaacccc tttgatgatg
+     2401 atgcttcctc gtacgatgat acttcaatag caagaagatt ggctgctttg aacactttga
+     2461 aattggataa ccactctgcc actgaatctg atatttccag cgtggatgaa aagagagatt
+     2521 ctctatcagg tatgaataca tacaatgatc agttccaatc ccaaagtaaa gaagaattat
+     2581 tagcaaaacc cccagtacag cctccagaga gcccgttctt tgacccacag aataggtctt
+     2641 cttctgtgta tatggatagt gaaccagcag taaataaatc ctggcgatat actggcaacc
+     2701 tgtcaccagt ctctgatatt gtcagagaca gttacggatc acaaaaaact gttgatacag
+     2761 aaaaactttt cgatttagaa gcaccagaga aggaaaaacg tacgtcaagg gatgtcacta
+     2821 tgtcttcact ggacccttgg aacagcaata ttagcccttc tcccgtaaga aaatcagtaa
+     2881 caccatcacc atataacgta acgaagcatc gtaaccgcca cttacaaaat attcaagact
+     2941 ctcaaagcgg taaaaacgga atcactccca caacaatgtc aacttcatct tctgacgatt
+     3001 ttgttccggt taaagatggt gaaaattttt gctgggtcca tagcatggaa ccagacagaa
+     3061 gaccaagtaa gaaaaggtta gtagattttt caaataagag taatgtcaat gttggtcaag
+     3121 ttaaggacat tcacggacgc atcccagaaa tgctgtgatt atacgcaacg atattttgct
+     3181 taattttatt ttcctgtttt attttttatt agtggtttac agatacccta tattttattt
+     3241 agtttttata cttagagaca tttaatttta attccattct tcaaatttca tttttgcact
+     3301 taaaacaaag atccaaaaat gctctcgccc tcttcatatt gagaatacac tccattcaaa
+     3361 attttgtcgt caccgctgat taatttttca ctaaactgat gaataatcaa aggccccacg
+     3421 tcagaaccga ctaaagaagt gagttttatt ttaggaggtt gaaaaccatt attgtctggt
+     3481 aaattttcat cttcttgaca tttaacccag tttgaatccc tttcaatttc tgctttttcc
+     3541 tccaaactat cgaccctcct gtttctgtcc aacttatgtc ctagttccaa ttcgatcgca
+     3601 ttaataactg cttcaaatgt tattgtgtca tcgttgactt taggtaattt ctccaaatgc
+     3661 ataatcaaac tatttaagga agatcggaat tcgtcgaaca cttcagtttc cgtaatgatc
+     3721 tgatcgtctt tatccacatg ttgtaattca ctaaaatcta aaacgtattt ttcaatgcat
+     3781 aaatcgttct ttttattaat aatgcagatg gaaaatctgt aaacgtgcgt taatttagaa
+     3841 agaacatcca gtataagttc ttctatatag tcaattaaag caggatgcct attaatggga
+     3901 acgaactgcg gcaagttgaa tgactggtaa gtagtgtagt cgaatgactg aggtgggtat
+     3961 acatttctat aaaataaaat caaattaatg tagcatttta agtataccct cagccacttc
+     4021 tctacccatc tattcataaa gctgacgcaa cgattactat tttttttttc ttcttggatc
+     4081 tcagtcgtcg caaaaacgta taccttcttt ttccgacctt ttttttagct ttctggaaaa
+     4141 gtttatatta gttaaacagg gtctagtctt agtgtgaaag ctagtggttt cgattgactg
+     4201 atattaagaa agtggaaatt aaattagtag tgtagacgta tatgcatatg tatttctcgc
+     4261 ctgtttatgt ttctacgtac ttttgattta tagcaagggg aaaagaaata catactattt
+     4321 tttggtaaag gtgaaagcat aatgtaaaag ctagaataaa atggacgaaa taaagagagg
+     4381 cttagttcat cttttttcca aaaagcaccc aatgataata actaaaatga aaaggatttg
+     4441 ccatctgtca gcaacatcag ttgtgtgagc aataataaaa tcatcacctc cgttgccttt
+     4501 agcgcgtttg tcgtttgtat cttccgtaat tttagtctta tcaatgggaa tcataaattt
+     4561 tccaatgaat tagcaatttc gtccaattct ttttgagctt cttcatattt gctttggaat
+     4621 tcttcgcact tcttttccca ttcatctctt tcttcttcca aagcaacgat ccttctaccc
+     4681 atttgctcag agttcaaatc ggcctctttc agtttatcca ttgcttcctt cagtttggct
+     4741 tcactgtctt ctagctgttg ttctagatcc tggtttttct tggtgtagtt ctcattatta
+     4801 gatctcaagt tattggagtc ttcagccaat tgctttgtat cagacaattg actctctaac
+     4861 ttctccactt cactgtcgag ttgctcgttt ttagcggaca aagatttaat ctcgttttct
+     4921 ttttcagtgt tagattgctc taattctttg agctgttctc tcagctcctc atatttttct
+     4981 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc
+//
+

data/test/data/litdb/1717226.litdb

@@ -0,0 +1,13 @@
+CODE        1717226
+TITLE       Characterization of an Escherichia coli gene encoding 
+            betaine aldehyde dehydrogenase (BADH). Structural similarity 
+            to mammalian ALDHs and a plant BADH.
+FIELD       q (sequence analysis)
+JOURNAL     Gene
+VOLUME      Vol.103, No.1, 45-52 (1991)
+KEYWORD     *Betaine Aldehyde Dehydrogenase;;*betB Gene;E.coli;;
+            Seq Determination;1854bp;491AAs;;Hydropathy Plot;*EC1.2.1.8;;
+            Seq Comparison
+AUTHOR      Boyd,L.A.;Adam,L.;Pelcher,L.E.;McHughen,A.;Hirji,R.;
+            Selvaraj,G.
+END

data/test/data/pir/CRAB_ANAPL.pir

@@ -0,0 +1,6 @@
+>P1;CRAB_ANAPL
+ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
+  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR 
+  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH 
+  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ 
+  SDVPERSIPI TREEKPAIAG AQRK*

data/test/functional/bio/appl/blast/test_remote.rb

@@ -0,0 +1,93 @@
+#
+# = test/functional/bio/appl/blast/test_remote.rb - Unit test for Bio::Blast::Remote::Genomenet and Bio::Blast::Remote::DDBJ with network connection
+#
+# Copyright::   Copyright (C) 2011
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/sequence'
+require 'bio/appl/blast'
+
+module Bio
+module FuncTestBlastRemote
+
+  module NetTestBlastRemoteCommon
+
+    Programs = %w( blastn tblastn tblastx blastp blastx ).freeze
+    Programs.each { |x| x.freeze }
+
+    def test_databases
+      Programs.each do |prog|
+        databases = nil
+        assert_nothing_raised {
+          databases = @klass.databases(prog)
+        }
+        assert_kind_of(Array, databases, "wrong data type for #{prog}")
+        assert(!databases.empty?, "no database found for #{prog}")
+      end
+    end
+
+    # sampling test for blastn database
+    def test_databases_blastn
+      databases = @klass.databases("blastn")
+      self.class::BLASTN_DBNAME_KEYWORDS.each do |re|
+        assert(databases.find { |x| re =~ x })
+      end
+    end
+
+    # sampling test for blastp database
+    def test_databases_blastp
+      databases = @klass.databases("blastp")
+      self.class::BLASTP_DBNAME_KEYWORDS.each do |re|
+        assert(databases.find { |x| re =~ x })
+      end
+    end
+
+    def test_database_description
+      Programs.each do |prog|
+        @klass.databases(prog).each do |db|
+          assert_kind_of(String, @klass.database_description(prog, db))
+        end
+      end
+    end
+  end #module NetTestBlastRemoteCommon
+
+  # This test class only contains tests for meta information.
+  # BLAST execution tests are written in ../test_blast.rb 
+  class NetTestBlastRemoteGenomeNet < Test::Unit::TestCase
+
+    include NetTestBlastRemoteCommon
+
+    BLASTN_DBNAME_KEYWORDS = [ /genes/, /nt/ ]
+    BLASTP_DBNAME_KEYWORDS = [ /genes/, /uniprot/, /nr/ ]
+
+    def setup
+      @klass = Bio::Blast::Remote::GenomeNet
+    end
+  end #class NetTestBlastRemoteGenomeNet
+
+  # This test class only contains tests for meta information.
+  # BLAST execution tests are written in ../test_blast.rb 
+  class NetTestBlastRemoteDDBJ < Test::Unit::TestCase
+
+    include NetTestBlastRemoteCommon
+
+    BLASTN_DBNAME_KEYWORDS = [ /ddbj/i, /nt/i ]
+    BLASTP_DBNAME_KEYWORDS = [ /uniprot/i, /pdb/i ]
+
+    def setup
+      @klass = Bio::Blast::Remote::DDBJ
+    end
+  end #class NetTestBlastRemoteDDBJ
+
+end #module FuncTestBlastRemote
+end #module Bio
+

data/test/functional/bio/appl/test_blast.rb

@@ -0,0 +1,61 @@
+#
+# = test/functional/bio/appl/test_blast.rb - Unit test for Bio::Blast with network connection
+#
+# Copyright::   Copyright (C) 2011
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/sequence'
+require 'bio/appl/blast'
+
+module Bio
+module FunctTestBlast
+
+  module NetTestBlastCommonProteinQuery
+    filename = File.join(BioRubyTestDataPath, 'fasta', 'EFTU_BACSU.fasta')
+    QuerySequence = File.read(filename).freeze
+
+    def test_query
+      report = nil
+      assert_nothing_raised {
+        report = @blast.query(QuerySequence)
+      }
+      assert(report.hits.size > 0)
+    end
+  end #module NetTestBlastCommonProteinQuery
+
+  class NetTestBlast_GenomeNet < Test::Unit::TestCase
+    include NetTestBlastCommonProteinQuery
+
+    def setup
+      @blast = Bio::Blast.new('blastp', 'mine-aa eco',
+                              [ '-e', '1e-10',
+                                '-v', '10',
+                                '-b', '10' ],
+                              'genomenet')
+    end
+  end #class NetTestBlast_GenomeNet
+
+  class NetTestBlast_DDBJ < Test::Unit::TestCase
+    include NetTestBlastCommonProteinQuery
+
+    def setup
+      @blast = Bio::Blast.new('blastp', 'SWISS',
+                              ['-e', '1e-10',
+                              '-v', '10',
+                              '-b', '10' ],
+                              'ddbj')
+    end
+  end #class NetTestBlast_DDBJ
+
+end #module FuncTestBlast
+end #module Bio
+

data/test/functional/bio/io/test_ddbjrest.rb

@@ -0,0 +1,47 @@
+#
+# test/functional/bio/io/test_ddbjrest.rb - Functional test for Bio::DDBJ::REST
+#
+# Copyright::   Copyright (C) 2011
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'bio/io/ddbjrest'
+require 'test/unit'
+
+module Bio
+module NetTestDDBJREST
+
+  class TestDDBJ < Test::Unit::TestCase
+
+    def setup
+      @obj = Bio::DDBJ::REST::DDBJ.new
+    end
+
+    def test_countBasePair
+      text = @obj.countBasePair("AF237819")
+      expected = {
+        "a" => 47,
+        "t" => 38,
+        "g" => 48,
+        "c" => 38
+      }
+      h = {}
+      text.each_line do |line|
+        base, count, percent = line.split(/\t/)
+        count = count.to_i
+        h[base] = count if count > 0
+      end
+      assert_equal(expected, h)
+    end
+
+  end #class TestDDBJ
+
+end #module NetTestDDBJREST
+end #module Bio