jandot-bio 1.2.1

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

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+#
+# test/unit/bio/db/embl/test_uniprot.rb - Unit test for Bio::UniProt
+#
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id: test_uniprot.rb,v 1.5 2007/04/05 23:35:43 trevor 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

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+#
+# test/unit/bio/db/kegg/test_genes.rb - Unit test for Bio::KEGG::GENES
+#
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id: test_genes.rb,v 1.5 2007/04/05 23:35:43 trevor 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/pdb/test_pdb.rb

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+#
+# = test/unit/bio/db/pdb/test_pdb.rb - Unit test for Bio::PDB classes
+#
+# Copyright:: Copyright (C) 2006
+#             Naohisa Goto <ng@bioruby.org>
+#
+# License:: The Ruby License
+#
+#  $Id: test_pdb.rb,v 1.3 2007/04/05 23:35:43 trevor 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'
+
+module Bio
+  #class TestPDB < Test::Unit::TestCase
+  #end #class TestPDB
+
+  module TestPDBRecord
+
+    # test of Bio::PDB::Record::ATOM
+    class TestATOM < Test::Unit::TestCase
+      def setup
+        # the data is taken from
+        # http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_62.html
+        @str = 'ATOM    154  CG2BVAL A  25      29.909  16.996  55.922  0.72 13.25      A1   C  '
+        @atom = Bio::PDB::Record::ATOM.new.initialize_from_string(@str)
+      end
+
+      def test_record_name
+        assert_equal('ATOM', @atom.record_name)
+      end
+
+      def test_serial
+        assert_equal(154, @atom.serial)
+      end
+
+      def test_name
+        assert_equal('CG2', @atom.name)
+      end
+
+      def test_altLoc
+        assert_equal('B', @atom.altLoc)
+      end
+
+      def test_resName
+        assert_equal('VAL', @atom.resName)
+      end
+
+      def test_chainID
+        assert_equal('A', @atom.chainID)
+      end
+
+      def test_resSeq
+        assert_equal(25, @atom.resSeq)
+      end
+
+      def test_iCode
+        assert_equal('', @atom.iCode)
+      end
+
+      def test_x
+        assert_in_delta(29.909, @atom.x, Float::EPSILON)
+      end
+
+      def test_y
+        assert_in_delta(16.996, @atom.y, Float::EPSILON)
+      end
+
+      def test_z
+        assert_in_delta(55.922, @atom.z, Float::EPSILON)
+      end
+
+      def test_occupancy
+        assert_in_delta(0.72, @atom.occupancy, Float::EPSILON)
+      end
+
+      def test_tempFactor
+        assert_in_delta(13.25, @atom.tempFactor, Float::EPSILON)
+      end
+
+      def test_segID
+        assert_equal('A1', @atom.segID)
+      end
+
+      def test_element
+        assert_equal('C', @atom.element)
+      end
+
+      def test_charge
+        assert_equal('', @atom.charge)
+      end
+
+      def test_xyz
+        assert_equal(Bio::PDB::Coordinate[
+                       "29.909".to_f,
+                       "16.996".to_f,
+                       "55.922".to_f ], @atom.xyz)
+      end
+
+      def test_to_a
+        assert_equal([ "29.909".to_f,
+                       "16.996".to_f,
+                       "55.922".to_f ], @atom.to_a)
+      end
+
+      def test_comparable
+        a = Bio::PDB::Record::ATOM.new
+        a.serial = 999
+        assert_equal(-1, @atom <=> a)
+        a.serial = 154
+        assert_equal( 0, @atom <=> a)
+        a.serial = 111
+        assert_equal( 1, @atom <=> a)
+      end
+
+      def test_to_s
+        assert_equal(@str + "\n", @atom.to_s)
+      end
+
+      def test_original_data
+        assert_equal([ @str ], @atom.original_data)
+      end
+
+      def test_do_parse
+        assert_equal(@atom, @atom.do_parse)
+      end
+
+      def test_residue
+        assert_equal(nil, @atom.residue)
+      end
+
+      def test_sigatm
+        assert_equal(nil, @atom.sigatm)
+      end
+
+      def test_anisou
+        assert_equal(nil, @atom.anisou)
+      end
+
+      def test_ter
+        assert_equal(nil, @atom.ter)
+      end
+    end #class TestATOM
+
+  end #module TestPDBRecord
+
+end #module Bio

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

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+#
+# test/unit/bio/db/test_aaindex.rb - Unit test for Bio::AAindex
+#
+# Copyright::  Copyright (C) 2006 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+# $Id: test_aaindex.rb,v 1.4 2007/04/05 23:35:43 trevor 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/io/fetch'
+require 'bio/db/aaindex'
+
+module Bio
+  class DataAAindex
+    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s    
+    TestDataAAindex = Pathname.new(File.join(bioruby_root, 'test', 'data', 'aaindex')).cleanpath.to_s
+
+    def self.aax1
+      File.read(File.join(TestDataAAindex, "PRAM900102"))
+    end
+
+    def self.aax2
+      File.read(File.join(TestDataAAindex, "DAYM780301"))
+    end
+  end
+
+  # A super class for Bio::AAindex1 and Bio::AAindex2
+  class TestAAindexConstant < Test::Unit::TestCase
+    def test_delimiter
+      rs = "\n//\n"
+      assert_equal(rs, Bio::AAindex::DELIMITER)
+      assert_equal(rs, Bio::AAindex::RS)
+    end
+
+    def test_tagsize
+      assert_equal(2, Bio::AAindex::TAGSIZE)
+    end
+  end
+
+  class TestAAindex < Test::Unit::TestCase
+    def test_api
+      api_methods = ['entry_id', 'definition', 'dblinks', 'author',
+             'title', 'journal', 'comment']
+      api_methods.each do |m|
+      end
+    end
+
+    def test_auto_aax1
+      assert_equal(Bio::AAindex1, Bio::AAindex.auto(DataAAindex.aax1).class)
+    end
+
+    def test_auto_aax2
+      assert_equal(Bio::AAindex2, Bio::AAindex.auto(DataAAindex.aax2).class)
+    end
+  end
+
+  class TestAAindex1 < Test::Unit::TestCase
+    def setup
+      str = DataAAindex.aax1
+      @obj = Bio::AAindex1.new(str)
+    end
+    
+    def test_entry_id
+      assert_equal('PRAM900102', @obj.entry_id)
+    end
+
+    def test_definition
+      assert_equal('Relative frequency in alpha-helix (Prabhakaran, 1990)', @obj.definition)
+    end
+
+    def test_dblinks
+      assert_equal(['LIT:1614053b', 'PMID:2390062'], @obj.dblinks)
+    end
+
+    def test_author
+      assert_equal('Prabhakaran, M.', @obj.author)
+    end
+
+    def test_title
+      assert_equal('The distribution of physical, chemical and conformational properties in signal and nascent peptides', @obj.title)
+    end
+
+    def test_journal
+      assert_equal('Biochem. J. 269, 691-696 (1990) Original reference of these three data: Creighton, T.E. In "Protein Structure and Melecular Properties", (Freeman, W.H., ed.), San Francisco P.235 (1983)', @obj.journal)
+    end
+
+    def test_comment
+      assert_equal("", @obj.comment)
+    end
+
+    def test_correlation_coefficient
+#      str = "LEVM780101 1.000 LEVM780104 0.964 PALJ810101 0.943 KANM800101 0.942 ISOY800101 0.929 MAXF760101 0.924 ROBB760101 0.916 GEIM800101 0.912 GEIM800104 0.907 RACS820108 0.904 PALJ810102 0.902 PALJ810109 0.898 NAGK730101 0.894 CRAJ730101 0.887 CHOP780201 0.873 TANS770101 0.854 KANM800103 0.850 QIAN880107 0.829 QIAN880106 0.827 BURA740101 0.805 NAGK730103 -0.809"
+#      assert_equal(str, @obj.correlation_coefficient)
+      # to be this ?
+      hash = {'LEVM780101' => 1.000, 'LEVM780104' => 0.964, 'PALJ810101' => 0.943,  'KANM800101' => 0.942, 'ISOY800101' => 0.929, 'MAXF760101' => 0.924, 'ROBB760101' => 0.916, 'GEIM800101' => 0.912, 'GEIM800104' => 0.907, 'RACS820108' => 0.904, 'PALJ810102' => 0.902, 'PALJ810109' => 0.898, 'NAGK730101' => 0.894, 'CRAJ730101' => 0.887, 'CHOP780201' => 0.873, 'TANS770101' => 0.854, 'KANM800103' => 0.850, 'QIAN880107' => 0.829, 'QIAN880106' => 0.827,  'BURA740101' => 0.805, 'NAGK730103' => -0.809}
+      assert_equal(hash, @obj.correlation_coefficient)
+    end
+
+    def test_index
+      hash = {"V"=>0.91, "K"=>1.23, "W"=>0.99, "L"=>1.3, "A"=>1.29, "M"=>1.47, "Y"=>0.72, "C"=>1.11, "N"=>0.9, "D"=>1.04, "P"=>0.52, "E"=>1.44, "F"=>1.07, "Q"=>1.27, "G"=>0.56, "R"=>0.96, "S"=>0.82, "H"=>1.22, "T"=>0.82, "I"=>0.97}
+      assert_equal(hash, @obj.index)
+    end
+  end
+
+
+  class TestAAindex2 < Test::Unit::TestCase
+    def setup
+      str = DataAAindex.aax2
+      @obj = Bio::AAindex2.new(str)
+    end
+
+    def test_entry_id
+      assert_equal('DAYM780301', @obj.entry_id)
+    end
+
+    def test_definition
+      assert_equal('Log odds matrix for 250 PAMs (Dayhoff et al., 1978)', @obj.definition)
+    end
+
+    def test_dblinks
+      assert_equal([], @obj.dblinks)
+    end
+
+    def test_author
+      assert_equal("Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C.", @obj.author)
+    end
+
+    def test_title
+      assert_equal("A model of evolutionary change in proteins", @obj.title)
+    end
+
+    def test_journal
+      assert_equal('In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff, M.O., ed.), National Biomedical Research Foundation, Washington, D.C., p.352 (1978)', @obj.journal)
+    end
+
+    def test_comment
+      assert_equal("", @obj.comment)
+    end
+
+    def test_rows
+      ary = ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"]
+      assert_equal(ary, @obj.rows)
+    end
+
+    def test_cols
+      ary = ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"]
+      assert_equal(ary, @obj.cols)
+    end
+
+    def test_matrix
+      assert_equal(Matrix, @obj.matrix.class)
+    end
+
+    def test_matrix_2_2
+      assert_equal(2.0, @obj.matrix[2, 2])
+    end
+
+    def test_matrix_1_2
+      assert_equal(nil, @obj.matrix[1, 2])
+    end
+
+    def test_access_A_R
+      assert_equal(nil, @obj['A', 'R'])
+    end
+
+    def test_access_R_A
+      assert_equal(-2.0, @obj['R', 'A'])
+    end
+
+    def test_matrix_A_R
+      assert_equal(nil, @obj.matrix('A', 'R'))
+    end
+
+    def test_matrix_R_A
+      assert_equal(-2.0, @obj.matrix('R', 'A'))
+    end
+
+    def test_matrix_determinant
+      assert_equal(0, @obj.matrix.determinant)
+    end
+
+    def test_matrix_rank
+      assert_equal(1, @obj.matrix.rank)
+    end
+
+    def test_matrix_transpose
+      ary = Matrix[[2.0, -2.0, 0.0, 0.0, -2.0, 0.0, 0.0, 1.0, -1.0, -1.0, -2.0, -1.0, -1.0, -4.0, 1.0, 1.0, 1.0, -6.0, -3.0, 0.0]]
+      assert_equal(ary, @obj.matrix.transpose)
+    end
+  end    
+end

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

@@ -0,0 +1,250 @@
+#
+# test/unit/bio/db/test_fasta.rb - Unit test for Bio::FastaFormat
+#
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id: test_fasta.rb,v 1.5 2007/04/05 23:35:43 trevor 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