[BioRuby-cvs] bioruby/test/unit/bio/db test_fasta.rb,1.2,1.3

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/test/unit/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv30126/test/unit/bio/db

Modified Files:
	test_fasta.rb 
Log Message:
* fixed to pass all test, replaced the data with suitable one


Index: test_fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_fasta.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_fasta.rb	23 Nov 2005 11:21:15 -0000	1.2
--- test_fasta.rb	18 Dec 2005 17:55:13 -0000	1.3
***************
*** 39,44 ****
  
  
!   class TestFastaFormat < Test::Unit::TestCase
  
      def setup
        text =<<END
--- 39,82 ----
  
  
!   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
***************
*** 66,69 ****
--- 104,115 ----
      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"
***************
*** 71,78 ****
      end
  
-     def test_entry_id
-       assert_equal('sce:YBR160W', @obj.entry_id)
-     end
- 
      def test_definition
        data = "sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]"
--- 117,120 ----
***************
*** 84,137 ****
        assert_equal(data, @obj.data)
      end
  
!     def test_seq
!       seq = 'MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES'
!       assert_equal(seq, @obj.seq)
      end
  
!     def test_length
!       assert_equal(298, @obj.length)
      end
  
!     def test_naseq
!       seq = 'msgelanykrlekvgegtygvvykaldlrpgqgqrvvalkkirlesedegvpstaireisllkelkddnivrlydivhsdahklylvfefldldlkrymegipkdqplgadivkkfmmqlckgiaychshrilhrdlkpqnllinkdgnlklgdfglarafgvplraytheivtlwyrapevllggkqystgvdtwsigcifaemcnrkpifsgdseidqifkifrvlgtpneaiwpdivylpdfkpsfpqwrrkdlsqvvpsldprgidlldkllaydpinrisarraaihpyfqes'
!       assert_equal(seq, @obj.naseq)
      end
  
!     def test_nalen
!       assert_equal(298, @obj.nalen)
      end
  
      def test_aaseq
!       seq = "MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES"
        assert_equal(seq, @obj.aaseq)
      end
  
      def test_aalen
!       assert_equal(298, @obj.aalen)
      end
  
      def test_identifiers
!       assert_equal('', @obj.identifiers)
      end
  
      def test_gi
!       assert_equal('', @obj.gi)
      end
  
      def test_accession
!       assert_equal('', @obj.accession)
      end
  
      def test_accessions
!       assert_equal('', @obj.accessions)
      end
  
      def test_acc_version
!       assert_equal('', @obj.acc_version)
!     end
! 
!     def test_locus
!       assert_equal('', @obj.locus)
      end
  
--- 126,205 ----
        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