bio 0.7.0

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

@@ -0,0 +1,268 @@
+#
+# test/unit/bio/db/embl/test_sptr.rb - Unit test for Bio::SPTR
+#
+#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_sptr.rb,v 1.2 2005/11/23 10:06:12 nakao Exp $
+#
+
+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_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
+      assert_equal(["Tumor suppressor p53", "Phosphoprotein p53", "Antigen NY-CO-13"], @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::EMBL::COMMON#ref
+      @obj.ref
+    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"=>nil, "Named isoforms"=>"2", "Variants"=>  [{"IsoId"=>"P04637-1", "Name"=>"1", "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"=>nil, "From"=>102, "diff"=>[], "To"=>292, "Description"=>nil}], @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
+end

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

@@ -0,0 +1,44 @@
+#
+# test/unit/bio/db/embl/test_uniprot.rb - Unit test for Bio::UniProt
+#
+#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_uniprot.rb,v 1.3 2005/12/18 17:43:51 nakao Exp $
+#
+
+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/uniprot'
+
+module Bio
+  class TestUniProt < 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::UniProt.new(data)
+    end
+
+    def test_gene_name
+      assert_equal('TP53', @obj.gene_name)
+    end
+
+  end
+end

data/test/unit/bio/db/kegg/test_genes.rb

@@ -0,0 +1,58 @@
+#
+# test/unit/bio/db/kegg/test_genes.rb - Unit test for Bio::KEGG::GENES
+#
+#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_genes.rb,v 1.3 2005/11/09 13:20:09 nakao Exp $
+#
+
+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/kegg/genes'
+
+module Bio
+  class TestGenesDblinks < Test::Unit::TestCase
+
+    def setup
+      entry =<<END
+DBLINKS     TIGR: At3g05560
+            NCBI-GI: 15230008  42572267
+END
+      @obj = Bio::KEGG::GENES.new(entry)
+    end
+
+    def test_data
+      str = "DBLINKS     TIGR: At3g05560\n            NCBI-GI: 15230008  42572267"
+      assert_equal(str, @obj.instance_eval('get("DBLINKS")'))
+    end
+
+    def test_dblinks_0
+      assert_equal(Hash, @obj.dblinks.class)
+    end
+
+    def test_dblinks_1
+      assert_equal(['At3g05560'], @obj.dblinks['TIGR'])
+    end
+
+    def test_dblinks_2
+      assert_equal(['15230008', '42572267'], @obj.dblinks['NCBI-GI'])
+    end
+  end
+end

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

@@ -0,0 +1,263 @@
+#
+# test/unit/bio/db/test_fasta.rb - Unit test for Bio::FastaFormat
+#
+#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_fasta.rb,v 1.3 2005/12/18 17:55:13 k Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/db/fasta'
+
+module Bio
+  class TestFastaFormatConst < Test::Unit::TestCase
+
+    def test_delimiter
+      assert_equal("\n>", Bio::FastaFormat::DELIMITER)
+      assert_equal("\n>", Bio::FastaFormat::RS)
+    end
+
+  end # class TestFastaFormatConst
+
+
+  class TestFastaFormatSwissProt < Test::Unit::TestCase
+    def setup
+      text =<<END
+>gi|1171674|sp|P42267|NDD_BPR69 NUCLEAR DISRUPTION PROTEIN
+MKYMTVTDLNNAGATVIGTIKGGEWFLGTPHKDILSKPGFYFLVSKLDGRPFSNPCVSARFYVGNQRSKQGFSAVLSHIR
+QRRSQLARTIANNNMVYTVFYLPASKMKPLTTGFGKGQLALAFTRNHHSEYQTLEEMNRMLADNFKFVLQAY
+END
+      @obj = Bio::FastaFormat.new(text)
+    end
+
+    def test_locus
+      assert_equal(nil, @obj.locus)
+    end
+  end
+
+  class TestFastaFormatKeggGenesNT < Test::Unit::TestCase
+    def setup
+      text =<<END
+>eco:b0001 thrL; thr operon leader peptide (N)
+atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcg
+ggctga
+END
+      @obj = Bio::FastaFormat.new(text)
+    end
+
+    def test_naseq_class
+      assert_equal(Bio::Sequence::NA, @obj.naseq.class)
+    end
+
+    def test_naseq
+      seq = 'atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcgggctga'
+      assert_equal(seq, @obj.naseq)
+    end
+
+    def test_nalen
+      assert_equal(66, @obj.nalen)
+    end
+  end
+
+  class TestFastaFormatKeggGenesAA < Test::Unit::TestCase
+    def setup
+      text =<<END
+>sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
+MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
+VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
+GIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL
+KLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC
+IFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP
+QWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES
+>sce:YBR274W  CHK1; probable serine/threonine-protein kinase [EC:2.7.1.-] [SP:KB9S_YEAST]
+MSLSQVSPLPHIKDVVLGDTVGQGAFACVKNAHLQMDPSIILAVKFIHVP
+TCKKMGLSDKDITKEVVLQSKCSKHPNVLRLIDCNVSKEYMWIILEMADG
+GDLFDKIEPDVGVDSDVAQFYFQQLVSAINYLHVECGVAHRDIKPENILL
+DKNGNLKLADFGLASQFRRKDGTLRVSMDQRGSPPYMAPEVLYSEEGYYA
+DRTDIWSIGILLFVLLTGQTPWELPSLENEDFVFFIENDGNLNWGPWSKI
+EFTHLNLLRKILQPDPNKRVTLKALKLHPWVLRRASFSGDDGLCNDPELL
+AKKLFSHLKVSLSNENYLKFTQDTNSNNRYISTQPIGNELAELEHDSMHF
+QTVSNTQRAFTSYDSNTNYNSGTGMTQEAKWTQFISYDIAALQFHSDEND
+CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
+FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
+KTGDPLEWRRLFKKISTICRDIILIPN
+END
+      @obj = Bio::FastaFormat.new(text)
+    end
+
+    def test_entry_id
+      assert_equal('sce:YBR160W', @obj.entry_id)
+    end
+
+    def test_acc_version
+      assert_equal(nil, @obj.acc_version)
+    end
+
+    def test_entry
+      data = ">sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]\nMSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG\nVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME\nGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL\nKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC\nIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP\nQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES\n"
+      assert_equal(data, @obj.entry)
+    end
+
+    def test_definition
+      data = "sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]"
+      assert_equal(data, @obj.definition)
+    end
+
+    def test_data
+      data = "\nMSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG\nVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME\nGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL\nKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC\nIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP\nQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES\n"
+      assert_equal(data, @obj.data)
+    end
+  end
+
+  class TestFastaFormat < Test::Unit::TestCase
+
+    def setup
+      text =<<END
+>gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]
+MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT
+IALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF
+TLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI
+LFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL
+>gi|55416190|gb|AAV50057.1| NADH dehydrogenase subunit 2 [Dasyurus hallucatus]
+MSPYVLMILTLSLFIGTCLTIFSNHWFTAWMGLEINTLAIIPLMTAPNNPRSTEAATKYFLTQATASMLMMFAIIYNAWS
+TNQWALPQLSDDWISLLMTVALAIKLGLAPFHFWVPEVTQGIPLLTGMILLTWQKIAPTAILFQIAPYLNMKFLVILAIL
+STLVGGWGGLNQTHLRKILAYSSIAHMGWMIIIVQINPTLSIFTLTIYVMATLTTFLTLNLSNSTKIKSLGNLWNKSATA
+TIIIFLTLLSLGGLPPLTGFMPKWLILQELINNGNIITATMMALSALLNLFFYMRLIYASSLTMFPSINNSKMQWYNNSM
+KTTTLIPTATVISSLLLPLTPLFVTLY
+END
+      @obj = Bio::FastaFormat.new(text)
+    end
+
+    def test_entry
+      data = ">gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]\nMFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT\nIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF\nTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI\nLFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL\n"
+      assert_equal(data, @obj.entry)
+    end
+
+    def test_entry_id
+      assert_equal('gi|55416189', @obj.entry_id)
+    end
+
+    def test_definition
+      data = "gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]"
+      assert_equal(data, @obj.definition)
+    end
+
+    def test_data
+      data = "\nMFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT\nIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF\nTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI\nLFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL\n"
+      assert_equal(data, @obj.data)
+    end
+
+    def test_seq
+      seq = 'MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALTIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSFTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTILFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL'
+      assert_equal(seq, @obj.seq)
+    end
+
+    def test_length
+      assert_equal(318, @obj.length)
+    end
+
+    def test_aaseq
+      seq = "MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALTIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSFTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTILFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL"
+      assert_equal(seq, @obj.aaseq)
+    end
+
+    def test_aalen
+      assert_equal(318, @obj.aalen)
+    end
+
+    def test_identifiers
+      assert_equal(Bio::FastaDefline, @obj.identifiers.class)
+    end
+
+    def test_gi
+      assert_equal('55416189', @obj.gi)
+    end
+
+    def test_accession
+      assert_equal('AAV50056', @obj.accession)
+    end
+
+    def test_accessions
+      assert_equal(['AAV50056'], @obj.accessions)
+    end
+
+    def test_acc_version
+      assert_equal('AAV50056.1', @obj.acc_version)
+    end
+
+  end # class TestFastaFormat
+
+
+  class TestFastaNumericFormat < Test::Unit::TestCase
+
+    def setup
+      text =<<END
+>CRA3575282.F 
+24 15 23 29 20 13 20 21 21 23 22 25 13 22 17 15 25 27 32 26  
+32 29 29 25
+END
+      @obj = Bio::FastaNumericFormat.new(text)
+    end
+
+    def test_entry
+      assert_equal(">CRA3575282.F\n24 15 23 29 20 13 20 21 21 23 22 25 13 22 17 15 25 27 32 26  \n32 29 29 25\n", @obj.entry)
+    end
+
+    def test_entry_id
+      assert_equal('CRA3575282.F', @obj.entry_id) 
+    end
+
+    def test_definition
+      assert_equal('CRA3575282.F', @obj.definition)
+    end
+
+    def test_data
+      data = [24, 15, 23, 29, 20, 13, 20, 21, 21, 23, 22, 25, 13, 22, 17, 15, 25, 27, 32, 26, 32, 29, 29, 25]
+      assert_equal(data, @obj.data)
+    end
+
+    def test_length
+      assert_equal(24, @obj.length)
+    end
+
+    def test_each
+      assert(@obj.each {|x| })
+    end
+
+    def test_arg
+      assert(@obj[0], '')
+      assert(@obj[-1], '')
+    end
+
+
+  end # class TestFastaFormatNumeric
+
+
+  class TestFastaDefinition < Test::Unit::TestCase
+
+    def setup
+    end
+
+    def test_defline
+    end
+  end # class TestFastaDefinition
+
+end